17 import builtins
as __builtin__
21 strthis =
"proxy of " + self.this.__repr__()
22 except __builtin__.Exception:
24 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
27 def _swig_setattr_nondynamic_instance_variable(set):
28 def set_instance_attr(self, name, value):
30 set(self, name, value)
31 elif name ==
"thisown":
33 elif hasattr(self, name)
and isinstance(getattr(type(self), name), property):
34 set(self, name, value)
36 raise AttributeError(
"You cannot add instance attributes to %s" % self)
37 return set_instance_attr
40 def _swig_setattr_nondynamic_class_variable(set):
41 def set_class_attr(cls, name, value):
42 if hasattr(cls, name)
and not isinstance(getattr(cls, name), property):
45 raise AttributeError(
"You cannot add class attributes to %s" % cls)
49 class _SwigNonDynamicMeta(type):
50 """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
51 __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
56 class IMP_KERNEL_SwigPyIterator(object):
57 r"""Proxy of C++ swig::IMP_KERNEL_SwigPyIterator class."""
59 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
61 def __init__(self, *args, **kwargs):
62 raise AttributeError(
"No constructor defined - class is abstract")
64 __swig_destroy__ = _IMP_kernel.delete_IMP_KERNEL_SwigPyIterator
67 r"""value(IMP_KERNEL_SwigPyIterator self) -> PyObject *"""
68 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_value(self)
71 r"""incr(IMP_KERNEL_SwigPyIterator self, size_t n=1) -> IMP_KERNEL_SwigPyIterator"""
72 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_incr(self, n)
75 r"""decr(IMP_KERNEL_SwigPyIterator self, size_t n=1) -> IMP_KERNEL_SwigPyIterator"""
76 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_decr(self, n)
78 def distance(self, x):
79 r"""distance(IMP_KERNEL_SwigPyIterator self, IMP_KERNEL_SwigPyIterator x) -> ptrdiff_t"""
80 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_distance(self, x)
83 r"""equal(IMP_KERNEL_SwigPyIterator self, IMP_KERNEL_SwigPyIterator x) -> bool"""
84 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_equal(self, x)
87 r"""copy(IMP_KERNEL_SwigPyIterator self) -> IMP_KERNEL_SwigPyIterator"""
88 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_copy(self)
91 r"""__next__(IMP_KERNEL_SwigPyIterator self) -> PyObject *"""
92 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___next__(self)
95 r"""previous(IMP_KERNEL_SwigPyIterator self) -> PyObject *"""
96 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_previous(self)
99 r"""advance(IMP_KERNEL_SwigPyIterator self, ptrdiff_t n) -> IMP_KERNEL_SwigPyIterator"""
100 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_advance(self, n)
103 r"""__eq__(IMP_KERNEL_SwigPyIterator self, IMP_KERNEL_SwigPyIterator x) -> bool"""
104 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___eq__(self, x)
107 r"""__ne__(IMP_KERNEL_SwigPyIterator self, IMP_KERNEL_SwigPyIterator x) -> bool"""
108 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___ne__(self, x)
110 def __iadd__(self, n):
111 r"""__iadd__(IMP_KERNEL_SwigPyIterator self, ptrdiff_t n) -> IMP_KERNEL_SwigPyIterator"""
112 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___iadd__(self, n)
114 def __isub__(self, n):
115 r"""__isub__(IMP_KERNEL_SwigPyIterator self, ptrdiff_t n) -> IMP_KERNEL_SwigPyIterator"""
116 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___isub__(self, n)
118 def __add__(self, n):
119 r"""__add__(IMP_KERNEL_SwigPyIterator self, ptrdiff_t n) -> IMP_KERNEL_SwigPyIterator"""
120 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___add__(self, n)
122 def __sub__(self, *args):
124 __sub__(IMP_KERNEL_SwigPyIterator self, ptrdiff_t n) -> IMP_KERNEL_SwigPyIterator
125 __sub__(IMP_KERNEL_SwigPyIterator self, IMP_KERNEL_SwigPyIterator x) -> ptrdiff_t
127 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___sub__(self, *args)
132 _IMP_kernel.IMP_KERNEL_SwigPyIterator_swigregister(IMP_KERNEL_SwigPyIterator)
139 IMP_DEBUG = _IMP_kernel.IMP_DEBUG
141 IMP_RELEASE = _IMP_kernel.IMP_RELEASE
143 IMP_SILENT = _IMP_kernel.IMP_SILENT
145 IMP_PROGRESS = _IMP_kernel.IMP_PROGRESS
147 IMP_TERSE = _IMP_kernel.IMP_TERSE
149 IMP_VERBOSE = _IMP_kernel.IMP_VERBOSE
151 IMP_MEMORY = _IMP_kernel.IMP_MEMORY
153 IMP_NONE = _IMP_kernel.IMP_NONE
155 IMP_USAGE = _IMP_kernel.IMP_USAGE
157 IMP_INTERNAL = _IMP_kernel.IMP_INTERNAL
159 IMP_KERNEL_HAS_LOG4CXX = _IMP_kernel.IMP_KERNEL_HAS_LOG4CXX
161 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_kernel.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
163 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_kernel.IMP_COMPILER_HAS_DEBUG_VECTOR
165 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_kernel.IMP_COMPILER_HAS_RANDOM_SHUFFLE
167 IMP_COMPILER_HAS_THREE_WAY = _IMP_kernel.IMP_COMPILER_HAS_THREE_WAY
169 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_kernel.IMP_KERNEL_HAS_BOOST_RANDOM
171 IMP_KERNEL_HAS_NUMPY = _IMP_kernel.IMP_KERNEL_HAS_NUMPY
173 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_kernel.IMP_KERNEL_HAS_BOOST_SYSTEM
175 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_kernel.IMP_KERNEL_HAS_GPERFTOOLS
177 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_kernel.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
179 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_kernel.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
181 IMPKERNEL_SHOW_WARNINGS = _IMP_kernel.IMPKERNEL_SHOW_WARNINGS
185 class _DirectorObjects:
186 """@internal Simple class to keep references to director objects
187 to prevent premature deletion."""
190 def register(self, obj):
191 """Take a reference to a director object; will only work for
192 refcounted C++ classes"""
193 if hasattr(obj,
'get_ref_count'):
194 self._objects.append(obj)
196 """Only drop our reference and allow cleanup by Python if no other
197 Python references exist (we hold 3 references: one in self._objects,
198 one in x, and one in the argument list for getrefcount) *and* no
199 other C++ references exist (the Python object always holds one)"""
200 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
201 or x.get_ref_count() > 1]
205 def get_object_count(self):
206 """Get number of director objects (useful for testing only)"""
207 return len(self._objects)
208 _director_objects = _DirectorObjects()
210 DEFAULT_CHECK = _IMP_kernel.DEFAULT_CHECK
212 NONE = _IMP_kernel.NONE
214 USAGE = _IMP_kernel.USAGE
216 USAGE_AND_INTERNAL = _IMP_kernel.USAGE_AND_INTERNAL
220 r"""set_check_level(IMP::CheckLevel tf)"""
221 return _IMP_kernel.set_check_level(tf)
224 r"""get_check_level() -> IMP::CheckLevel"""
225 return _IMP_kernel.get_check_level()
227 from _IMP_kernel
import Exception, InternalException, ModelException, EventException
228 from _IMP_kernel
import UsageException, IndexException, IOException, ValueException
229 from _IMP_kernel
import TypeException
231 class _ostream(object):
232 r"""Proxy of C++ std::ostream class."""
234 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
236 def __init__(self, *args, **kwargs):
237 raise AttributeError(
"No constructor defined")
238 __repr__ = _swig_repr
240 def write(self, osa_buf):
241 r"""write(_ostream self, char const * osa_buf)"""
242 return _IMP_kernel._ostream_write(self, osa_buf)
245 _IMP_kernel._ostream_swigregister(_ostream)
246 IMP_C_OPEN_BINARY = _IMP_kernel.IMP_C_OPEN_BINARY
249 from .
import _list_util
252 _models_set = weakref.WeakSet()
254 def _models_set_get(m):
255 for x
in _models_set:
260 _raii_types.append(
"SetLogState")
263 _raii_types.append(
"SetNumberOfThreads")
266 _raii_types.append(
"SetCheckState")
269 _object_types.append(
"Object")
272 def _object_cast_to_Object(o):
273 r"""_object_cast_to_Object(Object * o) -> Object"""
274 return _IMP_kernel._object_cast_to_Object(o)
276 _object_types.append(
"_TestObject")
279 def _object_cast_to__TestObject(o):
280 r"""_object_cast_to__TestObject(Object * o) -> _TestObject"""
281 return _IMP_kernel._object_cast_to__TestObject(o)
284 _plural_types.append(
"VersionInfos")
285 _value_types.append(
"VersionInfo")
288 _raii_types.append(
"CreateLogContext")
291 _raii_types.append(
"WarningContext")
294 _raii_types.append(
"SetLogTarget")
298 _plural_types.append(
"_TestValues")
299 _value_types.append(
"_TestValue")
303 _plural_types.append(
"Floats")
304 _value_types.append(
"Float")
308 _plural_types.append(
"Ints")
309 _value_types.append(
"Int")
313 _plural_types.append(
"Strings")
314 _value_types.append(
"String")
318 _plural_types.append(
"_Protections")
319 _value_types.append(
"_Protection")
321 class _GeometricPrimitive1D(object):
322 r"""Proxy of C++ IMP::GeometricPrimitiveD< 1 > class."""
324 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
326 def __init__(self, *args, **kwargs):
327 raise AttributeError(
"No constructor defined")
328 __repr__ = _swig_repr
329 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive1D
332 _IMP_kernel._GeometricPrimitive1D_swigregister(_GeometricPrimitive1D)
333 class _GeometricPrimitive2D(object):
334 r"""Proxy of C++ IMP::GeometricPrimitiveD< 2 > class."""
336 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
338 def __init__(self, *args, **kwargs):
339 raise AttributeError(
"No constructor defined")
340 __repr__ = _swig_repr
341 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive2D
344 _IMP_kernel._GeometricPrimitive2D_swigregister(_GeometricPrimitive2D)
345 class _GeometricPrimitive3D(object):
346 r"""Proxy of C++ IMP::GeometricPrimitiveD< 3 > class."""
348 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
350 def __init__(self, *args, **kwargs):
351 raise AttributeError(
"No constructor defined")
352 __repr__ = _swig_repr
353 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive3D
356 _IMP_kernel._GeometricPrimitive3D_swigregister(_GeometricPrimitive3D)
357 class _GeometricPrimitive4D(object):
358 r"""Proxy of C++ IMP::GeometricPrimitiveD< 4 > class."""
360 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
362 def __init__(self, *args, **kwargs):
363 raise AttributeError(
"No constructor defined")
364 __repr__ = _swig_repr
365 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive4D
368 _IMP_kernel._GeometricPrimitive4D_swigregister(_GeometricPrimitive4D)
369 class _GeometricPrimitive5D(object):
370 r"""Proxy of C++ IMP::GeometricPrimitiveD< 5 > class."""
372 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
374 def __init__(self, *args, **kwargs):
375 raise AttributeError(
"No constructor defined")
376 __repr__ = _swig_repr
377 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive5D
380 _IMP_kernel._GeometricPrimitive5D_swigregister(_GeometricPrimitive5D)
381 class _GeometricPrimitive6D(object):
382 r"""Proxy of C++ IMP::GeometricPrimitiveD< 6 > class."""
384 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
386 def __init__(self, *args, **kwargs):
387 raise AttributeError(
"No constructor defined")
388 __repr__ = _swig_repr
389 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive6D
392 _IMP_kernel._GeometricPrimitive6D_swigregister(_GeometricPrimitive6D)
393 class _GeometricPrimitiveKD(object):
394 r"""Proxy of C++ IMP::GeometricPrimitiveD< -1 > class."""
396 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
398 def __init__(self, *args, **kwargs):
399 raise AttributeError(
"No constructor defined")
400 __repr__ = _swig_repr
401 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitiveKD
404 _IMP_kernel._GeometricPrimitiveKD_swigregister(_GeometricPrimitiveKD)
405 class _VectorBaseKD(_GeometricPrimitiveKD):
406 r"""Proxy of C++ IMP::internal::VectorBaseD< -1 > class."""
408 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
409 __repr__ = _swig_repr
412 r"""__init__(_VectorBaseKD self) -> _VectorBaseKD"""
413 _IMP_kernel._VectorBaseKD_swiginit(self, _IMP_kernel.new__VectorBaseKD())
415 def get_scalar_product(self, o):
416 r"""get_scalar_product(_VectorBaseKD self, _VectorBaseKD o) -> double"""
417 return _IMP_kernel._VectorBaseKD_get_scalar_product(self, o)
419 def get_squared_magnitude(self):
420 r"""get_squared_magnitude(_VectorBaseKD self) -> double"""
421 return _IMP_kernel._VectorBaseKD_get_squared_magnitude(self)
423 def get_magnitude(self):
424 r"""get_magnitude(_VectorBaseKD self) -> double"""
425 return _IMP_kernel._VectorBaseKD_get_magnitude(self)
428 r"""get_distance(_VectorBaseKD self, _VectorBaseKD o) -> double"""
429 return _IMP_kernel._VectorBaseKD_get_distance(self, o)
431 def __mul__(self, o):
432 r"""__mul__(_VectorBaseKD self, _VectorBaseKD o) -> double"""
433 return _IMP_kernel._VectorBaseKD___mul__(self, o)
435 def __iadd__(self, o):
436 r"""__iadd__(_VectorBaseKD self, _VectorBaseKD o) -> _VectorBaseKD"""
437 return _IMP_kernel._VectorBaseKD___iadd__(self, o)
439 def __isub__(self, o):
440 r"""__isub__(_VectorBaseKD self, _VectorBaseKD o) -> _VectorBaseKD"""
441 return _IMP_kernel._VectorBaseKD___isub__(self, o)
443 def __itruediv__(self, *args):
444 return _IMP_kernel._VectorBaseKD___itruediv__(self, *args)
445 __idiv__ = __itruediv__
449 def __imul__(self, f):
450 r"""__imul__(_VectorBaseKD self, double f) -> _VectorBaseKD"""
451 return _IMP_kernel._VectorBaseKD___imul__(self, f)
453 def show(self, *args):
455 show(_VectorBaseKD self, _ostream out, std::string delim, bool parens=True)
456 show(_VectorBaseKD self, _ostream out=std::cout)
458 return _IMP_kernel._VectorBaseKD_show(self, *args)
460 def get_dimension(self):
461 r"""get_dimension(_VectorBaseKD self) -> unsigned int"""
462 return _IMP_kernel._VectorBaseKD_get_dimension(self)
463 __swig_destroy__ = _IMP_kernel.delete__VectorBaseKD
466 _IMP_kernel._VectorBaseKD_swigregister(_VectorBaseKD)
467 class _VectorBase1D(_GeometricPrimitive1D):
468 r"""Proxy of C++ IMP::internal::VectorBaseD< 1 > class."""
470 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
471 __repr__ = _swig_repr
474 r"""__init__(_VectorBase1D self) -> _VectorBase1D"""
475 _IMP_kernel._VectorBase1D_swiginit(self, _IMP_kernel.new__VectorBase1D())
477 def get_scalar_product(self, o):
478 r"""get_scalar_product(_VectorBase1D self, _VectorBase1D o) -> double"""
479 return _IMP_kernel._VectorBase1D_get_scalar_product(self, o)
481 def get_squared_magnitude(self):
482 r"""get_squared_magnitude(_VectorBase1D self) -> double"""
483 return _IMP_kernel._VectorBase1D_get_squared_magnitude(self)
485 def get_magnitude(self):
486 r"""get_magnitude(_VectorBase1D self) -> double"""
487 return _IMP_kernel._VectorBase1D_get_magnitude(self)
490 r"""get_distance(_VectorBase1D self, _VectorBase1D o) -> double"""
491 return _IMP_kernel._VectorBase1D_get_distance(self, o)
493 def __mul__(self, o):
494 r"""__mul__(_VectorBase1D self, _VectorBase1D o) -> double"""
495 return _IMP_kernel._VectorBase1D___mul__(self, o)
497 def __iadd__(self, o):
498 r"""__iadd__(_VectorBase1D self, _VectorBase1D o) -> _VectorBase1D"""
499 return _IMP_kernel._VectorBase1D___iadd__(self, o)
501 def __isub__(self, o):
502 r"""__isub__(_VectorBase1D self, _VectorBase1D o) -> _VectorBase1D"""
503 return _IMP_kernel._VectorBase1D___isub__(self, o)
505 def __itruediv__(self, *args):
506 return _IMP_kernel._VectorBase1D___itruediv__(self, *args)
507 __idiv__ = __itruediv__
511 def __imul__(self, f):
512 r"""__imul__(_VectorBase1D self, double f) -> _VectorBase1D"""
513 return _IMP_kernel._VectorBase1D___imul__(self, f)
515 def show(self, *args):
517 show(_VectorBase1D self, _ostream out, std::string delim, bool parens=True)
518 show(_VectorBase1D self, _ostream out=std::cout)
520 return _IMP_kernel._VectorBase1D_show(self, *args)
522 def get_dimension(self):
523 r"""get_dimension(_VectorBase1D self) -> unsigned int"""
524 return _IMP_kernel._VectorBase1D_get_dimension(self)
525 __swig_destroy__ = _IMP_kernel.delete__VectorBase1D
528 _IMP_kernel._VectorBase1D_swigregister(_VectorBase1D)
529 class _VectorBase2D(_GeometricPrimitive2D):
530 r"""Proxy of C++ IMP::internal::VectorBaseD< 2 > class."""
532 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
533 __repr__ = _swig_repr
536 r"""__init__(_VectorBase2D self) -> _VectorBase2D"""
537 _IMP_kernel._VectorBase2D_swiginit(self, _IMP_kernel.new__VectorBase2D())
539 def get_scalar_product(self, o):
540 r"""get_scalar_product(_VectorBase2D self, _VectorBase2D o) -> double"""
541 return _IMP_kernel._VectorBase2D_get_scalar_product(self, o)
543 def get_squared_magnitude(self):
544 r"""get_squared_magnitude(_VectorBase2D self) -> double"""
545 return _IMP_kernel._VectorBase2D_get_squared_magnitude(self)
547 def get_magnitude(self):
548 r"""get_magnitude(_VectorBase2D self) -> double"""
549 return _IMP_kernel._VectorBase2D_get_magnitude(self)
552 r"""get_distance(_VectorBase2D self, _VectorBase2D o) -> double"""
553 return _IMP_kernel._VectorBase2D_get_distance(self, o)
555 def __mul__(self, o):
556 r"""__mul__(_VectorBase2D self, _VectorBase2D o) -> double"""
557 return _IMP_kernel._VectorBase2D___mul__(self, o)
559 def __iadd__(self, o):
560 r"""__iadd__(_VectorBase2D self, _VectorBase2D o) -> _VectorBase2D"""
561 return _IMP_kernel._VectorBase2D___iadd__(self, o)
563 def __isub__(self, o):
564 r"""__isub__(_VectorBase2D self, _VectorBase2D o) -> _VectorBase2D"""
565 return _IMP_kernel._VectorBase2D___isub__(self, o)
567 def __itruediv__(self, *args):
568 return _IMP_kernel._VectorBase2D___itruediv__(self, *args)
569 __idiv__ = __itruediv__
573 def __imul__(self, f):
574 r"""__imul__(_VectorBase2D self, double f) -> _VectorBase2D"""
575 return _IMP_kernel._VectorBase2D___imul__(self, f)
577 def show(self, *args):
579 show(_VectorBase2D self, _ostream out, std::string delim, bool parens=True)
580 show(_VectorBase2D self, _ostream out=std::cout)
582 return _IMP_kernel._VectorBase2D_show(self, *args)
584 def get_dimension(self):
585 r"""get_dimension(_VectorBase2D self) -> unsigned int"""
586 return _IMP_kernel._VectorBase2D_get_dimension(self)
587 __swig_destroy__ = _IMP_kernel.delete__VectorBase2D
590 _IMP_kernel._VectorBase2D_swigregister(_VectorBase2D)
591 class _VectorBase3D(_GeometricPrimitive3D):
592 r"""Proxy of C++ IMP::internal::VectorBaseD< 3 > class."""
594 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
595 __repr__ = _swig_repr
598 r"""__init__(_VectorBase3D self) -> _VectorBase3D"""
599 _IMP_kernel._VectorBase3D_swiginit(self, _IMP_kernel.new__VectorBase3D())
601 def get_scalar_product(self, o):
602 r"""get_scalar_product(_VectorBase3D self, _VectorBase3D o) -> double"""
603 return _IMP_kernel._VectorBase3D_get_scalar_product(self, o)
605 def get_squared_magnitude(self):
606 r"""get_squared_magnitude(_VectorBase3D self) -> double"""
607 return _IMP_kernel._VectorBase3D_get_squared_magnitude(self)
609 def get_magnitude(self):
610 r"""get_magnitude(_VectorBase3D self) -> double"""
611 return _IMP_kernel._VectorBase3D_get_magnitude(self)
614 r"""get_distance(_VectorBase3D self, _VectorBase3D o) -> double"""
615 return _IMP_kernel._VectorBase3D_get_distance(self, o)
617 def __mul__(self, o):
618 r"""__mul__(_VectorBase3D self, _VectorBase3D o) -> double"""
619 return _IMP_kernel._VectorBase3D___mul__(self, o)
621 def __iadd__(self, o):
622 r"""__iadd__(_VectorBase3D self, _VectorBase3D o) -> _VectorBase3D"""
623 return _IMP_kernel._VectorBase3D___iadd__(self, o)
625 def __isub__(self, o):
626 r"""__isub__(_VectorBase3D self, _VectorBase3D o) -> _VectorBase3D"""
627 return _IMP_kernel._VectorBase3D___isub__(self, o)
629 def __itruediv__(self, *args):
630 return _IMP_kernel._VectorBase3D___itruediv__(self, *args)
631 __idiv__ = __itruediv__
635 def __imul__(self, f):
636 r"""__imul__(_VectorBase3D self, double f) -> _VectorBase3D"""
637 return _IMP_kernel._VectorBase3D___imul__(self, f)
639 def show(self, *args):
641 show(_VectorBase3D self, _ostream out, std::string delim, bool parens=True)
642 show(_VectorBase3D self, _ostream out=std::cout)
644 return _IMP_kernel._VectorBase3D_show(self, *args)
646 def get_dimension(self):
647 r"""get_dimension(_VectorBase3D self) -> unsigned int"""
648 return _IMP_kernel._VectorBase3D_get_dimension(self)
649 __swig_destroy__ = _IMP_kernel.delete__VectorBase3D
652 _IMP_kernel._VectorBase3D_swigregister(_VectorBase3D)
653 class _VectorBase4D(_GeometricPrimitive4D):
654 r"""Proxy of C++ IMP::internal::VectorBaseD< 4 > class."""
656 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
657 __repr__ = _swig_repr
660 r"""__init__(_VectorBase4D self) -> _VectorBase4D"""
661 _IMP_kernel._VectorBase4D_swiginit(self, _IMP_kernel.new__VectorBase4D())
663 def get_scalar_product(self, o):
664 r"""get_scalar_product(_VectorBase4D self, _VectorBase4D o) -> double"""
665 return _IMP_kernel._VectorBase4D_get_scalar_product(self, o)
667 def get_squared_magnitude(self):
668 r"""get_squared_magnitude(_VectorBase4D self) -> double"""
669 return _IMP_kernel._VectorBase4D_get_squared_magnitude(self)
671 def get_magnitude(self):
672 r"""get_magnitude(_VectorBase4D self) -> double"""
673 return _IMP_kernel._VectorBase4D_get_magnitude(self)
676 r"""get_distance(_VectorBase4D self, _VectorBase4D o) -> double"""
677 return _IMP_kernel._VectorBase4D_get_distance(self, o)
679 def __mul__(self, o):
680 r"""__mul__(_VectorBase4D self, _VectorBase4D o) -> double"""
681 return _IMP_kernel._VectorBase4D___mul__(self, o)
683 def __iadd__(self, o):
684 r"""__iadd__(_VectorBase4D self, _VectorBase4D o) -> _VectorBase4D"""
685 return _IMP_kernel._VectorBase4D___iadd__(self, o)
687 def __isub__(self, o):
688 r"""__isub__(_VectorBase4D self, _VectorBase4D o) -> _VectorBase4D"""
689 return _IMP_kernel._VectorBase4D___isub__(self, o)
691 def __itruediv__(self, *args):
692 return _IMP_kernel._VectorBase4D___itruediv__(self, *args)
693 __idiv__ = __itruediv__
697 def __imul__(self, f):
698 r"""__imul__(_VectorBase4D self, double f) -> _VectorBase4D"""
699 return _IMP_kernel._VectorBase4D___imul__(self, f)
701 def show(self, *args):
703 show(_VectorBase4D self, _ostream out, std::string delim, bool parens=True)
704 show(_VectorBase4D self, _ostream out=std::cout)
706 return _IMP_kernel._VectorBase4D_show(self, *args)
708 def get_dimension(self):
709 r"""get_dimension(_VectorBase4D self) -> unsigned int"""
710 return _IMP_kernel._VectorBase4D_get_dimension(self)
711 __swig_destroy__ = _IMP_kernel.delete__VectorBase4D
714 _IMP_kernel._VectorBase4D_swigregister(_VectorBase4D)
715 class _VectorBase5D(_GeometricPrimitive5D):
716 r"""Proxy of C++ IMP::internal::VectorBaseD< 5 > class."""
718 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
719 __repr__ = _swig_repr
722 r"""__init__(_VectorBase5D self) -> _VectorBase5D"""
723 _IMP_kernel._VectorBase5D_swiginit(self, _IMP_kernel.new__VectorBase5D())
725 def get_scalar_product(self, o):
726 r"""get_scalar_product(_VectorBase5D self, _VectorBase5D o) -> double"""
727 return _IMP_kernel._VectorBase5D_get_scalar_product(self, o)
729 def get_squared_magnitude(self):
730 r"""get_squared_magnitude(_VectorBase5D self) -> double"""
731 return _IMP_kernel._VectorBase5D_get_squared_magnitude(self)
733 def get_magnitude(self):
734 r"""get_magnitude(_VectorBase5D self) -> double"""
735 return _IMP_kernel._VectorBase5D_get_magnitude(self)
738 r"""get_distance(_VectorBase5D self, _VectorBase5D o) -> double"""
739 return _IMP_kernel._VectorBase5D_get_distance(self, o)
741 def __mul__(self, o):
742 r"""__mul__(_VectorBase5D self, _VectorBase5D o) -> double"""
743 return _IMP_kernel._VectorBase5D___mul__(self, o)
745 def __iadd__(self, o):
746 r"""__iadd__(_VectorBase5D self, _VectorBase5D o) -> _VectorBase5D"""
747 return _IMP_kernel._VectorBase5D___iadd__(self, o)
749 def __isub__(self, o):
750 r"""__isub__(_VectorBase5D self, _VectorBase5D o) -> _VectorBase5D"""
751 return _IMP_kernel._VectorBase5D___isub__(self, o)
753 def __itruediv__(self, *args):
754 return _IMP_kernel._VectorBase5D___itruediv__(self, *args)
755 __idiv__ = __itruediv__
759 def __imul__(self, f):
760 r"""__imul__(_VectorBase5D self, double f) -> _VectorBase5D"""
761 return _IMP_kernel._VectorBase5D___imul__(self, f)
763 def show(self, *args):
765 show(_VectorBase5D self, _ostream out, std::string delim, bool parens=True)
766 show(_VectorBase5D self, _ostream out=std::cout)
768 return _IMP_kernel._VectorBase5D_show(self, *args)
770 def get_dimension(self):
771 r"""get_dimension(_VectorBase5D self) -> unsigned int"""
772 return _IMP_kernel._VectorBase5D_get_dimension(self)
773 __swig_destroy__ = _IMP_kernel.delete__VectorBase5D
776 _IMP_kernel._VectorBase5D_swigregister(_VectorBase5D)
777 class _VectorBase6D(_GeometricPrimitive6D):
778 r"""Proxy of C++ IMP::internal::VectorBaseD< 6 > class."""
780 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
781 __repr__ = _swig_repr
784 r"""__init__(_VectorBase6D self) -> _VectorBase6D"""
785 _IMP_kernel._VectorBase6D_swiginit(self, _IMP_kernel.new__VectorBase6D())
787 def get_scalar_product(self, o):
788 r"""get_scalar_product(_VectorBase6D self, _VectorBase6D o) -> double"""
789 return _IMP_kernel._VectorBase6D_get_scalar_product(self, o)
791 def get_squared_magnitude(self):
792 r"""get_squared_magnitude(_VectorBase6D self) -> double"""
793 return _IMP_kernel._VectorBase6D_get_squared_magnitude(self)
795 def get_magnitude(self):
796 r"""get_magnitude(_VectorBase6D self) -> double"""
797 return _IMP_kernel._VectorBase6D_get_magnitude(self)
800 r"""get_distance(_VectorBase6D self, _VectorBase6D o) -> double"""
801 return _IMP_kernel._VectorBase6D_get_distance(self, o)
803 def __mul__(self, o):
804 r"""__mul__(_VectorBase6D self, _VectorBase6D o) -> double"""
805 return _IMP_kernel._VectorBase6D___mul__(self, o)
807 def __iadd__(self, o):
808 r"""__iadd__(_VectorBase6D self, _VectorBase6D o) -> _VectorBase6D"""
809 return _IMP_kernel._VectorBase6D___iadd__(self, o)
811 def __isub__(self, o):
812 r"""__isub__(_VectorBase6D self, _VectorBase6D o) -> _VectorBase6D"""
813 return _IMP_kernel._VectorBase6D___isub__(self, o)
815 def __itruediv__(self, *args):
816 return _IMP_kernel._VectorBase6D___itruediv__(self, *args)
817 __idiv__ = __itruediv__
821 def __imul__(self, f):
822 r"""__imul__(_VectorBase6D self, double f) -> _VectorBase6D"""
823 return _IMP_kernel._VectorBase6D___imul__(self, f)
825 def show(self, *args):
827 show(_VectorBase6D self, _ostream out, std::string delim, bool parens=True)
828 show(_VectorBase6D self, _ostream out=std::cout)
830 return _IMP_kernel._VectorBase6D_show(self, *args)
832 def get_dimension(self):
833 r"""get_dimension(_VectorBase6D self) -> unsigned int"""
834 return _IMP_kernel._VectorBase6D_get_dimension(self)
835 __swig_destroy__ = _IMP_kernel.delete__VectorBase6D
838 _IMP_kernel._VectorBase6D_swigregister(_VectorBase6D)
839 class _InputAdaptor(object):
840 r"""Proxy of C++ IMP::InputAdaptor class."""
842 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
844 def __init__(self, *args, **kwargs):
845 raise AttributeError(
"No constructor defined")
846 __repr__ = _swig_repr
848 def __getstate__(self):
849 raise NotImplementedError(str(self.__class__)
850 +
" does not support serialization")
852 __swig_destroy__ = _IMP_kernel.delete__InputAdaptor
855 _IMP_kernel._InputAdaptor_swigregister(_InputAdaptor)
856 class _NonCopyable(object):
857 r"""Proxy of C++ IMP::NonCopyable class."""
859 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
861 def __init__(self, *args, **kwargs):
862 raise AttributeError(
"No constructor defined")
863 __repr__ = _swig_repr
864 __swig_destroy__ = _IMP_kernel.delete__NonCopyable
867 _IMP_kernel._NonCopyable_swigregister(_NonCopyable)
868 class _RAII(_NonCopyable):
869 r"""Proxy of C++ IMP::RAII class."""
871 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
873 def __init__(self, *args, **kwargs):
874 raise AttributeError(
"No constructor defined")
875 __repr__ = _swig_repr
876 __swig_destroy__ = _IMP_kernel.delete__RAII
879 _IMP_kernel._RAII_swigregister(_RAII)
880 class _Value(object):
881 r"""Proxy of C++ IMP::Value class."""
883 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
885 def __init__(self, *args, **kwargs):
886 raise AttributeError(
"No constructor defined")
887 __repr__ = _swig_repr
889 def __getstate__(self):
890 raise NotImplementedError(str(self.__class__)
891 +
" does not support serialization")
893 __swig_destroy__ = _IMP_kernel.delete__Value
896 _IMP_kernel._Value_swigregister(_Value)
899 r"""get_executable_name() -> std::string"""
900 return _IMP_kernel.get_executable_name()
904 setup_from_argv(IMP::Strings const & argv, std::string description)
905 setup_from_argv(IMP::Strings const & argv, std::string description, std::string positional_description, int num_positional) -> IMP::Strings
907 return _IMP_kernel.setup_from_argv(*args)
910 r"""add_string_flag(std::string name, std::string default_value, std::string description)"""
911 return _IMP_kernel.add_string_flag(name, default_value, description)
914 r"""get_string_flag(std::string name) -> std::string"""
915 return _IMP_kernel.get_string_flag(name)
918 r"""add_int_flag(std::string name, size_t default_value, std::string description)"""
919 return _IMP_kernel.add_int_flag(name, default_value, description)
922 r"""get_int_flag(std::string name) -> size_t"""
923 return _IMP_kernel.get_int_flag(name)
926 r"""add_bool_flag(std::string name, std::string description)"""
927 return _IMP_kernel.add_bool_flag(name, description)
930 r"""get_bool_flag(std::string name) -> bool"""
931 return _IMP_kernel.get_bool_flag(name)
934 r"""add_float_flag(std::string name, double default_value, std::string description)"""
935 return _IMP_kernel.add_float_flag(name, default_value, description)
938 r"""get_float_flag(std::string name) -> double"""
939 return _IMP_kernel.get_float_flag(name)
942 r"""write_help(_ostream out=std::cerr)"""
943 return _IMP_kernel.write_help(*args)
946 r"""get_is_quick_test() -> bool"""
947 return _IMP_kernel.get_is_quick_test()
948 DEFAULT = _IMP_kernel.DEFAULT
950 SILENT = _IMP_kernel.SILENT
952 WARNING = _IMP_kernel.WARNING
954 PROGRESS = _IMP_kernel.PROGRESS
956 TERSE = _IMP_kernel.TERSE
958 VERBOSE = _IMP_kernel.VERBOSE
960 MEMORY = _IMP_kernel.MEMORY
962 ALL_LOG = _IMP_kernel.ALL_LOG
964 class VersionInfo(_Value):
965 r"""Proxy of C++ IMP::VersionInfo class."""
967 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
969 def __init__(self, *args):
971 __init__(VersionInfo self, std::string module, std::string version) -> VersionInfo
972 __init__(VersionInfo self) -> VersionInfo
974 _IMP_kernel.VersionInfo_swiginit(self, _IMP_kernel.new_VersionInfo(*args))
976 def get_module(self):
977 r"""get_module(VersionInfo self) -> std::string"""
978 return _IMP_kernel.VersionInfo_get_module(self)
980 def get_version(self):
981 r"""get_version(VersionInfo self) -> std::string"""
982 return _IMP_kernel.VersionInfo_get_version(self)
984 def show(self, *args):
985 r"""show(VersionInfo self, _ostream out=std::cout)"""
986 return _IMP_kernel.VersionInfo_show(self, *args)
989 r"""__eq__(VersionInfo self, VersionInfo o) -> bool"""
990 return _IMP_kernel.VersionInfo___eq__(self, o)
993 r"""__ne__(VersionInfo self, VersionInfo o) -> bool"""
994 return _IMP_kernel.VersionInfo___ne__(self, o)
997 r"""__lt__(VersionInfo self, VersionInfo o) -> bool"""
998 return _IMP_kernel.VersionInfo___lt__(self, o)
1000 def __gt__(self, o):
1001 r"""__gt__(VersionInfo self, VersionInfo o) -> bool"""
1002 return _IMP_kernel.VersionInfo___gt__(self, o)
1004 def __ge__(self, o):
1005 r"""__ge__(VersionInfo self, VersionInfo o) -> bool"""
1006 return _IMP_kernel.VersionInfo___ge__(self, o)
1008 def __le__(self, o):
1009 r"""__le__(VersionInfo self, VersionInfo o) -> bool"""
1010 return _IMP_kernel.VersionInfo___le__(self, o)
1013 r"""__str__(VersionInfo self) -> std::string"""
1014 return _IMP_kernel.VersionInfo___str__(self)
1017 r"""__repr__(VersionInfo self) -> std::string"""
1018 return _IMP_kernel.VersionInfo___repr__(self)
1020 def _get_as_binary(self):
1021 r"""_get_as_binary(VersionInfo self) -> PyObject *"""
1022 return _IMP_kernel.VersionInfo__get_as_binary(self)
1024 def _set_from_binary(self, p):
1025 r"""_set_from_binary(VersionInfo self, PyObject * p)"""
1026 return _IMP_kernel.VersionInfo__set_from_binary(self, p)
1028 def __getstate__(self):
1029 p = self._get_as_binary()
1030 if len(self.__dict__) > 1:
1031 d = self.__dict__.copy()
1036 def __setstate__(self, p):
1037 if not hasattr(self,
'this'):
1039 if isinstance(p, tuple):
1041 self.__dict__.update(d)
1042 return self._set_from_binary(p)
1044 __swig_destroy__ = _IMP_kernel.delete_VersionInfo
1047 _IMP_kernel.VersionInfo_swigregister(VersionInfo)
1048 class TextOutput(_InputAdaptor):
1049 r"""Proxy of C++ IMP::TextOutput class."""
1051 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1052 __repr__ = _swig_repr
1054 def __init__(self, *args):
1056 __init__(TextOutput self, int arg2) -> TextOutput
1057 __init__(TextOutput self, double arg2) -> TextOutput
1058 __init__(TextOutput self, char const * c, bool append=False) -> TextOutput
1059 __init__(TextOutput self, IMP::TextProxy< std::ostream > p) -> TextOutput
1060 __init__(TextOutput self) -> TextOutput
1061 __init__(TextOutput self, std::string file_name, bool append=False) -> TextOutput
1063 _IMP_kernel.TextOutput_swiginit(self, _IMP_kernel.new_TextOutput(*args))
1065 def show(self, *args):
1066 r"""show(TextOutput self, _ostream out=std::cout)"""
1067 return _IMP_kernel.TextOutput_show(self, *args)
1070 r"""get_name(TextOutput self) -> std::string"""
1071 return _IMP_kernel.TextOutput_get_name(self)
1072 __swig_destroy__ = _IMP_kernel.delete_TextOutput
1075 _IMP_kernel.TextOutput_swigregister(TextOutput)
1076 class TextInput(_InputAdaptor):
1077 r"""Proxy of C++ IMP::TextInput class."""
1079 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1080 __repr__ = _swig_repr
1082 def __init__(self, *args):
1084 __init__(TextInput self, int arg2) -> TextInput
1085 __init__(TextInput self, double arg2) -> TextInput
1086 __init__(TextInput self, char const * c) -> TextInput
1087 __init__(TextInput self, IMP::TextProxy< std::istream > p) -> TextInput
1088 __init__(TextInput self) -> TextInput
1089 __init__(TextInput self, std::string file_name) -> TextInput
1091 _IMP_kernel.TextInput_swiginit(self, _IMP_kernel.new_TextInput(*args))
1093 def show(self, *args):
1094 r"""show(TextInput self, _ostream out=std::cout)"""
1095 return _IMP_kernel.TextInput_show(self, *args)
1098 r"""get_name(TextInput self) -> std::string"""
1099 return _IMP_kernel.TextInput_get_name(self)
1101 def set_binary_open_mode(self, binary):
1102 r"""set_binary_open_mode(TextInput self, bool binary)"""
1103 return _IMP_kernel.TextInput_set_binary_open_mode(self, binary)
1104 __swig_destroy__ = _IMP_kernel.delete_TextInput
1107 _IMP_kernel.TextInput_swigregister(TextInput)
1108 class SetLogTarget(_RAII):
1109 r"""Proxy of C++ IMP::SetLogTarget class."""
1111 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1113 def __init__(self, *args):
1115 __init__(SetLogTarget self) -> SetLogTarget
1116 __init__(SetLogTarget self, TextOutput to) -> SetLogTarget
1118 _IMP_kernel.SetLogTarget_swiginit(self, _IMP_kernel.new_SetLogTarget(*args))
1121 r"""set(SetLogTarget self, TextOutput to)"""
1122 return _IMP_kernel.SetLogTarget_set(self, to)
1125 r"""reset(SetLogTarget self)"""
1126 return _IMP_kernel.SetLogTarget_reset(self)
1127 __swig_destroy__ = _IMP_kernel.delete_SetLogTarget
1129 def show(self, *args):
1130 r"""show(SetLogTarget self, _ostream out=std::cout)"""
1131 return _IMP_kernel.SetLogTarget_show(self, *args)
1133 def __enter__(self):
1135 def __exit__(self, exc_type, exc_val, exc_tb):
1141 r"""__str__(SetLogTarget self) -> std::string"""
1142 return _IMP_kernel.SetLogTarget___str__(self)
1145 r"""__repr__(SetLogTarget self) -> std::string"""
1146 return _IMP_kernel.SetLogTarget___repr__(self)
1149 _IMP_kernel.SetLogTarget_swigregister(SetLogTarget)
1152 r"""create_temporary_file(std::string prefix="imp_temp", std::string suffix="") -> TextOutput"""
1153 return _IMP_kernel.create_temporary_file(*args)
1156 r"""create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="") -> std::string"""
1157 return _IMP_kernel.create_temporary_file_name(*args)
1160 r"""get_relative_path(std::string base, std::string relative) -> std::string"""
1161 return _IMP_kernel.get_relative_path(base, relative)
1164 r"""get_absolute_path(std::string file) -> std::string"""
1165 return _IMP_kernel.get_absolute_path(file)
1167 def push_log_context(functionname, object):
1168 r"""push_log_context(char const * functionname, void const * object)"""
1169 return _IMP_kernel.push_log_context(functionname, object)
1171 def pop_log_context():
1172 r"""pop_log_context()"""
1173 return _IMP_kernel.pop_log_context()
1177 add_to_log(std::string to_write)
1178 add_to_log(IMP::LogLevel level, std::string to_write)
1180 return _IMP_kernel.add_to_log(*args)
1183 r"""set_log_level(IMP::LogLevel l)"""
1184 return _IMP_kernel.set_log_level(l)
1187 r"""set_log_timer(bool tb)"""
1188 return _IMP_kernel.set_log_timer(tb)
1191 r"""reset_log_timer()"""
1192 return _IMP_kernel.reset_log_timer()
1195 r"""get_log_level() -> IMP::LogLevel"""
1196 return _IMP_kernel.get_log_level()
1199 r"""set_progress_display(std::string description, unsigned int steps)"""
1200 return _IMP_kernel.set_progress_display(description, steps)
1203 r"""add_to_progress_display(unsigned int step=1)"""
1204 return _IMP_kernel.add_to_progress_display(step)
1205 class Object(_NonCopyable):
1206 r"""Proxy of C++ IMP::Object class."""
1208 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1210 def __init__(self, name):
1211 r"""__init__(Object self, std::string name) -> Object"""
1212 if self.__class__ == Object:
1216 _IMP_kernel.Object_swiginit(self, _IMP_kernel.new_Object(_self, name))
1218 if self.__class__ != Object:
1219 _director_objects.register(self)
1223 __swig_destroy__ = _IMP_kernel.delete_Object
1226 r"""__hash__(Object self) -> std::size_t"""
1227 return _IMP_kernel.Object___hash__(self)
1230 r"""set_log_level(Object self, IMP::LogLevel l)"""
1231 return _IMP_kernel.Object_set_log_level(self, l)
1234 r"""set_check_level(Object self, IMP::CheckLevel l)"""
1235 return _IMP_kernel.Object_set_check_level(self, l)
1238 r"""get_log_level(Object self) -> IMP::LogLevel"""
1239 return _IMP_kernel.Object_get_log_level(self)
1242 r"""get_check_level(Object self) -> IMP::CheckLevel"""
1243 return _IMP_kernel.Object_get_check_level(self)
1245 def get_version_info(self):
1246 r"""get_version_info(Object self) -> VersionInfo"""
1247 val = _IMP_kernel.Object_get_version_info(self)
1248 if val.get_module() ==
'none':
1255 r"""get_name(Object self) -> std::string const &"""
1256 return _IMP_kernel.Object_get_name(self)
1258 def set_name(self, name):
1259 r"""set_name(Object self, std::string name)"""
1260 return _IMP_kernel.Object_set_name(self, name)
1262 def get_type_name(self):
1263 r"""get_type_name(Object self) -> std::string"""
1264 val = _IMP_kernel.Object_get_type_name(self)
1265 if val ==
'unknown object type':
1266 val = self.__class__.__name__
1269 def set_was_used(self, tf):
1270 r"""set_was_used(Object self, bool tf)"""
1271 return _IMP_kernel.Object_set_was_used(self, tf)
1273 def show(self, *args):
1274 r"""show(Object self, _ostream out=std::cout)"""
1275 return _IMP_kernel.Object_show(self, *args)
1277 def get_string(self):
1278 r"""get_string(Object self) -> std::string"""
1279 return _IMP_kernel.Object_get_string(self)
1281 def _on_destruction(self):
1282 r"""_on_destruction(Object self)"""
1283 return _IMP_kernel.Object__on_destruction(self)
1285 def get_is_valid(self):
1286 r"""get_is_valid(Object self) -> bool"""
1287 return _IMP_kernel.Object_get_is_valid(self)
1289 def get_ref_count(self):
1290 r"""get_ref_count(Object self) -> unsigned int"""
1291 return _IMP_kernel.Object_get_ref_count(self)
1294 def get_number_of_live_objects():
1295 r"""get_number_of_live_objects() -> unsigned int"""
1296 return _IMP_kernel.Object_get_number_of_live_objects()
1298 def get_is_shared(self):
1299 r"""get_is_shared(Object self) -> bool"""
1300 return _IMP_kernel.Object_get_is_shared(self)
1302 def clear_caches(self):
1303 r"""clear_caches(Object self)"""
1304 return _IMP_kernel.Object_clear_caches(self)
1306 def do_destroy(self):
1307 r"""do_destroy(Object self)"""
1308 return _IMP_kernel.Object_do_destroy(self)
1310 def __getstate__(self):
1311 raise NotImplementedError(str(self.__class__)
1312 +
" does not support serialization")
1315 def __eq__(self, o):
1316 r"""__eq__(Object self, Object o) -> bool"""
1317 return _IMP_kernel.Object___eq__(self, o)
1319 def __ne__(self, o):
1320 r"""__ne__(Object self, Object o) -> bool"""
1321 return _IMP_kernel.Object___ne__(self, o)
1323 def __le__(self, o):
1324 r"""__le__(Object self, Object o) -> bool"""
1325 return _IMP_kernel.Object___le__(self, o)
1327 def __lt__(self, o):
1328 r"""__lt__(Object self, Object o) -> bool"""
1329 return _IMP_kernel.Object___lt__(self, o)
1331 def __ge__(self, o):
1332 r"""__ge__(Object self, Object o) -> bool"""
1333 return _IMP_kernel.Object___ge__(self, o)
1335 def __gt__(self, o):
1336 r"""__gt__(Object self, Object o) -> bool"""
1337 return _IMP_kernel.Object___gt__(self, o)
1339 def _get_director_object(self):
1340 r"""_get_director_object(Object self) -> PyObject *"""
1341 return _IMP_kernel.Object__get_director_object(self)
1344 """Return this object cast to the most derived subclass."""
1346 pyobj = self._get_director_object()
1347 if pyobj
is not None:
1351 modname = self.get_version_info().get_module().replace(
'::',
'.')
1352 type_name = self.get_type_name()
1353 if (modname ==
'IMP.core'
1354 and type_name ==
'GenericBoundingBox3DSingletonScore'):
1355 type_name =
'BoundingBox3DSingletonScore'
1356 elif (modname ==
'IMP.core'
1357 and type_name ==
'GenericAttributeSingletonScore'):
1358 type_name =
'AttributeSingletonScore'
1359 elif (modname ==
'IMP.core'
1360 and type_name ==
'GenericBoundingSphere3DSingletonScore'):
1361 type_name =
'BoundingSphere3DSingletonScore'
1362 elif modname ==
'IMP' and type_name ==
'RestraintScoringFunction':
1366 elif modname ==
'IMP' and type_name ==
'GenericRestraintsScoringFunction':
1368 if self.get_single_restraint():
1371 type_name =
'_RestraintsScoringFunction'
1372 modobj = sys.modules[modname]
1373 clsobj = getattr(modobj, type_name)
1374 return clsobj.get_from(self)
1378 r"""__str__(Object self) -> std::string"""
1379 return _IMP_kernel.Object___str__(self)
1382 r"""__repr__(Object self) -> std::string"""
1383 return _IMP_kernel.Object___repr__(self)
1387 return _object_cast_to_Object(o)
1389 def __disown__(self):
1391 _IMP_kernel.disown_Object(self)
1392 return weakref.proxy(self)
1395 _IMP_kernel.Object_swigregister(Object)
1396 class SetLogState(_RAII):
1397 r"""Proxy of C++ IMP::SetLogState class."""
1399 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1402 r"""reset(SetLogState self)"""
1403 return _IMP_kernel.SetLogState_reset(self)
1404 __swig_destroy__ = _IMP_kernel.delete_SetLogState
1406 def show(self, *args):
1407 r"""show(SetLogState self, _ostream out=std::cout)"""
1408 return _IMP_kernel.SetLogState_show(self, *args)
1410 def __init__(self, *args):
1412 __init__(SetLogState self) -> SetLogState
1413 __init__(SetLogState self, Object o, IMP::LogLevel l) -> SetLogState
1414 __init__(SetLogState self, IMP::LogLevel l) -> SetLogState
1416 _IMP_kernel.SetLogState_swiginit(self, _IMP_kernel.new_SetLogState(*args))
1418 def set(self, *args):
1420 set(SetLogState self, Object o, IMP::LogLevel l)
1421 set(SetLogState self, IMP::LogLevel l)
1423 return _IMP_kernel.SetLogState_set(self, *args)
1425 def __enter__(self):
1427 def __exit__(self, exc_type, exc_val, exc_tb):
1433 r"""__str__(SetLogState self) -> std::string"""
1434 return _IMP_kernel.SetLogState___str__(self)
1437 r"""__repr__(SetLogState self) -> std::string"""
1438 return _IMP_kernel.SetLogState___repr__(self)
1441 _IMP_kernel.SetLogState_swigregister(SetLogState)
1442 class WarningContext(object):
1443 r"""Proxy of C++ IMP::WarningContext class."""
1445 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1446 data_ = property(_IMP_kernel.WarningContext_data__get, _IMP_kernel.WarningContext_data__set, doc=
r"""data_ : boost::unordered_set<(std::string)>""")
1448 def add_warning(self, key, warning):
1449 r"""add_warning(WarningContext self, std::string key, std::string warning)"""
1450 return _IMP_kernel.WarningContext_add_warning(self, key, warning)
1452 def clear_warnings(self):
1453 r"""clear_warnings(WarningContext self)"""
1454 return _IMP_kernel.WarningContext_clear_warnings(self)
1456 def dump_warnings(self):
1457 r"""dump_warnings(WarningContext self)"""
1458 return _IMP_kernel.WarningContext_dump_warnings(self)
1459 __swig_destroy__ = _IMP_kernel.delete_WarningContext
1461 def show(self, *args):
1462 r"""show(WarningContext self, _ostream out=std::cout)"""
1463 return _IMP_kernel.WarningContext_show(self, *args)
1465 def __enter__(self):
1467 def __exit__(self, exc_type, exc_val, exc_tb):
1473 r"""__str__(WarningContext self) -> std::string"""
1474 return _IMP_kernel.WarningContext___str__(self)
1477 r"""__repr__(WarningContext self) -> std::string"""
1478 return _IMP_kernel.WarningContext___repr__(self)
1481 r"""__init__(WarningContext self) -> WarningContext"""
1482 _IMP_kernel.WarningContext_swiginit(self, _IMP_kernel.new_WarningContext())
1485 _IMP_kernel.WarningContext_swigregister(WarningContext)
1486 class CreateLogContext(_RAII):
1487 r"""Proxy of C++ IMP::CreateLogContext class."""
1489 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1491 def __init__(self, *args):
1493 __init__(CreateLogContext self, std::string fname, Object object=None) -> CreateLogContext
1494 __init__(CreateLogContext self) -> CreateLogContext
1495 __init__(CreateLogContext self, char const * fname, Object object=None) -> CreateLogContext
1497 _IMP_kernel.CreateLogContext_swiginit(self, _IMP_kernel.new_CreateLogContext(*args))
1499 def set(self, fname, object=None):
1500 r"""set(CreateLogContext self, char const * fname, Object object=None)"""
1501 return _IMP_kernel.CreateLogContext_set(self, fname, object)
1504 r"""reset(CreateLogContext self)"""
1505 return _IMP_kernel.CreateLogContext_reset(self)
1506 __swig_destroy__ = _IMP_kernel.delete_CreateLogContext
1508 def show(self, *args):
1509 r"""show(CreateLogContext self, _ostream out=std::cout)"""
1510 return _IMP_kernel.CreateLogContext_show(self, *args)
1512 def __enter__(self):
1514 def __exit__(self, exc_type, exc_val, exc_tb):
1520 r"""__str__(CreateLogContext self) -> std::string"""
1521 return _IMP_kernel.CreateLogContext___str__(self)
1524 r"""__repr__(CreateLogContext self) -> std::string"""
1525 return _IMP_kernel.CreateLogContext___repr__(self)
1528 _IMP_kernel.CreateLogContext_swigregister(CreateLogContext)
1529 class SetCheckState(_RAII):
1530 r"""Proxy of C++ IMP::SetCheckState class."""
1532 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1535 r"""reset(SetCheckState self)"""
1536 return _IMP_kernel.SetCheckState_reset(self)
1537 __swig_destroy__ = _IMP_kernel.delete_SetCheckState
1539 def show(self, *args):
1540 r"""show(SetCheckState self, _ostream out=std::cout)"""
1541 return _IMP_kernel.SetCheckState_show(self, *args)
1543 def __init__(self, *args):
1545 __init__(SetCheckState self) -> SetCheckState
1546 __init__(SetCheckState self, Object o, IMP::CheckLevel l) -> SetCheckState
1547 __init__(SetCheckState self, IMP::CheckLevel l) -> SetCheckState
1549 _IMP_kernel.SetCheckState_swiginit(self, _IMP_kernel.new_SetCheckState(*args))
1551 def set(self, *args):
1553 set(SetCheckState self, Object o, IMP::CheckLevel l)
1554 set(SetCheckState self, IMP::CheckLevel l)
1556 return _IMP_kernel.SetCheckState_set(self, *args)
1558 def __enter__(self):
1560 def __exit__(self, exc_type, exc_val, exc_tb):
1566 r"""__str__(SetCheckState self) -> std::string"""
1567 return _IMP_kernel.SetCheckState___str__(self)
1570 r"""__repr__(SetCheckState self) -> std::string"""
1571 return _IMP_kernel.SetCheckState___repr__(self)
1574 _IMP_kernel.SetCheckState_swigregister(SetCheckState)
1577 r"""get_unique_name(std::string templ) -> std::string"""
1578 return _IMP_kernel.get_unique_name(templ)
1581 r"""get_copyright() -> std::string"""
1582 return _IMP_kernel.get_copyright()
1583 class _Protection(object):
1584 r"""Proxy of C++ IMP::internal::_Protection class."""
1586 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1588 def __init__(self, *args, **kwargs):
1589 raise AttributeError(
"No constructor defined")
1591 def show(self, *args):
1592 r"""show(_Protection self, _ostream out=std::cout)"""
1593 return _IMP_kernel._Protection_show(self, *args)
1596 r"""__str__(_Protection self) -> std::string"""
1597 return _IMP_kernel._Protection___str__(self)
1600 r"""__repr__(_Protection self) -> std::string"""
1601 return _IMP_kernel._Protection___repr__(self)
1602 __swig_destroy__ = _IMP_kernel.delete__Protection
1605 _IMP_kernel._Protection_swigregister(_Protection)
1609 return _IMP_kernel._test_log()
1611 def _test_intranges(ips):
1612 r"""_test_intranges(IMP::IntRanges const & ips) -> int"""
1613 return _IMP_kernel._test_intranges(ips)
1615 def _test_intrange(*args):
1617 _test_intrange(IMP::IntRange const & ips) -> IMP::IntRange
1618 _test_intrange() -> IMP::IntRange
1620 return _IMP_kernel._test_intrange(*args)
1623 r"""_test_ifile(TextInput a) -> std::string"""
1624 return _IMP_kernel._test_ifile(a)
1627 r"""_test_ofile(TextOutput a) -> std::string"""
1628 return _IMP_kernel._test_ofile(a)
1630 def _test_ifile_overloaded(*args):
1632 _test_ifile_overloaded(TextInput a, int i) -> std::string
1633 _test_ifile_overloaded(TextInput a, std::string st) -> std::string
1635 return _IMP_kernel._test_ifile_overloaded(*args)
1637 def _test_ofile_overloaded(*args):
1639 _test_ofile_overloaded(TextOutput a, int i) -> std::string
1640 _test_ofile_overloaded(TextOutput a, std::string st) -> std::string
1642 return _IMP_kernel._test_ofile_overloaded(*args)
1643 class _TestValue(object):
1644 r"""Proxy of C++ IMP::internal::_TestValue class."""
1646 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1648 def __init__(self, i):
1649 r"""__init__(_TestValue self, int i) -> _TestValue"""
1650 _IMP_kernel._TestValue_swiginit(self, _IMP_kernel.new__TestValue(i))
1652 def show(self, *args):
1653 r"""show(_TestValue self, _ostream out=std::cout)"""
1654 return _IMP_kernel._TestValue_show(self, *args)
1656 def __eq__(self, o):
1657 r"""__eq__(_TestValue self, _TestValue o) -> bool"""
1658 return _IMP_kernel._TestValue___eq__(self, o)
1660 def __ne__(self, o):
1661 r"""__ne__(_TestValue self, _TestValue o) -> bool"""
1662 return _IMP_kernel._TestValue___ne__(self, o)
1664 def __lt__(self, o):
1665 r"""__lt__(_TestValue self, _TestValue o) -> bool"""
1666 return _IMP_kernel._TestValue___lt__(self, o)
1668 def __gt__(self, o):
1669 r"""__gt__(_TestValue self, _TestValue o) -> bool"""
1670 return _IMP_kernel._TestValue___gt__(self, o)
1672 def __ge__(self, o):
1673 r"""__ge__(_TestValue self, _TestValue o) -> bool"""
1674 return _IMP_kernel._TestValue___ge__(self, o)
1676 def __le__(self, o):
1677 r"""__le__(_TestValue self, _TestValue o) -> bool"""
1678 return _IMP_kernel._TestValue___le__(self, o)
1681 r"""get(_TestValue self) -> int"""
1682 return _IMP_kernel._TestValue_get(self)
1684 def get_float(self):
1685 r"""get_float(_TestValue self) -> float const &"""
1686 return _IMP_kernel._TestValue_get_float(self)
1688 def get_double(self):
1689 r"""get_double(_TestValue self) -> double const &"""
1690 return _IMP_kernel._TestValue_get_double(self)
1692 def get_Float(self):
1693 r"""get_Float(_TestValue self) -> IMP::Float const &"""
1694 return _IMP_kernel._TestValue_get_Float(self)
1697 r"""get_int(_TestValue self) -> int const &"""
1698 return _IMP_kernel._TestValue_get_int(self)
1701 r"""get_Int(_TestValue self) -> IMP::Int const &"""
1702 return _IMP_kernel._TestValue_get_Int(self)
1704 def get_string(self):
1705 r"""get_string(_TestValue self) -> std::string const &"""
1706 return _IMP_kernel._TestValue_get_string(self)
1708 def get_String(self):
1709 r"""get_String(_TestValue self) -> IMP::String const &"""
1710 return _IMP_kernel._TestValue_get_String(self)
1713 r"""__str__(_TestValue self) -> std::string"""
1714 return _IMP_kernel._TestValue___str__(self)
1717 r"""__repr__(_TestValue self) -> std::string"""
1718 return _IMP_kernel._TestValue___repr__(self)
1719 __swig_destroy__ = _IMP_kernel.delete__TestValue
1722 _IMP_kernel._TestValue_swigregister(_TestValue)
1724 def _pass_plain_pair(p):
1725 r"""_pass_plain_pair(IMP::FloatPair p) -> IMP::FloatPair"""
1726 return _IMP_kernel._pass_plain_pair(p)
1728 def _pass_overloaded_strings(*args):
1730 _pass_overloaded_strings(IMP::Strings const & a, int arg2) -> IMP::Strings
1731 _pass_overloaded_strings(IMP::Strings const & a) -> IMP::Strings
1733 return _IMP_kernel._pass_overloaded_strings(*args)
1736 r"""_pass_pair(IMP::DerivativePair const & p) -> IMP::DerivativePair"""
1737 return _IMP_kernel._pass_pair(p)
1739 def _pass_floats(input):
1740 r"""_pass_floats(IMP::Floats const & input) -> IMP::Floats"""
1741 return _IMP_kernel._pass_floats(input)
1743 def _pass_ints(input):
1744 r"""_pass_ints(IMP::Ints input) -> IMP::Ints"""
1745 return _IMP_kernel._pass_ints(input)
1747 def _pass_ints_list(input):
1748 r"""_pass_ints_list(IMP::IntsList const & input) -> IMP::IntsList"""
1749 return _IMP_kernel._pass_ints_list(input)
1751 def _pass_ints_lists(input):
1752 r"""_pass_ints_lists(IMP::IntsLists const & input) -> IMP::IntsLists"""
1753 return _IMP_kernel._pass_ints_lists(input)
1755 def _pass_strings(input):
1756 r"""_pass_strings(IMP::Strings const & input) -> IMP::Strings const &"""
1757 return _IMP_kernel._pass_strings(input)
1758 class _TestObject(
Object):
1759 r"""Proxy of C++ IMP::internal::_TestObject class."""
1761 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1764 r"""__init__(_TestObject self) -> _TestObject"""
1765 _IMP_kernel._TestObject_swiginit(self, _IMP_kernel.new__TestObject())
1768 r"""get_version_info(_TestObject self) -> VersionInfo"""
1769 return _IMP_kernel._TestObject_get_version_info(self)
1770 __swig_destroy__ = _IMP_kernel.delete__TestObject
1773 r"""__str__(_TestObject self) -> std::string"""
1774 return _IMP_kernel._TestObject___str__(self)
1777 r"""__repr__(_TestObject self) -> std::string"""
1778 return _IMP_kernel._TestObject___repr__(self)
1782 return _object_cast_to__TestObject(o)
1786 _IMP_kernel._TestObject_swigregister(_TestObject)
1789 r"""get_live_object_names() -> IMP::Strings"""
1790 return _IMP_kernel.get_live_object_names()
1793 r"""get_live_objects() -> IMP::Objects"""
1794 return _IMP_kernel.get_live_objects()
1797 r"""set_show_leaked_objects(bool tf)"""
1798 return _IMP_kernel.set_show_leaked_objects(tf)
1801 r"""set_deprecation_warnings(bool tf)"""
1802 return _IMP_kernel.set_deprecation_warnings(tf)
1805 r"""set_deprecation_exceptions(bool tf)"""
1806 return _IMP_kernel.set_deprecation_exceptions(tf)
1809 r"""get_deprecation_exceptions() -> bool"""
1810 return _IMP_kernel.get_deprecation_exceptions()
1813 r"""handle_use_deprecated(std::string message)"""
1814 return _IMP_kernel.handle_use_deprecated(message)
1817 r"""get_number_of_threads() -> unsigned int"""
1818 return _IMP_kernel.get_number_of_threads()
1821 r"""set_number_of_threads(unsigned int n)"""
1822 return _IMP_kernel.set_number_of_threads(n)
1823 class SetNumberOfThreads(_RAII):
1824 r"""Proxy of C++ IMP::SetNumberOfThreads class."""
1826 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1828 def __init__(self, *args):
1830 __init__(SetNumberOfThreads self) -> SetNumberOfThreads
1831 __init__(SetNumberOfThreads self, unsigned int n) -> SetNumberOfThreads
1833 _IMP_kernel.SetNumberOfThreads_swiginit(self, _IMP_kernel.new_SetNumberOfThreads(*args))
1836 r"""set(SetNumberOfThreads self, unsigned int n)"""
1837 return _IMP_kernel.SetNumberOfThreads_set(self, n)
1840 r"""reset(SetNumberOfThreads self)"""
1841 return _IMP_kernel.SetNumberOfThreads_reset(self)
1842 __swig_destroy__ = _IMP_kernel.delete_SetNumberOfThreads
1844 def show(self, *args):
1845 r"""show(SetNumberOfThreads self, _ostream out=std::cout)"""
1846 return _IMP_kernel.SetNumberOfThreads_show(self, *args)
1848 def __enter__(self):
1850 def __exit__(self, exc_type, exc_val, exc_tb):
1856 r"""__str__(SetNumberOfThreads self) -> std::string"""
1857 return _IMP_kernel.SetNumberOfThreads___str__(self)
1860 r"""__repr__(SetNumberOfThreads self) -> std::string"""
1861 return _IMP_kernel.SetNumberOfThreads___repr__(self)
1864 _IMP_kernel.SetNumberOfThreads_swigregister(SetNumberOfThreads)
1867 i_m_p=
"IMP_MODULE_PATH"
1868 if i_m_p
in os.environ.keys():
1869 __path__.insert(0, os.environ[i_m_p])
1871 def _forward_add_attribute(self, name, value, opt=None):
1873 self.get_particle().add_attribute(name, value, opt)
1875 self.get_particle().add_attribute(name, value)
1876 def _forward_get_value(self, name):
1877 self.get_particle().get_value(name)
1878 def _forward_set_value(self, name, value):
1879 self.get_particle().set_value(name, value)
1885 _object_types.append(
"Constraint")
1888 def _object_cast_to_Constraint(o):
1889 r"""_object_cast_to_Constraint(Object o) -> Constraint"""
1890 return _IMP_kernel._object_cast_to_Constraint(o)
1892 _object_types.append(
"Undecorator")
1895 def _object_cast_to_Undecorator(o):
1896 r"""_object_cast_to_Undecorator(Object o) -> Undecorator"""
1897 return _IMP_kernel._object_cast_to_Undecorator(o)
1899 _object_types.append(
"Container")
1902 def _object_cast_to_Container(o):
1903 r"""_object_cast_to_Container(Object o) -> Container"""
1904 return _IMP_kernel._object_cast_to_Container(o)
1906 _object_types.append(
"Optimizer")
1909 def _object_cast_to_Optimizer(o):
1910 r"""_object_cast_to_Optimizer(Object o) -> Optimizer"""
1911 return _IMP_kernel._object_cast_to_Optimizer(o)
1913 _object_types.append(
"AttributeOptimizer")
1916 def _object_cast_to_AttributeOptimizer(o):
1917 r"""_object_cast_to_AttributeOptimizer(Object o) -> AttributeOptimizer"""
1918 return _IMP_kernel._object_cast_to_AttributeOptimizer(o)
1920 _object_types.append(
"OptimizerState")
1923 def _object_cast_to_OptimizerState(o):
1924 r"""_object_cast_to_OptimizerState(Object o) -> OptimizerState"""
1925 return _IMP_kernel._object_cast_to_OptimizerState(o)
1927 _object_types.append(
"PairContainer")
1930 def _object_cast_to_PairContainer(o):
1931 r"""_object_cast_to_PairContainer(Object o) -> PairContainer"""
1932 return _IMP_kernel._object_cast_to_PairContainer(o)
1934 _object_types.append(
"PairModifier")
1937 def _object_cast_to_PairModifier(o):
1938 r"""_object_cast_to_PairModifier(Object o) -> PairModifier"""
1939 return _IMP_kernel._object_cast_to_PairModifier(o)
1941 _object_types.append(
"PairScore")
1944 def _object_cast_to_PairScore(o):
1945 r"""_object_cast_to_PairScore(Object o) -> PairScore"""
1946 return _IMP_kernel._object_cast_to_PairScore(o)
1948 _object_types.append(
"QuadContainer")
1951 def _object_cast_to_QuadContainer(o):
1952 r"""_object_cast_to_QuadContainer(Object o) -> QuadContainer"""
1953 return _IMP_kernel._object_cast_to_QuadContainer(o)
1955 _object_types.append(
"QuadModifier")
1958 def _object_cast_to_QuadModifier(o):
1959 r"""_object_cast_to_QuadModifier(Object o) -> QuadModifier"""
1960 return _IMP_kernel._object_cast_to_QuadModifier(o)
1962 _object_types.append(
"QuadScore")
1965 def _object_cast_to_QuadScore(o):
1966 r"""_object_cast_to_QuadScore(Object o) -> QuadScore"""
1967 return _IMP_kernel._object_cast_to_QuadScore(o)
1969 _object_types.append(
"Refiner")
1972 def _object_cast_to_Refiner(o):
1973 r"""_object_cast_to_Refiner(Object o) -> Refiner"""
1974 return _IMP_kernel._object_cast_to_Refiner(o)
1976 _object_types.append(
"Restraint")
1979 def _object_cast_to_Restraint(o):
1980 r"""_object_cast_to_Restraint(Object o) -> Restraint"""
1981 return _IMP_kernel._object_cast_to_Restraint(o)
1983 _object_types.append(
"Sampler")
1986 def _object_cast_to_Sampler(o):
1987 r"""_object_cast_to_Sampler(Object o) -> Sampler"""
1988 return _IMP_kernel._object_cast_to_Sampler(o)
1990 _object_types.append(
"ScoreState")
1993 def _object_cast_to_ScoreState(o):
1994 r"""_object_cast_to_ScoreState(Object o) -> ScoreState"""
1995 return _IMP_kernel._object_cast_to_ScoreState(o)
1997 _object_types.append(
"SingletonContainer")
2000 def _object_cast_to_SingletonContainer(o):
2001 r"""_object_cast_to_SingletonContainer(Object o) -> SingletonContainer"""
2002 return _IMP_kernel._object_cast_to_SingletonContainer(o)
2004 _object_types.append(
"SingletonModifier")
2007 def _object_cast_to_SingletonModifier(o):
2008 r"""_object_cast_to_SingletonModifier(Object o) -> SingletonModifier"""
2009 return _IMP_kernel._object_cast_to_SingletonModifier(o)
2011 _object_types.append(
"SingletonScore")
2014 def _object_cast_to_SingletonScore(o):
2015 r"""_object_cast_to_SingletonScore(Object o) -> SingletonScore"""
2016 return _IMP_kernel._object_cast_to_SingletonScore(o)
2018 _object_types.append(
"TripletContainer")
2021 def _object_cast_to_TripletContainer(o):
2022 r"""_object_cast_to_TripletContainer(Object o) -> TripletContainer"""
2023 return _IMP_kernel._object_cast_to_TripletContainer(o)
2025 _object_types.append(
"TripletModifier")
2028 def _object_cast_to_TripletModifier(o):
2029 r"""_object_cast_to_TripletModifier(Object o) -> TripletModifier"""
2030 return _IMP_kernel._object_cast_to_TripletModifier(o)
2032 _object_types.append(
"TripletScore")
2035 def _object_cast_to_TripletScore(o):
2036 r"""_object_cast_to_TripletScore(Object o) -> TripletScore"""
2037 return _IMP_kernel._object_cast_to_TripletScore(o)
2039 _object_types.append(
"UnaryFunction")
2042 def _object_cast_to_UnaryFunction(o):
2043 r"""_object_cast_to_UnaryFunction(Object o) -> UnaryFunction"""
2044 return _IMP_kernel._object_cast_to_UnaryFunction(o)
2046 _object_types.append(
"RestraintInfo")
2049 def _object_cast_to_RestraintInfo(o):
2050 r"""_object_cast_to_RestraintInfo(Object o) -> RestraintInfo"""
2051 return _IMP_kernel._object_cast_to_RestraintInfo(o)
2053 _object_types.append(
"ConfigurationSet")
2056 def _object_cast_to_ConfigurationSet(o):
2057 r"""_object_cast_to_ConfigurationSet(Object o) -> ConfigurationSet"""
2058 return _IMP_kernel._object_cast_to_ConfigurationSet(o)
2060 _object_types.append(
"Configuration")
2063 def _object_cast_to_Configuration(o):
2064 r"""_object_cast_to_Configuration(Object o) -> Configuration"""
2065 return _IMP_kernel._object_cast_to_Configuration(o)
2067 _object_types.append(
"Model")
2070 def _object_cast_to_Model(o):
2071 r"""_object_cast_to_Model(Object o) -> Model"""
2072 return _IMP_kernel._object_cast_to_Model(o)
2074 _object_types.append(
"Particle")
2077 def _object_cast_to_Particle(o):
2078 r"""_object_cast_to_Particle(Object o) -> Particle"""
2079 return _IMP_kernel._object_cast_to_Particle(o)
2081 _object_types.append(
"RestraintSet")
2084 def _object_cast_to_RestraintSet(o):
2085 r"""_object_cast_to_RestraintSet(Object o) -> RestraintSet"""
2086 return _IMP_kernel._object_cast_to_RestraintSet(o)
2088 ParticlePairsTemp=list
2089 _plural_types.append(
"ParticlePairsTemp")
2090 _value_types.append(
"ParticlePair")
2093 ParticleTripletsTemp=list
2094 _plural_types.append(
"ParticleTripletsTemp")
2095 _value_types.append(
"ParticleTriplet")
2098 ParticleQuadsTemp=list
2099 _plural_types.append(
"ParticleQuadsTemp")
2100 _value_types.append(
"ParticleQuad")
2103 ParticleIndexPairs=list
2104 _plural_types.append(
"ParticleIndexPairs")
2105 _value_types.append(
"ParticleIndexPair")
2108 ParticleIndexTriplets=list
2109 _plural_types.append(
"ParticleIndexTriplets")
2110 _value_types.append(
"ParticleIndexTriplet")
2113 ParticleIndexQuads=list
2114 _plural_types.append(
"ParticleIndexQuads")
2115 _value_types.append(
"ParticleIndexQuad")
2118 _object_types.append(
"SingletonPredicate")
2121 def _object_cast_to_SingletonPredicate(o):
2122 r"""_object_cast_to_SingletonPredicate(Object o) -> SingletonPredicate"""
2123 return _IMP_kernel._object_cast_to_SingletonPredicate(o)
2125 _object_types.append(
"PairPredicate")
2128 def _object_cast_to_PairPredicate(o):
2129 r"""_object_cast_to_PairPredicate(Object o) -> PairPredicate"""
2130 return _IMP_kernel._object_cast_to_PairPredicate(o)
2132 _object_types.append(
"TripletPredicate")
2135 def _object_cast_to_TripletPredicate(o):
2136 r"""_object_cast_to_TripletPredicate(Object o) -> TripletPredicate"""
2137 return _IMP_kernel._object_cast_to_TripletPredicate(o)
2139 _object_types.append(
"QuadPredicate")
2142 def _object_cast_to_QuadPredicate(o):
2143 r"""_object_cast_to_QuadPredicate(Object o) -> QuadPredicate"""
2144 return _IMP_kernel._object_cast_to_QuadPredicate(o)
2146 _object_types.append(
"SaveToConfigurationSetOptimizerState")
2149 def _object_cast_to_SaveToConfigurationSetOptimizerState(o):
2150 r"""_object_cast_to_SaveToConfigurationSetOptimizerState(Object o) -> SaveToConfigurationSetOptimizerState"""
2151 return _IMP_kernel._object_cast_to_SaveToConfigurationSetOptimizerState(o)
2153 EvaluationStates=list
2154 _plural_types.append(
"EvaluationStates")
2155 _value_types.append(
"EvaluationState")
2158 ScoreAccumulators=list
2159 _plural_types.append(
"ScoreAccumulators")
2160 _value_types.append(
"ScoreAccumulator")
2163 ParticleIndexes=list
2164 _plural_types.append(
"ParticleIndexes")
2165 _value_types.append(
"ParticleIndex")
2169 _plural_types.append(
"FloatIndexes")
2170 _value_types.append(
"FloatIndex")
2174 _plural_types.append(
"FloatKeys")
2175 _value_types.append(
"FloatKey")
2179 _plural_types.append(
"FloatsKeys")
2180 _value_types.append(
"FloatsKey")
2184 _plural_types.append(
"IntKeys")
2185 _value_types.append(
"IntKey")
2189 _plural_types.append(
"IntsKeys")
2190 _value_types.append(
"IntsKey")
2194 _plural_types.append(
"StringKeys")
2195 _value_types.append(
"StringKey")
2198 ParticleIndexKeys=list
2199 _plural_types.append(
"ParticleIndexKeys")
2200 _value_types.append(
"ParticleIndexKey")
2203 ParticleIndexesKeys=list
2204 _plural_types.append(
"ParticleIndexesKeys")
2205 _value_types.append(
"ParticleIndexesKey")
2209 _plural_types.append(
"ObjectKeys")
2210 _value_types.append(
"ObjectKey")
2214 _plural_types.append(
"ModelKeys")
2215 _value_types.append(
"ModelKey")
2219 _plural_types.append(
"TriggerKeys")
2220 _value_types.append(
"TriggerKey")
2223 SparseFloatKeys=list
2224 _plural_types.append(
"SparseFloatKeys")
2225 _value_types.append(
"SparseFloatKey")
2229 _plural_types.append(
"SparseIntKeys")
2230 _value_types.append(
"SparseIntKey")
2233 SparseStringKeys=list
2234 _plural_types.append(
"SparseStringKeys")
2235 _value_types.append(
"SparseStringKey")
2238 SparseParticleIndexKeys=list
2239 _plural_types.append(
"SparseParticleIndexKeys")
2240 _value_types.append(
"SparseParticleIndexKey")
2244 _plural_types.append(
"Vector3DKeys")
2245 _value_types.append(
"Vector3DKey")
2249 _plural_types.append(
"Vector4DKeys")
2250 _value_types.append(
"Vector4DKey")
2253 Vector3DDerivKeys=list
2254 _plural_types.append(
"Vector3DDerivKeys")
2255 _value_types.append(
"Vector3DDerivKey")
2258 Vector4DDerivKeys=list
2259 _plural_types.append(
"Vector4DDerivKeys")
2260 _value_types.append(
"Vector4DDerivKey")
2263 _raii_types.append(
"ScopedSetFloatAttribute")
2266 _object_types.append(
"ScoringFunction")
2269 def _object_cast_to_ScoringFunction(o):
2270 r"""_object_cast_to_ScoringFunction(Object o) -> ScoringFunction"""
2271 return _IMP_kernel._object_cast_to_ScoringFunction(o)
2273 _object_types.append(
"ModelObject")
2276 def _object_cast_to_ModelObject(o):
2277 r"""_object_cast_to_ModelObject(Object o) -> ModelObject"""
2278 return _IMP_kernel._object_cast_to_ModelObject(o)
2280 _object_types.append(
"_RestraintsScoringFunction")
2283 def _object_cast_to__RestraintsScoringFunction(o):
2284 r"""_object_cast_to__RestraintsScoringFunction(Object o) -> _RestraintsScoringFunction"""
2285 return _IMP_kernel._object_cast_to__RestraintsScoringFunction(o)
2287 def _TrivialDecorators(l=[]):
2288 return [_TrivialDecorator(x)
for x
in l]
2289 _plural_types.append(
"_TrivialDecorators")
2292 _value_types.append(
"_TrivialDecorator")
2295 def _TrivialDerivedDecorators(l=[]):
2296 return [_TrivialDerivedDecorator(x)
for x
in l]
2297 _plural_types.append(
"_TrivialDerivedDecorators")
2300 _value_types.append(
"_TrivialDerivedDecorator")
2303 def _TrivialTraitsDecorators(l=[]):
2304 return [_TrivialTraitsDecorator(x)
for x
in l]
2305 _plural_types.append(
"_TrivialTraitsDecorators")
2308 _value_types.append(
"_TrivialTraitsDecorator")
2311 _object_types.append(
"_ConstRestraint")
2314 def _object_cast_to__ConstRestraint(o):
2315 r"""_object_cast_to__ConstRestraint(Object o) -> _ConstRestraint"""
2316 return _IMP_kernel._object_cast_to__ConstRestraint(o)
2318 _object_types.append(
"_ConstOptimizer")
2321 def _object_cast_to__ConstOptimizer(o):
2322 r"""_object_cast_to__ConstOptimizer(Object o) -> _ConstOptimizer"""
2323 return _IMP_kernel._object_cast_to__ConstOptimizer(o)
2325 _object_types.append(
"_ConstSingletonScore")
2328 def _object_cast_to__ConstSingletonScore(o):
2329 r"""_object_cast_to__ConstSingletonScore(Object o) -> _ConstSingletonScore"""
2330 return _IMP_kernel._object_cast_to__ConstSingletonScore(o)
2332 _object_types.append(
"_ConstPairScore")
2335 def _object_cast_to__ConstPairScore(o):
2336 r"""_object_cast_to__ConstPairScore(Object o) -> _ConstPairScore"""
2337 return _IMP_kernel._object_cast_to__ConstPairScore(o)
2339 r"""Proxy of C++ IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex > class."""
2341 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2342 __repr__ = _swig_repr
2345 r"""__init__(DependencyGraph self) -> DependencyGraph"""
2346 _IMP_kernel.DependencyGraph_swiginit(self, _IMP_kernel.new_DependencyGraph())
2348 def get_graph(self):
2349 r"""get_graph(DependencyGraph self) -> IMP::DependencyGraph const &"""
2350 return _IMP_kernel.DependencyGraph_get_graph(self)
2353 r"""get_vertices(DependencyGraph self) -> IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptors"""
2354 return _IMP_kernel.DependencyGraph_get_vertices(self)
2356 def get_vertex_name(self, i):
2357 r"""get_vertex_name(DependencyGraph self, IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor i) -> ModelObject"""
2358 return _IMP_kernel.DependencyGraph_get_vertex_name(self, i)
2360 def get_in_neighbors(self, v):
2361 r"""get_in_neighbors(DependencyGraph self, IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptors"""
2362 return _IMP_kernel.DependencyGraph_get_in_neighbors(self, v)
2364 def get_out_neighbors(self, v):
2365 r"""get_out_neighbors(DependencyGraph self, IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor v) -> IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptors"""
2366 return _IMP_kernel.DependencyGraph_get_out_neighbors(self, v)
2369 r"""show_graphviz(DependencyGraph self, _ostream out=std::cout)"""
2370 return _IMP_kernel.DependencyGraph_show_graphviz(self, *args)
2372 def get_graphviz_string(self):
2373 r"""get_graphviz_string(DependencyGraph self) -> std::string"""
2374 return _IMP_kernel.DependencyGraph_get_graphviz_string(self)
2376 def add_edge(self, v0, v1):
2377 r"""add_edge(DependencyGraph self, IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor v0, IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor v1)"""
2378 return _IMP_kernel.DependencyGraph_add_edge(self, v0, v1)
2380 def add_vertex(self, l):
2381 r"""add_vertex(DependencyGraph self, ModelObject l) -> IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor"""
2382 return _IMP_kernel.DependencyGraph_add_vertex(self, l)
2384 def remove_vertex(self, l):
2385 r"""remove_vertex(DependencyGraph self, IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor l)"""
2386 return _IMP_kernel.DependencyGraph_remove_vertex(self, l)
2387 __swig_destroy__ = _IMP_kernel.delete_DependencyGraph
2390 _IMP_kernel.DependencyGraph_swigregister(DependencyGraph)
2392 _value_types.append(
"DependencyGraph")
2395 r"""Proxy of C++ IMP::Key< 0 > class."""
2397 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2399 def __init__(self, *args):
2401 __init__(FloatKey self) -> FloatKey
2402 __init__(FloatKey self, std::string const & c, bool is_implicit_add_permitted=True) -> FloatKey
2403 __init__(FloatKey self, unsigned int i) -> FloatKey
2405 _IMP_kernel.FloatKey_swiginit(self, _IMP_kernel.new_FloatKey(*args))
2409 r"""add_key(std::string const & sc) -> unsigned int"""
2410 return _IMP_kernel.FloatKey_add_key(sc)
2413 def get_existing_key(sc):
2414 r"""get_existing_key(std::string const & sc) -> FloatKey"""
2415 return _IMP_kernel.FloatKey_get_existing_key(sc)
2418 def get_key_exists(sc):
2419 r"""get_key_exists(std::string const & sc) -> bool"""
2420 return _IMP_kernel.FloatKey_get_key_exists(sc)
2422 def get_string(self):
2423 r"""get_string(FloatKey self) -> std::string const"""
2424 return _IMP_kernel.FloatKey_get_string(self)
2426 def __eq__(self, o):
2427 r"""__eq__(FloatKey self, FloatKey o) -> bool"""
2428 return _IMP_kernel.FloatKey___eq__(self, o)
2430 def __ne__(self, o):
2431 r"""__ne__(FloatKey self, FloatKey o) -> bool"""
2432 return _IMP_kernel.FloatKey___ne__(self, o)
2434 def __lt__(self, o):
2435 r"""__lt__(FloatKey self, FloatKey o) -> bool"""
2436 return _IMP_kernel.FloatKey___lt__(self, o)
2438 def __gt__(self, o):
2439 r"""__gt__(FloatKey self, FloatKey o) -> bool"""
2440 return _IMP_kernel.FloatKey___gt__(self, o)
2442 def __ge__(self, o):
2443 r"""__ge__(FloatKey self, FloatKey o) -> bool"""
2444 return _IMP_kernel.FloatKey___ge__(self, o)
2446 def __le__(self, o):
2447 r"""__le__(FloatKey self, FloatKey o) -> bool"""
2448 return _IMP_kernel.FloatKey___le__(self, o)
2451 r"""__hash__(FloatKey self) -> std::size_t"""
2452 return _IMP_kernel.FloatKey___hash__(self)
2454 def show(self, *args):
2455 r"""show(FloatKey self, _ostream out=std::cout)"""
2456 return _IMP_kernel.FloatKey_show(self, *args)
2459 def add_alias(old_key, new_name):
2460 r"""add_alias(FloatKey old_key, std::string new_name) -> FloatKey"""
2461 return _IMP_kernel.FloatKey_add_alias(old_key, new_name)
2464 def get_number_of_keys():
2465 r"""get_number_of_keys() -> unsigned int"""
2466 return _IMP_kernel.FloatKey_get_number_of_keys()
2469 r"""get_index(FloatKey self) -> unsigned int"""
2470 return _IMP_kernel.FloatKey_get_index(self)
2474 r"""show_all(_ostream out)"""
2475 return _IMP_kernel.FloatKey_show_all(out)
2478 def get_all_strings():
2479 r"""get_all_strings() -> IMP::Vector< std::string >"""
2480 return _IMP_kernel.FloatKey_get_all_strings()
2483 def get_number_unique():
2484 r"""get_number_unique() -> unsigned int"""
2485 return _IMP_kernel.FloatKey_get_number_unique()
2488 r"""__str__(FloatKey self) -> std::string"""
2489 return _IMP_kernel.FloatKey___str__(self)
2492 r"""__repr__(FloatKey self) -> std::string"""
2493 return _IMP_kernel.FloatKey___repr__(self)
2494 __swig_destroy__ = _IMP_kernel.delete_FloatKey
2497 _IMP_kernel.FloatKey_swigregister(FloatKey)
2499 r"""Proxy of C++ IMP::Key< 1 > class."""
2501 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2503 def __init__(self, *args):
2505 __init__(IntKey self) -> IntKey
2506 __init__(IntKey self, std::string const & c, bool is_implicit_add_permitted=True) -> IntKey
2507 __init__(IntKey self, unsigned int i) -> IntKey
2509 _IMP_kernel.IntKey_swiginit(self, _IMP_kernel.new_IntKey(*args))
2513 r"""add_key(std::string const & sc) -> unsigned int"""
2514 return _IMP_kernel.IntKey_add_key(sc)
2517 def get_existing_key(sc):
2518 r"""get_existing_key(std::string const & sc) -> IntKey"""
2519 return _IMP_kernel.IntKey_get_existing_key(sc)
2522 def get_key_exists(sc):
2523 r"""get_key_exists(std::string const & sc) -> bool"""
2524 return _IMP_kernel.IntKey_get_key_exists(sc)
2526 def get_string(self):
2527 r"""get_string(IntKey self) -> std::string const"""
2528 return _IMP_kernel.IntKey_get_string(self)
2530 def __eq__(self, o):
2531 r"""__eq__(IntKey self, IntKey o) -> bool"""
2532 return _IMP_kernel.IntKey___eq__(self, o)
2534 def __ne__(self, o):
2535 r"""__ne__(IntKey self, IntKey o) -> bool"""
2536 return _IMP_kernel.IntKey___ne__(self, o)
2538 def __lt__(self, o):
2539 r"""__lt__(IntKey self, IntKey o) -> bool"""
2540 return _IMP_kernel.IntKey___lt__(self, o)
2542 def __gt__(self, o):
2543 r"""__gt__(IntKey self, IntKey o) -> bool"""
2544 return _IMP_kernel.IntKey___gt__(self, o)
2546 def __ge__(self, o):
2547 r"""__ge__(IntKey self, IntKey o) -> bool"""
2548 return _IMP_kernel.IntKey___ge__(self, o)
2550 def __le__(self, o):
2551 r"""__le__(IntKey self, IntKey o) -> bool"""
2552 return _IMP_kernel.IntKey___le__(self, o)
2555 r"""__hash__(IntKey self) -> std::size_t"""
2556 return _IMP_kernel.IntKey___hash__(self)
2558 def show(self, *args):
2559 r"""show(IntKey self, _ostream out=std::cout)"""
2560 return _IMP_kernel.IntKey_show(self, *args)
2563 def add_alias(old_key, new_name):
2564 r"""add_alias(IntKey old_key, std::string new_name) -> IntKey"""
2565 return _IMP_kernel.IntKey_add_alias(old_key, new_name)
2568 def get_number_of_keys():
2569 r"""get_number_of_keys() -> unsigned int"""
2570 return _IMP_kernel.IntKey_get_number_of_keys()
2573 r"""get_index(IntKey self) -> unsigned int"""
2574 return _IMP_kernel.IntKey_get_index(self)
2578 r"""show_all(_ostream out)"""
2579 return _IMP_kernel.IntKey_show_all(out)
2582 def get_all_strings():
2583 r"""get_all_strings() -> IMP::Vector< std::string >"""
2584 return _IMP_kernel.IntKey_get_all_strings()
2587 def get_number_unique():
2588 r"""get_number_unique() -> unsigned int"""
2589 return _IMP_kernel.IntKey_get_number_unique()
2592 r"""__str__(IntKey self) -> std::string"""
2593 return _IMP_kernel.IntKey___str__(self)
2596 r"""__repr__(IntKey self) -> std::string"""
2597 return _IMP_kernel.IntKey___repr__(self)
2598 __swig_destroy__ = _IMP_kernel.delete_IntKey
2601 _IMP_kernel.IntKey_swigregister(IntKey)
2603 r"""Proxy of C++ IMP::Key< 2 > class."""
2605 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2607 def __init__(self, *args):
2609 __init__(StringKey self) -> StringKey
2610 __init__(StringKey self, std::string const & c, bool is_implicit_add_permitted=True) -> StringKey
2611 __init__(StringKey self, unsigned int i) -> StringKey
2613 _IMP_kernel.StringKey_swiginit(self, _IMP_kernel.new_StringKey(*args))
2617 r"""add_key(std::string const & sc) -> unsigned int"""
2618 return _IMP_kernel.StringKey_add_key(sc)
2621 def get_existing_key(sc):
2622 r"""get_existing_key(std::string const & sc) -> StringKey"""
2623 return _IMP_kernel.StringKey_get_existing_key(sc)
2626 def get_key_exists(sc):
2627 r"""get_key_exists(std::string const & sc) -> bool"""
2628 return _IMP_kernel.StringKey_get_key_exists(sc)
2630 def get_string(self):
2631 r"""get_string(StringKey self) -> std::string const"""
2632 return _IMP_kernel.StringKey_get_string(self)
2634 def __eq__(self, o):
2635 r"""__eq__(StringKey self, StringKey o) -> bool"""
2636 return _IMP_kernel.StringKey___eq__(self, o)
2638 def __ne__(self, o):
2639 r"""__ne__(StringKey self, StringKey o) -> bool"""
2640 return _IMP_kernel.StringKey___ne__(self, o)
2642 def __lt__(self, o):
2643 r"""__lt__(StringKey self, StringKey o) -> bool"""
2644 return _IMP_kernel.StringKey___lt__(self, o)
2646 def __gt__(self, o):
2647 r"""__gt__(StringKey self, StringKey o) -> bool"""
2648 return _IMP_kernel.StringKey___gt__(self, o)
2650 def __ge__(self, o):
2651 r"""__ge__(StringKey self, StringKey o) -> bool"""
2652 return _IMP_kernel.StringKey___ge__(self, o)
2654 def __le__(self, o):
2655 r"""__le__(StringKey self, StringKey o) -> bool"""
2656 return _IMP_kernel.StringKey___le__(self, o)
2659 r"""__hash__(StringKey self) -> std::size_t"""
2660 return _IMP_kernel.StringKey___hash__(self)
2662 def show(self, *args):
2663 r"""show(StringKey self, _ostream out=std::cout)"""
2664 return _IMP_kernel.StringKey_show(self, *args)
2667 def add_alias(old_key, new_name):
2668 r"""add_alias(StringKey old_key, std::string new_name) -> StringKey"""
2669 return _IMP_kernel.StringKey_add_alias(old_key, new_name)
2672 def get_number_of_keys():
2673 r"""get_number_of_keys() -> unsigned int"""
2674 return _IMP_kernel.StringKey_get_number_of_keys()
2677 r"""get_index(StringKey self) -> unsigned int"""
2678 return _IMP_kernel.StringKey_get_index(self)
2682 r"""show_all(_ostream out)"""
2683 return _IMP_kernel.StringKey_show_all(out)
2686 def get_all_strings():
2687 r"""get_all_strings() -> IMP::Vector< std::string >"""
2688 return _IMP_kernel.StringKey_get_all_strings()
2691 def get_number_unique():
2692 r"""get_number_unique() -> unsigned int"""
2693 return _IMP_kernel.StringKey_get_number_unique()
2696 r"""__str__(StringKey self) -> std::string"""
2697 return _IMP_kernel.StringKey___str__(self)
2700 r"""__repr__(StringKey self) -> std::string"""
2701 return _IMP_kernel.StringKey___repr__(self)
2702 __swig_destroy__ = _IMP_kernel.delete_StringKey
2705 _IMP_kernel.StringKey_swigregister(StringKey)
2707 r"""Proxy of C++ IMP::Key< 3 > class."""
2709 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2711 def __init__(self, *args):
2713 __init__(ParticleIndexKey self) -> ParticleIndexKey
2714 __init__(ParticleIndexKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ParticleIndexKey
2715 __init__(ParticleIndexKey self, unsigned int i) -> ParticleIndexKey
2717 _IMP_kernel.ParticleIndexKey_swiginit(self, _IMP_kernel.new_ParticleIndexKey(*args))
2721 r"""add_key(std::string const & sc) -> unsigned int"""
2722 return _IMP_kernel.ParticleIndexKey_add_key(sc)
2725 def get_existing_key(sc):
2726 r"""get_existing_key(std::string const & sc) -> ParticleIndexKey"""
2727 return _IMP_kernel.ParticleIndexKey_get_existing_key(sc)
2730 def get_key_exists(sc):
2731 r"""get_key_exists(std::string const & sc) -> bool"""
2732 return _IMP_kernel.ParticleIndexKey_get_key_exists(sc)
2734 def get_string(self):
2735 r"""get_string(ParticleIndexKey self) -> std::string const"""
2736 return _IMP_kernel.ParticleIndexKey_get_string(self)
2738 def __eq__(self, o):
2739 r"""__eq__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2740 return _IMP_kernel.ParticleIndexKey___eq__(self, o)
2742 def __ne__(self, o):
2743 r"""__ne__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2744 return _IMP_kernel.ParticleIndexKey___ne__(self, o)
2746 def __lt__(self, o):
2747 r"""__lt__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2748 return _IMP_kernel.ParticleIndexKey___lt__(self, o)
2750 def __gt__(self, o):
2751 r"""__gt__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2752 return _IMP_kernel.ParticleIndexKey___gt__(self, o)
2754 def __ge__(self, o):
2755 r"""__ge__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2756 return _IMP_kernel.ParticleIndexKey___ge__(self, o)
2758 def __le__(self, o):
2759 r"""__le__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2760 return _IMP_kernel.ParticleIndexKey___le__(self, o)
2763 r"""__hash__(ParticleIndexKey self) -> std::size_t"""
2764 return _IMP_kernel.ParticleIndexKey___hash__(self)
2766 def show(self, *args):
2767 r"""show(ParticleIndexKey self, _ostream out=std::cout)"""
2768 return _IMP_kernel.ParticleIndexKey_show(self, *args)
2771 def add_alias(old_key, new_name):
2772 r"""add_alias(ParticleIndexKey old_key, std::string new_name) -> ParticleIndexKey"""
2773 return _IMP_kernel.ParticleIndexKey_add_alias(old_key, new_name)
2776 def get_number_of_keys():
2777 r"""get_number_of_keys() -> unsigned int"""
2778 return _IMP_kernel.ParticleIndexKey_get_number_of_keys()
2781 r"""get_index(ParticleIndexKey self) -> unsigned int"""
2782 return _IMP_kernel.ParticleIndexKey_get_index(self)
2786 r"""show_all(_ostream out)"""
2787 return _IMP_kernel.ParticleIndexKey_show_all(out)
2790 def get_all_strings():
2791 r"""get_all_strings() -> IMP::Vector< std::string >"""
2792 return _IMP_kernel.ParticleIndexKey_get_all_strings()
2795 def get_number_unique():
2796 r"""get_number_unique() -> unsigned int"""
2797 return _IMP_kernel.ParticleIndexKey_get_number_unique()
2800 r"""__str__(ParticleIndexKey self) -> std::string"""
2801 return _IMP_kernel.ParticleIndexKey___str__(self)
2804 r"""__repr__(ParticleIndexKey self) -> std::string"""
2805 return _IMP_kernel.ParticleIndexKey___repr__(self)
2806 __swig_destroy__ = _IMP_kernel.delete_ParticleIndexKey
2809 _IMP_kernel.ParticleIndexKey_swigregister(ParticleIndexKey)
2811 r"""Proxy of C++ IMP::Key< 4 > class."""
2813 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2815 def __init__(self, *args):
2817 __init__(ObjectKey self) -> ObjectKey
2818 __init__(ObjectKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ObjectKey
2819 __init__(ObjectKey self, unsigned int i) -> ObjectKey
2821 _IMP_kernel.ObjectKey_swiginit(self, _IMP_kernel.new_ObjectKey(*args))
2825 r"""add_key(std::string const & sc) -> unsigned int"""
2826 return _IMP_kernel.ObjectKey_add_key(sc)
2829 def get_existing_key(sc):
2830 r"""get_existing_key(std::string const & sc) -> ObjectKey"""
2831 return _IMP_kernel.ObjectKey_get_existing_key(sc)
2834 def get_key_exists(sc):
2835 r"""get_key_exists(std::string const & sc) -> bool"""
2836 return _IMP_kernel.ObjectKey_get_key_exists(sc)
2838 def get_string(self):
2839 r"""get_string(ObjectKey self) -> std::string const"""
2840 return _IMP_kernel.ObjectKey_get_string(self)
2842 def __eq__(self, o):
2843 r"""__eq__(ObjectKey self, ObjectKey o) -> bool"""
2844 return _IMP_kernel.ObjectKey___eq__(self, o)
2846 def __ne__(self, o):
2847 r"""__ne__(ObjectKey self, ObjectKey o) -> bool"""
2848 return _IMP_kernel.ObjectKey___ne__(self, o)
2850 def __lt__(self, o):
2851 r"""__lt__(ObjectKey self, ObjectKey o) -> bool"""
2852 return _IMP_kernel.ObjectKey___lt__(self, o)
2854 def __gt__(self, o):
2855 r"""__gt__(ObjectKey self, ObjectKey o) -> bool"""
2856 return _IMP_kernel.ObjectKey___gt__(self, o)
2858 def __ge__(self, o):
2859 r"""__ge__(ObjectKey self, ObjectKey o) -> bool"""
2860 return _IMP_kernel.ObjectKey___ge__(self, o)
2862 def __le__(self, o):
2863 r"""__le__(ObjectKey self, ObjectKey o) -> bool"""
2864 return _IMP_kernel.ObjectKey___le__(self, o)
2867 r"""__hash__(ObjectKey self) -> std::size_t"""
2868 return _IMP_kernel.ObjectKey___hash__(self)
2870 def show(self, *args):
2871 r"""show(ObjectKey self, _ostream out=std::cout)"""
2872 return _IMP_kernel.ObjectKey_show(self, *args)
2875 def add_alias(old_key, new_name):
2876 r"""add_alias(ObjectKey old_key, std::string new_name) -> ObjectKey"""
2877 return _IMP_kernel.ObjectKey_add_alias(old_key, new_name)
2880 def get_number_of_keys():
2881 r"""get_number_of_keys() -> unsigned int"""
2882 return _IMP_kernel.ObjectKey_get_number_of_keys()
2885 r"""get_index(ObjectKey self) -> unsigned int"""
2886 return _IMP_kernel.ObjectKey_get_index(self)
2890 r"""show_all(_ostream out)"""
2891 return _IMP_kernel.ObjectKey_show_all(out)
2894 def get_all_strings():
2895 r"""get_all_strings() -> IMP::Vector< std::string >"""
2896 return _IMP_kernel.ObjectKey_get_all_strings()
2899 def get_number_unique():
2900 r"""get_number_unique() -> unsigned int"""
2901 return _IMP_kernel.ObjectKey_get_number_unique()
2904 r"""__str__(ObjectKey self) -> std::string"""
2905 return _IMP_kernel.ObjectKey___str__(self)
2908 r"""__repr__(ObjectKey self) -> std::string"""
2909 return _IMP_kernel.ObjectKey___repr__(self)
2910 __swig_destroy__ = _IMP_kernel.delete_ObjectKey
2913 _IMP_kernel.ObjectKey_swigregister(ObjectKey)
2915 r"""Proxy of C++ IMP::Key< 5 > class."""
2917 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2919 def __init__(self, *args):
2921 __init__(IntsKey self) -> IntsKey
2922 __init__(IntsKey self, std::string const & c, bool is_implicit_add_permitted=True) -> IntsKey
2923 __init__(IntsKey self, unsigned int i) -> IntsKey
2925 _IMP_kernel.IntsKey_swiginit(self, _IMP_kernel.new_IntsKey(*args))
2929 r"""add_key(std::string const & sc) -> unsigned int"""
2930 return _IMP_kernel.IntsKey_add_key(sc)
2933 def get_existing_key(sc):
2934 r"""get_existing_key(std::string const & sc) -> IntsKey"""
2935 return _IMP_kernel.IntsKey_get_existing_key(sc)
2938 def get_key_exists(sc):
2939 r"""get_key_exists(std::string const & sc) -> bool"""
2940 return _IMP_kernel.IntsKey_get_key_exists(sc)
2942 def get_string(self):
2943 r"""get_string(IntsKey self) -> std::string const"""
2944 return _IMP_kernel.IntsKey_get_string(self)
2946 def __eq__(self, o):
2947 r"""__eq__(IntsKey self, IntsKey o) -> bool"""
2948 return _IMP_kernel.IntsKey___eq__(self, o)
2950 def __ne__(self, o):
2951 r"""__ne__(IntsKey self, IntsKey o) -> bool"""
2952 return _IMP_kernel.IntsKey___ne__(self, o)
2954 def __lt__(self, o):
2955 r"""__lt__(IntsKey self, IntsKey o) -> bool"""
2956 return _IMP_kernel.IntsKey___lt__(self, o)
2958 def __gt__(self, o):
2959 r"""__gt__(IntsKey self, IntsKey o) -> bool"""
2960 return _IMP_kernel.IntsKey___gt__(self, o)
2962 def __ge__(self, o):
2963 r"""__ge__(IntsKey self, IntsKey o) -> bool"""
2964 return _IMP_kernel.IntsKey___ge__(self, o)
2966 def __le__(self, o):
2967 r"""__le__(IntsKey self, IntsKey o) -> bool"""
2968 return _IMP_kernel.IntsKey___le__(self, o)
2971 r"""__hash__(IntsKey self) -> std::size_t"""
2972 return _IMP_kernel.IntsKey___hash__(self)
2974 def show(self, *args):
2975 r"""show(IntsKey self, _ostream out=std::cout)"""
2976 return _IMP_kernel.IntsKey_show(self, *args)
2979 def add_alias(old_key, new_name):
2980 r"""add_alias(IntsKey old_key, std::string new_name) -> IntsKey"""
2981 return _IMP_kernel.IntsKey_add_alias(old_key, new_name)
2984 def get_number_of_keys():
2985 r"""get_number_of_keys() -> unsigned int"""
2986 return _IMP_kernel.IntsKey_get_number_of_keys()
2989 r"""get_index(IntsKey self) -> unsigned int"""
2990 return _IMP_kernel.IntsKey_get_index(self)
2994 r"""show_all(_ostream out)"""
2995 return _IMP_kernel.IntsKey_show_all(out)
2998 def get_all_strings():
2999 r"""get_all_strings() -> IMP::Vector< std::string >"""
3000 return _IMP_kernel.IntsKey_get_all_strings()
3003 def get_number_unique():
3004 r"""get_number_unique() -> unsigned int"""
3005 return _IMP_kernel.IntsKey_get_number_unique()
3008 r"""__str__(IntsKey self) -> std::string"""
3009 return _IMP_kernel.IntsKey___str__(self)
3012 r"""__repr__(IntsKey self) -> std::string"""
3013 return _IMP_kernel.IntsKey___repr__(self)
3014 __swig_destroy__ = _IMP_kernel.delete_IntsKey
3017 _IMP_kernel.IntsKey_swigregister(IntsKey)
3019 r"""Proxy of C++ IMP::Key< 6 > class."""
3021 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3023 def __init__(self, *args):
3025 __init__(ParticleIndexesKey self) -> ParticleIndexesKey
3026 __init__(ParticleIndexesKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ParticleIndexesKey
3027 __init__(ParticleIndexesKey self, unsigned int i) -> ParticleIndexesKey
3029 _IMP_kernel.ParticleIndexesKey_swiginit(self, _IMP_kernel.new_ParticleIndexesKey(*args))
3033 r"""add_key(std::string const & sc) -> unsigned int"""
3034 return _IMP_kernel.ParticleIndexesKey_add_key(sc)
3037 def get_existing_key(sc):
3038 r"""get_existing_key(std::string const & sc) -> ParticleIndexesKey"""
3039 return _IMP_kernel.ParticleIndexesKey_get_existing_key(sc)
3042 def get_key_exists(sc):
3043 r"""get_key_exists(std::string const & sc) -> bool"""
3044 return _IMP_kernel.ParticleIndexesKey_get_key_exists(sc)
3046 def get_string(self):
3047 r"""get_string(ParticleIndexesKey self) -> std::string const"""
3048 return _IMP_kernel.ParticleIndexesKey_get_string(self)
3050 def __eq__(self, o):
3051 r"""__eq__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3052 return _IMP_kernel.ParticleIndexesKey___eq__(self, o)
3054 def __ne__(self, o):
3055 r"""__ne__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3056 return _IMP_kernel.ParticleIndexesKey___ne__(self, o)
3058 def __lt__(self, o):
3059 r"""__lt__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3060 return _IMP_kernel.ParticleIndexesKey___lt__(self, o)
3062 def __gt__(self, o):
3063 r"""__gt__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3064 return _IMP_kernel.ParticleIndexesKey___gt__(self, o)
3066 def __ge__(self, o):
3067 r"""__ge__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3068 return _IMP_kernel.ParticleIndexesKey___ge__(self, o)
3070 def __le__(self, o):
3071 r"""__le__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3072 return _IMP_kernel.ParticleIndexesKey___le__(self, o)
3075 r"""__hash__(ParticleIndexesKey self) -> std::size_t"""
3076 return _IMP_kernel.ParticleIndexesKey___hash__(self)
3078 def show(self, *args):
3079 r"""show(ParticleIndexesKey self, _ostream out=std::cout)"""
3080 return _IMP_kernel.ParticleIndexesKey_show(self, *args)
3083 def add_alias(old_key, new_name):
3084 r"""add_alias(ParticleIndexesKey old_key, std::string new_name) -> ParticleIndexesKey"""
3085 return _IMP_kernel.ParticleIndexesKey_add_alias(old_key, new_name)
3088 def get_number_of_keys():
3089 r"""get_number_of_keys() -> unsigned int"""
3090 return _IMP_kernel.ParticleIndexesKey_get_number_of_keys()
3093 r"""get_index(ParticleIndexesKey self) -> unsigned int"""
3094 return _IMP_kernel.ParticleIndexesKey_get_index(self)
3098 r"""show_all(_ostream out)"""
3099 return _IMP_kernel.ParticleIndexesKey_show_all(out)
3102 def get_all_strings():
3103 r"""get_all_strings() -> IMP::Vector< std::string >"""
3104 return _IMP_kernel.ParticleIndexesKey_get_all_strings()
3107 def get_number_unique():
3108 r"""get_number_unique() -> unsigned int"""
3109 return _IMP_kernel.ParticleIndexesKey_get_number_unique()
3112 r"""__str__(ParticleIndexesKey self) -> std::string"""
3113 return _IMP_kernel.ParticleIndexesKey___str__(self)
3116 r"""__repr__(ParticleIndexesKey self) -> std::string"""
3117 return _IMP_kernel.ParticleIndexesKey___repr__(self)
3118 __swig_destroy__ = _IMP_kernel.delete_ParticleIndexesKey
3121 _IMP_kernel.ParticleIndexesKey_swigregister(ParticleIndexesKey)
3123 r"""Proxy of C++ IMP::Key< 8 > class."""
3125 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3127 def __init__(self, *args):
3129 __init__(ModelKey self) -> ModelKey
3130 __init__(ModelKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ModelKey
3131 __init__(ModelKey self, unsigned int i) -> ModelKey
3133 _IMP_kernel.ModelKey_swiginit(self, _IMP_kernel.new_ModelKey(*args))
3137 r"""add_key(std::string const & sc) -> unsigned int"""
3138 return _IMP_kernel.ModelKey_add_key(sc)
3141 def get_existing_key(sc):
3142 r"""get_existing_key(std::string const & sc) -> ModelKey"""
3143 return _IMP_kernel.ModelKey_get_existing_key(sc)
3146 def get_key_exists(sc):
3147 r"""get_key_exists(std::string const & sc) -> bool"""
3148 return _IMP_kernel.ModelKey_get_key_exists(sc)
3150 def get_string(self):
3151 r"""get_string(ModelKey self) -> std::string const"""
3152 return _IMP_kernel.ModelKey_get_string(self)
3154 def __eq__(self, o):
3155 r"""__eq__(ModelKey self, ModelKey o) -> bool"""
3156 return _IMP_kernel.ModelKey___eq__(self, o)
3158 def __ne__(self, o):
3159 r"""__ne__(ModelKey self, ModelKey o) -> bool"""
3160 return _IMP_kernel.ModelKey___ne__(self, o)
3162 def __lt__(self, o):
3163 r"""__lt__(ModelKey self, ModelKey o) -> bool"""
3164 return _IMP_kernel.ModelKey___lt__(self, o)
3166 def __gt__(self, o):
3167 r"""__gt__(ModelKey self, ModelKey o) -> bool"""
3168 return _IMP_kernel.ModelKey___gt__(self, o)
3170 def __ge__(self, o):
3171 r"""__ge__(ModelKey self, ModelKey o) -> bool"""
3172 return _IMP_kernel.ModelKey___ge__(self, o)
3174 def __le__(self, o):
3175 r"""__le__(ModelKey self, ModelKey o) -> bool"""
3176 return _IMP_kernel.ModelKey___le__(self, o)
3179 r"""__hash__(ModelKey self) -> std::size_t"""
3180 return _IMP_kernel.ModelKey___hash__(self)
3182 def show(self, *args):
3183 r"""show(ModelKey self, _ostream out=std::cout)"""
3184 return _IMP_kernel.ModelKey_show(self, *args)
3187 def add_alias(old_key, new_name):
3188 r"""add_alias(ModelKey old_key, std::string new_name) -> ModelKey"""
3189 return _IMP_kernel.ModelKey_add_alias(old_key, new_name)
3192 def get_number_of_keys():
3193 r"""get_number_of_keys() -> unsigned int"""
3194 return _IMP_kernel.ModelKey_get_number_of_keys()
3197 r"""get_index(ModelKey self) -> unsigned int"""
3198 return _IMP_kernel.ModelKey_get_index(self)
3202 r"""show_all(_ostream out)"""
3203 return _IMP_kernel.ModelKey_show_all(out)
3206 def get_all_strings():
3207 r"""get_all_strings() -> IMP::Vector< std::string >"""
3208 return _IMP_kernel.ModelKey_get_all_strings()
3211 def get_number_unique():
3212 r"""get_number_unique() -> unsigned int"""
3213 return _IMP_kernel.ModelKey_get_number_unique()
3216 r"""__str__(ModelKey self) -> std::string"""
3217 return _IMP_kernel.ModelKey___str__(self)
3220 r"""__repr__(ModelKey self) -> std::string"""
3221 return _IMP_kernel.ModelKey___repr__(self)
3222 __swig_destroy__ = _IMP_kernel.delete_ModelKey
3225 _IMP_kernel.ModelKey_swigregister(ModelKey)
3227 r"""Proxy of C++ IMP::Key< 11 > class."""
3229 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3231 def __init__(self, *args):
3233 __init__(TriggerKey self) -> TriggerKey
3234 __init__(TriggerKey self, std::string const & c, bool is_implicit_add_permitted=True) -> TriggerKey
3235 __init__(TriggerKey self, unsigned int i) -> TriggerKey
3237 _IMP_kernel.TriggerKey_swiginit(self, _IMP_kernel.new_TriggerKey(*args))
3241 r"""add_key(std::string const & sc) -> unsigned int"""
3242 return _IMP_kernel.TriggerKey_add_key(sc)
3245 def get_existing_key(sc):
3246 r"""get_existing_key(std::string const & sc) -> TriggerKey"""
3247 return _IMP_kernel.TriggerKey_get_existing_key(sc)
3250 def get_key_exists(sc):
3251 r"""get_key_exists(std::string const & sc) -> bool"""
3252 return _IMP_kernel.TriggerKey_get_key_exists(sc)
3254 def get_string(self):
3255 r"""get_string(TriggerKey self) -> std::string const"""
3256 return _IMP_kernel.TriggerKey_get_string(self)
3258 def __eq__(self, o):
3259 r"""__eq__(TriggerKey self, TriggerKey o) -> bool"""
3260 return _IMP_kernel.TriggerKey___eq__(self, o)
3262 def __ne__(self, o):
3263 r"""__ne__(TriggerKey self, TriggerKey o) -> bool"""
3264 return _IMP_kernel.TriggerKey___ne__(self, o)
3266 def __lt__(self, o):
3267 r"""__lt__(TriggerKey self, TriggerKey o) -> bool"""
3268 return _IMP_kernel.TriggerKey___lt__(self, o)
3270 def __gt__(self, o):
3271 r"""__gt__(TriggerKey self, TriggerKey o) -> bool"""
3272 return _IMP_kernel.TriggerKey___gt__(self, o)
3274 def __ge__(self, o):
3275 r"""__ge__(TriggerKey self, TriggerKey o) -> bool"""
3276 return _IMP_kernel.TriggerKey___ge__(self, o)
3278 def __le__(self, o):
3279 r"""__le__(TriggerKey self, TriggerKey o) -> bool"""
3280 return _IMP_kernel.TriggerKey___le__(self, o)
3283 r"""__hash__(TriggerKey self) -> std::size_t"""
3284 return _IMP_kernel.TriggerKey___hash__(self)
3286 def show(self, *args):
3287 r"""show(TriggerKey self, _ostream out=std::cout)"""
3288 return _IMP_kernel.TriggerKey_show(self, *args)
3291 def add_alias(old_key, new_name):
3292 r"""add_alias(TriggerKey old_key, std::string new_name) -> TriggerKey"""
3293 return _IMP_kernel.TriggerKey_add_alias(old_key, new_name)
3296 def get_number_of_keys():
3297 r"""get_number_of_keys() -> unsigned int"""
3298 return _IMP_kernel.TriggerKey_get_number_of_keys()
3301 r"""get_index(TriggerKey self) -> unsigned int"""
3302 return _IMP_kernel.TriggerKey_get_index(self)
3306 r"""show_all(_ostream out)"""
3307 return _IMP_kernel.TriggerKey_show_all(out)
3310 def get_all_strings():
3311 r"""get_all_strings() -> IMP::Vector< std::string >"""
3312 return _IMP_kernel.TriggerKey_get_all_strings()
3315 def get_number_unique():
3316 r"""get_number_unique() -> unsigned int"""
3317 return _IMP_kernel.TriggerKey_get_number_unique()
3320 r"""__str__(TriggerKey self) -> std::string"""
3321 return _IMP_kernel.TriggerKey___str__(self)
3324 r"""__repr__(TriggerKey self) -> std::string"""
3325 return _IMP_kernel.TriggerKey___repr__(self)
3326 __swig_destroy__ = _IMP_kernel.delete_TriggerKey
3329 _IMP_kernel.TriggerKey_swigregister(TriggerKey)
3331 r"""Proxy of C++ IMP::Index< IMP::ParticleIndexTag > class."""
3333 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3335 def __init__(self, *args):
3337 __init__(ParticleIndex self, int i) -> ParticleIndex
3338 __init__(ParticleIndex self) -> ParticleIndex
3340 _IMP_kernel.ParticleIndex_swiginit(self, _IMP_kernel.new_ParticleIndex(*args))
3343 r"""get_index(ParticleIndex self) -> int"""
3344 return _IMP_kernel.ParticleIndex_get_index(self)
3346 def __eq__(self, o):
3347 r"""__eq__(ParticleIndex self, ParticleIndex o) -> bool"""
3348 return _IMP_kernel.ParticleIndex___eq__(self, o)
3350 def __ne__(self, o):
3351 r"""__ne__(ParticleIndex self, ParticleIndex o) -> bool"""
3352 return _IMP_kernel.ParticleIndex___ne__(self, o)
3354 def __lt__(self, o):
3355 r"""__lt__(ParticleIndex self, ParticleIndex o) -> bool"""
3356 return _IMP_kernel.ParticleIndex___lt__(self, o)
3358 def __gt__(self, o):
3359 r"""__gt__(ParticleIndex self, ParticleIndex o) -> bool"""
3360 return _IMP_kernel.ParticleIndex___gt__(self, o)
3362 def __ge__(self, o):
3363 r"""__ge__(ParticleIndex self, ParticleIndex o) -> bool"""
3364 return _IMP_kernel.ParticleIndex___ge__(self, o)
3366 def __le__(self, o):
3367 r"""__le__(ParticleIndex self, ParticleIndex o) -> bool"""
3368 return _IMP_kernel.ParticleIndex___le__(self, o)
3370 def show(self, *args):
3371 r"""show(ParticleIndex self, _ostream out=std::cout)"""
3372 return _IMP_kernel.ParticleIndex_show(self, *args)
3375 r"""__hash__(ParticleIndex self) -> std::size_t"""
3376 return _IMP_kernel.ParticleIndex___hash__(self)
3379 r"""__str__(ParticleIndex self) -> std::string"""
3380 return _IMP_kernel.ParticleIndex___str__(self)
3383 r"""__repr__(ParticleIndex self) -> std::string"""
3384 return _IMP_kernel.ParticleIndex___repr__(self)
3385 __swig_destroy__ = _IMP_kernel.delete_ParticleIndex
3388 _IMP_kernel.ParticleIndex_swigregister(ParticleIndex)
3390 r"""Proxy of C++ IMP::Key< 10 > class."""
3392 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3394 def __init__(self, *args):
3396 __init__(FloatsKey self) -> FloatsKey
3397 __init__(FloatsKey self, std::string const & c, bool is_implicit_add_permitted=True) -> FloatsKey
3398 __init__(FloatsKey self, unsigned int i) -> FloatsKey
3400 _IMP_kernel.FloatsKey_swiginit(self, _IMP_kernel.new_FloatsKey(*args))
3404 r"""add_key(std::string const & sc) -> unsigned int"""
3405 return _IMP_kernel.FloatsKey_add_key(sc)
3408 def get_existing_key(sc):
3409 r"""get_existing_key(std::string const & sc) -> FloatsKey"""
3410 return _IMP_kernel.FloatsKey_get_existing_key(sc)
3413 def get_key_exists(sc):
3414 r"""get_key_exists(std::string const & sc) -> bool"""
3415 return _IMP_kernel.FloatsKey_get_key_exists(sc)
3417 def get_string(self):
3418 r"""get_string(FloatsKey self) -> std::string const"""
3419 return _IMP_kernel.FloatsKey_get_string(self)
3421 def __eq__(self, o):
3422 r"""__eq__(FloatsKey self, FloatsKey o) -> bool"""
3423 return _IMP_kernel.FloatsKey___eq__(self, o)
3425 def __ne__(self, o):
3426 r"""__ne__(FloatsKey self, FloatsKey o) -> bool"""
3427 return _IMP_kernel.FloatsKey___ne__(self, o)
3429 def __lt__(self, o):
3430 r"""__lt__(FloatsKey self, FloatsKey o) -> bool"""
3431 return _IMP_kernel.FloatsKey___lt__(self, o)
3433 def __gt__(self, o):
3434 r"""__gt__(FloatsKey self, FloatsKey o) -> bool"""
3435 return _IMP_kernel.FloatsKey___gt__(self, o)
3437 def __ge__(self, o):
3438 r"""__ge__(FloatsKey self, FloatsKey o) -> bool"""
3439 return _IMP_kernel.FloatsKey___ge__(self, o)
3441 def __le__(self, o):
3442 r"""__le__(FloatsKey self, FloatsKey o) -> bool"""
3443 return _IMP_kernel.FloatsKey___le__(self, o)
3446 r"""__hash__(FloatsKey self) -> std::size_t"""
3447 return _IMP_kernel.FloatsKey___hash__(self)
3449 def show(self, *args):
3450 r"""show(FloatsKey self, _ostream out=std::cout)"""
3451 return _IMP_kernel.FloatsKey_show(self, *args)
3454 def add_alias(old_key, new_name):
3455 r"""add_alias(FloatsKey old_key, std::string new_name) -> FloatsKey"""
3456 return _IMP_kernel.FloatsKey_add_alias(old_key, new_name)
3459 def get_number_of_keys():
3460 r"""get_number_of_keys() -> unsigned int"""
3461 return _IMP_kernel.FloatsKey_get_number_of_keys()
3464 r"""get_index(FloatsKey self) -> unsigned int"""
3465 return _IMP_kernel.FloatsKey_get_index(self)
3469 r"""show_all(_ostream out)"""
3470 return _IMP_kernel.FloatsKey_show_all(out)
3473 def get_all_strings():
3474 r"""get_all_strings() -> IMP::Vector< std::string >"""
3475 return _IMP_kernel.FloatsKey_get_all_strings()
3478 def get_number_unique():
3479 r"""get_number_unique() -> unsigned int"""
3480 return _IMP_kernel.FloatsKey_get_number_unique()
3483 r"""__str__(FloatsKey self) -> std::string"""
3484 return _IMP_kernel.FloatsKey___str__(self)
3487 r"""__repr__(FloatsKey self) -> std::string"""
3488 return _IMP_kernel.FloatsKey___repr__(self)
3489 __swig_destroy__ = _IMP_kernel.delete_FloatsKey
3492 _IMP_kernel.FloatsKey_swigregister(FloatsKey)
3494 r"""Proxy of C++ IMP::Key< 12 > class."""
3496 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3498 def __init__(self, *args):
3500 __init__(SparseStringKey self) -> SparseStringKey
3501 __init__(SparseStringKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseStringKey
3502 __init__(SparseStringKey self, unsigned int i) -> SparseStringKey
3504 _IMP_kernel.SparseStringKey_swiginit(self, _IMP_kernel.new_SparseStringKey(*args))
3508 r"""add_key(std::string const & sc) -> unsigned int"""
3509 return _IMP_kernel.SparseStringKey_add_key(sc)
3512 def get_existing_key(sc):
3513 r"""get_existing_key(std::string const & sc) -> SparseStringKey"""
3514 return _IMP_kernel.SparseStringKey_get_existing_key(sc)
3517 def get_key_exists(sc):
3518 r"""get_key_exists(std::string const & sc) -> bool"""
3519 return _IMP_kernel.SparseStringKey_get_key_exists(sc)
3521 def get_string(self):
3522 r"""get_string(SparseStringKey self) -> std::string const"""
3523 return _IMP_kernel.SparseStringKey_get_string(self)
3525 def __eq__(self, o):
3526 r"""__eq__(SparseStringKey self, SparseStringKey o) -> bool"""
3527 return _IMP_kernel.SparseStringKey___eq__(self, o)
3529 def __ne__(self, o):
3530 r"""__ne__(SparseStringKey self, SparseStringKey o) -> bool"""
3531 return _IMP_kernel.SparseStringKey___ne__(self, o)
3533 def __lt__(self, o):
3534 r"""__lt__(SparseStringKey self, SparseStringKey o) -> bool"""
3535 return _IMP_kernel.SparseStringKey___lt__(self, o)
3537 def __gt__(self, o):
3538 r"""__gt__(SparseStringKey self, SparseStringKey o) -> bool"""
3539 return _IMP_kernel.SparseStringKey___gt__(self, o)
3541 def __ge__(self, o):
3542 r"""__ge__(SparseStringKey self, SparseStringKey o) -> bool"""
3543 return _IMP_kernel.SparseStringKey___ge__(self, o)
3545 def __le__(self, o):
3546 r"""__le__(SparseStringKey self, SparseStringKey o) -> bool"""
3547 return _IMP_kernel.SparseStringKey___le__(self, o)
3550 r"""__hash__(SparseStringKey self) -> std::size_t"""
3551 return _IMP_kernel.SparseStringKey___hash__(self)
3553 def show(self, *args):
3554 r"""show(SparseStringKey self, _ostream out=std::cout)"""
3555 return _IMP_kernel.SparseStringKey_show(self, *args)
3558 def add_alias(old_key, new_name):
3559 r"""add_alias(SparseStringKey old_key, std::string new_name) -> SparseStringKey"""
3560 return _IMP_kernel.SparseStringKey_add_alias(old_key, new_name)
3563 def get_number_of_keys():
3564 r"""get_number_of_keys() -> unsigned int"""
3565 return _IMP_kernel.SparseStringKey_get_number_of_keys()
3568 r"""get_index(SparseStringKey self) -> unsigned int"""
3569 return _IMP_kernel.SparseStringKey_get_index(self)
3573 r"""show_all(_ostream out)"""
3574 return _IMP_kernel.SparseStringKey_show_all(out)
3577 def get_all_strings():
3578 r"""get_all_strings() -> IMP::Vector< std::string >"""
3579 return _IMP_kernel.SparseStringKey_get_all_strings()
3582 def get_number_unique():
3583 r"""get_number_unique() -> unsigned int"""
3584 return _IMP_kernel.SparseStringKey_get_number_unique()
3587 r"""__str__(SparseStringKey self) -> std::string"""
3588 return _IMP_kernel.SparseStringKey___str__(self)
3591 r"""__repr__(SparseStringKey self) -> std::string"""
3592 return _IMP_kernel.SparseStringKey___repr__(self)
3593 __swig_destroy__ = _IMP_kernel.delete_SparseStringKey
3596 _IMP_kernel.SparseStringKey_swigregister(SparseStringKey)
3598 r"""Proxy of C++ IMP::Key< 13 > class."""
3600 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3602 def __init__(self, *args):
3604 __init__(SparseIntKey self) -> SparseIntKey
3605 __init__(SparseIntKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseIntKey
3606 __init__(SparseIntKey self, unsigned int i) -> SparseIntKey
3608 _IMP_kernel.SparseIntKey_swiginit(self, _IMP_kernel.new_SparseIntKey(*args))
3612 r"""add_key(std::string const & sc) -> unsigned int"""
3613 return _IMP_kernel.SparseIntKey_add_key(sc)
3616 def get_existing_key(sc):
3617 r"""get_existing_key(std::string const & sc) -> SparseIntKey"""
3618 return _IMP_kernel.SparseIntKey_get_existing_key(sc)
3621 def get_key_exists(sc):
3622 r"""get_key_exists(std::string const & sc) -> bool"""
3623 return _IMP_kernel.SparseIntKey_get_key_exists(sc)
3625 def get_string(self):
3626 r"""get_string(SparseIntKey self) -> std::string const"""
3627 return _IMP_kernel.SparseIntKey_get_string(self)
3629 def __eq__(self, o):
3630 r"""__eq__(SparseIntKey self, SparseIntKey o) -> bool"""
3631 return _IMP_kernel.SparseIntKey___eq__(self, o)
3633 def __ne__(self, o):
3634 r"""__ne__(SparseIntKey self, SparseIntKey o) -> bool"""
3635 return _IMP_kernel.SparseIntKey___ne__(self, o)
3637 def __lt__(self, o):
3638 r"""__lt__(SparseIntKey self, SparseIntKey o) -> bool"""
3639 return _IMP_kernel.SparseIntKey___lt__(self, o)
3641 def __gt__(self, o):
3642 r"""__gt__(SparseIntKey self, SparseIntKey o) -> bool"""
3643 return _IMP_kernel.SparseIntKey___gt__(self, o)
3645 def __ge__(self, o):
3646 r"""__ge__(SparseIntKey self, SparseIntKey o) -> bool"""
3647 return _IMP_kernel.SparseIntKey___ge__(self, o)
3649 def __le__(self, o):
3650 r"""__le__(SparseIntKey self, SparseIntKey o) -> bool"""
3651 return _IMP_kernel.SparseIntKey___le__(self, o)
3654 r"""__hash__(SparseIntKey self) -> std::size_t"""
3655 return _IMP_kernel.SparseIntKey___hash__(self)
3657 def show(self, *args):
3658 r"""show(SparseIntKey self, _ostream out=std::cout)"""
3659 return _IMP_kernel.SparseIntKey_show(self, *args)
3662 def add_alias(old_key, new_name):
3663 r"""add_alias(SparseIntKey old_key, std::string new_name) -> SparseIntKey"""
3664 return _IMP_kernel.SparseIntKey_add_alias(old_key, new_name)
3667 def get_number_of_keys():
3668 r"""get_number_of_keys() -> unsigned int"""
3669 return _IMP_kernel.SparseIntKey_get_number_of_keys()
3672 r"""get_index(SparseIntKey self) -> unsigned int"""
3673 return _IMP_kernel.SparseIntKey_get_index(self)
3677 r"""show_all(_ostream out)"""
3678 return _IMP_kernel.SparseIntKey_show_all(out)
3681 def get_all_strings():
3682 r"""get_all_strings() -> IMP::Vector< std::string >"""
3683 return _IMP_kernel.SparseIntKey_get_all_strings()
3686 def get_number_unique():
3687 r"""get_number_unique() -> unsigned int"""
3688 return _IMP_kernel.SparseIntKey_get_number_unique()
3691 r"""__str__(SparseIntKey self) -> std::string"""
3692 return _IMP_kernel.SparseIntKey___str__(self)
3695 r"""__repr__(SparseIntKey self) -> std::string"""
3696 return _IMP_kernel.SparseIntKey___repr__(self)
3697 __swig_destroy__ = _IMP_kernel.delete_SparseIntKey
3700 _IMP_kernel.SparseIntKey_swigregister(SparseIntKey)
3702 r"""Proxy of C++ IMP::Key< 14 > class."""
3704 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3706 def __init__(self, *args):
3708 __init__(SparseFloatKey self) -> SparseFloatKey
3709 __init__(SparseFloatKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseFloatKey
3710 __init__(SparseFloatKey self, unsigned int i) -> SparseFloatKey
3712 _IMP_kernel.SparseFloatKey_swiginit(self, _IMP_kernel.new_SparseFloatKey(*args))
3716 r"""add_key(std::string const & sc) -> unsigned int"""
3717 return _IMP_kernel.SparseFloatKey_add_key(sc)
3720 def get_existing_key(sc):
3721 r"""get_existing_key(std::string const & sc) -> SparseFloatKey"""
3722 return _IMP_kernel.SparseFloatKey_get_existing_key(sc)
3725 def get_key_exists(sc):
3726 r"""get_key_exists(std::string const & sc) -> bool"""
3727 return _IMP_kernel.SparseFloatKey_get_key_exists(sc)
3729 def get_string(self):
3730 r"""get_string(SparseFloatKey self) -> std::string const"""
3731 return _IMP_kernel.SparseFloatKey_get_string(self)
3733 def __eq__(self, o):
3734 r"""__eq__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3735 return _IMP_kernel.SparseFloatKey___eq__(self, o)
3737 def __ne__(self, o):
3738 r"""__ne__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3739 return _IMP_kernel.SparseFloatKey___ne__(self, o)
3741 def __lt__(self, o):
3742 r"""__lt__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3743 return _IMP_kernel.SparseFloatKey___lt__(self, o)
3745 def __gt__(self, o):
3746 r"""__gt__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3747 return _IMP_kernel.SparseFloatKey___gt__(self, o)
3749 def __ge__(self, o):
3750 r"""__ge__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3751 return _IMP_kernel.SparseFloatKey___ge__(self, o)
3753 def __le__(self, o):
3754 r"""__le__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3755 return _IMP_kernel.SparseFloatKey___le__(self, o)
3758 r"""__hash__(SparseFloatKey self) -> std::size_t"""
3759 return _IMP_kernel.SparseFloatKey___hash__(self)
3761 def show(self, *args):
3762 r"""show(SparseFloatKey self, _ostream out=std::cout)"""
3763 return _IMP_kernel.SparseFloatKey_show(self, *args)
3766 def add_alias(old_key, new_name):
3767 r"""add_alias(SparseFloatKey old_key, std::string new_name) -> SparseFloatKey"""
3768 return _IMP_kernel.SparseFloatKey_add_alias(old_key, new_name)
3771 def get_number_of_keys():
3772 r"""get_number_of_keys() -> unsigned int"""
3773 return _IMP_kernel.SparseFloatKey_get_number_of_keys()
3776 r"""get_index(SparseFloatKey self) -> unsigned int"""
3777 return _IMP_kernel.SparseFloatKey_get_index(self)
3781 r"""show_all(_ostream out)"""
3782 return _IMP_kernel.SparseFloatKey_show_all(out)
3785 def get_all_strings():
3786 r"""get_all_strings() -> IMP::Vector< std::string >"""
3787 return _IMP_kernel.SparseFloatKey_get_all_strings()
3790 def get_number_unique():
3791 r"""get_number_unique() -> unsigned int"""
3792 return _IMP_kernel.SparseFloatKey_get_number_unique()
3795 r"""__str__(SparseFloatKey self) -> std::string"""
3796 return _IMP_kernel.SparseFloatKey___str__(self)
3799 r"""__repr__(SparseFloatKey self) -> std::string"""
3800 return _IMP_kernel.SparseFloatKey___repr__(self)
3801 __swig_destroy__ = _IMP_kernel.delete_SparseFloatKey
3804 _IMP_kernel.SparseFloatKey_swigregister(SparseFloatKey)
3806 r"""Proxy of C++ IMP::Key< 15 > class."""
3808 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3810 def __init__(self, *args):
3812 __init__(SparseParticleIndexKey self) -> SparseParticleIndexKey
3813 __init__(SparseParticleIndexKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseParticleIndexKey
3814 __init__(SparseParticleIndexKey self, unsigned int i) -> SparseParticleIndexKey
3816 _IMP_kernel.SparseParticleIndexKey_swiginit(self, _IMP_kernel.new_SparseParticleIndexKey(*args))
3820 r"""add_key(std::string const & sc) -> unsigned int"""
3821 return _IMP_kernel.SparseParticleIndexKey_add_key(sc)
3824 def get_existing_key(sc):
3825 r"""get_existing_key(std::string const & sc) -> SparseParticleIndexKey"""
3826 return _IMP_kernel.SparseParticleIndexKey_get_existing_key(sc)
3829 def get_key_exists(sc):
3830 r"""get_key_exists(std::string const & sc) -> bool"""
3831 return _IMP_kernel.SparseParticleIndexKey_get_key_exists(sc)
3833 def get_string(self):
3834 r"""get_string(SparseParticleIndexKey self) -> std::string const"""
3835 return _IMP_kernel.SparseParticleIndexKey_get_string(self)
3837 def __eq__(self, o):
3838 r"""__eq__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3839 return _IMP_kernel.SparseParticleIndexKey___eq__(self, o)
3841 def __ne__(self, o):
3842 r"""__ne__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3843 return _IMP_kernel.SparseParticleIndexKey___ne__(self, o)
3845 def __lt__(self, o):
3846 r"""__lt__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3847 return _IMP_kernel.SparseParticleIndexKey___lt__(self, o)
3849 def __gt__(self, o):
3850 r"""__gt__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3851 return _IMP_kernel.SparseParticleIndexKey___gt__(self, o)
3853 def __ge__(self, o):
3854 r"""__ge__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3855 return _IMP_kernel.SparseParticleIndexKey___ge__(self, o)
3857 def __le__(self, o):
3858 r"""__le__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3859 return _IMP_kernel.SparseParticleIndexKey___le__(self, o)
3862 r"""__hash__(SparseParticleIndexKey self) -> std::size_t"""
3863 return _IMP_kernel.SparseParticleIndexKey___hash__(self)
3865 def show(self, *args):
3866 r"""show(SparseParticleIndexKey self, _ostream out=std::cout)"""
3867 return _IMP_kernel.SparseParticleIndexKey_show(self, *args)
3870 def add_alias(old_key, new_name):
3871 r"""add_alias(SparseParticleIndexKey old_key, std::string new_name) -> SparseParticleIndexKey"""
3872 return _IMP_kernel.SparseParticleIndexKey_add_alias(old_key, new_name)
3875 def get_number_of_keys():
3876 r"""get_number_of_keys() -> unsigned int"""
3877 return _IMP_kernel.SparseParticleIndexKey_get_number_of_keys()
3880 r"""get_index(SparseParticleIndexKey self) -> unsigned int"""
3881 return _IMP_kernel.SparseParticleIndexKey_get_index(self)
3885 r"""show_all(_ostream out)"""
3886 return _IMP_kernel.SparseParticleIndexKey_show_all(out)
3889 def get_all_strings():
3890 r"""get_all_strings() -> IMP::Vector< std::string >"""
3891 return _IMP_kernel.SparseParticleIndexKey_get_all_strings()
3894 def get_number_unique():
3895 r"""get_number_unique() -> unsigned int"""
3896 return _IMP_kernel.SparseParticleIndexKey_get_number_unique()
3899 r"""__str__(SparseParticleIndexKey self) -> std::string"""
3900 return _IMP_kernel.SparseParticleIndexKey___str__(self)
3903 r"""__repr__(SparseParticleIndexKey self) -> std::string"""
3904 return _IMP_kernel.SparseParticleIndexKey___repr__(self)
3905 __swig_destroy__ = _IMP_kernel.delete_SparseParticleIndexKey
3908 _IMP_kernel.SparseParticleIndexKey_swigregister(SparseParticleIndexKey)
3910 r"""Proxy of C++ IMP::Key< 16 > class."""
3912 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3914 def __init__(self, *args):
3916 __init__(Vector3DKey self) -> Vector3DKey
3917 __init__(Vector3DKey self, std::string const & c, bool is_implicit_add_permitted=True) -> Vector3DKey
3918 __init__(Vector3DKey self, unsigned int i) -> Vector3DKey
3920 _IMP_kernel.Vector3DKey_swiginit(self, _IMP_kernel.new_Vector3DKey(*args))
3924 r"""add_key(std::string const & sc) -> unsigned int"""
3925 return _IMP_kernel.Vector3DKey_add_key(sc)
3928 def get_existing_key(sc):
3929 r"""get_existing_key(std::string const & sc) -> Vector3DKey"""
3930 return _IMP_kernel.Vector3DKey_get_existing_key(sc)
3933 def get_key_exists(sc):
3934 r"""get_key_exists(std::string const & sc) -> bool"""
3935 return _IMP_kernel.Vector3DKey_get_key_exists(sc)
3937 def get_string(self):
3938 r"""get_string(Vector3DKey self) -> std::string const"""
3939 return _IMP_kernel.Vector3DKey_get_string(self)
3941 def __eq__(self, o):
3942 r"""__eq__(Vector3DKey self, Vector3DKey o) -> bool"""
3943 return _IMP_kernel.Vector3DKey___eq__(self, o)
3945 def __ne__(self, o):
3946 r"""__ne__(Vector3DKey self, Vector3DKey o) -> bool"""
3947 return _IMP_kernel.Vector3DKey___ne__(self, o)
3949 def __lt__(self, o):
3950 r"""__lt__(Vector3DKey self, Vector3DKey o) -> bool"""
3951 return _IMP_kernel.Vector3DKey___lt__(self, o)
3953 def __gt__(self, o):
3954 r"""__gt__(Vector3DKey self, Vector3DKey o) -> bool"""
3955 return _IMP_kernel.Vector3DKey___gt__(self, o)
3957 def __ge__(self, o):
3958 r"""__ge__(Vector3DKey self, Vector3DKey o) -> bool"""
3959 return _IMP_kernel.Vector3DKey___ge__(self, o)
3961 def __le__(self, o):
3962 r"""__le__(Vector3DKey self, Vector3DKey o) -> bool"""
3963 return _IMP_kernel.Vector3DKey___le__(self, o)
3966 r"""__hash__(Vector3DKey self) -> std::size_t"""
3967 return _IMP_kernel.Vector3DKey___hash__(self)
3969 def show(self, *args):
3970 r"""show(Vector3DKey self, _ostream out=std::cout)"""
3971 return _IMP_kernel.Vector3DKey_show(self, *args)
3974 def add_alias(old_key, new_name):
3975 r"""add_alias(Vector3DKey old_key, std::string new_name) -> Vector3DKey"""
3976 return _IMP_kernel.Vector3DKey_add_alias(old_key, new_name)
3979 def get_number_of_keys():
3980 r"""get_number_of_keys() -> unsigned int"""
3981 return _IMP_kernel.Vector3DKey_get_number_of_keys()
3984 r"""get_index(Vector3DKey self) -> unsigned int"""
3985 return _IMP_kernel.Vector3DKey_get_index(self)
3989 r"""show_all(_ostream out)"""
3990 return _IMP_kernel.Vector3DKey_show_all(out)
3993 def get_all_strings():
3994 r"""get_all_strings() -> IMP::Vector< std::string >"""
3995 return _IMP_kernel.Vector3DKey_get_all_strings()
3998 def get_number_unique():
3999 r"""get_number_unique() -> unsigned int"""
4000 return _IMP_kernel.Vector3DKey_get_number_unique()
4003 r"""__str__(Vector3DKey self) -> std::string"""
4004 return _IMP_kernel.Vector3DKey___str__(self)
4007 r"""__repr__(Vector3DKey self) -> std::string"""
4008 return _IMP_kernel.Vector3DKey___repr__(self)
4009 __swig_destroy__ = _IMP_kernel.delete_Vector3DKey
4012 _IMP_kernel.Vector3DKey_swigregister(Vector3DKey)
4014 r"""Proxy of C++ IMP::Key< 17 > class."""
4016 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4018 def __init__(self, *args):
4020 __init__(Vector3DDerivKey self) -> Vector3DDerivKey
4021 __init__(Vector3DDerivKey self, std::string const & c, bool is_implicit_add_permitted=True) -> Vector3DDerivKey
4022 __init__(Vector3DDerivKey self, unsigned int i) -> Vector3DDerivKey
4024 _IMP_kernel.Vector3DDerivKey_swiginit(self, _IMP_kernel.new_Vector3DDerivKey(*args))
4028 r"""add_key(std::string const & sc) -> unsigned int"""
4029 return _IMP_kernel.Vector3DDerivKey_add_key(sc)
4032 def get_existing_key(sc):
4033 r"""get_existing_key(std::string const & sc) -> Vector3DDerivKey"""
4034 return _IMP_kernel.Vector3DDerivKey_get_existing_key(sc)
4037 def get_key_exists(sc):
4038 r"""get_key_exists(std::string const & sc) -> bool"""
4039 return _IMP_kernel.Vector3DDerivKey_get_key_exists(sc)
4041 def get_string(self):
4042 r"""get_string(Vector3DDerivKey self) -> std::string const"""
4043 return _IMP_kernel.Vector3DDerivKey_get_string(self)
4045 def __eq__(self, o):
4046 r"""__eq__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4047 return _IMP_kernel.Vector3DDerivKey___eq__(self, o)
4049 def __ne__(self, o):
4050 r"""__ne__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4051 return _IMP_kernel.Vector3DDerivKey___ne__(self, o)
4053 def __lt__(self, o):
4054 r"""__lt__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4055 return _IMP_kernel.Vector3DDerivKey___lt__(self, o)
4057 def __gt__(self, o):
4058 r"""__gt__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4059 return _IMP_kernel.Vector3DDerivKey___gt__(self, o)
4061 def __ge__(self, o):
4062 r"""__ge__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4063 return _IMP_kernel.Vector3DDerivKey___ge__(self, o)
4065 def __le__(self, o):
4066 r"""__le__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4067 return _IMP_kernel.Vector3DDerivKey___le__(self, o)
4070 r"""__hash__(Vector3DDerivKey self) -> std::size_t"""
4071 return _IMP_kernel.Vector3DDerivKey___hash__(self)
4073 def show(self, *args):
4074 r"""show(Vector3DDerivKey self, _ostream out=std::cout)"""
4075 return _IMP_kernel.Vector3DDerivKey_show(self, *args)
4078 def add_alias(old_key, new_name):
4079 r"""add_alias(Vector3DDerivKey old_key, std::string new_name) -> Vector3DDerivKey"""
4080 return _IMP_kernel.Vector3DDerivKey_add_alias(old_key, new_name)
4083 def get_number_of_keys():
4084 r"""get_number_of_keys() -> unsigned int"""
4085 return _IMP_kernel.Vector3DDerivKey_get_number_of_keys()
4088 r"""get_index(Vector3DDerivKey self) -> unsigned int"""
4089 return _IMP_kernel.Vector3DDerivKey_get_index(self)
4093 r"""show_all(_ostream out)"""
4094 return _IMP_kernel.Vector3DDerivKey_show_all(out)
4097 def get_all_strings():
4098 r"""get_all_strings() -> IMP::Vector< std::string >"""
4099 return _IMP_kernel.Vector3DDerivKey_get_all_strings()
4102 def get_number_unique():
4103 r"""get_number_unique() -> unsigned int"""
4104 return _IMP_kernel.Vector3DDerivKey_get_number_unique()
4107 r"""__str__(Vector3DDerivKey self) -> std::string"""
4108 return _IMP_kernel.Vector3DDerivKey___str__(self)
4111 r"""__repr__(Vector3DDerivKey self) -> std::string"""
4112 return _IMP_kernel.Vector3DDerivKey___repr__(self)
4113 __swig_destroy__ = _IMP_kernel.delete_Vector3DDerivKey
4116 _IMP_kernel.Vector3DDerivKey_swigregister(Vector3DDerivKey)
4118 r"""Proxy of C++ IMP::Key< 18 > class."""
4120 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4122 def __init__(self, *args):
4124 __init__(Vector4DKey self) -> Vector4DKey
4125 __init__(Vector4DKey self, std::string const & c, bool is_implicit_add_permitted=True) -> Vector4DKey
4126 __init__(Vector4DKey self, unsigned int i) -> Vector4DKey
4128 _IMP_kernel.Vector4DKey_swiginit(self, _IMP_kernel.new_Vector4DKey(*args))
4132 r"""add_key(std::string const & sc) -> unsigned int"""
4133 return _IMP_kernel.Vector4DKey_add_key(sc)
4136 def get_existing_key(sc):
4137 r"""get_existing_key(std::string const & sc) -> Vector4DKey"""
4138 return _IMP_kernel.Vector4DKey_get_existing_key(sc)
4141 def get_key_exists(sc):
4142 r"""get_key_exists(std::string const & sc) -> bool"""
4143 return _IMP_kernel.Vector4DKey_get_key_exists(sc)
4145 def get_string(self):
4146 r"""get_string(Vector4DKey self) -> std::string const"""
4147 return _IMP_kernel.Vector4DKey_get_string(self)
4149 def __eq__(self, o):
4150 r"""__eq__(Vector4DKey self, Vector4DKey o) -> bool"""
4151 return _IMP_kernel.Vector4DKey___eq__(self, o)
4153 def __ne__(self, o):
4154 r"""__ne__(Vector4DKey self, Vector4DKey o) -> bool"""
4155 return _IMP_kernel.Vector4DKey___ne__(self, o)
4157 def __lt__(self, o):
4158 r"""__lt__(Vector4DKey self, Vector4DKey o) -> bool"""
4159 return _IMP_kernel.Vector4DKey___lt__(self, o)
4161 def __gt__(self, o):
4162 r"""__gt__(Vector4DKey self, Vector4DKey o) -> bool"""
4163 return _IMP_kernel.Vector4DKey___gt__(self, o)
4165 def __ge__(self, o):
4166 r"""__ge__(Vector4DKey self, Vector4DKey o) -> bool"""
4167 return _IMP_kernel.Vector4DKey___ge__(self, o)
4169 def __le__(self, o):
4170 r"""__le__(Vector4DKey self, Vector4DKey o) -> bool"""
4171 return _IMP_kernel.Vector4DKey___le__(self, o)
4174 r"""__hash__(Vector4DKey self) -> std::size_t"""
4175 return _IMP_kernel.Vector4DKey___hash__(self)
4177 def show(self, *args):
4178 r"""show(Vector4DKey self, _ostream out=std::cout)"""
4179 return _IMP_kernel.Vector4DKey_show(self, *args)
4182 def add_alias(old_key, new_name):
4183 r"""add_alias(Vector4DKey old_key, std::string new_name) -> Vector4DKey"""
4184 return _IMP_kernel.Vector4DKey_add_alias(old_key, new_name)
4187 def get_number_of_keys():
4188 r"""get_number_of_keys() -> unsigned int"""
4189 return _IMP_kernel.Vector4DKey_get_number_of_keys()
4192 r"""get_index(Vector4DKey self) -> unsigned int"""
4193 return _IMP_kernel.Vector4DKey_get_index(self)
4197 r"""show_all(_ostream out)"""
4198 return _IMP_kernel.Vector4DKey_show_all(out)
4201 def get_all_strings():
4202 r"""get_all_strings() -> IMP::Vector< std::string >"""
4203 return _IMP_kernel.Vector4DKey_get_all_strings()
4206 def get_number_unique():
4207 r"""get_number_unique() -> unsigned int"""
4208 return _IMP_kernel.Vector4DKey_get_number_unique()
4211 r"""__str__(Vector4DKey self) -> std::string"""
4212 return _IMP_kernel.Vector4DKey___str__(self)
4215 r"""__repr__(Vector4DKey self) -> std::string"""
4216 return _IMP_kernel.Vector4DKey___repr__(self)
4217 __swig_destroy__ = _IMP_kernel.delete_Vector4DKey
4220 _IMP_kernel.Vector4DKey_swigregister(Vector4DKey)
4222 r"""Proxy of C++ IMP::Key< 19 > class."""
4224 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4226 def __init__(self, *args):
4228 __init__(Vector4DDerivKey self) -> Vector4DDerivKey
4229 __init__(Vector4DDerivKey self, std::string const & c, bool is_implicit_add_permitted=True) -> Vector4DDerivKey
4230 __init__(Vector4DDerivKey self, unsigned int i) -> Vector4DDerivKey
4232 _IMP_kernel.Vector4DDerivKey_swiginit(self, _IMP_kernel.new_Vector4DDerivKey(*args))
4236 r"""add_key(std::string const & sc) -> unsigned int"""
4237 return _IMP_kernel.Vector4DDerivKey_add_key(sc)
4240 def get_existing_key(sc):
4241 r"""get_existing_key(std::string const & sc) -> Vector4DDerivKey"""
4242 return _IMP_kernel.Vector4DDerivKey_get_existing_key(sc)
4245 def get_key_exists(sc):
4246 r"""get_key_exists(std::string const & sc) -> bool"""
4247 return _IMP_kernel.Vector4DDerivKey_get_key_exists(sc)
4249 def get_string(self):
4250 r"""get_string(Vector4DDerivKey self) -> std::string const"""
4251 return _IMP_kernel.Vector4DDerivKey_get_string(self)
4253 def __eq__(self, o):
4254 r"""__eq__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4255 return _IMP_kernel.Vector4DDerivKey___eq__(self, o)
4257 def __ne__(self, o):
4258 r"""__ne__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4259 return _IMP_kernel.Vector4DDerivKey___ne__(self, o)
4261 def __lt__(self, o):
4262 r"""__lt__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4263 return _IMP_kernel.Vector4DDerivKey___lt__(self, o)
4265 def __gt__(self, o):
4266 r"""__gt__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4267 return _IMP_kernel.Vector4DDerivKey___gt__(self, o)
4269 def __ge__(self, o):
4270 r"""__ge__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4271 return _IMP_kernel.Vector4DDerivKey___ge__(self, o)
4273 def __le__(self, o):
4274 r"""__le__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4275 return _IMP_kernel.Vector4DDerivKey___le__(self, o)
4278 r"""__hash__(Vector4DDerivKey self) -> std::size_t"""
4279 return _IMP_kernel.Vector4DDerivKey___hash__(self)
4281 def show(self, *args):
4282 r"""show(Vector4DDerivKey self, _ostream out=std::cout)"""
4283 return _IMP_kernel.Vector4DDerivKey_show(self, *args)
4286 def add_alias(old_key, new_name):
4287 r"""add_alias(Vector4DDerivKey old_key, std::string new_name) -> Vector4DDerivKey"""
4288 return _IMP_kernel.Vector4DDerivKey_add_alias(old_key, new_name)
4291 def get_number_of_keys():
4292 r"""get_number_of_keys() -> unsigned int"""
4293 return _IMP_kernel.Vector4DDerivKey_get_number_of_keys()
4296 r"""get_index(Vector4DDerivKey self) -> unsigned int"""
4297 return _IMP_kernel.Vector4DDerivKey_get_index(self)
4301 r"""show_all(_ostream out)"""
4302 return _IMP_kernel.Vector4DDerivKey_show_all(out)
4305 def get_all_strings():
4306 r"""get_all_strings() -> IMP::Vector< std::string >"""
4307 return _IMP_kernel.Vector4DDerivKey_get_all_strings()
4310 def get_number_unique():
4311 r"""get_number_unique() -> unsigned int"""
4312 return _IMP_kernel.Vector4DDerivKey_get_number_unique()
4315 r"""__str__(Vector4DDerivKey self) -> std::string"""
4316 return _IMP_kernel.Vector4DDerivKey___str__(self)
4319 r"""__repr__(Vector4DDerivKey self) -> std::string"""
4320 return _IMP_kernel.Vector4DDerivKey___repr__(self)
4321 __swig_destroy__ = _IMP_kernel.delete_Vector4DDerivKey
4324 _IMP_kernel.Vector4DDerivKey_swigregister(Vector4DDerivKey)
4333 class FloatIndex(_Value):
4334 r"""Proxy of C++ IMP::FloatIndex class."""
4336 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4338 def __init__(self, *args):
4340 __init__(FloatIndex self, ParticleIndex pi, FloatKey k) -> FloatIndex
4341 __init__(FloatIndex self, ParticleIndex pi, Vector3DDerivKey k, int index) -> FloatIndex
4342 __init__(FloatIndex self, ParticleIndex pi, Vector4DDerivKey k, int index) -> FloatIndex
4344 _IMP_kernel.FloatIndex_swiginit(self, _IMP_kernel.new_FloatIndex(*args))
4346 def get_float_key(self):
4347 r"""get_float_key(FloatIndex self) -> FloatKey"""
4348 return _IMP_kernel.FloatIndex_get_float_key(self)
4350 def set_value(self, m, v):
4351 r"""set_value(FloatIndex self, Model m, IMP::Float v)"""
4352 return _IMP_kernel.FloatIndex_set_value(self, m, v)
4354 def get_value(self, m):
4355 r"""get_value(FloatIndex self, Model m) -> IMP::Float"""
4356 return _IMP_kernel.FloatIndex_get_value(self, m)
4358 def get_derivative(self, m):
4359 r"""get_derivative(FloatIndex self, Model m) -> IMP::Float"""
4360 return _IMP_kernel.FloatIndex_get_derivative(self, m)
4362 def show(self, *args):
4363 r"""show(FloatIndex self, _ostream out=std::cout)"""
4364 return _IMP_kernel.FloatIndex_show(self, *args)
4367 r"""__str__(FloatIndex self) -> std::string"""
4368 return _IMP_kernel.FloatIndex___str__(self)
4371 r"""__repr__(FloatIndex self) -> std::string"""
4372 return _IMP_kernel.FloatIndex___repr__(self)
4373 __swig_destroy__ = _IMP_kernel.delete_FloatIndex
4376 _IMP_kernel.FloatIndex_swigregister(FloatIndex)
4377 class _ParticleIndexTag(object):
4378 r"""Proxy of C++ IMP::ParticleIndexTag class."""
4380 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4381 __repr__ = _swig_repr
4384 r"""__init__(_ParticleIndexTag self) -> _ParticleIndexTag"""
4385 _IMP_kernel._ParticleIndexTag_swiginit(self, _IMP_kernel.new__ParticleIndexTag())
4386 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexTag
4389 _IMP_kernel._ParticleIndexTag_swigregister(_ParticleIndexTag)
4390 class ModelObject(
Object):
4391 r"""Proxy of C++ IMP::ModelObject class."""
4393 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4395 def __init__(self, *args):
4397 __init__(ModelObject self, Model m, std::string name) -> ModelObject
4398 __init__(ModelObject self) -> ModelObject
4400 if self.__class__ == ModelObject:
4404 _IMP_kernel.ModelObject_swiginit(self, _IMP_kernel.new_ModelObject(_self, *args))
4406 if self.__class__ != ModelObject:
4407 _director_objects.register(self)
4411 __swig_destroy__ = _IMP_kernel.delete_ModelObject
4413 def get_model(self):
4414 m = _IMP_kernel.ModelObject_get_model(self)
4415 if m
in _models_set:
4416 m = _models_set_get(m)
4421 def get_inputs(self):
4422 r"""get_inputs(ModelObject self) -> IMP::ModelObjectsTemp"""
4423 return _IMP_kernel.ModelObject_get_inputs(self)
4425 def get_outputs(self):
4426 r"""get_outputs(ModelObject self) -> IMP::ModelObjectsTemp"""
4427 return _IMP_kernel.ModelObject_get_outputs(self)
4429 def get_interactions(self):
4430 r"""get_interactions(ModelObject self) -> IMP::ModelObjectsTemps"""
4431 return _IMP_kernel.ModelObject_get_interactions(self)
4433 def get_has_dependencies(self):
4434 r"""get_has_dependencies(ModelObject self) -> bool"""
4435 return _IMP_kernel.ModelObject_get_has_dependencies(self)
4437 def set_has_dependencies(self, tf):
4438 r"""set_has_dependencies(ModelObject self, bool tf)"""
4439 return _IMP_kernel.ModelObject_set_has_dependencies(self, tf)
4441 def set_has_required_score_states(self, tf):
4442 r"""set_has_required_score_states(ModelObject self, bool tf)"""
4443 return _IMP_kernel.ModelObject_set_has_required_score_states(self, tf)
4445 def get_has_required_score_states(self):
4446 r"""get_has_required_score_states(ModelObject self) -> bool"""
4447 return _IMP_kernel.ModelObject_get_has_required_score_states(self)
4449 def get_required_score_states(self):
4450 r"""get_required_score_states(ModelObject self) -> IMP::ScoreStatesTemp const &"""
4451 return _IMP_kernel.ModelObject_get_required_score_states(self)
4453 def handle_set_has_required_score_states(self, arg0):
4454 r"""handle_set_has_required_score_states(ModelObject self, bool arg0)"""
4455 return _IMP_kernel.ModelObject_handle_set_has_required_score_states(self, arg0)
4457 def do_get_inputs(self):
4458 r"""do_get_inputs(ModelObject self) -> IMP::ModelObjectsTemp"""
4459 return _IMP_kernel.ModelObject_do_get_inputs(self)
4461 def do_get_outputs(self):
4462 r"""do_get_outputs(ModelObject self) -> IMP::ModelObjectsTemp"""
4463 return _IMP_kernel.ModelObject_do_get_outputs(self)
4465 def do_get_interactions(self):
4466 r"""do_get_interactions(ModelObject self) -> IMP::ModelObjectsTemps"""
4467 return _IMP_kernel.ModelObject_do_get_interactions(self)
4470 r"""__str__(ModelObject self) -> std::string"""
4471 return _IMP_kernel.ModelObject___str__(self)
4474 r"""__repr__(ModelObject self) -> std::string"""
4475 return _IMP_kernel.ModelObject___repr__(self)
4479 return _object_cast_to_ModelObject(o)
4482 def do_show(self, out):
4487 return _object_cast_to_ModelObject(o)
4489 def __disown__(self):
4491 _IMP_kernel.disown_ModelObject(self)
4492 return weakref.proxy(self)
4495 r"""do_destroy(ModelObject self)"""
4496 return _IMP_kernel.ModelObject_do_destroy(self)
4499 _IMP_kernel.ModelObject_swigregister(ModelObject)
4500 cvar = _IMP_kernel.cvar
4501 NO_MAX = cvar.NO_MAX
4502 BAD_SCORE = cvar.BAD_SCORE
4504 class _ParticleInputs(object):
4505 r"""Proxy of C++ IMP::ParticleInputs class."""
4507 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4509 def __init__(self, *args, **kwargs):
4510 raise AttributeError(
"No constructor defined - class is abstract")
4511 __repr__ = _swig_repr
4513 def get_inputs(self, m, pis):
4514 r"""get_inputs(_ParticleInputs self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4515 return _IMP_kernel._ParticleInputs_get_inputs(self, m, pis)
4518 _IMP_kernel._ParticleInputs_swigregister(_ParticleInputs)
4519 class _ParticleOutputs(object):
4520 r"""Proxy of C++ IMP::ParticleOutputs class."""
4522 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4524 def __init__(self, *args, **kwargs):
4525 raise AttributeError(
"No constructor defined - class is abstract")
4526 __repr__ = _swig_repr
4528 def get_outputs(self, m, pis):
4529 r"""get_outputs(_ParticleOutputs self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4530 return _IMP_kernel._ParticleOutputs_get_outputs(self, m, pis)
4533 _IMP_kernel._ParticleOutputs_swigregister(_ParticleOutputs)
4536 r"""get_input_particles(IMP::ModelObjectsTemp const & mos) -> IMP::ParticlesTemp"""
4537 return _IMP_kernel.get_input_particles(mos)
4540 r"""get_input_containers(IMP::ModelObjectsTemp const & mos) -> IMP::ContainersTemp"""
4541 return _IMP_kernel.get_input_containers(mos)
4544 r"""get_output_particles(IMP::ModelObjectsTemp const & mos) -> IMP::ParticlesTemp"""
4545 return _IMP_kernel.get_output_particles(mos)
4548 r"""get_output_containers(IMP::ModelObjectsTemp const & mos) -> IMP::ContainersTemp"""
4549 return _IMP_kernel.get_output_containers(mos)
4552 _plural_types.append(
"Vector1Ds")
4553 _value_types.append(
"Vector1D")
4557 _plural_types.append(
"Vector2Ds")
4558 _value_types.append(
"Vector2D")
4562 _plural_types.append(
"Vector3Ds")
4563 _value_types.append(
"Vector3D")
4567 _plural_types.append(
"Vector4Ds")
4568 _value_types.append(
"Vector4D")
4572 _plural_types.append(
"Vector5Ds")
4573 _value_types.append(
"Vector5D")
4577 _plural_types.append(
"Vector6Ds")
4578 _value_types.append(
"Vector6D")
4582 _plural_types.append(
"Vector1Ds")
4583 _value_types.append(
"VectorD<1>")
4587 _plural_types.append(
"Vector2Ds")
4588 _value_types.append(
"VectorD<2>")
4592 _plural_types.append(
"Vector3Ds")
4593 _value_types.append(
"VectorD<3>")
4597 _plural_types.append(
"Vector4Ds")
4598 _value_types.append(
"VectorD<4>")
4602 _plural_types.append(
"Vector5Ds")
4603 _value_types.append(
"VectorD<5>")
4607 _plural_types.append(
"Vector6Ds")
4608 _value_types.append(
"VectorD<6>")
4612 _plural_types.append(
"VectorKDs")
4613 _value_types.append(
"VectorKD")
4617 _plural_types.append(
"VectorKDs")
4618 _value_types.append(
"VectorD<-1>")
4622 r"""get_basis_vector_kd(int D, unsigned int coordinate) -> VectorKD"""
4623 return _IMP_kernel.get_basis_vector_kd(D, coordinate)
4626 r"""get_zero_vector_kd(int D) -> VectorKD"""
4627 return _IMP_kernel.get_zero_vector_kd(D)
4630 r"""get_ones_vector_kd(unsigned int D, double v=1) -> VectorKD"""
4631 return _IMP_kernel.get_ones_vector_kd(D, v)
4634 r"""get_vector_product(Vector3D p1, Vector3D p2) -> Vector3D"""
4635 return _IMP_kernel.get_vector_product(p1, p2)
4638 r"""get_orthogonal_vector(Vector3D v) -> Vector3D"""
4639 return _IMP_kernel.get_orthogonal_vector(v)
4642 r"""get_centroid(IMP::Vector3Ds const & ps) -> Vector3D"""
4643 return _IMP_kernel.get_centroid(ps)
4646 r"""get_radius_of_gyration(IMP::Vector3Ds const & ps) -> double"""
4647 return _IMP_kernel.get_radius_of_gyration(ps)
4648 class DerivativeAccumulator(object):
4649 r"""Proxy of C++ IMP::DerivativeAccumulator class."""
4651 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4652 __repr__ = _swig_repr
4654 def __init__(self, *args):
4656 __init__(DerivativeAccumulator self, DerivativeAccumulator arg2) -> DerivativeAccumulator
4657 __init__(DerivativeAccumulator self, double weight=1.0) -> DerivativeAccumulator
4658 __init__(DerivativeAccumulator self, DerivativeAccumulator copy, double weight) -> DerivativeAccumulator
4660 _IMP_kernel.DerivativeAccumulator_swiginit(self, _IMP_kernel.new_DerivativeAccumulator(*args))
4662 def __call__(self, *args):
4664 __call__(DerivativeAccumulator self, double const value) -> double
4665 __call__(DerivativeAccumulator self, Vector3D value) -> Vector3D
4666 __call__(DerivativeAccumulator self, Vector4D value) -> Vector4D
4668 return _IMP_kernel.DerivativeAccumulator___call__(self, *args)
4670 def get_weight(self):
4671 r"""get_weight(DerivativeAccumulator self) -> double"""
4672 return _IMP_kernel.DerivativeAccumulator_get_weight(self)
4674 def show(self, *args):
4675 r"""show(DerivativeAccumulator self, _ostream out=std::cout)"""
4676 return _IMP_kernel.DerivativeAccumulator_show(self, *args)
4677 __swig_destroy__ = _IMP_kernel.delete_DerivativeAccumulator
4680 _IMP_kernel.DerivativeAccumulator_swigregister(DerivativeAccumulator)
4681 class EvaluationState(object):
4682 r"""Proxy of C++ IMP::EvaluationState class."""
4684 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4685 score = property(_IMP_kernel.EvaluationState_score_get, _IMP_kernel.EvaluationState_score_set, doc=
r"""score : double""")
4686 good = property(_IMP_kernel.EvaluationState_good_get, _IMP_kernel.EvaluationState_good_set, doc=
r"""good : bool""")
4688 def __init__(self, *args):
4690 __init__(EvaluationState self, double oscore, bool ogood) -> EvaluationState
4691 __init__(EvaluationState self) -> EvaluationState
4693 _IMP_kernel.EvaluationState_swiginit(self, _IMP_kernel.new_EvaluationState(*args))
4695 def show(self, *args):
4696 r"""show(EvaluationState self, _ostream out=std::cout)"""
4697 return _IMP_kernel.EvaluationState_show(self, *args)
4700 r"""__str__(EvaluationState self) -> std::string"""
4701 return _IMP_kernel.EvaluationState___str__(self)
4704 r"""__repr__(EvaluationState self) -> std::string"""
4705 return _IMP_kernel.EvaluationState___repr__(self)
4706 __swig_destroy__ = _IMP_kernel.delete_EvaluationState
4709 _IMP_kernel.EvaluationState_swigregister(EvaluationState)
4710 class ScoreAccumulator(_Value):
4711 r"""Proxy of C++ IMP::ScoreAccumulator class."""
4713 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4715 def __init__(self, *args):
4717 __init__(ScoreAccumulator self, ScoreAccumulator arg2) -> ScoreAccumulator
4718 __init__(ScoreAccumulator self) -> ScoreAccumulator
4719 __init__(ScoreAccumulator self, ScoreAccumulator o, Restraint r) -> ScoreAccumulator
4720 __init__(ScoreAccumulator self, ScoreAccumulator o, double weight, double local_max) -> ScoreAccumulator
4722 _IMP_kernel.ScoreAccumulator_swiginit(self, _IMP_kernel.new_ScoreAccumulator(*args))
4724 def add_score(self, score):
4725 r"""add_score(ScoreAccumulator self, double score)"""
4726 return _IMP_kernel.ScoreAccumulator_add_score(self, score)
4728 def get_abort_evaluation(self):
4729 r"""get_abort_evaluation(ScoreAccumulator self) -> bool"""
4730 return _IMP_kernel.ScoreAccumulator_get_abort_evaluation(self)
4732 def get_is_evaluate_if_below(self):
4733 r"""get_is_evaluate_if_below(ScoreAccumulator self) -> bool"""
4734 return _IMP_kernel.ScoreAccumulator_get_is_evaluate_if_below(self)
4736 def get_is_evaluate_if_good(self):
4737 r"""get_is_evaluate_if_good(ScoreAccumulator self) -> bool"""
4738 return _IMP_kernel.ScoreAccumulator_get_is_evaluate_if_good(self)
4740 def get_maximum(self):
4741 r"""get_maximum(ScoreAccumulator self) -> double"""
4742 return _IMP_kernel.ScoreAccumulator_get_maximum(self)
4744 def get_derivative_accumulator(self):
4745 r"""get_derivative_accumulator(ScoreAccumulator self) -> DerivativeAccumulator"""
4746 return _IMP_kernel.ScoreAccumulator_get_derivative_accumulator(self)
4748 def show(self, *args):
4749 r"""show(ScoreAccumulator self, _ostream out=std::cout)"""
4750 return _IMP_kernel.ScoreAccumulator_show(self, *args)
4753 r"""__str__(ScoreAccumulator self) -> std::string"""
4754 return _IMP_kernel.ScoreAccumulator___str__(self)
4757 r"""__repr__(ScoreAccumulator self) -> std::string"""
4758 return _IMP_kernel.ScoreAccumulator___repr__(self)
4759 __swig_destroy__ = _IMP_kernel.delete_ScoreAccumulator
4762 _IMP_kernel.ScoreAccumulator_swigregister(ScoreAccumulator)
4763 class ScoreState(ModelObject):
4764 r"""Proxy of C++ IMP::ScoreState class."""
4766 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4767 is_ignored_by_jax_ = property(_IMP_kernel.ScoreState_is_ignored_by_jax__get, _IMP_kernel.ScoreState_is_ignored_by_jax__set, doc=
r"""is_ignored_by_jax_ : bool""")
4769 def set_can_skip(self, can_skip):
4770 r"""set_can_skip(ScoreState self, bool can_skip)"""
4771 return _IMP_kernel.ScoreState_set_can_skip(self, can_skip)
4773 def __init__(self, *args):
4775 __init__(ScoreState self, Model m, std::string name) -> ScoreState
4776 __init__(ScoreState self) -> ScoreState
4778 if self.__class__ == ScoreState:
4782 _IMP_kernel.ScoreState_swiginit(self, _IMP_kernel.new_ScoreState(_self, *args))
4784 if self.__class__ != ScoreState:
4785 _director_objects.register(self)
4790 def before_evaluate(self):
4791 r"""before_evaluate(ScoreState self)"""
4792 return _IMP_kernel.ScoreState_before_evaluate(self)
4794 def after_evaluate(self, accpt):
4795 r"""after_evaluate(ScoreState self, DerivativeAccumulator accpt)"""
4796 return _IMP_kernel.ScoreState_after_evaluate(self, accpt)
4798 def get_can_skip(self):
4799 r"""get_can_skip(ScoreState self) -> bool"""
4800 return _IMP_kernel.ScoreState_get_can_skip(self)
4802 def get_has_update_order(self):
4803 r"""get_has_update_order(ScoreState self) -> bool"""
4804 return _IMP_kernel.ScoreState_get_has_update_order(self)
4807 r"""get_update_order(ScoreState self) -> unsigned int"""
4808 return _IMP_kernel.ScoreState_get_update_order(self)
4810 def handle_set_has_required_score_states(self, tf):
4811 r"""handle_set_has_required_score_states(ScoreState self, bool tf)"""
4812 return _IMP_kernel.ScoreState_handle_set_has_required_score_states(self, tf)
4814 def get_is_ignored_by_jax(self):
4815 r"""get_is_ignored_by_jax(ScoreState self) -> bool"""
4816 return _IMP_kernel.ScoreState_get_is_ignored_by_jax(self)
4818 def do_before_evaluate(self):
4819 r"""do_before_evaluate(ScoreState self)"""
4820 return _IMP_kernel.ScoreState_do_before_evaluate(self)
4822 def do_after_evaluate(self, accpt):
4823 r"""do_after_evaluate(ScoreState self, DerivativeAccumulator accpt)"""
4824 return _IMP_kernel.ScoreState_do_after_evaluate(self, accpt)
4825 __swig_destroy__ = _IMP_kernel.delete_ScoreState
4828 r"""__str__(ScoreState self) -> std::string"""
4829 return _IMP_kernel.ScoreState___str__(self)
4832 r"""__repr__(ScoreState self) -> std::string"""
4833 return _IMP_kernel.ScoreState___repr__(self)
4837 return _object_cast_to_ScoreState(o)
4840 def do_show(self, out):
4845 return _object_cast_to_ScoreState(o)
4848 def _wrap_jax(self, apply_func, keys=None):
4849 """Create the return value for _get_jax.
4850 Use this method in _get_jax() to wrap the JAX apply function
4851 with other model- and ScoreState-specific information.
4853 @param apply_func A function implemented using JAX that takes
4854 a single argument (the current JAX Model) and returns
4855 a new JAX Model with the ScoreState's transformation
4857 @param keys If given, a set of IMP::Key objects describing Model
4858 attributes (other than xyz and radius) that the ScoreState
4861 from IMP._jax_util
import JAXScoreStateInfo
4862 return JAXScoreStateInfo(m=self.get_model(), apply_func=apply_func,
4866 """Return a JAX implementation of this ScoreState.
4867 Implement this method in a ScoreState subclass to provide
4868 an equivalent function using [JAX](https://docs.jax.dev/)
4869 that modifies the JAX Model. See also _wrap_jax.
4871 if self.get_is_ignored_by_jax():
4872 return self._wrap_jax(
lambda jm: jm)
4874 raise NotImplementedError(
4875 f
"No JAX implementation for {self} ({type(self)})")
4877 def __disown__(self):
4879 _IMP_kernel.disown_ScoreState(self)
4880 return weakref.proxy(self)
4883 r"""do_destroy(ScoreState self)"""
4884 return _IMP_kernel.ScoreState_do_destroy(self)
4886 def do_get_inputs(self):
4887 r"""do_get_inputs(ScoreState self) -> IMP::ModelObjectsTemp"""
4888 return _IMP_kernel.ScoreState_do_get_inputs(self)
4890 def do_get_outputs(self):
4891 r"""do_get_outputs(ScoreState self) -> IMP::ModelObjectsTemp"""
4892 return _IMP_kernel.ScoreState_do_get_outputs(self)
4894 def do_get_interactions(self):
4895 r"""do_get_interactions(ScoreState self) -> IMP::ModelObjectsTemps"""
4896 return _IMP_kernel.ScoreState_do_get_interactions(self)
4899 _IMP_kernel.ScoreState_swigregister(ScoreState)
4902 r"""get_update_order(IMP::ScoreStatesTemp input) -> IMP::ScoreStatesTemp"""
4903 return _IMP_kernel.get_update_order(input)
4904 class Constraint(ScoreState):
4905 r"""Proxy of C++ IMP::Constraint class."""
4907 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4909 def __init__(self, *args):
4911 __init__(Constraint self, Model m, std::string name="Constraint %1%") -> Constraint
4912 __init__(Constraint self) -> Constraint
4914 if self.__class__ == Constraint:
4918 _IMP_kernel.Constraint_swiginit(self, _IMP_kernel.new_Constraint(_self, *args))
4920 if self.__class__ != Constraint:
4921 _director_objects.register(self)
4926 def do_update_attributes(self):
4927 r"""do_update_attributes(Constraint self)"""
4928 return _IMP_kernel.Constraint_do_update_attributes(self)
4930 def do_update_derivatives(self, da):
4931 r"""do_update_derivatives(Constraint self, DerivativeAccumulator da)"""
4932 return _IMP_kernel.Constraint_do_update_derivatives(self, da)
4934 def do_before_evaluate(self):
4935 r"""do_before_evaluate(Constraint self)"""
4936 return _IMP_kernel.Constraint_do_before_evaluate(self)
4938 def do_after_evaluate(self, da):
4939 r"""do_after_evaluate(Constraint self, DerivativeAccumulator da)"""
4940 return _IMP_kernel.Constraint_do_after_evaluate(self, da)
4941 __swig_destroy__ = _IMP_kernel.delete_Constraint
4944 r"""__str__(Constraint self) -> std::string"""
4945 return _IMP_kernel.Constraint___str__(self)
4948 r"""__repr__(Constraint self) -> std::string"""
4949 return _IMP_kernel.Constraint___repr__(self)
4953 return _object_cast_to_Constraint(o)
4956 def do_show(self, out):
4961 return _object_cast_to_Constraint(o)
4963 def __disown__(self):
4965 _IMP_kernel.disown_Constraint(self)
4966 return weakref.proxy(self)
4969 r"""do_destroy(Constraint self)"""
4970 return _IMP_kernel.Constraint_do_destroy(self)
4972 def do_get_inputs(self):
4973 r"""do_get_inputs(Constraint self) -> IMP::ModelObjectsTemp"""
4974 return _IMP_kernel.Constraint_do_get_inputs(self)
4976 def do_get_outputs(self):
4977 r"""do_get_outputs(Constraint self) -> IMP::ModelObjectsTemp"""
4978 return _IMP_kernel.Constraint_do_get_outputs(self)
4980 def do_get_interactions(self):
4981 r"""do_get_interactions(Constraint self) -> IMP::ModelObjectsTemps"""
4982 return _IMP_kernel.Constraint_do_get_interactions(self)
4985 _IMP_kernel.Constraint_swigregister(Constraint)
4986 class Container(ModelObject):
4987 r"""Proxy of C++ IMP::Container class."""
4989 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4991 def __init__(self, *args):
4993 __init__(Container self, Model m, std::string name="Container %1%") -> Container
4994 __init__(Container self) -> Container
4996 if self.__class__ == Container:
5000 _IMP_kernel.Container_swiginit(self, _IMP_kernel.new_Container(_self, *args))
5002 if self.__class__ != Container:
5003 _director_objects.register(self)
5008 def do_get_contents_hash(self):
5009 r"""do_get_contents_hash(Container self) -> std::size_t"""
5010 return _IMP_kernel.Container_do_get_contents_hash(self)
5012 def get_all_possible_indexes(self):
5013 r"""get_all_possible_indexes(Container self) -> IMP::ParticleIndexes"""
5014 return _IMP_kernel.Container_get_all_possible_indexes(self)
5016 def get_contents_hash(self):
5017 r"""get_contents_hash(Container self) -> std::size_t"""
5018 return _IMP_kernel.Container_get_contents_hash(self)
5020 def do_get_outputs(self):
5021 r"""do_get_outputs(Container self) -> IMP::ModelObjectsTemp"""
5022 return _IMP_kernel.Container_do_get_outputs(self)
5024 def get_is_decomposable(self):
5025 r"""get_is_decomposable(Container self) -> bool"""
5026 return _IMP_kernel.Container_get_is_decomposable(self)
5028 def validate_readable(self):
5029 r"""validate_readable(Container self)"""
5030 return _IMP_kernel.Container_validate_readable(self)
5032 def validate_writable(self):
5033 r"""validate_writable(Container self)"""
5034 return _IMP_kernel.Container_validate_writable(self)
5036 def set_is_readable(self, tf):
5037 r"""set_is_readable(Container self, bool tf)"""
5038 return _IMP_kernel.Container_set_is_readable(self, tf)
5040 def set_is_writable(self, tf):
5041 r"""set_is_writable(Container self, bool tf)"""
5042 return _IMP_kernel.Container_set_is_writable(self, tf)
5043 __swig_destroy__ = _IMP_kernel.delete_Container
5046 r"""__str__(Container self) -> std::string"""
5047 return _IMP_kernel.Container___str__(self)
5050 r"""__repr__(Container self) -> std::string"""
5051 return _IMP_kernel.Container___repr__(self)
5055 return _object_cast_to_Container(o)
5058 def do_show(self, out):
5063 return _object_cast_to_Container(o)
5065 def __disown__(self):
5067 _IMP_kernel.disown_Container(self)
5068 return weakref.proxy(self)
5071 r"""do_destroy(Container self)"""
5072 return _IMP_kernel.Container_do_destroy(self)
5074 def handle_set_has_required_score_states(self, arg0):
5075 r"""handle_set_has_required_score_states(Container self, bool arg0)"""
5076 return _IMP_kernel.Container_handle_set_has_required_score_states(self, arg0)
5078 def do_get_inputs(self):
5079 r"""do_get_inputs(Container self) -> IMP::ModelObjectsTemp"""
5080 return _IMP_kernel.Container_do_get_inputs(self)
5082 def do_get_interactions(self):
5083 r"""do_get_interactions(Container self) -> IMP::ModelObjectsTemps"""
5084 return _IMP_kernel.Container_do_get_interactions(self)
5087 _IMP_kernel.Container_swigregister(Container)
5088 class RestraintInfo(
Object):
5089 r"""Proxy of C++ IMP::RestraintInfo class."""
5091 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5093 def __init__(self, *args):
5094 r"""__init__(RestraintInfo self, std::string name="RestraintInfo %1%") -> RestraintInfo"""
5095 _IMP_kernel.RestraintInfo_swiginit(self, _IMP_kernel.new_RestraintInfo(*args))
5098 r"""clear(RestraintInfo self)"""
5099 return _IMP_kernel.RestraintInfo_clear(self)
5101 def add_int(self, key, value):
5102 r"""add_int(RestraintInfo self, std::string key, int value)"""
5103 return _IMP_kernel.RestraintInfo_add_int(self, key, value)
5105 def get_number_of_int(self):
5106 r"""get_number_of_int(RestraintInfo self) -> unsigned int"""
5107 return _IMP_kernel.RestraintInfo_get_number_of_int(self)
5109 def get_int_key(self, i):
5110 r"""get_int_key(RestraintInfo self, unsigned int i) -> std::string"""
5111 return _IMP_kernel.RestraintInfo_get_int_key(self, i)
5113 def get_int_value(self, i):
5114 r"""get_int_value(RestraintInfo self, unsigned int i) -> int"""
5115 return _IMP_kernel.RestraintInfo_get_int_value(self, i)
5117 def add_float(self, key, value):
5118 r"""add_float(RestraintInfo self, std::string key, double value)"""
5119 return _IMP_kernel.RestraintInfo_add_float(self, key, value)
5121 def get_number_of_float(self):
5122 r"""get_number_of_float(RestraintInfo self) -> unsigned int"""
5123 return _IMP_kernel.RestraintInfo_get_number_of_float(self)
5125 def get_float_key(self, i):
5126 r"""get_float_key(RestraintInfo self, unsigned int i) -> std::string"""
5127 return _IMP_kernel.RestraintInfo_get_float_key(self, i)
5129 def get_float_value(self, i):
5130 r"""get_float_value(RestraintInfo self, unsigned int i) -> double"""
5131 return _IMP_kernel.RestraintInfo_get_float_value(self, i)
5133 def add_string(self, key, value):
5134 r"""add_string(RestraintInfo self, std::string key, std::string value)"""
5135 return _IMP_kernel.RestraintInfo_add_string(self, key, value)
5137 def get_number_of_string(self):
5138 r"""get_number_of_string(RestraintInfo self) -> unsigned int"""
5139 return _IMP_kernel.RestraintInfo_get_number_of_string(self)
5141 def get_string_key(self, i):
5142 r"""get_string_key(RestraintInfo self, unsigned int i) -> std::string"""
5143 return _IMP_kernel.RestraintInfo_get_string_key(self, i)
5145 def get_string_value(self, i):
5146 r"""get_string_value(RestraintInfo self, unsigned int i) -> std::string"""
5147 return _IMP_kernel.RestraintInfo_get_string_value(self, i)
5149 def add_filename(self, key, value):
5150 r"""add_filename(RestraintInfo self, std::string key, std::string value)"""
5151 return _IMP_kernel.RestraintInfo_add_filename(self, key, value)
5153 def get_number_of_filename(self):
5154 r"""get_number_of_filename(RestraintInfo self) -> unsigned int"""
5155 return _IMP_kernel.RestraintInfo_get_number_of_filename(self)
5157 def get_filename_key(self, i):
5158 r"""get_filename_key(RestraintInfo self, unsigned int i) -> std::string"""
5159 return _IMP_kernel.RestraintInfo_get_filename_key(self, i)
5161 def get_filename_value(self, i):
5162 r"""get_filename_value(RestraintInfo self, unsigned int i) -> std::string"""
5163 return _IMP_kernel.RestraintInfo_get_filename_value(self, i)
5165 def add_floats(self, key, value):
5166 r"""add_floats(RestraintInfo self, std::string key, IMP::Floats value)"""
5167 return _IMP_kernel.RestraintInfo_add_floats(self, key, value)
5169 def get_number_of_floats(self):
5170 r"""get_number_of_floats(RestraintInfo self) -> unsigned int"""
5171 return _IMP_kernel.RestraintInfo_get_number_of_floats(self)
5173 def get_floats_key(self, i):
5174 r"""get_floats_key(RestraintInfo self, unsigned int i) -> std::string"""
5175 return _IMP_kernel.RestraintInfo_get_floats_key(self, i)
5177 def get_floats_value(self, i):
5178 r"""get_floats_value(RestraintInfo self, unsigned int i) -> IMP::Floats"""
5179 return _IMP_kernel.RestraintInfo_get_floats_value(self, i)
5181 def add_ints(self, key, value):
5182 r"""add_ints(RestraintInfo self, std::string key, IMP::Ints value)"""
5183 return _IMP_kernel.RestraintInfo_add_ints(self, key, value)
5185 def get_number_of_ints(self):
5186 r"""get_number_of_ints(RestraintInfo self) -> unsigned int"""
5187 return _IMP_kernel.RestraintInfo_get_number_of_ints(self)
5189 def get_ints_key(self, i):
5190 r"""get_ints_key(RestraintInfo self, unsigned int i) -> std::string"""
5191 return _IMP_kernel.RestraintInfo_get_ints_key(self, i)
5193 def get_ints_value(self, i):
5194 r"""get_ints_value(RestraintInfo self, unsigned int i) -> IMP::Ints"""
5195 return _IMP_kernel.RestraintInfo_get_ints_value(self, i)
5197 def add_strings(self, key, value):
5198 r"""add_strings(RestraintInfo self, std::string key, IMP::Strings value)"""
5199 return _IMP_kernel.RestraintInfo_add_strings(self, key, value)
5201 def get_number_of_strings(self):
5202 r"""get_number_of_strings(RestraintInfo self) -> unsigned int"""
5203 return _IMP_kernel.RestraintInfo_get_number_of_strings(self)
5205 def get_strings_key(self, i):
5206 r"""get_strings_key(RestraintInfo self, unsigned int i) -> std::string"""
5207 return _IMP_kernel.RestraintInfo_get_strings_key(self, i)
5209 def get_strings_value(self, i):
5210 r"""get_strings_value(RestraintInfo self, unsigned int i) -> IMP::Strings"""
5211 return _IMP_kernel.RestraintInfo_get_strings_value(self, i)
5213 def add_filenames(self, key, value):
5214 r"""add_filenames(RestraintInfo self, std::string key, IMP::Strings value)"""
5215 return _IMP_kernel.RestraintInfo_add_filenames(self, key, value)
5217 def get_number_of_filenames(self):
5218 r"""get_number_of_filenames(RestraintInfo self) -> unsigned int"""
5219 return _IMP_kernel.RestraintInfo_get_number_of_filenames(self)
5221 def get_filenames_key(self, i):
5222 r"""get_filenames_key(RestraintInfo self, unsigned int i) -> std::string"""
5223 return _IMP_kernel.RestraintInfo_get_filenames_key(self, i)
5225 def get_filenames_value(self, i):
5226 r"""get_filenames_value(RestraintInfo self, unsigned int i) -> IMP::Strings"""
5227 return _IMP_kernel.RestraintInfo_get_filenames_value(self, i)
5229 def add_particle_indexes(self, key, value):
5230 r"""add_particle_indexes(RestraintInfo self, std::string key, IMP::ParticleIndexes value)"""
5231 return _IMP_kernel.RestraintInfo_add_particle_indexes(self, key, value)
5233 def get_number_of_particle_indexes(self):
5234 r"""get_number_of_particle_indexes(RestraintInfo self) -> unsigned int"""
5235 return _IMP_kernel.RestraintInfo_get_number_of_particle_indexes(self)
5237 def get_particle_indexes_key(self, i):
5238 r"""get_particle_indexes_key(RestraintInfo self, unsigned int i) -> std::string"""
5239 return _IMP_kernel.RestraintInfo_get_particle_indexes_key(self, i)
5241 def get_particle_indexes_value(self, i):
5242 r"""get_particle_indexes_value(RestraintInfo self, unsigned int i) -> IMP::ParticleIndexes"""
5243 return _IMP_kernel.RestraintInfo_get_particle_indexes_value(self, i)
5246 r"""get_version_info(RestraintInfo self) -> VersionInfo"""
5247 return _IMP_kernel.RestraintInfo_get_version_info(self)
5248 __swig_destroy__ = _IMP_kernel.delete_RestraintInfo
5251 r"""__str__(RestraintInfo self) -> std::string"""
5252 return _IMP_kernel.RestraintInfo___str__(self)
5255 r"""__repr__(RestraintInfo self) -> std::string"""
5256 return _IMP_kernel.RestraintInfo___repr__(self)
5260 return _object_cast_to_RestraintInfo(o)
5264 _IMP_kernel.RestraintInfo_swigregister(RestraintInfo)
5265 class Restraint(ModelObject):
5266 r"""Proxy of C++ IMP::Restraint class."""
5268 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5270 def __init__(self, *args):
5272 __init__(Restraint self, Model m, std::string name) -> Restraint
5273 __init__(Restraint self) -> Restraint
5275 if self.__class__ == Restraint:
5279 _IMP_kernel.Restraint_swiginit(self, _IMP_kernel.new_Restraint(_self, *args))
5281 if self.__class__ != Restraint:
5282 _director_objects.register(self)
5287 def get_score(self):
5288 r"""get_score(Restraint self) -> double"""
5289 return _IMP_kernel.Restraint_get_score(self)
5291 def evaluate(self, calc_derivs):
5292 r"""evaluate(Restraint self, bool calc_derivs) -> double"""
5293 return _IMP_kernel.Restraint_evaluate(self, calc_derivs)
5295 def evaluate_moved(self, calc_derivs, moved_pis, reset_pis):
5296 r"""evaluate_moved(Restraint self, bool calc_derivs, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
5297 return _IMP_kernel.Restraint_evaluate_moved(self, calc_derivs, moved_pis, reset_pis)
5299 def evaluate_moved_if_below(self, calc_derivatives, moved_pis, reset_pis, max):
5300 r"""evaluate_moved_if_below(Restraint self, bool calc_derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
5301 return _IMP_kernel.Restraint_evaluate_moved_if_below(self, calc_derivatives, moved_pis, reset_pis, max)
5303 def evaluate_moved_if_good(self, calc_derivatives, moved_pis, reset_pis):
5304 r"""evaluate_moved_if_good(Restraint self, bool calc_derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
5305 return _IMP_kernel.Restraint_evaluate_moved_if_good(self, calc_derivatives, moved_pis, reset_pis)
5307 def evaluate_if_good(self, calc_derivatives):
5308 r"""evaluate_if_good(Restraint self, bool calc_derivatives) -> double"""
5309 return _IMP_kernel.Restraint_evaluate_if_good(self, calc_derivatives)
5311 def evaluate_if_below(self, calc_derivatives, max):
5312 r"""evaluate_if_below(Restraint self, bool calc_derivatives, double max) -> double"""
5313 return _IMP_kernel.Restraint_evaluate_if_below(self, calc_derivatives, max)
5315 def unprotected_evaluate(self, da):
5316 r"""unprotected_evaluate(Restraint self, DerivativeAccumulator da) -> double"""
5317 return _IMP_kernel.Restraint_unprotected_evaluate(self, da)
5319 def unprotected_evaluate_moved(self, da, moved_pis, reset_pis):
5320 r"""unprotected_evaluate_moved(Restraint self, DerivativeAccumulator da, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
5321 return _IMP_kernel.Restraint_unprotected_evaluate_moved(self, da, moved_pis, reset_pis)
5323 def clear_moved_cache(self):
5324 r"""clear_moved_cache(Restraint self)"""
5325 return _IMP_kernel.Restraint_clear_moved_cache(self)
5327 def unprotected_evaluate_if_good(self, da, max):
5328 r"""unprotected_evaluate_if_good(Restraint self, DerivativeAccumulator da, double max) -> double"""
5329 return _IMP_kernel.Restraint_unprotected_evaluate_if_good(self, da, max)
5331 def unprotected_evaluate_if_below(self, da, max):
5332 r"""unprotected_evaluate_if_below(Restraint self, DerivativeAccumulator da, double max) -> double"""
5333 return _IMP_kernel.Restraint_unprotected_evaluate_if_below(self, da, max)
5335 def unprotected_evaluate_moved_if_below(self, da, moved_pis, reset_pis, max):
5336 r"""unprotected_evaluate_moved_if_below(Restraint self, DerivativeAccumulator da, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
5337 return _IMP_kernel.Restraint_unprotected_evaluate_moved_if_below(self, da, moved_pis, reset_pis, max)
5339 def unprotected_evaluate_moved_if_good(self, da, moved_pis, reset_pis, max):
5340 r"""unprotected_evaluate_moved_if_good(Restraint self, DerivativeAccumulator da, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
5341 return _IMP_kernel.Restraint_unprotected_evaluate_moved_if_good(self, da, moved_pis, reset_pis, max)
5343 def get_static_info(self):
5344 r"""get_static_info(Restraint self) -> RestraintInfo"""
5345 return _IMP_kernel.Restraint_get_static_info(self)
5347 def get_dynamic_info(self):
5348 r"""get_dynamic_info(Restraint self) -> RestraintInfo"""
5349 return _IMP_kernel.Restraint_get_dynamic_info(self)
5351 def add_score_and_derivatives(self, sa):
5352 r"""add_score_and_derivatives(Restraint self, ScoreAccumulator sa)"""
5353 return _IMP_kernel.Restraint_add_score_and_derivatives(self, sa)
5355 def add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
5356 r"""add_score_and_derivatives_moved(Restraint self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
5357 return _IMP_kernel.Restraint_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
5360 r"""create_decomposition(Restraint self) -> Restraint"""
5361 return _IMP_kernel.Restraint_create_decomposition(self)
5363 def create_current_decomposition(self):
5364 r"""create_current_decomposition(Restraint self) -> Restraint"""
5365 return _IMP_kernel.Restraint_create_current_decomposition(self)
5367 def set_weight(self, weight):
5368 r"""set_weight(Restraint self, IMP::Float weight)"""
5369 return _IMP_kernel.Restraint_set_weight(self, weight)
5371 def get_weight(self):
5372 r"""get_weight(Restraint self) -> IMP::Float"""
5373 return _IMP_kernel.Restraint_get_weight(self)
5375 def get_maximum_score(self):
5376 r"""get_maximum_score(Restraint self) -> double"""
5377 return _IMP_kernel.Restraint_get_maximum_score(self)
5379 def set_maximum_score(self, s):
5380 r"""set_maximum_score(Restraint self, double s)"""
5381 return _IMP_kernel.Restraint_set_maximum_score(self, s)
5384 r"""create_scoring_function(Restraint self, double weight=1.0, double max=NO_MAX) -> ScoringFunction"""
5385 return _IMP_kernel.Restraint_create_scoring_function(self, *args)
5387 def set_last_score(self, s):
5388 r"""set_last_score(Restraint self, double s)"""
5389 return _IMP_kernel.Restraint_set_last_score(self, s)
5391 def set_last_last_score(self, s):
5392 r"""set_last_last_score(Restraint self, double s)"""
5393 return _IMP_kernel.Restraint_set_last_last_score(self, s)
5395 def get_last_score(self):
5396 r"""get_last_score(Restraint self) -> double"""
5397 return _IMP_kernel.Restraint_get_last_score(self)
5399 def get_last_last_score(self):
5400 r"""get_last_last_score(Restraint self) -> double"""
5401 return _IMP_kernel.Restraint_get_last_last_score(self)
5403 def get_is_aggregate(self):
5404 r"""get_is_aggregate(Restraint self) -> bool"""
5405 return _IMP_kernel.Restraint_get_is_aggregate(self)
5407 def get_is_custom_reset(self):
5408 r"""get_is_custom_reset(Restraint self) -> bool"""
5409 return _IMP_kernel.Restraint_get_is_custom_reset(self)
5411 def get_was_good(self):
5412 r"""get_was_good(Restraint self) -> bool"""
5413 return _IMP_kernel.Restraint_get_was_good(self)
5414 __swig_destroy__ = _IMP_kernel.delete_Restraint
5416 def do_create_decomposition(self):
5417 r"""do_create_decomposition(Restraint self) -> IMP::Restraints"""
5418 return _IMP_kernel.Restraint_do_create_decomposition(self)
5420 def do_create_current_decomposition(self):
5421 r"""do_create_current_decomposition(Restraint self) -> IMP::Restraints"""
5422 return _IMP_kernel.Restraint_do_create_current_decomposition(self)
5424 def do_add_score_and_derivatives(self, sa):
5425 r"""do_add_score_and_derivatives(Restraint self, ScoreAccumulator sa)"""
5426 return _IMP_kernel.Restraint_do_add_score_and_derivatives(self, sa)
5428 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
5429 r"""do_add_score_and_derivatives_moved(Restraint self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
5430 return _IMP_kernel.Restraint_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
5432 def do_get_outputs(self):
5433 r"""do_get_outputs(Restraint self) -> IMP::ModelObjectsTemp"""
5434 return _IMP_kernel.Restraint_do_get_outputs(self)
5435 is_aggregate_ = property(_IMP_kernel.Restraint_is_aggregate__get, _IMP_kernel.Restraint_is_aggregate__set, doc=
r"""is_aggregate_ : bool""")
5436 is_custom_reset_ = property(_IMP_kernel.Restraint_is_custom_reset__get, _IMP_kernel.Restraint_is_custom_reset__set, doc=
r"""is_custom_reset_ : bool""")
5439 r"""__str__(Restraint self) -> std::string"""
5440 return _IMP_kernel.Restraint___str__(self)
5443 r"""__repr__(Restraint self) -> std::string"""
5444 return _IMP_kernel.Restraint___repr__(self)
5448 return _object_cast_to_Restraint(o)
5451 def do_show(self, out):
5456 return _object_cast_to_Restraint(o)
5459 def _wrap_jax(self, score_func, keys=None):
5460 """Create the return value for _get_jax.
5461 Use this method in _get_jax() to wrap the JAX scoring function
5462 with other model- and restraint-specific information.
5464 @param score_func A function implemented using JAX that takes
5465 a single argument (the current JAX Model) and returns
5466 the score of the restraint.
5467 @param keys If given, a set of IMP::Key objects describing Model
5468 attributes (other than xyz and radius) that the restraint
5469 uses. For example, a restraint that uses electrostatic charge
5470 would pass IMP::atom::Charged::get_charge_key() here.
5472 from IMP._jax_util
import JAXRestraintInfo
5473 return JAXRestraintInfo(m=self.get_model(), score_func=score_func,
5474 weight=self.get_weight(), keys=keys)
5477 def _wrap_jax_multiple(cls, restraint, score_func, keys=None):
5478 """Create the return value for _get_jax_multiple.
5479 This is similar to _wrap_jax but is used to handle the JAX scoring
5480 function for multiple restraints at once. It is designed to be
5481 called from the _get_jax_multiple class method (if implemented).
5482 _get_jax_multiple is called (typically by RestraintSet) once for
5483 each type of restraint, and is given a list of all restraints.
5484 It should return a list of JAX functions that score some of the
5485 restraints using _wrap_jax_multiple (or None), and a list of the
5486 remaining unhandled restraints.
5488 @param restraint Any one of the restraints that is being scored.
5489 @param score_func A function implemented using JAX that takes
5490 a single argument (the current JAX Model) and returns
5491 an array of scores (one per restraint). Note that this array
5492 should be weighted by the restraint weights; that is not
5493 done in this method.
5494 @param keys As for _wrap_jax().
5496 from IMP._jax_util
import JAXRestraintInfo
5497 return JAXRestraintInfo(m=restraint.get_model(), score_func=score_func,
5498 weight=1.0, keys=keys)
5500 def _get_jax(self, space):
5501 """Return a JAX implementation of this Restraint.
5502 Implement this method in a Restraint subclass to provide
5503 an equivalent function using [JAX](https://docs.jax.dev/)
5504 that scores the current JAX Model. See also _wrap_jax.
5506 @param space The space in which the restraint is evaluated
5507 (e.g. a periodic box). See IMP._jax_util.Space.
5509 raise NotImplementedError(
5510 f
"No JAX implementation for {self} ({type(self)})")
5512 def _evaluate_jax(self, space=None):
5513 """Similar to evaluate(False), but using JAX.
5514 This is intended to be useful for testing purposes. It will likely
5515 not be particularly fast as it will copy the IMP Model and
5516 jax.jit-compile the scoring function each time.
5518 @param space The space in which the restraint is evaluated
5519 (e.g. a periodic box). See IMP._jax_util.Space. If not
5520 specified, an unbounded (free) space is used.
5525 jm = ji.get_jax_model()
5526 axes = jm.get_vmap_axes()
5528 j = jax.jit(ji.score_func)
5531 j = jax.jit(jax.vmap(ji.score_func, in_axes=(axes,)))
5534 def __disown__(self):
5536 _IMP_kernel.disown_Restraint(self)
5537 return weakref.proxy(self)
5540 r"""do_destroy(Restraint self)"""
5541 return _IMP_kernel.Restraint_do_destroy(self)
5543 def handle_set_has_required_score_states(self, arg0):
5544 r"""handle_set_has_required_score_states(Restraint self, bool arg0)"""
5545 return _IMP_kernel.Restraint_handle_set_has_required_score_states(self, arg0)
5547 def do_get_inputs(self):
5548 r"""do_get_inputs(Restraint self) -> IMP::ModelObjectsTemp"""
5549 return _IMP_kernel.Restraint_do_get_inputs(self)
5551 def do_get_interactions(self):
5552 r"""do_get_interactions(Restraint self) -> IMP::ModelObjectsTemps"""
5553 return _IMP_kernel.Restraint_do_get_interactions(self)
5556 _IMP_kernel.Restraint_swigregister(Restraint)
5557 class _RestraintsAdaptor(_InputAdaptor):
5558 r"""Proxy of C++ IMP::RestraintsAdaptor class."""
5560 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5561 __repr__ = _swig_repr
5563 def __init__(self, *args):
5565 __init__(_RestraintsAdaptor self) -> _RestraintsAdaptor
5566 __init__(_RestraintsAdaptor self, IMP::Restraints const & sf) -> _RestraintsAdaptor
5567 __init__(_RestraintsAdaptor self, IMP::RestraintsTemp const & sf) -> _RestraintsAdaptor
5568 __init__(_RestraintsAdaptor self, Restraint sf) -> _RestraintsAdaptor
5570 _IMP_kernel._RestraintsAdaptor_swiginit(self, _IMP_kernel.new__RestraintsAdaptor(*args))
5571 __swig_destroy__ = _IMP_kernel.delete__RestraintsAdaptor
5574 _IMP_kernel._RestraintsAdaptor_swigregister(_RestraintsAdaptor)
5575 class RestraintSet(Restraint):
5576 r"""Proxy of C++ IMP::RestraintSet class."""
5578 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5580 def __init__(self, *args):
5582 __init__(RestraintSet self, Model m, double weight, std::string const & name="RestraintSet %1%") -> RestraintSet
5583 __init__(RestraintSet self, Model m, std::string const & name="RestraintSet %1%") -> RestraintSet
5584 __init__(RestraintSet self, IMP::RestraintsTemp const & rs, double weight, std::string const & name="RestraintSet %1%") -> RestraintSet
5585 __init__(RestraintSet self) -> RestraintSet
5587 if self.__class__ == RestraintSet:
5591 _IMP_kernel.RestraintSet_swiginit(self, _IMP_kernel.new_RestraintSet(_self, *args))
5593 if self.__class__ != RestraintSet:
5594 _director_objects.register(self)
5599 def unprotected_evaluate(self, da):
5600 r"""unprotected_evaluate(RestraintSet self, DerivativeAccumulator da) -> double"""
5601 return _IMP_kernel.RestraintSet_unprotected_evaluate(self, da)
5603 def get_type_name(self):
5604 r"""get_type_name(RestraintSet self) -> std::string"""
5605 return _IMP_kernel.RestraintSet_get_type_name(self)
5608 r"""get_version_info(RestraintSet self) -> VersionInfo"""
5609 return _IMP_kernel.RestraintSet_get_version_info(self)
5610 __swig_destroy__ = _IMP_kernel.delete_RestraintSet
5611 def __get_restraints(self):
return _list_util.VarList(getdimfunc=self.get_number_of_restraints, getfunc=self.get_restraint, erasefunc=self.erase_restraint, appendfunc=self.add_restraint, extendfunc=self.add_restraints, clearfunc=self.clear_restraints, indexfunc=self._python_index_restraint)
5612 def __set_restraints(self, obj): _list_util.set_varlist(self.restraints, obj)
5613 def __del_restraints(self): _list_util.del_varlist(self.restraints)
5614 restraints = property(__get_restraints, __set_restraints, __del_restraints, doc=
"List of ##ucnames")
5616 def remove_restraint(self, d):
5617 r"""remove_restraint(RestraintSet self, Restraint d)"""
5618 return _IMP_kernel.RestraintSet_remove_restraint(self, d)
5620 def _python_index_restraint(self, d, start, stop):
5621 r"""_python_index_restraint(RestraintSet self, Restraint d, unsigned int start, unsigned int stop) -> unsigned int"""
5622 return _IMP_kernel.RestraintSet__python_index_restraint(self, d, start, stop)
5624 def remove_restraints(self, d):
5625 r"""remove_restraints(RestraintSet self, IMP::Restraints const & d)"""
5626 return _IMP_kernel.RestraintSet_remove_restraints(self, d)
5628 def set_restraints(self, ps):
5629 r"""set_restraints(RestraintSet self, IMP::Restraints const & ps)"""
5630 return _IMP_kernel.RestraintSet_set_restraints(self, ps)
5632 def set_restraints_order(self, objs):
5633 r"""set_restraints_order(RestraintSet self, IMP::Restraints const & objs)"""
5634 return _IMP_kernel.RestraintSet_set_restraints_order(self, objs)
5637 r"""add_restraint(RestraintSet self, Restraint obj) -> unsigned int"""
5638 return _IMP_kernel.RestraintSet_add_restraint(self, obj)
5641 r"""add_restraints(RestraintSet self, IMP::Restraints const & objs)"""
5642 return _IMP_kernel.RestraintSet_add_restraints(self, objs)
5644 def clear_restraints(self):
5645 r"""clear_restraints(RestraintSet self)"""
5646 return _IMP_kernel.RestraintSet_clear_restraints(self)
5648 def get_number_of_restraints(self):
5649 r"""get_number_of_restraints(RestraintSet self) -> unsigned int"""
5650 return _IMP_kernel.RestraintSet_get_number_of_restraints(self)
5652 def get_has_restraints(self):
5653 r"""get_has_restraints(RestraintSet self) -> bool"""
5654 return _IMP_kernel.RestraintSet_get_has_restraints(self)
5656 def get_restraint(self, i):
5657 r"""get_restraint(RestraintSet self, unsigned int i) -> Restraint"""
5658 return _IMP_kernel.RestraintSet_get_restraint(self, i)
5660 def get_restraints(self):
5661 r"""get_restraints(RestraintSet self) -> IMP::Restraints"""
5662 return _IMP_kernel.RestraintSet_get_restraints(self)
5664 def erase_restraint(self, i):
5665 r"""erase_restraint(RestraintSet self, unsigned int i)"""
5666 return _IMP_kernel.RestraintSet_erase_restraint(self, i)
5668 def reserve_restraints(self, sz):
5669 r"""reserve_restraints(RestraintSet self, unsigned int sz)"""
5670 return _IMP_kernel.RestraintSet_reserve_restraints(self, sz)
5672 def get_non_sets_and_sets(self):
5673 r"""get_non_sets_and_sets(RestraintSet self) -> std::pair< IMP::RestraintsTemp,IMP::RestraintSetsTemp >"""
5674 return _IMP_kernel.RestraintSet_get_non_sets_and_sets(self)
5676 def do_get_inputs(self):
5677 r"""do_get_inputs(RestraintSet self) -> IMP::ModelObjectsTemp"""
5678 return _IMP_kernel.RestraintSet_do_get_inputs(self)
5681 r"""create_scoring_function(RestraintSet self, double weight=1.0, double max=std::numeric_limits< double >::max()) -> ScoringFunction"""
5682 return _IMP_kernel.RestraintSet_create_scoring_function(self, *args)
5684 def get_last_score(self):
5685 r"""get_last_score(RestraintSet self) -> double"""
5686 return _IMP_kernel.RestraintSet_get_last_score(self)
5689 r"""__str__(RestraintSet self) -> std::string"""
5690 return _IMP_kernel.RestraintSet___str__(self)
5693 r"""__repr__(RestraintSet self) -> std::string"""
5694 return _IMP_kernel.RestraintSet___repr__(self)
5698 return _object_cast_to_RestraintSet(o)
5701 def do_show(self, out):
5706 return _object_cast_to_RestraintSet(o)
5709 def _get_as_binary(self):
5710 r"""_get_as_binary(RestraintSet self) -> PyObject *"""
5711 return _IMP_kernel.RestraintSet__get_as_binary(self)
5713 def _set_from_binary(self, p):
5714 r"""_set_from_binary(RestraintSet self, PyObject * p)"""
5715 return _IMP_kernel.RestraintSet__set_from_binary(self, p)
5717 def __getstate__(self):
5718 p = self._get_as_binary()
5719 if len(self.__dict__) > 1:
5720 d = self.__dict__.copy()
5725 def __setstate__(self, p):
5726 if not hasattr(self,
'this'):
5728 if isinstance(p, tuple):
5730 self.__dict__.update(d)
5731 return self._set_from_binary(p)
5734 def _get_jax(self, space):
5735 import jax.numpy
as jnp
5736 import IMP._jax_util
5737 restraints = [r.get_derived_object()
for r
in self.restraints]
5738 multi_funcs, funcs, keys = IMP._jax_util.get_restraints_jax_funcs_keys(
5741 if funcs
or multi_funcs:
5742 rets = [f(jm)
for f
in multi_funcs]
5744 rets.append(jnp.stack([f(jm)
for f
in funcs], axis=-1))
5745 scores = jnp.concatenate(rets, axis=-1)
5746 return jnp.sum(scores, axis=-1)
5750 return self._wrap_jax(jax_sf, keys=keys)
5752 def __disown__(self):
5754 _IMP_kernel.disown_RestraintSet(self)
5755 return weakref.proxy(self)
5758 r"""do_destroy(RestraintSet self)"""
5759 return _IMP_kernel.RestraintSet_do_destroy(self)
5761 def handle_set_has_required_score_states(self, arg0):
5762 r"""handle_set_has_required_score_states(RestraintSet self, bool arg0)"""
5763 return _IMP_kernel.RestraintSet_handle_set_has_required_score_states(self, arg0)
5765 def do_get_outputs(self):
5766 r"""do_get_outputs(RestraintSet self) -> IMP::ModelObjectsTemp"""
5767 return _IMP_kernel.RestraintSet_do_get_outputs(self)
5769 def do_get_interactions(self):
5770 r"""do_get_interactions(RestraintSet self) -> IMP::ModelObjectsTemps"""
5771 return _IMP_kernel.RestraintSet_do_get_interactions(self)
5773 def do_create_decomposition(self):
5774 r"""do_create_decomposition(RestraintSet self) -> IMP::Restraints"""
5775 return _IMP_kernel.RestraintSet_do_create_decomposition(self)
5777 def do_create_current_decomposition(self):
5778 r"""do_create_current_decomposition(RestraintSet self) -> IMP::Restraints"""
5779 return _IMP_kernel.RestraintSet_do_create_current_decomposition(self)
5781 def do_add_score_and_derivatives(self, sa):
5782 r"""do_add_score_and_derivatives(RestraintSet self, ScoreAccumulator sa)"""
5783 return _IMP_kernel.RestraintSet_do_add_score_and_derivatives(self, sa)
5785 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
5786 r"""do_add_score_and_derivatives_moved(RestraintSet self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
5787 return _IMP_kernel.RestraintSet_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
5790 _IMP_kernel.RestraintSet_swigregister(RestraintSet)
5792 def get_restraints(rs):
5793 r"""get_restraints(IMP::RestraintsTemp const & rs) -> IMP::RestraintsTemp"""
5794 return _IMP_kernel.get_restraints(rs)
5796 def _check_particle(p, a):
5797 if (
not p.get_is_active()):
5798 raise ValueError(
"Inactive Particle")
5799 if (type(a)() == a):
5800 raise IndexError(
"Cannot use default Index")
5801 if (
not p.has_attribute(a)):
5802 raise IndexError(
"Particle does not have attribute")
5804 class Particle(ModelObject):
5805 r"""Proxy of C++ IMP::Particle class."""
5807 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5810 r"""get_version_info(Particle self) -> VersionInfo"""
5811 return _IMP_kernel.Particle_get_version_info(self)
5812 __swig_destroy__ = _IMP_kernel.delete_Particle
5814 def __init__(self, *args):
5816 __init__(Particle self, Model m, std::string name) -> Particle
5817 __init__(Particle self, Model m) -> Particle
5818 __init__(Particle self) -> Particle
5820 _IMP_kernel.Particle_swiginit(self, _IMP_kernel.new_Particle(*args))
5822 def get_float_keys(self):
5823 r"""get_float_keys(Particle self) -> IMP::FloatKeys"""
5824 return _IMP_kernel.Particle_get_float_keys(self)
5826 def get_floats_keys(self):
5827 r"""get_floats_keys(Particle self) -> IMP::FloatsKeys"""
5828 return _IMP_kernel.Particle_get_floats_keys(self)
5830 def get_int_keys(self):
5831 r"""get_int_keys(Particle self) -> IMP::IntKeys"""
5832 return _IMP_kernel.Particle_get_int_keys(self)
5834 def get_ints_keys(self):
5835 r"""get_ints_keys(Particle self) -> IMP::IntsKeys"""
5836 return _IMP_kernel.Particle_get_ints_keys(self)
5838 def get_string_keys(self):
5839 r"""get_string_keys(Particle self) -> IMP::StringKeys"""
5840 return _IMP_kernel.Particle_get_string_keys(self)
5842 def get_object_keys(self):
5843 r"""get_object_keys(Particle self) -> IMP::ObjectKeys"""
5844 return _IMP_kernel.Particle_get_object_keys(self)
5846 def add_cache_attribute(self, *args):
5848 add_cache_attribute(Particle self, FloatKey name, IMP::Float value)
5849 add_cache_attribute(Particle self, FloatsKey name, IMP::Floats value)
5850 add_cache_attribute(Particle self, IntKey name, IMP::Int value)
5851 add_cache_attribute(Particle self, IntsKey name, IMP::Ints value)
5852 add_cache_attribute(Particle self, StringKey name, IMP::String value)
5853 add_cache_attribute(Particle self, ObjectKey name, Object value)
5854 add_cache_attribute(Particle self, IMP::WeakObjectKey name, Object value)
5856 return _IMP_kernel.Particle_add_cache_attribute(self, *args)
5858 def get_weak_object_keys(self):
5859 r"""get_weak_object_keys(Particle self) -> IMP::WeakObjectKeys"""
5860 return _IMP_kernel.Particle_get_weak_object_keys(self)
5862 def add_to_derivative(self, *args):
5864 add_to_derivative(Particle self, FloatKey key, IMP::Float value, DerivativeAccumulator da)
5865 add_to_derivative(Particle self, Vector3DDerivKey key, Vector3D value, DerivativeAccumulator da)
5866 add_to_derivative(Particle self, Vector4DDerivKey key, Vector4D value, DerivativeAccumulator da)
5868 return _IMP_kernel.Particle_add_to_derivative(self, *args)
5870 def set_is_optimized(self, *args):
5872 set_is_optimized(Particle self, FloatKey k, bool tf)
5873 set_is_optimized(Particle self, Vector3DDerivKey k, bool tf)
5874 set_is_optimized(Particle self, Vector4DDerivKey k, bool tf)
5876 return _IMP_kernel.Particle_set_is_optimized(self, *args)
5878 def get_is_optimized(self, *args):
5880 get_is_optimized(Particle self, FloatKey k) -> bool
5881 get_is_optimized(Particle self, Vector3DDerivKey k) -> bool
5882 get_is_optimized(Particle self, Vector4DDerivKey k) -> bool
5884 return _IMP_kernel.Particle_get_is_optimized(self, *args)
5886 def get_derivative(self, *args):
5888 get_derivative(Particle self, FloatKey k) -> IMP::Float
5889 get_derivative(Particle self, Vector3DDerivKey k) -> Vector3D
5890 get_derivative(Particle self, Vector4DDerivKey k) -> Vector4D
5892 return _IMP_kernel.Particle_get_derivative(self, *args)
5894 def add_attribute(self, *args):
5896 add_attribute(Particle self, FloatKey name, IMP::Float initial_value)
5897 add_attribute(Particle self, FloatsKey name, IMP::Floats initial_value)
5898 add_attribute(Particle self, IntKey name, IMP::Int initial_value)
5899 add_attribute(Particle self, IntsKey name, IMP::Ints initial_value)
5900 add_attribute(Particle self, StringKey name, IMP::String initial_value)
5901 add_attribute(Particle self, ObjectKey name, Object initial_value)
5902 add_attribute(Particle self, IMP::WeakObjectKey name, Object initial_value)
5903 add_attribute(Particle self, SparseStringKey name, IMP::String initial_value)
5904 add_attribute(Particle self, SparseIntKey name, IMP::Int initial_value)
5905 add_attribute(Particle self, SparseFloatKey name, IMP::Float initial_value)
5906 add_attribute(Particle self, SparseParticleIndexKey name, ParticleIndex initial_value)
5907 add_attribute(Particle self, FloatKey name, IMP::Float const initial_value, bool optimized)
5908 add_attribute(Particle self, ParticleIndexKey k, Particle v)
5910 return _IMP_kernel.Particle_add_attribute(self, *args)
5912 def has_attribute(self, *args):
5914 has_attribute(Particle self, FloatKey name) -> bool
5915 has_attribute(Particle self, FloatsKey name) -> bool
5916 has_attribute(Particle self, IntKey name) -> bool
5917 has_attribute(Particle self, IntsKey name) -> bool
5918 has_attribute(Particle self, StringKey name) -> bool
5919 has_attribute(Particle self, ObjectKey name) -> bool
5920 has_attribute(Particle self, IMP::WeakObjectKey name) -> bool
5921 has_attribute(Particle self, SparseStringKey name) -> bool
5922 has_attribute(Particle self, SparseIntKey name) -> bool
5923 has_attribute(Particle self, SparseFloatKey name) -> bool
5924 has_attribute(Particle self, SparseParticleIndexKey name) -> bool
5925 has_attribute(Particle self, ParticleIndexKey k) -> bool
5927 return _IMP_kernel.Particle_has_attribute(self, *args)
5929 def set_value(self, *args):
5931 set_value(Particle self, FloatKey name, IMP::Float value)
5932 set_value(Particle self, FloatsKey name, IMP::Floats value)
5933 set_value(Particle self, IntKey name, IMP::Int value)
5934 set_value(Particle self, IntsKey name, IMP::Ints value)
5935 set_value(Particle self, StringKey name, IMP::String value)
5936 set_value(Particle self, ObjectKey name, Object value)
5937 set_value(Particle self, IMP::WeakObjectKey name, Object value)
5938 set_value(Particle self, SparseStringKey name, IMP::String value)
5939 set_value(Particle self, SparseIntKey name, IMP::Int value)
5940 set_value(Particle self, SparseFloatKey name, IMP::Float value)
5941 set_value(Particle self, SparseParticleIndexKey name, ParticleIndex value)
5942 set_value(Particle self, ParticleIndexKey k, Particle v)
5944 return _IMP_kernel.Particle_set_value(self, *args)
5946 def get_value(self, *args):
5948 get_value(Particle self, FloatKey name) -> IMP::Float
5949 get_value(Particle self, FloatsKey name) -> IMP::Floats
5950 get_value(Particle self, IntKey name) -> IMP::Int
5951 get_value(Particle self, IntsKey name) -> IMP::Ints
5952 get_value(Particle self, StringKey name) -> IMP::String
5953 get_value(Particle self, ObjectKey name) -> Object
5954 get_value(Particle self, IMP::WeakObjectKey name) -> Object
5955 get_value(Particle self, SparseStringKey name) -> IMP::String
5956 get_value(Particle self, SparseIntKey name) -> IMP::Int
5957 get_value(Particle self, SparseFloatKey name) -> IMP::Float
5958 get_value(Particle self, SparseParticleIndexKey name) -> ParticleIndex
5959 get_value(Particle self, ParticleIndexKey k) -> Particle
5961 return _IMP_kernel.Particle_get_value(self, *args)
5963 def remove_attribute(self, *args):
5965 remove_attribute(Particle self, FloatKey name)
5966 remove_attribute(Particle self, FloatsKey name)
5967 remove_attribute(Particle self, IntKey name)
5968 remove_attribute(Particle self, IntsKey name)
5969 remove_attribute(Particle self, StringKey name)
5970 remove_attribute(Particle self, ObjectKey name)
5971 remove_attribute(Particle self, IMP::WeakObjectKey name)
5972 remove_attribute(Particle self, SparseStringKey name)
5973 remove_attribute(Particle self, SparseIntKey name)
5974 remove_attribute(Particle self, SparseFloatKey name)
5975 remove_attribute(Particle self, SparseParticleIndexKey name)
5976 remove_attribute(Particle self, ParticleIndexKey k)
5978 return _IMP_kernel.Particle_remove_attribute(self, *args)
5980 def get_particle_keys(self):
5981 r"""get_particle_keys(Particle self) -> IMP::ParticleIndexKeys"""
5982 return _IMP_kernel.Particle_get_particle_keys(self)
5984 def show(self, *args):
5985 r"""show(Particle self, _ostream out=std::cout)"""
5986 return _IMP_kernel.Particle_show(self, *args)
5988 def get_is_active(self):
5989 r"""get_is_active(Particle self) -> bool"""
5990 return _IMP_kernel.Particle_get_is_active(self)
5993 r"""get_index(Particle self) -> ParticleIndex"""
5994 return _IMP_kernel.Particle_get_index(self)
5996 def __eq__(self, *args):
5998 __eq__(Particle self, Particle o) -> bool
5999 __eq__(Particle self, Decorator d) -> bool
6001 return _IMP_kernel.Particle___eq__(self, *args)
6003 def __ne__(self, *args):
6005 __ne__(Particle self, Particle o) -> bool
6006 __ne__(Particle self, Decorator d) -> bool
6008 return _IMP_kernel.Particle___ne__(self, *args)
6010 def __le__(self, *args):
6012 __le__(Particle self, Particle o) -> bool
6013 __le__(Particle self, Decorator d) -> bool
6015 return _IMP_kernel.Particle___le__(self, *args)
6017 def __lt__(self, *args):
6019 __lt__(Particle self, Particle o) -> bool
6020 __lt__(Particle self, Decorator d) -> bool
6022 return _IMP_kernel.Particle___lt__(self, *args)
6024 def __ge__(self, *args):
6026 __ge__(Particle self, Particle o) -> bool
6027 __ge__(Particle self, Decorator d) -> bool
6029 return _IMP_kernel.Particle___ge__(self, *args)
6031 def __gt__(self, *args):
6033 __gt__(Particle self, Particle o) -> bool
6034 __gt__(Particle self, Decorator d) -> bool
6036 return _IMP_kernel.Particle___gt__(self, *args)
6038 __hash__ = ModelObject.__hash__
6042 r"""__str__(Particle self) -> std::string"""
6043 return _IMP_kernel.Particle___str__(self)
6046 r"""__repr__(Particle self) -> std::string"""
6047 return _IMP_kernel.Particle___repr__(self)
6051 return _object_cast_to_Particle(o)
6054 def _get_as_binary(self):
6055 r"""_get_as_binary(Particle self) -> PyObject *"""
6056 return _IMP_kernel.Particle__get_as_binary(self)
6058 def _set_from_binary(self, p):
6059 r"""_set_from_binary(Particle self, PyObject * p)"""
6060 return _IMP_kernel.Particle__set_from_binary(self, p)
6062 def __getstate__(self):
6063 p = self._get_as_binary()
6064 if len(self.__dict__) > 1:
6065 d = self.__dict__.copy()
6070 def __setstate__(self, p):
6071 if not hasattr(self,
'this'):
6073 if isinstance(p, tuple):
6075 self.__dict__.update(d)
6076 return self._set_from_binary(p)
6080 _IMP_kernel.Particle_swigregister(Particle)
6081 class _ParticleAdaptor(_InputAdaptor):
6082 r"""Proxy of C++ IMP::ParticleAdaptor class."""
6084 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6085 __repr__ = _swig_repr
6087 def __init__(self, *args):
6089 __init__(_ParticleAdaptor self) -> _ParticleAdaptor
6090 __init__(_ParticleAdaptor self, Particle p) -> _ParticleAdaptor
6091 __init__(_ParticleAdaptor self, Decorator d) -> _ParticleAdaptor
6093 _IMP_kernel._ParticleAdaptor_swiginit(self, _IMP_kernel.new__ParticleAdaptor(*args))
6095 def get_model(self):
6096 r"""get_model(_ParticleAdaptor self) -> Model"""
6097 return _IMP_kernel._ParticleAdaptor_get_model(self)
6099 def get_particle_index(self):
6100 r"""get_particle_index(_ParticleAdaptor self) -> ParticleIndex"""
6101 return _IMP_kernel._ParticleAdaptor_get_particle_index(self)
6102 __swig_destroy__ = _IMP_kernel.delete__ParticleAdaptor
6105 _IMP_kernel._ParticleAdaptor_swigregister(_ParticleAdaptor)
6106 class _DependencyGraphVertexIndex(object):
6107 r"""Proxy of C++ IMP::DependencyGraphVertexIndex class."""
6109 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6110 __repr__ = _swig_repr
6113 r"""__init__(_DependencyGraphVertexIndex self) -> _DependencyGraphVertexIndex"""
6114 _IMP_kernel._DependencyGraphVertexIndex_swiginit(self, _IMP_kernel.new__DependencyGraphVertexIndex())
6115 __swig_destroy__ = _IMP_kernel.delete__DependencyGraphVertexIndex
6118 _IMP_kernel._DependencyGraphVertexIndex_swigregister(_DependencyGraphVertexIndex)
6120 def show_as_graphviz(name, out):
6121 r"""show_as_graphviz(IMP::DependencyGraph const & name, TextOutput out)"""
6122 return _IMP_kernel.show_as_graphviz(name, out)
6124 def get_vertex_index(g):
6125 r"""get_vertex_index(IMP::DependencyGraph const & g) -> _DependencyGraphVertexIndex"""
6126 return _IMP_kernel.get_vertex_index(g)
6129 r"""get_dependency_graph(Model m) -> IMP::DependencyGraph"""
6130 return _IMP_kernel.get_dependency_graph(m)
6133 r"""get_pruned_dependency_graph(Model m) -> IMP::DependencyGraph"""
6134 return _IMP_kernel.get_pruned_dependency_graph(m)
6136 def get_dependent_particles(p, all, dg, index):
6137 r"""get_dependent_particles(ModelObject p, IMP::ModelObjectsTemp const & all, IMP::DependencyGraph const & dg, _DependencyGraphVertexIndex index) -> IMP::ParticlesTemp"""
6138 return _IMP_kernel.get_dependent_particles(p, all, dg, index)
6140 def get_required_score_states(*args):
6142 get_required_score_states(IMP::ModelObjectsTemp const & mos, IMP::ScoreStatesTemp exclude=IMP::ScoreStatesTemp()) -> IMP::ScoreStatesTemp
6143 get_required_score_states(ModelObject p, IMP::ModelObjectsTemp const & all, IMP::DependencyGraph const & dg, _DependencyGraphVertexIndex index) -> IMP::ScoreStatesTemp
6144 get_required_score_states(Model m, ParticleIndex pi) -> IMP::ScoreStatesTemp
6146 return _IMP_kernel.get_required_score_states(*args)
6147 class ScoringFunction(ModelObject):
6148 r"""Proxy of C++ IMP::ScoringFunction class."""
6150 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6152 def do_add_score_and_derivatives(self, sa, ss):
6153 r"""do_add_score_and_derivatives(ScoringFunction self, ScoreAccumulator sa, IMP::ScoreStatesTemp const & ss)"""
6154 return _IMP_kernel.ScoringFunction_do_add_score_and_derivatives(self, sa, ss)
6156 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss):
6157 r"""do_add_score_and_derivatives_moved(ScoringFunction self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, IMP::ScoreStatesTemp const & ss)"""
6158 return _IMP_kernel.ScoringFunction_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss)
6160 def get_score_accumulator_if_below(self, deriv, max):
6161 r"""get_score_accumulator_if_below(ScoringFunction self, bool deriv, double max) -> ScoreAccumulator"""
6162 return _IMP_kernel.ScoringFunction_get_score_accumulator_if_below(self, deriv, max)
6164 def get_score_accumulator_if_good(self, deriv):
6165 r"""get_score_accumulator_if_good(ScoringFunction self, bool deriv) -> ScoreAccumulator"""
6166 return _IMP_kernel.ScoringFunction_get_score_accumulator_if_good(self, deriv)
6168 def get_score_accumulator(self, deriv):
6169 r"""get_score_accumulator(ScoringFunction self, bool deriv) -> ScoreAccumulator"""
6170 return _IMP_kernel.ScoringFunction_get_score_accumulator(self, deriv)
6172 def __init__(self, *args):
6174 __init__(ScoringFunction self, Model m, std::string name) -> ScoringFunction
6175 __init__(ScoringFunction self) -> ScoringFunction
6177 if self.__class__ == ScoringFunction:
6181 _IMP_kernel.ScoringFunction_swiginit(self, _IMP_kernel.new_ScoringFunction(_self, *args))
6183 if self.__class__ != ScoringFunction:
6184 _director_objects.register(self)
6189 def do_get_outputs(self):
6190 r"""do_get_outputs(ScoringFunction self) -> IMP::ModelObjectsTemp"""
6191 return _IMP_kernel.ScoringFunction_do_get_outputs(self)
6193 def evaluate(self, derivatives):
6194 r"""evaluate(ScoringFunction self, bool derivatives) -> double"""
6195 return _IMP_kernel.ScoringFunction_evaluate(self, derivatives)
6197 def evaluate_if_good(self, derivatives):
6198 r"""evaluate_if_good(ScoringFunction self, bool derivatives) -> double"""
6199 return _IMP_kernel.ScoringFunction_evaluate_if_good(self, derivatives)
6201 def evaluate_if_below(self, derivatives, max):
6202 r"""evaluate_if_below(ScoringFunction self, bool derivatives, double max) -> double"""
6203 return _IMP_kernel.ScoringFunction_evaluate_if_below(self, derivatives, max)
6205 def evaluate_moved(self, derivatives, moved_pis, reset_pis):
6206 r"""evaluate_moved(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
6207 return _IMP_kernel.ScoringFunction_evaluate_moved(self, derivatives, moved_pis, reset_pis)
6209 def evaluate_moved_if_below(self, derivatives, moved_pis, reset_pis, max):
6210 r"""evaluate_moved_if_below(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
6211 return _IMP_kernel.ScoringFunction_evaluate_moved_if_below(self, derivatives, moved_pis, reset_pis, max)
6213 def evaluate_moved_if_good(self, derivatives, moved_pis, reset_pis):
6214 r"""evaluate_moved_if_good(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
6215 return _IMP_kernel.ScoringFunction_evaluate_moved_if_good(self, derivatives, moved_pis, reset_pis)
6217 def clear_moved_cache(self):
6218 r"""clear_moved_cache(ScoringFunction self)"""
6219 return _IMP_kernel.ScoringFunction_clear_moved_cache(self)
6221 def get_had_good_score(self):
6222 r"""get_had_good_score(ScoringFunction self) -> bool"""
6223 return _IMP_kernel.ScoringFunction_get_had_good_score(self)
6225 def get_last_score(self):
6226 r"""get_last_score(ScoringFunction self) -> double"""
6227 return _IMP_kernel.ScoringFunction_get_last_score(self)
6230 r"""create_restraints(ScoringFunction self) -> IMP::Restraints"""
6231 return _IMP_kernel.ScoringFunction_create_restraints(self)
6233 def get_single_restraint(self):
6234 r"""get_single_restraint(ScoringFunction self) -> Restraint"""
6235 return _IMP_kernel.ScoringFunction_get_single_restraint(self)
6238 r"""__str__(ScoringFunction self) -> std::string"""
6239 return _IMP_kernel.ScoringFunction___str__(self)
6242 r"""__repr__(ScoringFunction self) -> std::string"""
6243 return _IMP_kernel.ScoringFunction___repr__(self)
6247 return _object_cast_to_ScoringFunction(o)
6250 def do_show(self, out):
6255 return _object_cast_to_ScoringFunction(o)
6258 def _get_jax(self, space=None):
6261 r = self.get_single_restraint()
6263 raise NotImplementedError(
6264 f
"No JAX implementation for {self} ({type(self)})")
6266 return r.get_derived_object()._get_jax(space)
6268 def _evaluate_jax(self, space=None):
6269 """Similar to evaluate(False), but using JAX.
6270 This is intended to be useful for testing purposes. It will likely
6271 not be particularly fast as it will copy the IMP Model and
6272 jax.jit-compile the scoring function each time.
6274 @param space The space in which the scoring function is evaluated
6275 (e.g. a periodic box). See IMP._jax_util.Space. If not
6276 specified, an unbounded (free) space is used.
6279 ji = self._get_jax(space)
6280 jm = ji.get_jax_model()
6281 axes = jm.get_vmap_axes()
6283 j = jax.jit(ji.score_func)
6287 j = jax.jit(jax.vmap(ji.score_func, in_axes=(axes,)))
6290 __swig_destroy__ = _IMP_kernel.delete_ScoringFunction
6291 def __disown__(self):
6293 _IMP_kernel.disown_ScoringFunction(self)
6294 return weakref.proxy(self)
6297 r"""do_destroy(ScoringFunction self)"""
6298 return _IMP_kernel.ScoringFunction_do_destroy(self)
6300 def handle_set_has_required_score_states(self, arg0):
6301 r"""handle_set_has_required_score_states(ScoringFunction self, bool arg0)"""
6302 return _IMP_kernel.ScoringFunction_handle_set_has_required_score_states(self, arg0)
6304 def do_get_inputs(self):
6305 r"""do_get_inputs(ScoringFunction self) -> IMP::ModelObjectsTemp"""
6306 return _IMP_kernel.ScoringFunction_do_get_inputs(self)
6308 def do_get_interactions(self):
6309 r"""do_get_interactions(ScoringFunction self) -> IMP::ModelObjectsTemps"""
6310 return _IMP_kernel.ScoringFunction_do_get_interactions(self)
6313 _IMP_kernel.ScoringFunction_swigregister(ScoringFunction)
6317 create_decomposition(IMP::RestraintsTemp const & rs) -> IMP::Restraints
6318 create_decomposition(ScoringFunction sf) -> IMP::ScoringFunctions
6320 return _IMP_kernel.create_decomposition(*args)
6321 class _ScoringFunctionAdaptor(_InputAdaptor):
6322 r"""Proxy of C++ IMP::ScoringFunctionAdaptor class."""
6324 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6325 __repr__ = _swig_repr
6327 def __init__(self, *args):
6329 __init__(_ScoringFunctionAdaptor self) -> _ScoringFunctionAdaptor
6330 __init__(_ScoringFunctionAdaptor self, ScoringFunction sf) -> _ScoringFunctionAdaptor
6331 __init__(_ScoringFunctionAdaptor self, IMP::RestraintsTemp const & sf) -> _ScoringFunctionAdaptor
6332 __init__(_ScoringFunctionAdaptor self, IMP::Restraints const & sf) -> _ScoringFunctionAdaptor
6333 __init__(_ScoringFunctionAdaptor self, Restraint sf) -> _ScoringFunctionAdaptor
6335 _IMP_kernel._ScoringFunctionAdaptor_swiginit(self, _IMP_kernel.new__ScoringFunctionAdaptor(*args))
6336 __swig_destroy__ = _IMP_kernel.delete__ScoringFunctionAdaptor
6339 _IMP_kernel._ScoringFunctionAdaptor_swigregister(_ScoringFunctionAdaptor)
6342 r"""show_restraint_hierarchy(_ScoringFunctionAdaptor rs, _ostream out=std::cout)"""
6343 return _IMP_kernel.show_restraint_hierarchy(*args)
6344 class Undecorator(
Object):
6345 r"""Proxy of C++ IMP::Undecorator class."""
6347 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6349 def __init__(self, m, name):
6350 r"""__init__(Undecorator self, Model m, std::string name) -> Undecorator"""
6351 if self.__class__ == Undecorator:
6355 _IMP_kernel.Undecorator_swiginit(self, _IMP_kernel.new_Undecorator(_self, m, name))
6357 if self.__class__ != Undecorator:
6358 _director_objects.register(self)
6363 def teardown(self, pi):
6364 r"""teardown(Undecorator self, ParticleIndex pi)"""
6365 return _IMP_kernel.Undecorator_teardown(self, pi)
6368 r"""__str__(Undecorator self) -> std::string"""
6369 return _IMP_kernel.Undecorator___str__(self)
6372 r"""__repr__(Undecorator self) -> std::string"""
6373 return _IMP_kernel.Undecorator___repr__(self)
6377 return _object_cast_to_Undecorator(o)
6380 def do_show(self, out):
6385 return _object_cast_to_Undecorator(o)
6387 __swig_destroy__ = _IMP_kernel.delete_Undecorator
6388 def __disown__(self):
6390 _IMP_kernel.disown_Undecorator(self)
6391 return weakref.proxy(self)
6394 r"""do_destroy(Undecorator self)"""
6395 return _IMP_kernel.Undecorator_do_destroy(self)
6398 _IMP_kernel.Undecorator_swigregister(Undecorator)
6400 r"""Proxy of C++ IMP::Model class."""
6402 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6404 def __init__(self, *args):
6405 r"""__init__(Model self, std::string name="Model %1%") -> Model"""
6406 _IMP_kernel.Model_swiginit(self, _IMP_kernel.new_Model(*args))
6408 if self
not in _models_set:
6409 _models_set.add(self)
6414 def clear_particle_caches(self, pi):
6415 r"""clear_particle_caches(Model self, ParticleIndex pi)"""
6416 return _IMP_kernel.Model_clear_particle_caches(self, pi)
6419 r"""add_particle(Model self, std::string name) -> ParticleIndex"""
6420 return _IMP_kernel.Model_add_particle(self, name)
6422 def get_particle_name(self, pi):
6423 r"""get_particle_name(Model self, ParticleIndex pi) -> std::string"""
6424 return _IMP_kernel.Model_get_particle_name(self, pi)
6426 def add_undecorator(self, pi, d):
6427 r"""add_undecorator(Model self, ParticleIndex pi, Undecorator d)"""
6428 return _IMP_kernel.Model_add_undecorator(self, pi, d)
6430 def get_dependent_restraints_uncached(self, pi):
6431 r"""get_dependent_restraints_uncached(Model self, ParticleIndex pi) -> IMP::RestraintsTemp"""
6432 return _IMP_kernel.Model_get_dependent_restraints_uncached(self, pi)
6434 def get_dependent_particles_uncached(self, pi):
6435 r"""get_dependent_particles_uncached(Model self, ParticleIndex pi) -> IMP::ParticlesTemp"""
6436 return _IMP_kernel.Model_get_dependent_particles_uncached(self, pi)
6438 def get_dependent_score_states_uncached(self, pi):
6439 r"""get_dependent_score_states_uncached(Model self, ParticleIndex pi) -> IMP::ScoreStatesTemp"""
6440 return _IMP_kernel.Model_get_dependent_score_states_uncached(self, pi)
6441 def __get_score_states(self):
return _list_util.VarList(getdimfunc=self.get_number_of_score_states, getfunc=self.get_score_state, erasefunc=self.erase_score_state, appendfunc=self.add_score_state, extendfunc=self.add_score_states, clearfunc=self.clear_score_states, indexfunc=self._python_index_score_state)
6442 def __set_score_states(self, obj): _list_util.set_varlist(self.score_states, obj)
6443 def __del_score_states(self): _list_util.del_varlist(self.score_states)
6444 score_states = property(__get_score_states, __set_score_states, __del_score_states, doc=
"List of ##ucnames")
6446 def remove_score_state(self, d):
6447 r"""remove_score_state(Model self, ScoreState d)"""
6448 return _IMP_kernel.Model_remove_score_state(self, d)
6450 def _python_index_score_state(self, d, start, stop):
6451 r"""_python_index_score_state(Model self, ScoreState d, unsigned int start, unsigned int stop) -> unsigned int"""
6452 return _IMP_kernel.Model__python_index_score_state(self, d, start, stop)
6454 def remove_score_states(self, d):
6455 r"""remove_score_states(Model self, IMP::ScoreStates const & d)"""
6456 return _IMP_kernel.Model_remove_score_states(self, d)
6458 def set_score_states(self, ps):
6459 r"""set_score_states(Model self, IMP::ScoreStates const & ps)"""
6460 return _IMP_kernel.Model_set_score_states(self, ps)
6462 def set_score_states_order(self, objs):
6463 r"""set_score_states_order(Model self, IMP::ScoreStates const & objs)"""
6464 return _IMP_kernel.Model_set_score_states_order(self, objs)
6466 def add_score_state(self, obj):
6467 r"""add_score_state(Model self, ScoreState obj) -> unsigned int"""
6468 return _IMP_kernel.Model_add_score_state(self, obj)
6470 def add_score_states(self, objs):
6471 r"""add_score_states(Model self, IMP::ScoreStates const & objs)"""
6472 return _IMP_kernel.Model_add_score_states(self, objs)
6474 def clear_score_states(self):
6475 r"""clear_score_states(Model self)"""
6476 return _IMP_kernel.Model_clear_score_states(self)
6478 def get_number_of_score_states(self):
6479 r"""get_number_of_score_states(Model self) -> unsigned int"""
6480 return _IMP_kernel.Model_get_number_of_score_states(self)
6482 def get_has_score_states(self):
6483 r"""get_has_score_states(Model self) -> bool"""
6484 return _IMP_kernel.Model_get_has_score_states(self)
6486 def get_score_state(self, i):
6487 r"""get_score_state(Model self, unsigned int i) -> ScoreState"""
6488 return _IMP_kernel.Model_get_score_state(self, i)
6490 def get_score_states(self):
6491 r"""get_score_states(Model self) -> IMP::ScoreStates"""
6492 return _IMP_kernel.Model_get_score_states(self)
6494 def erase_score_state(self, i):
6495 r"""erase_score_state(Model self, unsigned int i)"""
6496 return _IMP_kernel.Model_erase_score_state(self, i)
6498 def reserve_score_states(self, sz):
6499 r"""reserve_score_states(Model self, unsigned int sz)"""
6500 return _IMP_kernel.Model_reserve_score_states(self, sz)
6503 r"""update(Model self)"""
6504 return _IMP_kernel.Model_update(self)
6506 def get_ordered_score_states(self):
6507 r"""get_ordered_score_states(Model self) -> IMP::ScoreStatesTemp"""
6508 return _IMP_kernel.Model_get_ordered_score_states(self)
6510 def add_cache_attribute(self, *args):
6512 add_cache_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
6513 add_cache_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
6514 add_cache_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
6515 add_cache_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, Vector3D value)
6516 add_cache_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle, Vector4D value)
6517 add_cache_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle, Vector3D value)
6518 add_cache_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle, Vector4D value)
6519 add_cache_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
6520 add_cache_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
6521 add_cache_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
6522 add_cache_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
6523 add_cache_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
6524 add_cache_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
6526 return _IMP_kernel.Model_add_cache_attribute(self, *args)
6528 def add_attribute(self, *args):
6530 add_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
6531 add_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
6532 add_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
6533 add_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, Vector3D value)
6534 add_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle, Vector4D value)
6535 add_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle, Vector3D value)
6536 add_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle, Vector4D value)
6537 add_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
6538 add_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
6539 add_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
6540 add_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
6541 add_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
6542 add_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
6543 add_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle, IMP::String value)
6544 add_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle, IMP::Int value)
6545 add_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle, IMP::Float value)
6546 add_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
6548 return _IMP_kernel.Model_add_attribute(self, *args)
6550 def remove_attribute(self, *args):
6552 remove_attribute(Model self, FloatKey attribute_key, ParticleIndex particle)
6553 remove_attribute(Model self, IntKey attribute_key, ParticleIndex particle)
6554 remove_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle)
6555 remove_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle)
6556 remove_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle)
6557 remove_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle)
6558 remove_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle)
6559 remove_attribute(Model self, IntsKey attribute_key, ParticleIndex particle)
6560 remove_attribute(Model self, StringKey attribute_key, ParticleIndex particle)
6561 remove_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle)
6562 remove_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle)
6563 remove_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle)
6564 remove_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle)
6565 remove_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle)
6566 remove_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle)
6567 remove_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle)
6568 remove_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle)
6570 return _IMP_kernel.Model_remove_attribute(self, *args)
6572 def get_has_attribute(self, *args):
6574 get_has_attribute(Model self, FloatKey attribute_key, ParticleIndex particle) -> bool
6575 get_has_attribute(Model self, IntKey attribute_key, ParticleIndex particle) -> bool
6576 get_has_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle) -> bool
6577 get_has_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle) -> bool
6578 get_has_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle) -> bool
6579 get_has_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle) -> bool
6580 get_has_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle) -> bool
6581 get_has_attribute(Model self, IntsKey attribute_key, ParticleIndex particle) -> bool
6582 get_has_attribute(Model self, StringKey attribute_key, ParticleIndex particle) -> bool
6583 get_has_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle) -> bool
6584 get_has_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle) -> bool
6585 get_has_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle) -> bool
6586 get_has_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle) -> bool
6587 get_has_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle) -> bool
6588 get_has_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle) -> bool
6589 get_has_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle) -> bool
6590 get_has_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle) -> bool
6592 return _IMP_kernel.Model_get_has_attribute(self, *args)
6594 def set_attribute(self, *args):
6596 set_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
6597 set_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
6598 set_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
6599 set_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, Vector3D value)
6600 set_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle, Vector4D value)
6601 set_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle, Vector3D value)
6602 set_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle, Vector4D value)
6603 set_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
6604 set_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
6605 set_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
6606 set_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
6607 set_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
6608 set_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
6609 set_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle, IMP::String value)
6610 set_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle, IMP::Int value)
6611 set_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle, IMP::Float value)
6612 set_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
6614 return _IMP_kernel.Model_set_attribute(self, *args)
6616 def get_attribute(self, *args):
6618 get_attribute(Model self, FloatKey attribute_key, ParticleIndex particle) -> IMP::Float
6619 get_attribute(Model self, IntKey attribute_key, ParticleIndex particle) -> IMP::Int
6620 get_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle) -> IMP::Floats
6621 get_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle) -> Vector3D
6622 get_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle) -> Vector4D
6623 get_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle) -> Vector3D
6624 get_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle) -> Vector4D
6625 get_attribute(Model self, IntsKey attribute_key, ParticleIndex particle) -> IMP::Ints
6626 get_attribute(Model self, StringKey attribute_key, ParticleIndex particle) -> IMP::String
6627 get_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle) -> IMP::ParticleIndexes
6628 get_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle) -> ParticleIndex
6629 get_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle) -> Object
6630 get_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle) -> Object
6631 get_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle) -> IMP::String
6632 get_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle) -> IMP::Int
6633 get_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle) -> IMP::Float
6634 get_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle) -> ParticleIndex
6636 return _IMP_kernel.Model_get_attribute(self, *args)
6638 def set_is_optimized(self, *args):
6640 set_is_optimized(Model self, Vector3DDerivKey arg2, ParticleIndex arg3, bool arg4)
6641 set_is_optimized(Model self, Vector4DDerivKey arg2, ParticleIndex arg3, bool arg4)
6642 set_is_optimized(Model self, FloatKey arg2, ParticleIndex arg3, bool arg4)
6644 return _IMP_kernel.Model_set_is_optimized(self, *args)
6646 def add_to_derivative(self, *args):
6648 add_to_derivative(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle, Vector3D v, DerivativeAccumulator da)
6649 add_to_derivative(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle, Vector4D v, DerivativeAccumulator da)
6650 add_to_derivative(Model self, FloatKey k, ParticleIndex particle, double v, DerivativeAccumulator da)
6652 return _IMP_kernel.Model_add_to_derivative(self, *args)
6654 def get_sphere_attribute_sets_external(self):
6655 r"""get_sphere_attribute_sets_external(Model self) -> bool"""
6656 return _IMP_kernel.Model_get_sphere_attribute_sets_external(self)
6658 def set_sphere_attribute_sets_external(self, external):
6659 r"""set_sphere_attribute_sets_external(Model self, bool external)"""
6660 return _IMP_kernel.Model_set_sphere_attribute_sets_external(self, external)
6662 def get_number_of_sphere_attribute_sets(self):
6663 r"""get_number_of_sphere_attribute_sets(Model self) -> int"""
6664 return _IMP_kernel.Model_get_number_of_sphere_attribute_sets(self)
6666 def set_number_of_sphere_attribute_sets(self, nsets):
6667 r"""set_number_of_sphere_attribute_sets(Model self, int nsets)"""
6668 return _IMP_kernel.Model_set_number_of_sphere_attribute_sets(self, nsets)
6670 def set_active_sphere_attribute_set(self, set):
6671 r"""set_active_sphere_attribute_set(Model self, int set)"""
6672 return _IMP_kernel.Model_set_active_sphere_attribute_set(self, set)
6674 def get_number_of_internal_coordinate_attribute_sets(self):
6675 r"""get_number_of_internal_coordinate_attribute_sets(Model self) -> int"""
6676 return _IMP_kernel.Model_get_number_of_internal_coordinate_attribute_sets(self)
6678 def set_number_of_internal_coordinate_attribute_sets(self, nsets):
6679 r"""set_number_of_internal_coordinate_attribute_sets(Model self, int nsets)"""
6680 return _IMP_kernel.Model_set_number_of_internal_coordinate_attribute_sets(self, nsets)
6682 def get_internal_coordinate_attribute_sets_external(self):
6683 r"""get_internal_coordinate_attribute_sets_external(Model self) -> bool"""
6684 return _IMP_kernel.Model_get_internal_coordinate_attribute_sets_external(self)
6686 def set_internal_coordinate_attribute_sets_external(self, external):
6687 r"""set_internal_coordinate_attribute_sets_external(Model self, bool external)"""
6688 return _IMP_kernel.Model_set_internal_coordinate_attribute_sets_external(self, external)
6690 def set_active_internal_coordinate_attribute_set(self, set):
6691 r"""set_active_internal_coordinate_attribute_set(Model self, int set)"""
6692 return _IMP_kernel.Model_set_active_internal_coordinate_attribute_set(self, set)
6694 def get_number_of_attribute_sets(self, *args):
6696 get_number_of_attribute_sets(Model self)
6697 get_number_of_attribute_sets(Model self, FloatKey k) -> int
6698 get_number_of_attribute_sets(Model self, Vector3DKey k) -> int
6699 get_number_of_attribute_sets(Model self, Vector4DKey k) -> int
6700 get_number_of_attribute_sets(Model self, Vector3DDerivKey k) -> int
6701 get_number_of_attribute_sets(Model self, Vector4DDerivKey k) -> int
6703 return _IMP_kernel.Model_get_number_of_attribute_sets(self, *args)
6705 def set_number_of_attribute_sets(self, *args):
6707 set_number_of_attribute_sets(Model self)
6708 set_number_of_attribute_sets(Model self, FloatKey k, int nsets)
6709 set_number_of_attribute_sets(Model self, Vector3DKey k, int nsets)
6710 set_number_of_attribute_sets(Model self, Vector4DKey k, int nsets)
6711 set_number_of_attribute_sets(Model self, Vector3DDerivKey k, int nsets)
6712 set_number_of_attribute_sets(Model self, Vector4DDerivKey k, int nsets)
6714 return _IMP_kernel.Model_set_number_of_attribute_sets(self, *args)
6716 def set_active_attribute_set(self, *args):
6718 set_active_attribute_set(Model self)
6719 set_active_attribute_set(Model self, FloatKey k, int set)
6720 set_active_attribute_set(Model self, Vector3DKey k, int set)
6721 set_active_attribute_set(Model self, Vector4DKey k, int set)
6722 set_active_attribute_set(Model self, Vector3DDerivKey k, int set)
6723 set_active_attribute_set(Model self, Vector4DDerivKey k, int set)
6725 return _IMP_kernel.Model_set_active_attribute_set(self, *args)
6727 def set_attribute_sets_external(self, *args):
6729 set_attribute_sets_external(Model self)
6730 set_attribute_sets_external(Model self, FloatKey k, bool external)
6731 set_attribute_sets_external(Model self, Vector3DKey k, bool external)
6732 set_attribute_sets_external(Model self, Vector4DKey k, bool external)
6733 set_attribute_sets_external(Model self, Vector3DDerivKey k, bool external)
6734 set_attribute_sets_external(Model self, Vector4DDerivKey k, bool external)
6736 return _IMP_kernel.Model_set_attribute_sets_external(self, *args)
6738 def get_attribute_sets_external(self, *args):
6740 get_attribute_sets_external(Model self)
6741 get_attribute_sets_external(Model self, FloatKey k) -> bool
6742 get_attribute_sets_external(Model self, Vector3DKey k) -> bool
6743 get_attribute_sets_external(Model self, Vector4DKey k) -> bool
6744 get_attribute_sets_external(Model self, Vector3DDerivKey k) -> bool
6745 get_attribute_sets_external(Model self, Vector4DDerivKey k) -> bool
6747 return _IMP_kernel.Model_get_attribute_sets_external(self, *args)
6749 def get_particle(self, p):
6750 r"""get_particle(Model self, ParticleIndex p) -> Particle"""
6751 return _IMP_kernel.Model_get_particle(self, p)
6753 def get_has_particle(self, p):
6754 r"""get_has_particle(Model self, ParticleIndex p) -> bool"""
6755 return _IMP_kernel.Model_get_has_particle(self, p)
6758 r"""get_particle_indexes(Model self) -> IMP::ParticleIndexes"""
6759 return _IMP_kernel.Model_get_particle_indexes(self)
6761 def get_model_objects(self):
6762 r"""get_model_objects(Model self) -> IMP::ModelObjectsTemp"""
6763 return _IMP_kernel.Model_get_model_objects(self)
6765 def remove_particle(self, pi):
6766 r"""remove_particle(Model self, ParticleIndex pi)"""
6767 return _IMP_kernel.Model_remove_particle(self, pi)
6769 def add_data(self, mk, o):
6770 r"""add_data(Model self, ModelKey mk, Object o)"""
6771 return _IMP_kernel.Model_add_data(self, mk, o)
6773 def get_data(self, mk):
6774 r"""get_data(Model self, ModelKey mk) -> Object"""
6775 return _IMP_kernel.Model_get_data(self, mk)
6777 def remove_data(self, mk):
6778 r"""remove_data(Model self, ModelKey mk)"""
6779 return _IMP_kernel.Model_remove_data(self, mk)
6781 def get_has_data(self, mk):
6782 r"""get_has_data(Model self, ModelKey mk) -> bool"""
6783 return _IMP_kernel.Model_get_has_data(self, mk)
6786 r"""get_age(Model self) -> unsigned int"""
6787 return _IMP_kernel.Model_get_age(self)
6789 def get_trigger_last_updated(self, tk):
6790 r"""get_trigger_last_updated(Model self, TriggerKey tk) -> unsigned int"""
6791 return _IMP_kernel.Model_get_trigger_last_updated(self, tk)
6793 def set_trigger_updated(self, tk):
6794 r"""set_trigger_updated(Model self, TriggerKey tk)"""
6795 return _IMP_kernel.Model_set_trigger_updated(self, tk)
6797 def get_dependencies_updated(self):
6798 r"""get_dependencies_updated(Model self) -> unsigned int"""
6799 return _IMP_kernel.Model_get_dependencies_updated(self)
6801 def get_removed_particles_attributes_age(self):
6802 r"""get_removed_particles_attributes_age(Model self) -> unsigned int"""
6803 return _IMP_kernel.Model_get_removed_particles_attributes_age(self)
6805 def save_dependencies(self):
6806 r"""save_dependencies(Model self)"""
6807 return _IMP_kernel.Model_save_dependencies(self)
6809 def restore_dependencies(self):
6810 r"""restore_dependencies(Model self)"""
6811 return _IMP_kernel.Model_restore_dependencies(self)
6813 def get_particles_size(self):
6814 r"""get_particles_size(Model self) -> unsigned int"""
6815 return _IMP_kernel.Model_get_particles_size(self)
6817 def get_unique_id(self):
6818 r"""get_unique_id(Model self) -> uint32_t"""
6819 return _IMP_kernel.Model_get_unique_id(self)
6822 def get_by_unique_id(id):
6823 r"""get_by_unique_id(uint32_t id) -> Model"""
6824 return _IMP_kernel.Model_get_by_unique_id(id)
6827 r"""get_version_info(Model self) -> VersionInfo"""
6828 return _IMP_kernel.Model_get_version_info(self)
6829 __swig_destroy__ = _IMP_kernel.delete_Model
6831 r"""__del__(Model self)"""
6833 _director_objects.cleanup()
6840 r"""do_destroy(Model self)"""
6841 return _IMP_kernel.Model_do_destroy(self)
6844 r"""__str__(Model self) -> std::string"""
6845 return _IMP_kernel.Model___str__(self)
6848 r"""__repr__(Model self) -> std::string"""
6849 return _IMP_kernel.Model___repr__(self)
6853 return _object_cast_to_Model(o)
6856 def _get_as_binary(self):
6857 r"""_get_as_binary(Model self) -> PyObject *"""
6858 return _IMP_kernel.Model__get_as_binary(self)
6860 def _set_from_binary(self, p):
6861 r"""_set_from_binary(Model self, PyObject * p)"""
6862 return _IMP_kernel.Model__set_from_binary(self, p)
6864 def __getstate__(self):
6865 p = self._get_as_binary()
6866 if len(self.__dict__) > 1:
6867 d = self.__dict__.copy()
6872 def __setstate__(self, p):
6873 if not hasattr(self,
'this'):
6875 if isinstance(p, tuple):
6877 self.__dict__.update(d)
6878 return self._set_from_binary(p)
6882 """Get the model's attribute array for IntKey k as a NumPy array.
6883 The array is indexed by ParticleIndex; particles that don't have
6884 this attribute will either be off the end of the array or will have
6886 This is a NumPy view that shares memory with the Model. Thus,
6887 any changes to values in this list will be reflected in the Model.
6888 Also, if the Model attribute array moves in memory (e.g. if particles
6889 or attributes are added) this array will be invalidated, so it is
6890 unsafe to keep it around long term.
6891 If read_only is set True, values in the array cannot be changed.
6893 return _get_ints_numpy(self, k, self, read_only)
6896 """Get the model's attribute array for any type of Key
6897 k as a NumPy array. See Model::get_ints_numpy() for more details.
6898 If this Key has multiple attribute sets defined for it,
6899 a multi-dimensional view over all sets is returned. If the storage
6900 of these sets is external, a read-only view is returned where each
6901 row points to data currently in the model for the first set."""
6902 _numpy_meth_map = {IntKey: (_get_ints_numpy,
False),
6903 FloatKey: (_get_floats_numpy,
True),
6904 Vector3DKey: (_get_vector3ds_numpy,
True),
6905 Vector3DDerivKey: (_get_vector3dderiv_numpy,
True),
6906 Vector4DKey: (_get_vector4ds_numpy,
True),
6907 Vector4DDerivKey: (_get_vector4dderiv_numpy,
True),
6908 ParticleIndexKey: (_get_particle_indexes_numpy,
6910 func, can_external = _numpy_meth_map[type(k)]
6911 n = func(self, k, self, read_only)
6912 if can_external
and self.get_attribute_sets_external(k):
6913 nsets = self.get_number_of_attribute_sets(k)
6914 return numpy.broadcast_to(n, (nsets,) + n.shape)
6919 """Get the model's attribute array for FloatKey k as a NumPy array.
6920 See Model::get_ints_numpy() for more details."""
6921 return _get_floats_numpy(self, k, self, read_only)
6924 """Get the model's attribute derivatives array for key k
6925 as a NumPy array. See Model::get_ints_numpy() for more details."""
6927 FloatKey: _get_derivatives_numpy,
6928 Vector3DDerivKey: _get_vector3dderiv_derivatives_numpy,
6929 Vector4DDerivKey: _get_vector4dderiv_derivatives_numpy}
6930 return _numpy_meth_map[type(k)](self, k, self, read_only)
6933 """Get the model's attribute array for Vector3DKey k as a NumPy array.
6934 See Model::get_ints_numpy() for more details."""
6935 return _get_vector3ds_numpy(self, k, self, read_only)
6938 """Get the model's XYZR attribute arrays as NumPy arrays.
6939 The attribute arrays for Cartesian coordinates and radii are
6940 stored separately from those for other FloatKeys. This function
6941 returns a tuple of two NumPy arrays, the first of coordinates and
6942 the second of radii. See Model::get_ints_numpy() for more details."""
6943 xyz, r = _get_spheres_numpy(self, self, read_only)
6944 if self.get_sphere_attribute_sets_external():
6945 nsets = self.get_number_of_sphere_attribute_sets()
6946 return (numpy.broadcast_to(xyz, (nsets,) + xyz.shape),
6947 numpy.broadcast_to(r, (nsets,) + r.shape))
6952 """Get the model's XYZR attribute derivatives arrays as NumPy arrays.
6953 See Model::get_ints_numpy() for more details."""
6954 return _get_sphere_derivatives_numpy(self, self, read_only)
6957 """Get the model's internal coordinate array as a NumPy array.
6958 The attribute arrays for rigid body internal coordinates are
6959 stored separately from those for other FloatKeys.
6960 See Model::get_ints_numpy() for more details."""
6961 return _get_internal_coordinates_numpy(self, self, read_only)
6964 """Get the model's internal coordinate derivative array as a
6966 See Model::get_ints_numpy() for more details."""
6967 return _get_internal_coordinate_derivatives_numpy(
6968 self, self, read_only)
6972 _IMP_kernel.Model_swigregister(Model)
6974 r"""Proxy of C++ IMP::Decorator class."""
6976 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6977 __repr__ = _swig_repr
6979 def __init__(self, p):
6980 r"""__init__(Decorator self, _ParticleAdaptor p) -> Decorator"""
6981 _IMP_kernel.Decorator_swiginit(self, _IMP_kernel.new_Decorator(p))
6983 def __ne__(self, o):
6984 r"""__ne__(Decorator self, Object o) -> bool"""
6985 return _IMP_kernel.Decorator___ne__(self, o)
6987 def __lt__(self, o):
6988 r"""__lt__(Decorator self, Object o) -> bool"""
6989 return _IMP_kernel.Decorator___lt__(self, o)
6991 def __gt__(self, o):
6992 r"""__gt__(Decorator self, Object o) -> bool"""
6993 return _IMP_kernel.Decorator___gt__(self, o)
6995 def __ge__(self, o):
6996 r"""__ge__(Decorator self, Object o) -> bool"""
6997 return _IMP_kernel.Decorator___ge__(self, o)
6999 def __le__(self, o):
7000 r"""__le__(Decorator self, Object o) -> bool"""
7001 return _IMP_kernel.Decorator___le__(self, o)
7004 r"""get_particle(Decorator self) -> Particle"""
7005 return _IMP_kernel.Decorator_get_particle(self)
7007 def get_particle_index(self):
7008 r"""get_particle_index(Decorator self) -> ParticleIndex"""
7009 return _IMP_kernel.Decorator_get_particle_index(self)
7011 def get_model(self):
7012 m = _IMP_kernel.Decorator_get_model(self)
7013 if m
in _models_set:
7014 m = _models_set_get(m)
7019 def get_is_valid(self):
7020 r"""get_is_valid(Decorator self) -> bool"""
7021 return _IMP_kernel.Decorator_get_is_valid(self)
7024 r"""__hash__(Decorator self) -> std::size_t"""
7025 return _IMP_kernel.Decorator___hash__(self)
7027 def __eq__(self, *args):
7029 __eq__(Decorator self, Object o) -> bool
7030 __eq__(Decorator self, Decorator o) -> bool
7031 __eq__(Decorator self, Particle o) -> bool
7033 return _IMP_kernel.Decorator___eq__(self, *args)
7036 r"""__bool__(Decorator self) -> bool"""
7037 return _IMP_kernel.Decorator___bool__(self)
7038 __swig_destroy__ = _IMP_kernel.delete_Decorator
7041 _IMP_kernel.Decorator_swigregister(Decorator)
7043 def check_particle(m, pi):
7044 r"""check_particle(Model m, ParticleIndex pi)"""
7045 return _IMP_kernel.check_particle(m, pi)
7047 r"""Proxy of C++ IMP::UnaryFunction class."""
7049 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7051 def __init__(self, *args):
7052 r"""__init__(UnaryFunction self, std::string name="UnaryFunction%1%") -> UnaryFunction"""
7053 if self.__class__ == UnaryFunction:
7057 _IMP_kernel.UnaryFunction_swiginit(self, _IMP_kernel.new_UnaryFunction(_self, *args))
7059 if self.__class__ != UnaryFunction:
7060 _director_objects.register(self)
7065 def evaluate(self, feature):
7066 r"""evaluate(UnaryFunction self, double feature) -> double"""
7067 return _IMP_kernel.UnaryFunction_evaluate(self, feature)
7069 def evaluate_with_derivative(self, feature):
7070 r"""evaluate_with_derivative(UnaryFunction self, double feature) -> IMP::DerivativePair"""
7071 return _IMP_kernel.UnaryFunction_evaluate_with_derivative(self, feature)
7072 __swig_destroy__ = _IMP_kernel.delete_UnaryFunction
7075 r"""__str__(UnaryFunction self) -> std::string"""
7076 return _IMP_kernel.UnaryFunction___str__(self)
7079 r"""__repr__(UnaryFunction self) -> std::string"""
7080 return _IMP_kernel.UnaryFunction___repr__(self)
7084 return _object_cast_to_UnaryFunction(o)
7087 def do_show(self, out):
7092 return _object_cast_to_UnaryFunction(o)
7096 """Return a JAX implementation of this UnaryFunction.
7097 Implement this method in a UnaryFunction subclass to provide
7098 an equivalent function using [JAX](https://docs.jax.dev/)
7099 that scores the provided feature value.
7101 raise NotImplementedError(
7102 f
"No JAX implementation for {self} ({type(self)})")
7104 def __disown__(self):
7106 _IMP_kernel.disown_UnaryFunction(self)
7107 return weakref.proxy(self)
7110 r"""do_destroy(UnaryFunction self)"""
7111 return _IMP_kernel.UnaryFunction_do_destroy(self)
7114 _IMP_kernel.UnaryFunction_swigregister(UnaryFunction)
7116 r"""Proxy of C++ IMP::OptimizerState class."""
7118 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7120 def __init__(self, *args):
7122 __init__(OptimizerState self, Model m, std::string name) -> OptimizerState
7123 __init__(OptimizerState self) -> OptimizerState
7125 if self.__class__ == OptimizerState:
7129 _IMP_kernel.OptimizerState_swiginit(self, _IMP_kernel.new_OptimizerState(_self, *args))
7131 if self.__class__ != OptimizerState:
7132 _director_objects.register(self)
7138 r"""update(OptimizerState self)"""
7139 return _IMP_kernel.OptimizerState_update(self)
7141 def set_is_optimizing(self, arg0):
7142 r"""set_is_optimizing(OptimizerState self, bool arg0)"""
7143 return _IMP_kernel.OptimizerState_set_is_optimizing(self, arg0)
7145 def get_optimizer(self):
7146 r"""get_optimizer(OptimizerState self) -> Optimizer"""
7147 return _IMP_kernel.OptimizerState_get_optimizer(self)
7149 def set_period(self, p):
7150 r"""set_period(OptimizerState self, unsigned int p)"""
7151 return _IMP_kernel.OptimizerState_set_period(self, p)
7153 def get_period(self):
7154 r"""get_period(OptimizerState self) -> unsigned int"""
7155 return _IMP_kernel.OptimizerState_get_period(self)
7158 r"""reset(OptimizerState self)"""
7159 return _IMP_kernel.OptimizerState_reset(self)
7161 def update_always(self):
7162 r"""update_always(OptimizerState self)"""
7163 return _IMP_kernel.OptimizerState_update_always(self)
7165 def get_number_of_updates(self):
7166 r"""get_number_of_updates(OptimizerState self) -> unsigned int"""
7167 return _IMP_kernel.OptimizerState_get_number_of_updates(self)
7169 def set_number_of_updates(self, n):
7170 r"""set_number_of_updates(OptimizerState self, unsigned int n)"""
7171 return _IMP_kernel.OptimizerState_set_number_of_updates(self, n)
7172 __swig_destroy__ = _IMP_kernel.delete_OptimizerState
7174 def do_update(self, arg0):
7175 r"""do_update(OptimizerState self, unsigned int arg0)"""
7176 return _IMP_kernel.OptimizerState_do_update(self, arg0)
7178 def do_set_is_optimizing(self, arg0):
7179 r"""do_set_is_optimizing(OptimizerState self, bool arg0)"""
7180 return _IMP_kernel.OptimizerState_do_set_is_optimizing(self, arg0)
7182 def do_get_inputs(self):
7183 r"""do_get_inputs(OptimizerState self) -> IMP::ModelObjectsTemp"""
7184 return _IMP_kernel.OptimizerState_do_get_inputs(self)
7186 def do_get_outputs(self):
7187 r"""do_get_outputs(OptimizerState self) -> IMP::ModelObjectsTemp"""
7188 return _IMP_kernel.OptimizerState_do_get_outputs(self)
7191 r"""__str__(OptimizerState self) -> std::string"""
7192 return _IMP_kernel.OptimizerState___str__(self)
7195 r"""__repr__(OptimizerState self) -> std::string"""
7196 return _IMP_kernel.OptimizerState___repr__(self)
7200 return _object_cast_to_OptimizerState(o)
7203 def do_show(self, out):
7208 return _object_cast_to_OptimizerState(o)
7211 def _get_jax(self, state_index):
7212 """Add JAX support for this OptimizerState.
7214 Each OptimizerState must explicitly support how it is going to
7215 be called when the Optimizer is run via JAX.
7217 OptimizerStates can run as traditional IMP CPU code
7218 on the IMP Model object, in which case None should be returned here.
7219 The Optimizer will sync any necessary information from JAX back
7220 with the IMP Model before calling the OptimizerState. However,
7221 the OptimizerState is not permitted to modify the Model; any
7222 changes will not be propagated back to the Optimizer.
7223 (For example, a thermostat which tries to change particle
7224 velocities will not function correctly.)
7226 Alternatively, a pure JAX implementation can be provided.
7227 See _wrap_jax for more information.
7229 raise NotImplementedError(
7230 f
"No JAX implementation for {self} ({type(self)})")
7232 def _wrap_jax(self, init_func, apply_func):
7233 """Create the return value for _get_jax.
7234 Use this method in _get_jax() to wrap the JAX function
7235 with other OptimizerState-specific information.
7237 @param init_func a JAX function which, given a JAX Optimizer,
7238 does any necessary setup and returns a (possibly modified)
7239 JAX Optimizer. If any OptimizerState-specific
7240 persistent state is needed, it can be stored in
7241 `opt.optimizer_states[state_index]` and later retrieved or
7242 modified in apply_func.
7243 @param apply_func a JAX function which, given a JAX Optimizer,
7244 does the JAX equivalent of do_update() and returns a new
7247 from IMP._jax_util
import JAXOptimizerStateInfo
7248 return JAXOptimizerStateInfo(self, init_func, apply_func)
7250 def __disown__(self):
7252 _IMP_kernel.disown_OptimizerState(self)
7253 return weakref.proxy(self)
7256 r"""do_destroy(OptimizerState self)"""
7257 return _IMP_kernel.OptimizerState_do_destroy(self)
7259 def handle_set_has_required_score_states(self, arg0):
7260 r"""handle_set_has_required_score_states(OptimizerState self, bool arg0)"""
7261 return _IMP_kernel.OptimizerState_handle_set_has_required_score_states(self, arg0)
7263 def do_get_interactions(self):
7264 r"""do_get_interactions(OptimizerState self) -> IMP::ModelObjectsTemps"""
7265 return _IMP_kernel.OptimizerState_do_get_interactions(self)
7268 _IMP_kernel.OptimizerState_swigregister(OptimizerState)
7270 r"""Proxy of C++ IMP::Refiner class."""
7272 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7274 def __init__(self, *args):
7275 r"""__init__(Refiner self, std::string name="Refiner %1%", bool is_by_ref=False) -> Refiner"""
7276 if self.__class__ == Refiner:
7280 _IMP_kernel.Refiner_swiginit(self, _IMP_kernel.new_Refiner(_self, *args))
7282 if self.__class__ != Refiner:
7283 _director_objects.register(self)
7288 def get_can_refine(self, arg0):
7289 r"""get_can_refine(Refiner self, Particle arg0) -> bool"""
7290 return _IMP_kernel.Refiner_get_can_refine(self, arg0)
7292 def get_refined_indexes(self, m, pi):
7293 r"""get_refined_indexes(Refiner self, Model m, ParticleIndex pi) -> IMP::ParticleIndexes"""
7294 return _IMP_kernel.Refiner_get_refined_indexes(self, m, pi)
7296 def get_refined_indexes_by_ref(self, m, pi):
7297 r"""get_refined_indexes_by_ref(Refiner self, Model m, ParticleIndex pi) -> IMP::ParticleIndexes const &"""
7298 return _IMP_kernel.Refiner_get_refined_indexes_by_ref(self, m, pi)
7300 def get_is_by_ref_supported(self):
7301 r"""get_is_by_ref_supported(Refiner self) -> bool"""
7302 return _IMP_kernel.Refiner_get_is_by_ref_supported(self)
7304 def get_refined(self, *args):
7306 get_refined(Refiner self, Particle a) -> IMP::ParticlesTemp const
7307 get_refined(Refiner self, Particle a, unsigned int i) -> Particle
7309 return _IMP_kernel.Refiner_get_refined(self, *args)
7311 def get_number_of_refined(self, a):
7312 r"""get_number_of_refined(Refiner self, Particle a) -> unsigned int"""
7313 return _IMP_kernel.Refiner_get_number_of_refined(self, a)
7316 r"""__str__(Refiner self) -> std::string"""
7317 return _IMP_kernel.Refiner___str__(self)
7320 r"""__repr__(Refiner self) -> std::string"""
7321 return _IMP_kernel.Refiner___repr__(self)
7325 return _object_cast_to_Refiner(o)
7328 def do_show(self, out):
7333 return _object_cast_to_Refiner(o)
7335 __swig_destroy__ = _IMP_kernel.delete_Refiner
7336 def __disown__(self):
7338 _IMP_kernel.disown_Refiner(self)
7339 return weakref.proxy(self)
7341 def do_get_inputs(self, m, pis):
7342 r"""do_get_inputs(Refiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7343 return _IMP_kernel.Refiner_do_get_inputs(self, m, pis)
7346 r"""do_destroy(Refiner self)"""
7347 return _IMP_kernel.Refiner_do_destroy(self)
7350 _IMP_kernel.Refiner_swigregister(Refiner)
7352 r"""Proxy of C++ IMP::Optimizer class."""
7354 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7356 def set_is_optimizing_states(self, tf):
7357 r"""set_is_optimizing_states(Optimizer self, bool tf)"""
7358 return _IMP_kernel.Optimizer_set_is_optimizing_states(self, tf)
7360 def get_optimizer_state_inputs(self):
7361 r"""get_optimizer_state_inputs(Optimizer self) -> IMP::ModelObjectsTemp"""
7362 return _IMP_kernel.Optimizer_get_optimizer_state_inputs(self)
7364 def do_get_inputs(self):
7365 r"""do_get_inputs(Optimizer self) -> IMP::ModelObjectsTemp"""
7366 return _IMP_kernel.Optimizer_do_get_inputs(self)
7368 def do_get_outputs(self):
7369 r"""do_get_outputs(Optimizer self) -> IMP::ModelObjectsTemp"""
7370 return _IMP_kernel.Optimizer_do_get_outputs(self)
7372 def __init__(self, *args):
7374 __init__(Optimizer self, Model m, std::string name="Optimizer %1%") -> Optimizer
7375 __init__(Optimizer self) -> Optimizer
7377 if self.__class__ == Optimizer:
7381 _IMP_kernel.Optimizer_swiginit(self, _IMP_kernel.new_Optimizer(_self, *args))
7383 if self.__class__ != Optimizer:
7384 _director_objects.register(self)
7389 def optimize(self, max_steps):
7390 r"""optimize(Optimizer self, unsigned int max_steps) -> double"""
7391 return _IMP_kernel.Optimizer_optimize(self, max_steps)
7393 def set_stop_on_good_score(self, tf):
7394 r"""set_stop_on_good_score(Optimizer self, bool tf)"""
7395 return _IMP_kernel.Optimizer_set_stop_on_good_score(self, tf)
7397 def get_stop_on_good_score(self):
7398 r"""get_stop_on_good_score(Optimizer self) -> bool"""
7399 return _IMP_kernel.Optimizer_get_stop_on_good_score(self)
7401 def get_last_score(self):
7402 r"""get_last_score(Optimizer self) -> double"""
7403 return _IMP_kernel.Optimizer_get_last_score(self)
7405 def get_scoring_function(self):
7406 r"""get_scoring_function(Optimizer self) -> ScoringFunction"""
7407 return _IMP_kernel.Optimizer_get_scoring_function(self)
7408 def __get_optimizer_states(self):
return _list_util.VarList(getdimfunc=self.get_number_of_optimizer_states, getfunc=self.get_optimizer_state, erasefunc=self.erase_optimizer_state, appendfunc=self.add_optimizer_state, extendfunc=self.add_optimizer_states, clearfunc=self.clear_optimizer_states, indexfunc=self._python_index_optimizer_state)
7409 def __set_optimizer_states(self, obj): _list_util.set_varlist(self.optimizer_states, obj)
7410 def __del_optimizer_states(self): _list_util.del_varlist(self.optimizer_states)
7411 optimizer_states = property(__get_optimizer_states, __set_optimizer_states, __del_optimizer_states, doc=
"List of ##ucnames")
7413 def remove_optimizer_state(self, d):
7414 r"""remove_optimizer_state(Optimizer self, OptimizerState d)"""
7415 return _IMP_kernel.Optimizer_remove_optimizer_state(self, d)
7417 def _python_index_optimizer_state(self, d, start, stop):
7418 r"""_python_index_optimizer_state(Optimizer self, OptimizerState d, unsigned int start, unsigned int stop) -> unsigned int"""
7419 return _IMP_kernel.Optimizer__python_index_optimizer_state(self, d, start, stop)
7421 def remove_optimizer_states(self, d):
7422 r"""remove_optimizer_states(Optimizer self, IMP::OptimizerStates const & d)"""
7423 return _IMP_kernel.Optimizer_remove_optimizer_states(self, d)
7425 def set_optimizer_states(self, ps):
7426 r"""set_optimizer_states(Optimizer self, IMP::OptimizerStates const & ps)"""
7427 return _IMP_kernel.Optimizer_set_optimizer_states(self, ps)
7429 def set_optimizer_states_order(self, objs):
7430 r"""set_optimizer_states_order(Optimizer self, IMP::OptimizerStates const & objs)"""
7431 return _IMP_kernel.Optimizer_set_optimizer_states_order(self, objs)
7433 def add_optimizer_state(self, obj):
7434 r"""add_optimizer_state(Optimizer self, OptimizerState obj) -> unsigned int"""
7435 return _IMP_kernel.Optimizer_add_optimizer_state(self, obj)
7437 def add_optimizer_states(self, objs):
7438 r"""add_optimizer_states(Optimizer self, IMP::OptimizerStates const & objs)"""
7439 return _IMP_kernel.Optimizer_add_optimizer_states(self, objs)
7441 def clear_optimizer_states(self):
7442 r"""clear_optimizer_states(Optimizer self)"""
7443 return _IMP_kernel.Optimizer_clear_optimizer_states(self)
7445 def get_number_of_optimizer_states(self):
7446 r"""get_number_of_optimizer_states(Optimizer self) -> unsigned int"""
7447 return _IMP_kernel.Optimizer_get_number_of_optimizer_states(self)
7449 def get_has_optimizer_states(self):
7450 r"""get_has_optimizer_states(Optimizer self) -> bool"""
7451 return _IMP_kernel.Optimizer_get_has_optimizer_states(self)
7453 def get_optimizer_state(self, i):
7454 r"""get_optimizer_state(Optimizer self, unsigned int i) -> OptimizerState"""
7455 return _IMP_kernel.Optimizer_get_optimizer_state(self, i)
7457 def get_optimizer_states(self):
7458 r"""get_optimizer_states(Optimizer self) -> IMP::OptimizerStates"""
7459 return _IMP_kernel.Optimizer_get_optimizer_states(self)
7461 def erase_optimizer_state(self, i):
7462 r"""erase_optimizer_state(Optimizer self, unsigned int i)"""
7463 return _IMP_kernel.Optimizer_erase_optimizer_state(self, i)
7465 def reserve_optimizer_states(self, sz):
7466 r"""reserve_optimizer_states(Optimizer self, unsigned int sz)"""
7467 return _IMP_kernel.Optimizer_reserve_optimizer_states(self, sz)
7469 def set_scoring_function(self, sf):
7470 r"""set_scoring_function(Optimizer self, _ScoringFunctionAdaptor sf)"""
7471 return _IMP_kernel.Optimizer_set_scoring_function(self, sf)
7472 __swig_destroy__ = _IMP_kernel.delete_Optimizer
7474 r"""__del__(Optimizer self)"""
7476 _director_objects.cleanup()
7482 def do_optimize(self, ns):
7483 r"""do_optimize(Optimizer self, unsigned int ns) -> double"""
7484 return _IMP_kernel.Optimizer_do_optimize(self, ns)
7486 def update_states(self):
7487 r"""update_states(Optimizer self)"""
7488 return _IMP_kernel.Optimizer_update_states(self)
7491 r"""__str__(Optimizer self) -> std::string"""
7492 return _IMP_kernel.Optimizer___str__(self)
7495 r"""__repr__(Optimizer self) -> std::string"""
7496 return _IMP_kernel.Optimizer___repr__(self)
7500 return _object_cast_to_Optimizer(o)
7503 def do_show(self, out):
7508 return _object_cast_to_Optimizer(o)
7510 def __disown__(self):
7512 _IMP_kernel.disown_Optimizer(self)
7513 return weakref.proxy(self)
7516 r"""do_destroy(Optimizer self)"""
7517 return _IMP_kernel.Optimizer_do_destroy(self)
7519 def handle_set_has_required_score_states(self, arg0):
7520 r"""handle_set_has_required_score_states(Optimizer self, bool arg0)"""
7521 return _IMP_kernel.Optimizer_handle_set_has_required_score_states(self, arg0)
7523 def do_get_interactions(self):
7524 r"""do_get_interactions(Optimizer self) -> IMP::ModelObjectsTemps"""
7525 return _IMP_kernel.Optimizer_do_get_interactions(self)
7528 _IMP_kernel.Optimizer_swigregister(Optimizer)
7530 r"""Proxy of C++ IMP::AttributeOptimizer class."""
7532 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7534 def __init__(self, *args):
7536 __init__(AttributeOptimizer self, Model m, std::string name="Optimizer %1%") -> AttributeOptimizer
7537 __init__(AttributeOptimizer self) -> AttributeOptimizer
7539 if self.__class__ == AttributeOptimizer:
7543 _IMP_kernel.AttributeOptimizer_swiginit(self, _IMP_kernel.new_AttributeOptimizer(_self, *args))
7545 if self.__class__ != AttributeOptimizer:
7546 _director_objects.register(self)
7551 def get_optimized_attributes(self):
7552 r"""get_optimized_attributes(AttributeOptimizer self) -> IMP::FloatIndexes"""
7553 return _IMP_kernel.AttributeOptimizer_get_optimized_attributes(self)
7555 def set_value(self, fi, v):
7556 r"""set_value(AttributeOptimizer self, FloatIndex fi, double v)"""
7557 return _IMP_kernel.AttributeOptimizer_set_value(self, fi, v)
7559 def get_value(self, fi):
7560 r"""get_value(AttributeOptimizer self, FloatIndex fi) -> IMP::Float"""
7561 return _IMP_kernel.AttributeOptimizer_get_value(self, fi)
7563 def get_derivative(self, fi):
7564 r"""get_derivative(AttributeOptimizer self, FloatIndex fi) -> IMP::Float"""
7565 return _IMP_kernel.AttributeOptimizer_get_derivative(self, fi)
7567 def get_width(self, k):
7568 r"""get_width(AttributeOptimizer self, FloatKey k) -> double"""
7569 return _IMP_kernel.AttributeOptimizer_get_width(self, k)
7571 def set_scaled_value(self, fi, v):
7572 r"""set_scaled_value(AttributeOptimizer self, FloatIndex fi, IMP::Float v)"""
7573 return _IMP_kernel.AttributeOptimizer_set_scaled_value(self, fi, v)
7575 def get_scaled_value(self, fi):
7576 r"""get_scaled_value(AttributeOptimizer self, FloatIndex fi) -> double"""
7577 return _IMP_kernel.AttributeOptimizer_get_scaled_value(self, fi)
7579 def get_scaled_derivative(self, fi):
7580 r"""get_scaled_derivative(AttributeOptimizer self, FloatIndex fi) -> double"""
7581 return _IMP_kernel.AttributeOptimizer_get_scaled_derivative(self, fi)
7583 def clear_range_cache(self):
7584 r"""clear_range_cache(AttributeOptimizer self)"""
7585 return _IMP_kernel.AttributeOptimizer_clear_range_cache(self)
7588 r"""__str__(AttributeOptimizer self) -> std::string"""
7589 return _IMP_kernel.AttributeOptimizer___str__(self)
7592 r"""__repr__(AttributeOptimizer self) -> std::string"""
7593 return _IMP_kernel.AttributeOptimizer___repr__(self)
7597 return _object_cast_to_AttributeOptimizer(o)
7600 def do_show(self, out):
7605 return _object_cast_to_AttributeOptimizer(o)
7607 __swig_destroy__ = _IMP_kernel.delete_AttributeOptimizer
7608 def __disown__(self):
7610 _IMP_kernel.disown_AttributeOptimizer(self)
7611 return weakref.proxy(self)
7614 r"""do_destroy(AttributeOptimizer self)"""
7615 return _IMP_kernel.AttributeOptimizer_do_destroy(self)
7617 def handle_set_has_required_score_states(self, arg0):
7618 r"""handle_set_has_required_score_states(AttributeOptimizer self, bool arg0)"""
7619 return _IMP_kernel.AttributeOptimizer_handle_set_has_required_score_states(self, arg0)
7621 def do_get_inputs(self):
7622 r"""do_get_inputs(AttributeOptimizer self) -> IMP::ModelObjectsTemp"""
7623 return _IMP_kernel.AttributeOptimizer_do_get_inputs(self)
7625 def do_get_outputs(self):
7626 r"""do_get_outputs(AttributeOptimizer self) -> IMP::ModelObjectsTemp"""
7627 return _IMP_kernel.AttributeOptimizer_do_get_outputs(self)
7629 def do_get_interactions(self):
7630 r"""do_get_interactions(AttributeOptimizer self) -> IMP::ModelObjectsTemps"""
7631 return _IMP_kernel.AttributeOptimizer_do_get_interactions(self)
7633 def do_optimize(self, ns):
7634 r"""do_optimize(AttributeOptimizer self, unsigned int ns) -> double"""
7635 return _IMP_kernel.AttributeOptimizer_do_optimize(self, ns)
7638 _IMP_kernel.AttributeOptimizer_swigregister(AttributeOptimizer)
7640 r"""Proxy of C++ IMP::ConfigurationSet class."""
7642 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7644 def __init__(self, *args):
7645 r"""__init__(ConfigurationSet self, Model m, std::string name="ConfigurationSet %1%") -> ConfigurationSet"""
7646 _IMP_kernel.ConfigurationSet_swiginit(self, _IMP_kernel.new_ConfigurationSet(*args))
7648 def save_configuration(self):
7649 r"""save_configuration(ConfigurationSet self)"""
7650 return _IMP_kernel.ConfigurationSet_save_configuration(self)
7652 def get_number_of_configurations(self):
7653 r"""get_number_of_configurations(ConfigurationSet self) -> unsigned int"""
7654 return _IMP_kernel.ConfigurationSet_get_number_of_configurations(self)
7656 def load_configuration(self, i):
7657 r"""load_configuration(ConfigurationSet self, int i)"""
7658 return _IMP_kernel.ConfigurationSet_load_configuration(self, i)
7660 def remove_configuration(self, i):
7661 r"""remove_configuration(ConfigurationSet self, unsigned int i)"""
7662 return _IMP_kernel.ConfigurationSet_remove_configuration(self, i)
7664 def get_model(self):
7665 r"""get_model(ConfigurationSet self) -> Model"""
7666 return _IMP_kernel.ConfigurationSet_get_model(self)
7669 r"""get_version_info(ConfigurationSet self) -> VersionInfo"""
7670 return _IMP_kernel.ConfigurationSet_get_version_info(self)
7671 __swig_destroy__ = _IMP_kernel.delete_ConfigurationSet
7674 r"""__str__(ConfigurationSet self) -> std::string"""
7675 return _IMP_kernel.ConfigurationSet___str__(self)
7678 r"""__repr__(ConfigurationSet self) -> std::string"""
7679 return _IMP_kernel.ConfigurationSet___repr__(self)
7683 return _object_cast_to_ConfigurationSet(o)
7687 _IMP_kernel.ConfigurationSet_swigregister(ConfigurationSet)
7689 r"""Proxy of C++ IMP::SaveToConfigurationSetOptimizerState class."""
7691 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7693 def __init__(self, cs):
7694 r"""__init__(SaveToConfigurationSetOptimizerState self, ConfigurationSet cs) -> SaveToConfigurationSetOptimizerState"""
7695 _IMP_kernel.SaveToConfigurationSetOptimizerState_swiginit(self, _IMP_kernel.new_SaveToConfigurationSetOptimizerState(cs))
7698 r"""get_version_info(SaveToConfigurationSetOptimizerState self) -> VersionInfo"""
7699 return _IMP_kernel.SaveToConfigurationSetOptimizerState_get_version_info(self)
7700 __swig_destroy__ = _IMP_kernel.delete_SaveToConfigurationSetOptimizerState
7703 r"""__str__(SaveToConfigurationSetOptimizerState self) -> std::string"""
7704 return _IMP_kernel.SaveToConfigurationSetOptimizerState___str__(self)
7707 r"""__repr__(SaveToConfigurationSetOptimizerState self) -> std::string"""
7708 return _IMP_kernel.SaveToConfigurationSetOptimizerState___repr__(self)
7712 return _object_cast_to_SaveToConfigurationSetOptimizerState(o)
7716 _IMP_kernel.SaveToConfigurationSetOptimizerState_swigregister(SaveToConfigurationSetOptimizerState)
7718 r"""Proxy of C++ IMP::Configuration class."""
7720 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7722 def __init__(self, *args):
7724 __init__(Configuration self, Model m, std::string name="Configuration %1%") -> Configuration
7725 __init__(Configuration self, Model m, Configuration base, std::string name="Configuration %1%") -> Configuration
7726 __init__(Configuration self) -> Configuration
7728 _IMP_kernel.Configuration_swiginit(self, _IMP_kernel.new_Configuration(*args))
7730 def load_configuration(self):
7731 r"""load_configuration(Configuration self)"""
7732 return _IMP_kernel.Configuration_load_configuration(self)
7734 def swap_configuration(self):
7735 r"""swap_configuration(Configuration self)"""
7736 return _IMP_kernel.Configuration_swap_configuration(self)
7739 r"""get_version_info(Configuration self) -> VersionInfo"""
7740 return _IMP_kernel.Configuration_get_version_info(self)
7741 __swig_destroy__ = _IMP_kernel.delete_Configuration
7744 r"""__str__(Configuration self) -> std::string"""
7745 return _IMP_kernel.Configuration___str__(self)
7748 r"""__repr__(Configuration self) -> std::string"""
7749 return _IMP_kernel.Configuration___repr__(self)
7753 return _object_cast_to_Configuration(o)
7756 def _get_as_binary(self):
7757 r"""_get_as_binary(Configuration self) -> PyObject *"""
7758 return _IMP_kernel.Configuration__get_as_binary(self)
7760 def _set_from_binary(self, p):
7761 r"""_set_from_binary(Configuration self, PyObject * p)"""
7762 return _IMP_kernel.Configuration__set_from_binary(self, p)
7764 def __getstate__(self):
7765 p = self._get_as_binary()
7766 if len(self.__dict__) > 1:
7767 d = self.__dict__.copy()
7772 def __setstate__(self, p):
7773 if not hasattr(self,
'this'):
7775 if isinstance(p, tuple):
7777 self.__dict__.update(d)
7778 return self._set_from_binary(p)
7782 _IMP_kernel.Configuration_swigregister(Configuration)
7784 r"""Proxy of C++ IMP::Sampler class."""
7786 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7788 def __init__(self, *args):
7789 r"""__init__(Sampler self, Model m, std::string name="Sampler %1%") -> Sampler"""
7790 if self.__class__ == Sampler:
7794 _IMP_kernel.Sampler_swiginit(self, _IMP_kernel.new_Sampler(_self, *args))
7796 if self.__class__ != Sampler:
7797 _director_objects.register(self)
7802 def create_sample(self):
7803 r"""create_sample(Sampler self) -> ConfigurationSet"""
7804 return _IMP_kernel.Sampler_create_sample(self)
7806 def get_scoring_function(self):
7807 r"""get_scoring_function(Sampler self) -> ScoringFunction"""
7808 return _IMP_kernel.Sampler_get_scoring_function(self)
7810 def set_scoring_function(self, sf):
7811 r"""set_scoring_function(Sampler self, _ScoringFunctionAdaptor sf)"""
7812 return _IMP_kernel.Sampler_set_scoring_function(self, sf)
7814 def get_model(self):
7815 r"""get_model(Sampler self) -> Model"""
7816 return _IMP_kernel.Sampler_get_model(self)
7818 def do_sample(self):
7819 r"""do_sample(Sampler self) -> ConfigurationSet"""
7820 return _IMP_kernel.Sampler_do_sample(self)
7821 __swig_destroy__ = _IMP_kernel.delete_Sampler
7824 r"""__str__(Sampler self) -> std::string"""
7825 return _IMP_kernel.Sampler___str__(self)
7828 r"""__repr__(Sampler self) -> std::string"""
7829 return _IMP_kernel.Sampler___repr__(self)
7833 return _object_cast_to_Sampler(o)
7836 def do_show(self, out):
7841 return _object_cast_to_Sampler(o)
7843 def __disown__(self):
7845 _IMP_kernel.disown_Sampler(self)
7846 return weakref.proxy(self)
7849 r"""do_destroy(Sampler self)"""
7850 return _IMP_kernel.Sampler_do_destroy(self)
7853 _IMP_kernel.Sampler_swigregister(Sampler)
7855 r"""Proxy of C++ IMP::PairModifier class."""
7857 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7859 def __init__(self, *args):
7860 r"""__init__(PairModifier self, std::string name="PairModifier %1%") -> PairModifier"""
7861 if self.__class__ == PairModifier:
7865 _IMP_kernel.PairModifier_swiginit(self, _IMP_kernel.new_PairModifier(_self, *args))
7867 if self.__class__ != PairModifier:
7868 _director_objects.register(self)
7873 def apply_index(self, m, v):
7874 r"""apply_index(PairModifier self, Model m, IMP::ParticleIndexPair const & v)"""
7875 return _IMP_kernel.PairModifier_apply_index(self, m, v)
7877 def apply_indexes(self, m, o, lower_bound, upper_bound):
7878 r"""apply_indexes(PairModifier self, Model m, IMP::ParticleIndexPairs const & o, unsigned int lower_bound, unsigned int upper_bound)"""
7879 return _IMP_kernel.PairModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
7881 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
7882 r"""apply_indexes_moved(PairModifier self, Model m, IMP::ParticleIndexPairs const & o, unsigned int lower_bound, unsigned int upper_bound, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7883 return _IMP_kernel.PairModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
7886 r"""__str__(PairModifier self) -> std::string"""
7887 return _IMP_kernel.PairModifier___str__(self)
7890 r"""__repr__(PairModifier self) -> std::string"""
7891 return _IMP_kernel.PairModifier___repr__(self)
7895 return _object_cast_to_PairModifier(o)
7898 def do_show(self, out):
7903 return _object_cast_to_PairModifier(o)
7905 __swig_destroy__ = _IMP_kernel.delete_PairModifier
7906 def __disown__(self):
7908 _IMP_kernel.disown_PairModifier(self)
7909 return weakref.proxy(self)
7911 def do_get_inputs(self, m, pis):
7912 r"""do_get_inputs(PairModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7913 return _IMP_kernel.PairModifier_do_get_inputs(self, m, pis)
7915 def do_get_outputs(self, m, pis):
7916 r"""do_get_outputs(PairModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7917 return _IMP_kernel.PairModifier_do_get_outputs(self, m, pis)
7920 r"""do_destroy(PairModifier self)"""
7921 return _IMP_kernel.PairModifier_do_destroy(self)
7924 _IMP_kernel.PairModifier_swigregister(PairModifier)
7926 r"""Proxy of C++ IMP::PairScore class."""
7928 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7930 def __init__(self, *args):
7931 r"""__init__(PairScore self, std::string name="PairScore %1%") -> PairScore"""
7932 if self.__class__ == PairScore:
7936 _IMP_kernel.PairScore_swiginit(self, _IMP_kernel.new_PairScore(_self, *args))
7938 if self.__class__ != PairScore:
7939 _director_objects.register(self)
7944 def evaluate_index(self, m, vt, da):
7945 r"""evaluate_index(PairScore self, Model m, IMP::ParticleIndexPair const & vt, DerivativeAccumulator da) -> double"""
7946 return _IMP_kernel.PairScore_evaluate_index(self, m, vt, da)
7948 def check_indexes(self, m, pis):
7949 r"""check_indexes(PairScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
7950 return _IMP_kernel.PairScore_check_indexes(self, m, pis)
7952 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
7953 r"""evaluate_indexes(PairScore self, Model m, IMP::ParticleIndexPairs const & o, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7954 return _IMP_kernel.PairScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
7956 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7957 r"""evaluate_indexes_scores(PairScore self, Model m, IMP::ParticleIndexPairs const & o, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7958 return _IMP_kernel.PairScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
7960 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
7961 r"""evaluate_indexes_delta(PairScore self, Model m, IMP::ParticleIndexPairs const & o, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
7962 return _IMP_kernel.PairScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
7964 def evaluate_if_good_index(self, m, vt, da, max):
7965 r"""evaluate_if_good_index(PairScore self, Model m, IMP::ParticleIndexPair const & vt, DerivativeAccumulator da, double max) -> double"""
7966 return _IMP_kernel.PairScore_evaluate_if_good_index(self, m, vt, da, max)
7968 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7969 r"""evaluate_if_good_indexes(PairScore self, Model m, IMP::ParticleIndexPairs const & o, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
7970 return _IMP_kernel.PairScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
7972 def create_current_decomposition(self, m, vt):
7973 r"""create_current_decomposition(PairScore self, Model m, IMP::ParticleIndexPair const & vt) -> IMP::Restraints"""
7974 return _IMP_kernel.PairScore_create_current_decomposition(self, m, vt)
7976 def do_create_current_decomposition(self, m, vt):
7977 r"""do_create_current_decomposition(PairScore self, Model m, IMP::ParticleIndexPair const & vt) -> IMP::Restraints"""
7978 return _IMP_kernel.PairScore_do_create_current_decomposition(self, m, vt)
7979 __swig_destroy__ = _IMP_kernel.delete_PairScore
7982 r"""__str__(PairScore self) -> std::string"""
7983 return _IMP_kernel.PairScore___str__(self)
7986 r"""__repr__(PairScore self) -> std::string"""
7987 return _IMP_kernel.PairScore___repr__(self)
7991 return _object_cast_to_PairScore(o)
7994 def do_show(self, out):
7999 return _object_cast_to_PairScore(o)
8002 def _wrap_jax(self, m, score_func, keys=None):
8003 """Create the return value for _get_jax.
8004 Use this method in _get_jax() to wrap the JAX scoring function
8005 with other score-specific information.
8007 @param m The IMP.Model that the score will act on.
8008 @param score_func A function implemented using JAX that takes
8009 one argument (the current JAX Model) and returns the total
8011 @param keys Model attributes used by the PairScore.
8012 See IMP::Restraint::_wrap_jax.
8014 from IMP._jax_util
import JAXScoreInfo
8015 return JAXScoreInfo(m, score_func=score_func, keys=keys)
8017 def _get_jax(self, m, indexes, space):
8018 """Return a JAX implementation of this PairScore.
8019 Implement this method in a PairScore subclass to provide
8020 an equivalent function using [JAX](https://docs.jax.dev/)
8021 that scores the current JAX Model with a given set of
8022 ParticlePairIndexes. See also _wrap_jax.
8024 @param m The IMP.Model that the score will act on.
8025 @param indexes The ParticlePairIndexes that the score will act on.
8026 @param space The space in which the score is evaluated
8027 (e.g. a periodic box). See IMP._jax_util.Space.
8029 raise NotImplementedError(
8030 f
"No JAX implementation for {self} ({type(self)})")
8032 def __disown__(self):
8034 _IMP_kernel.disown_PairScore(self)
8035 return weakref.proxy(self)
8037 def do_get_inputs(self, m, pis):
8038 r"""do_get_inputs(PairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8039 return _IMP_kernel.PairScore_do_get_inputs(self, m, pis)
8042 r"""do_destroy(PairScore self)"""
8043 return _IMP_kernel.PairScore_do_destroy(self)
8046 _IMP_kernel.PairScore_swigregister(PairScore)
8048 r"""Proxy of C++ IMP::PairPredicate class."""
8050 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8052 def __init__(self, *args):
8053 r"""__init__(PairPredicate self, std::string name="PairPredicate %1%") -> PairPredicate"""
8054 if self.__class__ == PairPredicate:
8058 _IMP_kernel.PairPredicate_swiginit(self, _IMP_kernel.new_PairPredicate(_self, *args))
8060 if self.__class__ != PairPredicate:
8061 _director_objects.register(self)
8066 def setup_for_get_value_index_in_batch(self, arg0):
8067 r"""setup_for_get_value_index_in_batch(PairPredicate self, Model arg0)"""
8068 return _IMP_kernel.PairPredicate_setup_for_get_value_index_in_batch(self, arg0)
8070 def get_value_index_in_batch(self, m, vt):
8071 r"""get_value_index_in_batch(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int"""
8072 return _IMP_kernel.PairPredicate_get_value_index_in_batch(self, m, vt)
8074 def __call__(self, m, vt):
8075 r"""__call__(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int"""
8076 return _IMP_kernel.PairPredicate___call__(self, m, vt)
8078 def get_value_index(self, *args):
8080 get_value_index(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int
8081 get_value_index(PairPredicate self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
8083 return _IMP_kernel.PairPredicate_get_value_index(self, *args)
8084 __swig_destroy__ = _IMP_kernel.delete_PairPredicate
8087 r"""__str__(PairPredicate self) -> std::string"""
8088 return _IMP_kernel.PairPredicate___str__(self)
8091 r"""__repr__(PairPredicate self) -> std::string"""
8092 return _IMP_kernel.PairPredicate___repr__(self)
8096 return _object_cast_to_PairPredicate(o)
8099 def do_show(self, out):
8104 return _object_cast_to_PairPredicate(o)
8106 def __disown__(self):
8108 _IMP_kernel.disown_PairPredicate(self)
8109 return weakref.proxy(self)
8111 def do_get_inputs(self, m, pis):
8112 r"""do_get_inputs(PairPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8113 return _IMP_kernel.PairPredicate_do_get_inputs(self, m, pis)
8116 r"""do_destroy(PairPredicate self)"""
8117 return _IMP_kernel.PairPredicate_do_destroy(self)
8120 _IMP_kernel.PairPredicate_swigregister(PairPredicate)
8122 r"""Proxy of C++ IMP::PairContainer class."""
8124 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8126 def apply_generic(self, m):
8127 r"""apply_generic(PairContainer self, PairModifier m)"""
8128 return _IMP_kernel.PairContainer_apply_generic(self, m)
8130 def apply_generic_moved(self, m, moved_pis, reset_pis):
8131 r"""apply_generic_moved(PairContainer self, PairModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8132 return _IMP_kernel.PairContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
8134 def apply(self, sm):
8135 r"""apply(PairContainer self, PairModifier sm)"""
8136 return _IMP_kernel.PairContainer_apply(self, sm)
8138 def apply_moved(self, sm, moved_pis, reset_pis):
8139 r"""apply_moved(PairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8140 return _IMP_kernel.PairContainer_apply_moved(self, sm, moved_pis, reset_pis)
8142 def get_range_indexes(self):
8143 r"""get_range_indexes(PairContainer self) -> IMP::ParticleIndexPairs"""
8144 return _IMP_kernel.PairContainer_get_range_indexes(self)
8146 def get_contents(self):
8147 r"""get_contents(PairContainer self) -> IMP::ParticleIndexPairs const &"""
8148 return _IMP_kernel.PairContainer_get_contents(self)
8151 r"""get_indexes(PairContainer self) -> IMP::ParticleIndexPairs"""
8152 return _IMP_kernel.PairContainer_get_indexes(self)
8154 def get(self, *args):
8156 get(PairContainer self) -> IMP::ParticlePairsTemp
8157 get(PairContainer self, unsigned int i) -> IMP::ParticlePair
8159 return _IMP_kernel.PairContainer_get(self, *args)
8161 def get_number(self):
8162 r"""get_number(PairContainer self) -> unsigned int"""
8163 return _IMP_kernel.PairContainer_get_number(self)
8165 def __init__(self, *args):
8167 __init__(PairContainer self, Model m, std::string name="PairContainer %1%") -> PairContainer
8168 __init__(PairContainer self) -> PairContainer
8170 if self.__class__ == PairContainer:
8174 _IMP_kernel.PairContainer_swiginit(self, _IMP_kernel.new_PairContainer(_self, *args))
8176 if self.__class__ != PairContainer:
8177 _director_objects.register(self)
8182 def do_apply(self, sm):
8183 r"""do_apply(PairContainer self, PairModifier sm)"""
8184 return _IMP_kernel.PairContainer_do_apply(self, sm)
8186 def do_apply_moved(self, sm, moved_pis, reset_pis):
8187 r"""do_apply_moved(PairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8188 return _IMP_kernel.PairContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
8190 def do_get_provides_access(self):
8191 r"""do_get_provides_access(PairContainer self) -> bool"""
8192 return _IMP_kernel.PairContainer_do_get_provides_access(self)
8193 __swig_destroy__ = _IMP_kernel.delete_PairContainer
8196 r"""__str__(PairContainer self) -> std::string"""
8197 return _IMP_kernel.PairContainer___str__(self)
8200 r"""__repr__(PairContainer self) -> std::string"""
8201 return _IMP_kernel.PairContainer___repr__(self)
8205 return _object_cast_to_PairContainer(o)
8208 def do_show(self, out):
8213 return _object_cast_to_PairContainer(o)
8215 def __disown__(self):
8217 _IMP_kernel.disown_PairContainer(self)
8218 return weakref.proxy(self)
8221 r"""do_destroy(PairContainer self)"""
8222 return _IMP_kernel.PairContainer_do_destroy(self)
8224 def handle_set_has_required_score_states(self, arg0):
8225 r"""handle_set_has_required_score_states(PairContainer self, bool arg0)"""
8226 return _IMP_kernel.PairContainer_handle_set_has_required_score_states(self, arg0)
8228 def do_get_inputs(self):
8229 r"""do_get_inputs(PairContainer self) -> IMP::ModelObjectsTemp"""
8230 return _IMP_kernel.PairContainer_do_get_inputs(self)
8232 def do_get_interactions(self):
8233 r"""do_get_interactions(PairContainer self) -> IMP::ModelObjectsTemps"""
8234 return _IMP_kernel.PairContainer_do_get_interactions(self)
8236 def do_get_contents_hash(self):
8237 r"""do_get_contents_hash(PairContainer self) -> std::size_t"""
8238 return _IMP_kernel.PairContainer_do_get_contents_hash(self)
8241 _IMP_kernel.PairContainer_swigregister(PairContainer)
8242 class _PairContainerAdaptor(_InputAdaptor):
8243 r"""Proxy of C++ IMP::PairContainerAdaptor class."""
8245 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8246 __repr__ = _swig_repr
8248 def __init__(self, *args):
8250 __init__(_PairContainerAdaptor self) -> _PairContainerAdaptor
8251 __init__(_PairContainerAdaptor self, PairContainer c) -> _PairContainerAdaptor
8252 __init__(_PairContainerAdaptor self, IMP::ParticlePairsTemp const & t) -> _PairContainerAdaptor
8254 _IMP_kernel._PairContainerAdaptor_swiginit(self, _IMP_kernel.new__PairContainerAdaptor(*args))
8256 def set_name_if_default(self, name):
8257 r"""set_name_if_default(_PairContainerAdaptor self, std::string name)"""
8258 return _IMP_kernel._PairContainerAdaptor_set_name_if_default(self, name)
8259 __swig_destroy__ = _IMP_kernel.delete__PairContainerAdaptor
8262 _IMP_kernel._PairContainerAdaptor_swigregister(_PairContainerAdaptor)
8264 r"""Proxy of C++ IMP::QuadModifier class."""
8266 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8268 def __init__(self, *args):
8269 r"""__init__(QuadModifier self, std::string name="QuadModifier %1%") -> QuadModifier"""
8270 if self.__class__ == QuadModifier:
8274 _IMP_kernel.QuadModifier_swiginit(self, _IMP_kernel.new_QuadModifier(_self, *args))
8276 if self.__class__ != QuadModifier:
8277 _director_objects.register(self)
8282 def apply_index(self, m, v):
8283 r"""apply_index(QuadModifier self, Model m, IMP::ParticleIndexQuad const & v)"""
8284 return _IMP_kernel.QuadModifier_apply_index(self, m, v)
8286 def apply_indexes(self, m, o, lower_bound, upper_bound):
8287 r"""apply_indexes(QuadModifier self, Model m, IMP::ParticleIndexQuads const & o, unsigned int lower_bound, unsigned int upper_bound)"""
8288 return _IMP_kernel.QuadModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
8290 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
8291 r"""apply_indexes_moved(QuadModifier self, Model m, IMP::ParticleIndexQuads const & o, unsigned int lower_bound, unsigned int upper_bound, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8292 return _IMP_kernel.QuadModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
8295 r"""__str__(QuadModifier self) -> std::string"""
8296 return _IMP_kernel.QuadModifier___str__(self)
8299 r"""__repr__(QuadModifier self) -> std::string"""
8300 return _IMP_kernel.QuadModifier___repr__(self)
8304 return _object_cast_to_QuadModifier(o)
8307 def do_show(self, out):
8312 return _object_cast_to_QuadModifier(o)
8314 __swig_destroy__ = _IMP_kernel.delete_QuadModifier
8315 def __disown__(self):
8317 _IMP_kernel.disown_QuadModifier(self)
8318 return weakref.proxy(self)
8320 def do_get_inputs(self, m, pis):
8321 r"""do_get_inputs(QuadModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8322 return _IMP_kernel.QuadModifier_do_get_inputs(self, m, pis)
8324 def do_get_outputs(self, m, pis):
8325 r"""do_get_outputs(QuadModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8326 return _IMP_kernel.QuadModifier_do_get_outputs(self, m, pis)
8329 r"""do_destroy(QuadModifier self)"""
8330 return _IMP_kernel.QuadModifier_do_destroy(self)
8333 _IMP_kernel.QuadModifier_swigregister(QuadModifier)
8335 r"""Proxy of C++ IMP::QuadScore class."""
8337 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8339 def __init__(self, *args):
8340 r"""__init__(QuadScore self, std::string name="QuadScore %1%") -> QuadScore"""
8341 if self.__class__ == QuadScore:
8345 _IMP_kernel.QuadScore_swiginit(self, _IMP_kernel.new_QuadScore(_self, *args))
8347 if self.__class__ != QuadScore:
8348 _director_objects.register(self)
8353 def evaluate_index(self, m, vt, da):
8354 r"""evaluate_index(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt, DerivativeAccumulator da) -> double"""
8355 return _IMP_kernel.QuadScore_evaluate_index(self, m, vt, da)
8357 def check_indexes(self, m, pis):
8358 r"""check_indexes(QuadScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
8359 return _IMP_kernel.QuadScore_check_indexes(self, m, pis)
8361 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
8362 r"""evaluate_indexes(QuadScore self, Model m, IMP::ParticleIndexQuads const & o, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
8363 return _IMP_kernel.QuadScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
8365 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
8366 r"""evaluate_indexes_scores(QuadScore self, Model m, IMP::ParticleIndexQuads const & o, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
8367 return _IMP_kernel.QuadScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
8369 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
8370 r"""evaluate_indexes_delta(QuadScore self, Model m, IMP::ParticleIndexQuads const & o, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
8371 return _IMP_kernel.QuadScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
8373 def evaluate_if_good_index(self, m, vt, da, max):
8374 r"""evaluate_if_good_index(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt, DerivativeAccumulator da, double max) -> double"""
8375 return _IMP_kernel.QuadScore_evaluate_if_good_index(self, m, vt, da, max)
8377 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
8378 r"""evaluate_if_good_indexes(QuadScore self, Model m, IMP::ParticleIndexQuads const & o, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
8379 return _IMP_kernel.QuadScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
8381 def create_current_decomposition(self, m, vt):
8382 r"""create_current_decomposition(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt) -> IMP::Restraints"""
8383 return _IMP_kernel.QuadScore_create_current_decomposition(self, m, vt)
8385 def do_create_current_decomposition(self, m, vt):
8386 r"""do_create_current_decomposition(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt) -> IMP::Restraints"""
8387 return _IMP_kernel.QuadScore_do_create_current_decomposition(self, m, vt)
8388 __swig_destroy__ = _IMP_kernel.delete_QuadScore
8391 r"""__str__(QuadScore self) -> std::string"""
8392 return _IMP_kernel.QuadScore___str__(self)
8395 r"""__repr__(QuadScore self) -> std::string"""
8396 return _IMP_kernel.QuadScore___repr__(self)
8400 return _object_cast_to_QuadScore(o)
8403 def do_show(self, out):
8408 return _object_cast_to_QuadScore(o)
8410 def __disown__(self):
8412 _IMP_kernel.disown_QuadScore(self)
8413 return weakref.proxy(self)
8415 def do_get_inputs(self, m, pis):
8416 r"""do_get_inputs(QuadScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8417 return _IMP_kernel.QuadScore_do_get_inputs(self, m, pis)
8420 r"""do_destroy(QuadScore self)"""
8421 return _IMP_kernel.QuadScore_do_destroy(self)
8424 _IMP_kernel.QuadScore_swigregister(QuadScore)
8426 r"""Proxy of C++ IMP::QuadPredicate class."""
8428 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8430 def __init__(self, *args):
8431 r"""__init__(QuadPredicate self, std::string name="QuadPredicate %1%") -> QuadPredicate"""
8432 if self.__class__ == QuadPredicate:
8436 _IMP_kernel.QuadPredicate_swiginit(self, _IMP_kernel.new_QuadPredicate(_self, *args))
8438 if self.__class__ != QuadPredicate:
8439 _director_objects.register(self)
8444 def setup_for_get_value_index_in_batch(self, arg0):
8445 r"""setup_for_get_value_index_in_batch(QuadPredicate self, Model arg0)"""
8446 return _IMP_kernel.QuadPredicate_setup_for_get_value_index_in_batch(self, arg0)
8448 def get_value_index_in_batch(self, m, vt):
8449 r"""get_value_index_in_batch(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int"""
8450 return _IMP_kernel.QuadPredicate_get_value_index_in_batch(self, m, vt)
8452 def __call__(self, m, vt):
8453 r"""__call__(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int"""
8454 return _IMP_kernel.QuadPredicate___call__(self, m, vt)
8456 def get_value_index(self, *args):
8458 get_value_index(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int
8459 get_value_index(QuadPredicate self, Model m, IMP::ParticleIndexQuads const & o) -> IMP::Ints
8461 return _IMP_kernel.QuadPredicate_get_value_index(self, *args)
8462 __swig_destroy__ = _IMP_kernel.delete_QuadPredicate
8465 r"""__str__(QuadPredicate self) -> std::string"""
8466 return _IMP_kernel.QuadPredicate___str__(self)
8469 r"""__repr__(QuadPredicate self) -> std::string"""
8470 return _IMP_kernel.QuadPredicate___repr__(self)
8474 return _object_cast_to_QuadPredicate(o)
8477 def do_show(self, out):
8482 return _object_cast_to_QuadPredicate(o)
8484 def __disown__(self):
8486 _IMP_kernel.disown_QuadPredicate(self)
8487 return weakref.proxy(self)
8489 def do_get_inputs(self, m, pis):
8490 r"""do_get_inputs(QuadPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8491 return _IMP_kernel.QuadPredicate_do_get_inputs(self, m, pis)
8494 r"""do_destroy(QuadPredicate self)"""
8495 return _IMP_kernel.QuadPredicate_do_destroy(self)
8498 _IMP_kernel.QuadPredicate_swigregister(QuadPredicate)
8500 r"""Proxy of C++ IMP::QuadContainer class."""
8502 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8504 def apply_generic(self, m):
8505 r"""apply_generic(QuadContainer self, QuadModifier m)"""
8506 return _IMP_kernel.QuadContainer_apply_generic(self, m)
8508 def apply_generic_moved(self, m, moved_pis, reset_pis):
8509 r"""apply_generic_moved(QuadContainer self, QuadModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8510 return _IMP_kernel.QuadContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
8512 def apply(self, sm):
8513 r"""apply(QuadContainer self, QuadModifier sm)"""
8514 return _IMP_kernel.QuadContainer_apply(self, sm)
8516 def apply_moved(self, sm, moved_pis, reset_pis):
8517 r"""apply_moved(QuadContainer self, QuadModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8518 return _IMP_kernel.QuadContainer_apply_moved(self, sm, moved_pis, reset_pis)
8520 def get_range_indexes(self):
8521 r"""get_range_indexes(QuadContainer self) -> IMP::ParticleIndexQuads"""
8522 return _IMP_kernel.QuadContainer_get_range_indexes(self)
8524 def get_contents(self):
8525 r"""get_contents(QuadContainer self) -> IMP::ParticleIndexQuads const &"""
8526 return _IMP_kernel.QuadContainer_get_contents(self)
8529 r"""get_indexes(QuadContainer self) -> IMP::ParticleIndexQuads"""
8530 return _IMP_kernel.QuadContainer_get_indexes(self)
8532 def get(self, *args):
8534 get(QuadContainer self) -> IMP::ParticleQuadsTemp
8535 get(QuadContainer self, unsigned int i) -> IMP::ParticleQuad
8537 return _IMP_kernel.QuadContainer_get(self, *args)
8539 def get_number(self):
8540 r"""get_number(QuadContainer self) -> unsigned int"""
8541 return _IMP_kernel.QuadContainer_get_number(self)
8543 def __init__(self, *args):
8545 __init__(QuadContainer self, Model m, std::string name="QuadContainer %1%") -> QuadContainer
8546 __init__(QuadContainer self) -> QuadContainer
8548 if self.__class__ == QuadContainer:
8552 _IMP_kernel.QuadContainer_swiginit(self, _IMP_kernel.new_QuadContainer(_self, *args))
8554 if self.__class__ != QuadContainer:
8555 _director_objects.register(self)
8560 def do_apply(self, sm):
8561 r"""do_apply(QuadContainer self, QuadModifier sm)"""
8562 return _IMP_kernel.QuadContainer_do_apply(self, sm)
8564 def do_apply_moved(self, sm, moved_pis, reset_pis):
8565 r"""do_apply_moved(QuadContainer self, QuadModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8566 return _IMP_kernel.QuadContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
8568 def do_get_provides_access(self):
8569 r"""do_get_provides_access(QuadContainer self) -> bool"""
8570 return _IMP_kernel.QuadContainer_do_get_provides_access(self)
8571 __swig_destroy__ = _IMP_kernel.delete_QuadContainer
8574 r"""__str__(QuadContainer self) -> std::string"""
8575 return _IMP_kernel.QuadContainer___str__(self)
8578 r"""__repr__(QuadContainer self) -> std::string"""
8579 return _IMP_kernel.QuadContainer___repr__(self)
8583 return _object_cast_to_QuadContainer(o)
8586 def do_show(self, out):
8591 return _object_cast_to_QuadContainer(o)
8593 def __disown__(self):
8595 _IMP_kernel.disown_QuadContainer(self)
8596 return weakref.proxy(self)
8599 r"""do_destroy(QuadContainer self)"""
8600 return _IMP_kernel.QuadContainer_do_destroy(self)
8602 def handle_set_has_required_score_states(self, arg0):
8603 r"""handle_set_has_required_score_states(QuadContainer self, bool arg0)"""
8604 return _IMP_kernel.QuadContainer_handle_set_has_required_score_states(self, arg0)
8606 def do_get_inputs(self):
8607 r"""do_get_inputs(QuadContainer self) -> IMP::ModelObjectsTemp"""
8608 return _IMP_kernel.QuadContainer_do_get_inputs(self)
8610 def do_get_interactions(self):
8611 r"""do_get_interactions(QuadContainer self) -> IMP::ModelObjectsTemps"""
8612 return _IMP_kernel.QuadContainer_do_get_interactions(self)
8614 def do_get_contents_hash(self):
8615 r"""do_get_contents_hash(QuadContainer self) -> std::size_t"""
8616 return _IMP_kernel.QuadContainer_do_get_contents_hash(self)
8619 _IMP_kernel.QuadContainer_swigregister(QuadContainer)
8620 class _QuadContainerAdaptor(_InputAdaptor):
8621 r"""Proxy of C++ IMP::QuadContainerAdaptor class."""
8623 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8624 __repr__ = _swig_repr
8626 def __init__(self, *args):
8628 __init__(_QuadContainerAdaptor self) -> _QuadContainerAdaptor
8629 __init__(_QuadContainerAdaptor self, QuadContainer c) -> _QuadContainerAdaptor
8630 __init__(_QuadContainerAdaptor self, IMP::ParticleQuadsTemp const & t) -> _QuadContainerAdaptor
8632 _IMP_kernel._QuadContainerAdaptor_swiginit(self, _IMP_kernel.new__QuadContainerAdaptor(*args))
8634 def set_name_if_default(self, name):
8635 r"""set_name_if_default(_QuadContainerAdaptor self, std::string name)"""
8636 return _IMP_kernel._QuadContainerAdaptor_set_name_if_default(self, name)
8637 __swig_destroy__ = _IMP_kernel.delete__QuadContainerAdaptor
8640 _IMP_kernel._QuadContainerAdaptor_swigregister(_QuadContainerAdaptor)
8642 r"""Proxy of C++ IMP::SingletonModifier class."""
8644 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8646 def __init__(self, *args):
8647 r"""__init__(SingletonModifier self, std::string name="SingletonModifier %1%") -> SingletonModifier"""
8648 if self.__class__ == SingletonModifier:
8652 _IMP_kernel.SingletonModifier_swiginit(self, _IMP_kernel.new_SingletonModifier(_self, *args))
8654 if self.__class__ != SingletonModifier:
8655 _director_objects.register(self)
8660 def apply_index(self, m, v):
8661 r"""apply_index(SingletonModifier self, Model m, ParticleIndex v)"""
8662 return _IMP_kernel.SingletonModifier_apply_index(self, m, v)
8664 def apply_indexes(self, m, o, lower_bound, upper_bound):
8665 r"""apply_indexes(SingletonModifier self, Model m, IMP::ParticleIndexes const & o, unsigned int lower_bound, unsigned int upper_bound)"""
8666 return _IMP_kernel.SingletonModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
8668 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
8669 r"""apply_indexes_moved(SingletonModifier self, Model m, IMP::ParticleIndexes const & o, unsigned int lower_bound, unsigned int upper_bound, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8670 return _IMP_kernel.SingletonModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
8673 r"""__str__(SingletonModifier self) -> std::string"""
8674 return _IMP_kernel.SingletonModifier___str__(self)
8677 r"""__repr__(SingletonModifier self) -> std::string"""
8678 return _IMP_kernel.SingletonModifier___repr__(self)
8682 return _object_cast_to_SingletonModifier(o)
8685 def do_show(self, out):
8690 return _object_cast_to_SingletonModifier(o)
8693 def _wrap_jax(self, apply_func, keys=None):
8694 """Create the return value for _get_jax.
8695 Use this method in _get_jax() to wrap the JAX function
8696 with other modifier-specific information.
8698 @param apply_func A function implemented using JAX that takes
8699 one argument (the current JAX Model) and returns a new
8701 @param keys Model attributes used by the SingletonModifier.
8702 See IMP::Restraint::_wrap_jax.
8704 from IMP._jax_util
import JAXModifierInfo
8705 return JAXModifierInfo(apply_func=apply_func, keys=keys)
8707 def _get_jax(self, m, indexes):
8708 """Return a JAX implementation of this SingletonModifier.
8709 Implement this method in a SingletonModifier subclass to provide
8710 an equivalent function using [JAX](https://docs.jax.dev/)
8711 that modifies the current JAX Model. See also _wrap_jax.
8713 @param m The IMP.Model that the modifier will act on.
8714 @param indexes The ParticleIndexes that the modifier will act on.
8716 raise NotImplementedError(
8717 f
"No JAX implementation for {self} ({type(self)})")
8719 __swig_destroy__ = _IMP_kernel.delete_SingletonModifier
8720 def __disown__(self):
8722 _IMP_kernel.disown_SingletonModifier(self)
8723 return weakref.proxy(self)
8725 def do_get_inputs(self, m, pis):
8726 r"""do_get_inputs(SingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8727 return _IMP_kernel.SingletonModifier_do_get_inputs(self, m, pis)
8729 def do_get_outputs(self, m, pis):
8730 r"""do_get_outputs(SingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8731 return _IMP_kernel.SingletonModifier_do_get_outputs(self, m, pis)
8734 r"""do_destroy(SingletonModifier self)"""
8735 return _IMP_kernel.SingletonModifier_do_destroy(self)
8738 _IMP_kernel.SingletonModifier_swigregister(SingletonModifier)
8740 r"""Proxy of C++ IMP::SingletonScore class."""
8742 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8744 def __init__(self, *args):
8745 r"""__init__(SingletonScore self, std::string name="SingletonScore %1%") -> SingletonScore"""
8746 if self.__class__ == SingletonScore:
8750 _IMP_kernel.SingletonScore_swiginit(self, _IMP_kernel.new_SingletonScore(_self, *args))
8752 if self.__class__ != SingletonScore:
8753 _director_objects.register(self)
8758 def evaluate_index(self, m, vt, da):
8759 r"""evaluate_index(SingletonScore self, Model m, ParticleIndex vt, DerivativeAccumulator da) -> double"""
8760 return _IMP_kernel.SingletonScore_evaluate_index(self, m, vt, da)
8762 def check_indexes(self, m, pis):
8763 r"""check_indexes(SingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
8764 return _IMP_kernel.SingletonScore_check_indexes(self, m, pis)
8766 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
8767 r"""evaluate_indexes(SingletonScore self, Model m, IMP::ParticleIndexes const & o, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
8768 return _IMP_kernel.SingletonScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
8770 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
8771 r"""evaluate_indexes_scores(SingletonScore self, Model m, IMP::ParticleIndexes const & o, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
8772 return _IMP_kernel.SingletonScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
8774 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
8775 r"""evaluate_indexes_delta(SingletonScore self, Model m, IMP::ParticleIndexes const & o, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
8776 return _IMP_kernel.SingletonScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
8778 def evaluate_if_good_index(self, m, vt, da, max):
8779 r"""evaluate_if_good_index(SingletonScore self, Model m, ParticleIndex vt, DerivativeAccumulator da, double max) -> double"""
8780 return _IMP_kernel.SingletonScore_evaluate_if_good_index(self, m, vt, da, max)
8782 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
8783 r"""evaluate_if_good_indexes(SingletonScore self, Model m, IMP::ParticleIndexes const & o, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
8784 return _IMP_kernel.SingletonScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
8786 def create_current_decomposition(self, m, vt):
8787 r"""create_current_decomposition(SingletonScore self, Model m, ParticleIndex vt) -> IMP::Restraints"""
8788 return _IMP_kernel.SingletonScore_create_current_decomposition(self, m, vt)
8790 def do_create_current_decomposition(self, m, vt):
8791 r"""do_create_current_decomposition(SingletonScore self, Model m, ParticleIndex vt) -> IMP::Restraints"""
8792 return _IMP_kernel.SingletonScore_do_create_current_decomposition(self, m, vt)
8793 __swig_destroy__ = _IMP_kernel.delete_SingletonScore
8796 r"""__str__(SingletonScore self) -> std::string"""
8797 return _IMP_kernel.SingletonScore___str__(self)
8800 r"""__repr__(SingletonScore self) -> std::string"""
8801 return _IMP_kernel.SingletonScore___repr__(self)
8805 return _object_cast_to_SingletonScore(o)
8808 def do_show(self, out):
8813 return _object_cast_to_SingletonScore(o)
8816 def _wrap_jax(self, m, score_func, keys=None):
8817 """See IMP::PairScore::_wrap_jax"""
8818 from IMP._jax_util
import JAXScoreInfo
8819 return JAXScoreInfo(m, score_func=score_func, keys=keys)
8821 def _get_jax(self, m, indexes, space):
8822 """See IMP::PairScore::_get_jax"""
8823 raise NotImplementedError(
8824 f
"No JAX implementation for {self} ({type(self)})")
8826 def __disown__(self):
8828 _IMP_kernel.disown_SingletonScore(self)
8829 return weakref.proxy(self)
8831 def do_get_inputs(self, m, pis):
8832 r"""do_get_inputs(SingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8833 return _IMP_kernel.SingletonScore_do_get_inputs(self, m, pis)
8836 r"""do_destroy(SingletonScore self)"""
8837 return _IMP_kernel.SingletonScore_do_destroy(self)
8840 _IMP_kernel.SingletonScore_swigregister(SingletonScore)
8842 r"""Proxy of C++ IMP::SingletonPredicate class."""
8844 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8846 def __init__(self, *args):
8847 r"""__init__(SingletonPredicate self, std::string name="SingletonPredicate %1%") -> SingletonPredicate"""
8848 if self.__class__ == SingletonPredicate:
8852 _IMP_kernel.SingletonPredicate_swiginit(self, _IMP_kernel.new_SingletonPredicate(_self, *args))
8854 if self.__class__ != SingletonPredicate:
8855 _director_objects.register(self)
8860 def setup_for_get_value_index_in_batch(self, arg0):
8861 r"""setup_for_get_value_index_in_batch(SingletonPredicate self, Model arg0)"""
8862 return _IMP_kernel.SingletonPredicate_setup_for_get_value_index_in_batch(self, arg0)
8864 def get_value_index_in_batch(self, m, vt):
8865 r"""get_value_index_in_batch(SingletonPredicate self, Model m, ParticleIndex vt) -> int"""
8866 return _IMP_kernel.SingletonPredicate_get_value_index_in_batch(self, m, vt)
8868 def __call__(self, m, vt):
8869 r"""__call__(SingletonPredicate self, Model m, ParticleIndex vt) -> int"""
8870 return _IMP_kernel.SingletonPredicate___call__(self, m, vt)
8872 def get_value_index(self, *args):
8874 get_value_index(SingletonPredicate self, Model m, ParticleIndex vt) -> int
8875 get_value_index(SingletonPredicate self, Model m, IMP::ParticleIndexes const & o) -> IMP::Ints
8877 return _IMP_kernel.SingletonPredicate_get_value_index(self, *args)
8878 __swig_destroy__ = _IMP_kernel.delete_SingletonPredicate
8881 r"""__str__(SingletonPredicate self) -> std::string"""
8882 return _IMP_kernel.SingletonPredicate___str__(self)
8885 r"""__repr__(SingletonPredicate self) -> std::string"""
8886 return _IMP_kernel.SingletonPredicate___repr__(self)
8890 return _object_cast_to_SingletonPredicate(o)
8893 def do_show(self, out):
8898 return _object_cast_to_SingletonPredicate(o)
8900 def __disown__(self):
8902 _IMP_kernel.disown_SingletonPredicate(self)
8903 return weakref.proxy(self)
8905 def do_get_inputs(self, m, pis):
8906 r"""do_get_inputs(SingletonPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8907 return _IMP_kernel.SingletonPredicate_do_get_inputs(self, m, pis)
8910 r"""do_destroy(SingletonPredicate self)"""
8911 return _IMP_kernel.SingletonPredicate_do_destroy(self)
8914 _IMP_kernel.SingletonPredicate_swigregister(SingletonPredicate)
8916 r"""Proxy of C++ IMP::SingletonContainer class."""
8918 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8920 def apply_generic(self, m):
8921 r"""apply_generic(SingletonContainer self, SingletonModifier m)"""
8922 return _IMP_kernel.SingletonContainer_apply_generic(self, m)
8924 def apply_generic_moved(self, m, moved_pis, reset_pis):
8925 r"""apply_generic_moved(SingletonContainer self, SingletonModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8926 return _IMP_kernel.SingletonContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
8928 def apply(self, sm):
8929 r"""apply(SingletonContainer self, SingletonModifier sm)"""
8930 return _IMP_kernel.SingletonContainer_apply(self, sm)
8932 def apply_moved(self, sm, moved_pis, reset_pis):
8933 r"""apply_moved(SingletonContainer self, SingletonModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8934 return _IMP_kernel.SingletonContainer_apply_moved(self, sm, moved_pis, reset_pis)
8936 def get_range_indexes(self):
8937 r"""get_range_indexes(SingletonContainer self) -> IMP::ParticleIndexes"""
8938 return _IMP_kernel.SingletonContainer_get_range_indexes(self)
8940 def get_contents(self):
8941 r"""get_contents(SingletonContainer self) -> IMP::ParticleIndexes const &"""
8942 return _IMP_kernel.SingletonContainer_get_contents(self)
8945 r"""get_indexes(SingletonContainer self) -> IMP::ParticleIndexes"""
8946 return _IMP_kernel.SingletonContainer_get_indexes(self)
8948 def get(self, *args):
8950 get(SingletonContainer self) -> IMP::ParticlesTemp
8951 get(SingletonContainer self, unsigned int i) -> Particle
8953 return _IMP_kernel.SingletonContainer_get(self, *args)
8955 def get_number(self):
8956 r"""get_number(SingletonContainer self) -> unsigned int"""
8957 return _IMP_kernel.SingletonContainer_get_number(self)
8959 def __init__(self, *args):
8961 __init__(SingletonContainer self, Model m, std::string name="SingletonContainer %1%") -> SingletonContainer
8962 __init__(SingletonContainer self) -> SingletonContainer
8964 if self.__class__ == SingletonContainer:
8968 _IMP_kernel.SingletonContainer_swiginit(self, _IMP_kernel.new_SingletonContainer(_self, *args))
8970 if self.__class__ != SingletonContainer:
8971 _director_objects.register(self)
8976 def do_apply(self, sm):
8977 r"""do_apply(SingletonContainer self, SingletonModifier sm)"""
8978 return _IMP_kernel.SingletonContainer_do_apply(self, sm)
8980 def do_apply_moved(self, sm, moved_pis, reset_pis):
8981 r"""do_apply_moved(SingletonContainer self, SingletonModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8982 return _IMP_kernel.SingletonContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
8984 def do_get_provides_access(self):
8985 r"""do_get_provides_access(SingletonContainer self) -> bool"""
8986 return _IMP_kernel.SingletonContainer_do_get_provides_access(self)
8987 __swig_destroy__ = _IMP_kernel.delete_SingletonContainer
8990 r"""__str__(SingletonContainer self) -> std::string"""
8991 return _IMP_kernel.SingletonContainer___str__(self)
8994 r"""__repr__(SingletonContainer self) -> std::string"""
8995 return _IMP_kernel.SingletonContainer___repr__(self)
8999 return _object_cast_to_SingletonContainer(o)
9002 def do_show(self, out):
9007 return _object_cast_to_SingletonContainer(o)
9009 def __disown__(self):
9011 _IMP_kernel.disown_SingletonContainer(self)
9012 return weakref.proxy(self)
9015 r"""do_destroy(SingletonContainer self)"""
9016 return _IMP_kernel.SingletonContainer_do_destroy(self)
9018 def handle_set_has_required_score_states(self, arg0):
9019 r"""handle_set_has_required_score_states(SingletonContainer self, bool arg0)"""
9020 return _IMP_kernel.SingletonContainer_handle_set_has_required_score_states(self, arg0)
9022 def do_get_inputs(self):
9023 r"""do_get_inputs(SingletonContainer self) -> IMP::ModelObjectsTemp"""
9024 return _IMP_kernel.SingletonContainer_do_get_inputs(self)
9026 def do_get_interactions(self):
9027 r"""do_get_interactions(SingletonContainer self) -> IMP::ModelObjectsTemps"""
9028 return _IMP_kernel.SingletonContainer_do_get_interactions(self)
9030 def do_get_contents_hash(self):
9031 r"""do_get_contents_hash(SingletonContainer self) -> std::size_t"""
9032 return _IMP_kernel.SingletonContainer_do_get_contents_hash(self)
9035 _IMP_kernel.SingletonContainer_swigregister(SingletonContainer)
9036 class _SingletonContainerAdaptor(_InputAdaptor):
9037 r"""Proxy of C++ IMP::SingletonContainerAdaptor class."""
9039 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9040 __repr__ = _swig_repr
9042 def __init__(self, *args):
9044 __init__(_SingletonContainerAdaptor self) -> _SingletonContainerAdaptor
9045 __init__(_SingletonContainerAdaptor self, SingletonContainer c) -> _SingletonContainerAdaptor
9046 __init__(_SingletonContainerAdaptor self, IMP::ParticlesTemp const & t) -> _SingletonContainerAdaptor
9048 _IMP_kernel._SingletonContainerAdaptor_swiginit(self, _IMP_kernel.new__SingletonContainerAdaptor(*args))
9050 def set_name_if_default(self, name):
9051 r"""set_name_if_default(_SingletonContainerAdaptor self, std::string name)"""
9052 return _IMP_kernel._SingletonContainerAdaptor_set_name_if_default(self, name)
9053 __swig_destroy__ = _IMP_kernel.delete__SingletonContainerAdaptor
9056 _IMP_kernel._SingletonContainerAdaptor_swigregister(_SingletonContainerAdaptor)
9058 r"""Proxy of C++ IMP::TripletModifier class."""
9060 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9062 def __init__(self, *args):
9063 r"""__init__(TripletModifier self, std::string name="TripletModifier %1%") -> TripletModifier"""
9064 if self.__class__ == TripletModifier:
9068 _IMP_kernel.TripletModifier_swiginit(self, _IMP_kernel.new_TripletModifier(_self, *args))
9070 if self.__class__ != TripletModifier:
9071 _director_objects.register(self)
9076 def apply_index(self, m, v):
9077 r"""apply_index(TripletModifier self, Model m, IMP::ParticleIndexTriplet const & v)"""
9078 return _IMP_kernel.TripletModifier_apply_index(self, m, v)
9080 def apply_indexes(self, m, o, lower_bound, upper_bound):
9081 r"""apply_indexes(TripletModifier self, Model m, IMP::ParticleIndexTriplets const & o, unsigned int lower_bound, unsigned int upper_bound)"""
9082 return _IMP_kernel.TripletModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
9084 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
9085 r"""apply_indexes_moved(TripletModifier self, Model m, IMP::ParticleIndexTriplets const & o, unsigned int lower_bound, unsigned int upper_bound, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
9086 return _IMP_kernel.TripletModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
9089 r"""__str__(TripletModifier self) -> std::string"""
9090 return _IMP_kernel.TripletModifier___str__(self)
9093 r"""__repr__(TripletModifier self) -> std::string"""
9094 return _IMP_kernel.TripletModifier___repr__(self)
9098 return _object_cast_to_TripletModifier(o)
9101 def do_show(self, out):
9106 return _object_cast_to_TripletModifier(o)
9108 __swig_destroy__ = _IMP_kernel.delete_TripletModifier
9109 def __disown__(self):
9111 _IMP_kernel.disown_TripletModifier(self)
9112 return weakref.proxy(self)
9114 def do_get_inputs(self, m, pis):
9115 r"""do_get_inputs(TripletModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
9116 return _IMP_kernel.TripletModifier_do_get_inputs(self, m, pis)
9118 def do_get_outputs(self, m, pis):
9119 r"""do_get_outputs(TripletModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
9120 return _IMP_kernel.TripletModifier_do_get_outputs(self, m, pis)
9123 r"""do_destroy(TripletModifier self)"""
9124 return _IMP_kernel.TripletModifier_do_destroy(self)
9127 _IMP_kernel.TripletModifier_swigregister(TripletModifier)
9129 r"""Proxy of C++ IMP::TripletScore class."""
9131 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9133 def __init__(self, *args):
9134 r"""__init__(TripletScore self, std::string name="TripletScore %1%") -> TripletScore"""
9135 if self.__class__ == TripletScore:
9139 _IMP_kernel.TripletScore_swiginit(self, _IMP_kernel.new_TripletScore(_self, *args))
9141 if self.__class__ != TripletScore:
9142 _director_objects.register(self)
9147 def evaluate_index(self, m, vt, da):
9148 r"""evaluate_index(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt, DerivativeAccumulator da) -> double"""
9149 return _IMP_kernel.TripletScore_evaluate_index(self, m, vt, da)
9151 def check_indexes(self, m, pis):
9152 r"""check_indexes(TripletScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
9153 return _IMP_kernel.TripletScore_check_indexes(self, m, pis)
9155 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
9156 r"""evaluate_indexes(TripletScore self, Model m, IMP::ParticleIndexTriplets const & o, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
9157 return _IMP_kernel.TripletScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
9159 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
9160 r"""evaluate_indexes_scores(TripletScore self, Model m, IMP::ParticleIndexTriplets const & o, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
9161 return _IMP_kernel.TripletScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
9163 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
9164 r"""evaluate_indexes_delta(TripletScore self, Model m, IMP::ParticleIndexTriplets const & o, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
9165 return _IMP_kernel.TripletScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
9167 def evaluate_if_good_index(self, m, vt, da, max):
9168 r"""evaluate_if_good_index(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt, DerivativeAccumulator da, double max) -> double"""
9169 return _IMP_kernel.TripletScore_evaluate_if_good_index(self, m, vt, da, max)
9171 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
9172 r"""evaluate_if_good_indexes(TripletScore self, Model m, IMP::ParticleIndexTriplets const & o, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
9173 return _IMP_kernel.TripletScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
9175 def create_current_decomposition(self, m, vt):
9176 r"""create_current_decomposition(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt) -> IMP::Restraints"""
9177 return _IMP_kernel.TripletScore_create_current_decomposition(self, m, vt)
9179 def do_create_current_decomposition(self, m, vt):
9180 r"""do_create_current_decomposition(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt) -> IMP::Restraints"""
9181 return _IMP_kernel.TripletScore_do_create_current_decomposition(self, m, vt)
9182 __swig_destroy__ = _IMP_kernel.delete_TripletScore
9185 r"""__str__(TripletScore self) -> std::string"""
9186 return _IMP_kernel.TripletScore___str__(self)
9189 r"""__repr__(TripletScore self) -> std::string"""
9190 return _IMP_kernel.TripletScore___repr__(self)
9194 return _object_cast_to_TripletScore(o)
9197 def do_show(self, out):
9202 return _object_cast_to_TripletScore(o)
9204 def __disown__(self):
9206 _IMP_kernel.disown_TripletScore(self)
9207 return weakref.proxy(self)
9209 def do_get_inputs(self, m, pis):
9210 r"""do_get_inputs(TripletScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
9211 return _IMP_kernel.TripletScore_do_get_inputs(self, m, pis)
9214 r"""do_destroy(TripletScore self)"""
9215 return _IMP_kernel.TripletScore_do_destroy(self)
9218 _IMP_kernel.TripletScore_swigregister(TripletScore)
9220 r"""Proxy of C++ IMP::TripletPredicate class."""
9222 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9224 def __init__(self, *args):
9225 r"""__init__(TripletPredicate self, std::string name="TripletPredicate %1%") -> TripletPredicate"""
9226 if self.__class__ == TripletPredicate:
9230 _IMP_kernel.TripletPredicate_swiginit(self, _IMP_kernel.new_TripletPredicate(_self, *args))
9232 if self.__class__ != TripletPredicate:
9233 _director_objects.register(self)
9238 def setup_for_get_value_index_in_batch(self, arg0):
9239 r"""setup_for_get_value_index_in_batch(TripletPredicate self, Model arg0)"""
9240 return _IMP_kernel.TripletPredicate_setup_for_get_value_index_in_batch(self, arg0)
9242 def get_value_index_in_batch(self, m, vt):
9243 r"""get_value_index_in_batch(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int"""
9244 return _IMP_kernel.TripletPredicate_get_value_index_in_batch(self, m, vt)
9246 def __call__(self, m, vt):
9247 r"""__call__(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int"""
9248 return _IMP_kernel.TripletPredicate___call__(self, m, vt)
9250 def get_value_index(self, *args):
9252 get_value_index(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int
9253 get_value_index(TripletPredicate self, Model m, IMP::ParticleIndexTriplets const & o) -> IMP::Ints
9255 return _IMP_kernel.TripletPredicate_get_value_index(self, *args)
9256 __swig_destroy__ = _IMP_kernel.delete_TripletPredicate
9259 r"""__str__(TripletPredicate self) -> std::string"""
9260 return _IMP_kernel.TripletPredicate___str__(self)
9263 r"""__repr__(TripletPredicate self) -> std::string"""
9264 return _IMP_kernel.TripletPredicate___repr__(self)
9268 return _object_cast_to_TripletPredicate(o)
9271 def do_show(self, out):
9276 return _object_cast_to_TripletPredicate(o)
9278 def __disown__(self):
9280 _IMP_kernel.disown_TripletPredicate(self)
9281 return weakref.proxy(self)
9283 def do_get_inputs(self, m, pis):
9284 r"""do_get_inputs(TripletPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
9285 return _IMP_kernel.TripletPredicate_do_get_inputs(self, m, pis)
9288 r"""do_destroy(TripletPredicate self)"""
9289 return _IMP_kernel.TripletPredicate_do_destroy(self)
9292 _IMP_kernel.TripletPredicate_swigregister(TripletPredicate)
9294 r"""Proxy of C++ IMP::TripletContainer class."""
9296 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9298 def apply_generic(self, m):
9299 r"""apply_generic(TripletContainer self, TripletModifier m)"""
9300 return _IMP_kernel.TripletContainer_apply_generic(self, m)
9302 def apply_generic_moved(self, m, moved_pis, reset_pis):
9303 r"""apply_generic_moved(TripletContainer self, TripletModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
9304 return _IMP_kernel.TripletContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
9306 def apply(self, sm):
9307 r"""apply(TripletContainer self, TripletModifier sm)"""
9308 return _IMP_kernel.TripletContainer_apply(self, sm)
9310 def apply_moved(self, sm, moved_pis, reset_pis):
9311 r"""apply_moved(TripletContainer self, TripletModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
9312 return _IMP_kernel.TripletContainer_apply_moved(self, sm, moved_pis, reset_pis)
9314 def get_range_indexes(self):
9315 r"""get_range_indexes(TripletContainer self) -> IMP::ParticleIndexTriplets"""
9316 return _IMP_kernel.TripletContainer_get_range_indexes(self)
9318 def get_contents(self):
9319 r"""get_contents(TripletContainer self) -> IMP::ParticleIndexTriplets const &"""
9320 return _IMP_kernel.TripletContainer_get_contents(self)
9323 r"""get_indexes(TripletContainer self) -> IMP::ParticleIndexTriplets"""
9324 return _IMP_kernel.TripletContainer_get_indexes(self)
9326 def get(self, *args):
9328 get(TripletContainer self) -> IMP::ParticleTripletsTemp
9329 get(TripletContainer self, unsigned int i) -> IMP::ParticleTriplet
9331 return _IMP_kernel.TripletContainer_get(self, *args)
9333 def get_number(self):
9334 r"""get_number(TripletContainer self) -> unsigned int"""
9335 return _IMP_kernel.TripletContainer_get_number(self)
9337 def __init__(self, *args):
9339 __init__(TripletContainer self, Model m, std::string name="TripletContainer %1%") -> TripletContainer
9340 __init__(TripletContainer self) -> TripletContainer
9342 if self.__class__ == TripletContainer:
9346 _IMP_kernel.TripletContainer_swiginit(self, _IMP_kernel.new_TripletContainer(_self, *args))
9348 if self.__class__ != TripletContainer:
9349 _director_objects.register(self)
9354 def do_apply(self, sm):
9355 r"""do_apply(TripletContainer self, TripletModifier sm)"""
9356 return _IMP_kernel.TripletContainer_do_apply(self, sm)
9358 def do_apply_moved(self, sm, moved_pis, reset_pis):
9359 r"""do_apply_moved(TripletContainer self, TripletModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
9360 return _IMP_kernel.TripletContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
9362 def do_get_provides_access(self):
9363 r"""do_get_provides_access(TripletContainer self) -> bool"""
9364 return _IMP_kernel.TripletContainer_do_get_provides_access(self)
9365 __swig_destroy__ = _IMP_kernel.delete_TripletContainer
9368 r"""__str__(TripletContainer self) -> std::string"""
9369 return _IMP_kernel.TripletContainer___str__(self)
9372 r"""__repr__(TripletContainer self) -> std::string"""
9373 return _IMP_kernel.TripletContainer___repr__(self)
9377 return _object_cast_to_TripletContainer(o)
9380 def do_show(self, out):
9385 return _object_cast_to_TripletContainer(o)
9387 def __disown__(self):
9389 _IMP_kernel.disown_TripletContainer(self)
9390 return weakref.proxy(self)
9393 r"""do_destroy(TripletContainer self)"""
9394 return _IMP_kernel.TripletContainer_do_destroy(self)
9396 def handle_set_has_required_score_states(self, arg0):
9397 r"""handle_set_has_required_score_states(TripletContainer self, bool arg0)"""
9398 return _IMP_kernel.TripletContainer_handle_set_has_required_score_states(self, arg0)
9400 def do_get_inputs(self):
9401 r"""do_get_inputs(TripletContainer self) -> IMP::ModelObjectsTemp"""
9402 return _IMP_kernel.TripletContainer_do_get_inputs(self)
9404 def do_get_interactions(self):
9405 r"""do_get_interactions(TripletContainer self) -> IMP::ModelObjectsTemps"""
9406 return _IMP_kernel.TripletContainer_do_get_interactions(self)
9408 def do_get_contents_hash(self):
9409 r"""do_get_contents_hash(TripletContainer self) -> std::size_t"""
9410 return _IMP_kernel.TripletContainer_do_get_contents_hash(self)
9413 _IMP_kernel.TripletContainer_swigregister(TripletContainer)
9414 class _TripletContainerAdaptor(_InputAdaptor):
9415 r"""Proxy of C++ IMP::TripletContainerAdaptor class."""
9417 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9418 __repr__ = _swig_repr
9420 def __init__(self, *args):
9422 __init__(_TripletContainerAdaptor self) -> _TripletContainerAdaptor
9423 __init__(_TripletContainerAdaptor self, TripletContainer c) -> _TripletContainerAdaptor
9424 __init__(_TripletContainerAdaptor self, IMP::ParticleTripletsTemp const & t) -> _TripletContainerAdaptor
9426 _IMP_kernel._TripletContainerAdaptor_swiginit(self, _IMP_kernel.new__TripletContainerAdaptor(*args))
9428 def set_name_if_default(self, name):
9429 r"""set_name_if_default(_TripletContainerAdaptor self, std::string name)"""
9430 return _IMP_kernel._TripletContainerAdaptor_set_name_if_default(self, name)
9431 __swig_destroy__ = _IMP_kernel.delete__TripletContainerAdaptor
9434 _IMP_kernel._TripletContainerAdaptor_swigregister(_TripletContainerAdaptor)
9437 r"""write_particles_to_buffer(IMP::ParticlesTemp const & particles, IMP::FloatKeys const & keys) -> IMP::Vector< char,std::allocator< char > >"""
9438 return _IMP_kernel.write_particles_to_buffer(particles, keys)
9441 r"""read_particles_from_buffer(IMP::Vector< char,std::allocator< char > > const & buffer, IMP::ParticlesTemp const & particles, IMP::FloatKeys const & keys)"""
9442 return _IMP_kernel.read_particles_from_buffer(buffer, particles, keys)
9445 r"""get_particles(Model m, IMP::ParticleIndexes const & ps) -> IMP::ParticlesTemp"""
9446 return _IMP_kernel.get_particles(m, ps)
9450 get_indexes(IMP::ParticlesTemp const & ps) -> IMP::ParticleIndexes
9451 get_indexes(IMP::ParticlePairsTemp const & ps) -> IMP::ParticleIndexPairs
9453 return _IMP_kernel.get_indexes(*args)
9454 class _ParticleIndexAdaptor(object):
9455 r"""Proxy of C++ IMP::ParticleIndexAdaptor class."""
9457 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9458 __repr__ = _swig_repr
9460 def __init__(self, *args):
9462 __init__(_ParticleIndexAdaptor self, Particle p) -> _ParticleIndexAdaptor
9463 __init__(_ParticleIndexAdaptor self, ParticleIndex pi) -> _ParticleIndexAdaptor
9464 __init__(_ParticleIndexAdaptor self, Decorator d) -> _ParticleIndexAdaptor
9466 _IMP_kernel._ParticleIndexAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexAdaptor(*args))
9467 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexAdaptor
9470 _IMP_kernel._ParticleIndexAdaptor_swigregister(_ParticleIndexAdaptor)
9471 class _ParticleIndexesAdaptor(_InputAdaptor):
9472 r"""Proxy of C++ IMP::ParticleIndexesAdaptor class."""
9474 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9475 __repr__ = _swig_repr
9477 def __init__(self, *args):
9479 __init__(_ParticleIndexesAdaptor self, IMP::ParticlesTemp const & ps) -> _ParticleIndexesAdaptor
9480 __init__(_ParticleIndexesAdaptor self, IMP::ParticleIndexes const & pi) -> _ParticleIndexesAdaptor
9481 __init__(_ParticleIndexesAdaptor self) -> _ParticleIndexesAdaptor
9483 _IMP_kernel._ParticleIndexesAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexesAdaptor(*args))
9484 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexesAdaptor
9487 _IMP_kernel._ParticleIndexesAdaptor_swigregister(_ParticleIndexesAdaptor)
9488 class _ParticleIndexPairsAdaptor(object):
9489 r"""Proxy of C++ IMP::ParticleIndexPairsAdaptor class."""
9491 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9492 __repr__ = _swig_repr
9494 def __init__(self, *args):
9496 __init__(_ParticleIndexPairsAdaptor self, IMP::ParticlePairsTemp const & ps) -> _ParticleIndexPairsAdaptor
9497 __init__(_ParticleIndexPairsAdaptor self, IMP::ParticleIndexPairs const & pi) -> _ParticleIndexPairsAdaptor
9498 __init__(_ParticleIndexPairsAdaptor self) -> _ParticleIndexPairsAdaptor
9500 _IMP_kernel._ParticleIndexPairsAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexPairsAdaptor(*args))
9501 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexPairsAdaptor
9504 _IMP_kernel._ParticleIndexPairsAdaptor_swigregister(_ParticleIndexPairsAdaptor)
9506 r"""Proxy of C++ IMP::internal::_ConstRestraint class."""
9508 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9510 def __init__(self, *args):
9512 __init__(_ConstRestraint self, Model m, IMP::ParticleIndexes const & pis, double v) -> _ConstRestraint
9513 __init__(_ConstRestraint self) -> _ConstRestraint
9515 _IMP_kernel._ConstRestraint_swiginit(self, _IMP_kernel.new__ConstRestraint(*args))
9517 def get_value(self):
9518 r"""get_value(_ConstRestraint self) -> double"""
9519 return _IMP_kernel._ConstRestraint_get_value(self)
9521 def do_create_decomposition(self):
9522 r"""do_create_decomposition(_ConstRestraint self) -> IMP::Restraints"""
9523 return _IMP_kernel._ConstRestraint_do_create_decomposition(self)
9525 def do_get_inputs(self):
9526 r"""do_get_inputs(_ConstRestraint self) -> IMP::ModelObjectsTemp"""
9527 return _IMP_kernel._ConstRestraint_do_get_inputs(self)
9530 r"""get_version_info(_ConstRestraint self) -> VersionInfo"""
9531 return _IMP_kernel._ConstRestraint_get_version_info(self)
9532 __swig_destroy__ = _IMP_kernel.delete__ConstRestraint
9535 r"""__str__(_ConstRestraint self) -> std::string"""
9536 return _IMP_kernel._ConstRestraint___str__(self)
9539 r"""__repr__(_ConstRestraint self) -> std::string"""
9540 return _IMP_kernel._ConstRestraint___repr__(self)
9544 return _object_cast_to__ConstRestraint(o)
9547 def _get_as_binary(self):
9548 r"""_get_as_binary(_ConstRestraint self) -> PyObject *"""
9549 return _IMP_kernel._ConstRestraint__get_as_binary(self)
9551 def _set_from_binary(self, p):
9552 r"""_set_from_binary(_ConstRestraint self, PyObject * p)"""
9553 return _IMP_kernel._ConstRestraint__set_from_binary(self, p)
9555 def __getstate__(self):
9556 p = self._get_as_binary()
9557 if len(self.__dict__) > 1:
9558 d = self.__dict__.copy()
9563 def __setstate__(self, p):
9564 if not hasattr(self,
'this'):
9566 if isinstance(p, tuple):
9568 self.__dict__.update(d)
9569 return self._set_from_binary(p)
9572 def _get_jax(self, space):
9573 value = self.get_value()
9575 return self._wrap_jax(
lambda jm: value)
9579 _IMP_kernel._ConstRestraint_swigregister(_ConstRestraint)
9581 r"""Proxy of C++ IMP::internal::_ConstSingletonScore class."""
9583 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9585 def __init__(self, *args):
9587 __init__(_ConstSingletonScore self, double v) -> _ConstSingletonScore
9588 __init__(_ConstSingletonScore self) -> _ConstSingletonScore
9590 _IMP_kernel._ConstSingletonScore_swiginit(self, _IMP_kernel.new__ConstSingletonScore(*args))
9592 def get_value(self):
9593 r"""get_value(_ConstSingletonScore self) -> double"""
9594 return _IMP_kernel._ConstSingletonScore_get_value(self)
9596 def do_get_inputs(self, arg2, arg3):
9597 r"""do_get_inputs(_ConstSingletonScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
9598 return _IMP_kernel._ConstSingletonScore_do_get_inputs(self, arg2, arg3)
9600 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
9601 r"""evaluate_indexes(_ConstSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
9602 return _IMP_kernel._ConstSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
9604 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
9605 r"""evaluate_indexes_scores(_ConstSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
9606 return _IMP_kernel._ConstSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
9608 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
9609 r"""evaluate_indexes_delta(_ConstSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
9610 return _IMP_kernel._ConstSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
9612 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
9613 r"""evaluate_if_good_indexes(_ConstSingletonScore self, Model m, IMP::ParticleIndexes const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
9614 return _IMP_kernel._ConstSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
9617 r"""get_version_info(_ConstSingletonScore self) -> VersionInfo"""
9618 return _IMP_kernel._ConstSingletonScore_get_version_info(self)
9619 __swig_destroy__ = _IMP_kernel.delete__ConstSingletonScore
9622 r"""__str__(_ConstSingletonScore self) -> std::string"""
9623 return _IMP_kernel._ConstSingletonScore___str__(self)
9626 r"""__repr__(_ConstSingletonScore self) -> std::string"""
9627 return _IMP_kernel._ConstSingletonScore___repr__(self)
9631 return _object_cast_to__ConstSingletonScore(o)
9634 def _get_as_binary(self):
9635 r"""_get_as_binary(_ConstSingletonScore self) -> PyObject *"""
9636 return _IMP_kernel._ConstSingletonScore__get_as_binary(self)
9638 def _set_from_binary(self, p):
9639 r"""_set_from_binary(_ConstSingletonScore self, PyObject * p)"""
9640 return _IMP_kernel._ConstSingletonScore__set_from_binary(self, p)
9642 def __getstate__(self):
9643 p = self._get_as_binary()
9644 if len(self.__dict__) > 1:
9645 d = self.__dict__.copy()
9650 def __setstate__(self, p):
9651 if not hasattr(self,
'this'):
9653 if isinstance(p, tuple):
9655 self.__dict__.update(d)
9656 return self._set_from_binary(p)
9659 def _get_jax(self, m, indexes, space):
9660 value = self.get_value()
9662 return self._wrap_jax(m,
lambda jm: value)
9666 _IMP_kernel._ConstSingletonScore_swigregister(_ConstSingletonScore)
9668 r"""Proxy of C++ IMP::internal::_ConstPairScore class."""
9670 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9672 def __init__(self, *args):
9674 __init__(_ConstPairScore self, double v) -> _ConstPairScore
9675 __init__(_ConstPairScore self) -> _ConstPairScore
9677 _IMP_kernel._ConstPairScore_swiginit(self, _IMP_kernel.new__ConstPairScore(*args))
9679 def get_value(self):
9680 r"""get_value(_ConstPairScore self) -> double"""
9681 return _IMP_kernel._ConstPairScore_get_value(self)
9683 def do_get_inputs(self, arg2, arg3):
9684 r"""do_get_inputs(_ConstPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
9685 return _IMP_kernel._ConstPairScore_do_get_inputs(self, arg2, arg3)
9687 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
9688 r"""evaluate_indexes(_ConstPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
9689 return _IMP_kernel._ConstPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
9691 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
9692 r"""evaluate_indexes_scores(_ConstPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
9693 return _IMP_kernel._ConstPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
9695 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
9696 r"""evaluate_indexes_delta(_ConstPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
9697 return _IMP_kernel._ConstPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
9699 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
9700 r"""evaluate_if_good_indexes(_ConstPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
9701 return _IMP_kernel._ConstPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
9704 r"""get_version_info(_ConstPairScore self) -> VersionInfo"""
9705 return _IMP_kernel._ConstPairScore_get_version_info(self)
9706 __swig_destroy__ = _IMP_kernel.delete__ConstPairScore
9709 r"""__str__(_ConstPairScore self) -> std::string"""
9710 return _IMP_kernel._ConstPairScore___str__(self)
9713 r"""__repr__(_ConstPairScore self) -> std::string"""
9714 return _IMP_kernel._ConstPairScore___repr__(self)
9718 return _object_cast_to__ConstPairScore(o)
9721 def _get_as_binary(self):
9722 r"""_get_as_binary(_ConstPairScore self) -> PyObject *"""
9723 return _IMP_kernel._ConstPairScore__get_as_binary(self)
9725 def _set_from_binary(self, p):
9726 r"""_set_from_binary(_ConstPairScore self, PyObject * p)"""
9727 return _IMP_kernel._ConstPairScore__set_from_binary(self, p)
9729 def __getstate__(self):
9730 p = self._get_as_binary()
9731 if len(self.__dict__) > 1:
9732 d = self.__dict__.copy()
9737 def __setstate__(self, p):
9738 if not hasattr(self,
'this'):
9740 if isinstance(p, tuple):
9742 self.__dict__.update(d)
9743 return self._set_from_binary(p)
9746 def _get_jax(self, m, indexes, space):
9747 value = self.get_value()
9749 return self._wrap_jax(m,
lambda jm: value)
9753 _IMP_kernel._ConstPairScore_swigregister(_ConstPairScore)
9755 r"""Proxy of C++ IMP::internal::_TrivialDecorator class."""
9757 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9759 def __init__(self, *args):
9761 __init__(_TrivialDecorator self) -> _TrivialDecorator
9762 __init__(_TrivialDecorator self, Model m, ParticleIndex id) -> _TrivialDecorator
9763 __init__(_TrivialDecorator self, _ParticleAdaptor d) -> _TrivialDecorator
9765 _IMP_kernel._TrivialDecorator_swiginit(self, _IMP_kernel.new__TrivialDecorator(*args))
9767 def show(self, *args):
9768 r"""show(_TrivialDecorator self, _ostream out=std::cout)"""
9769 return _IMP_kernel._TrivialDecorator_show(self, *args)
9772 def setup_particle(*args):
9774 setup_particle(Model m, ParticleIndex pi) -> _TrivialDecorator
9775 setup_particle(_ParticleAdaptor pa) -> _TrivialDecorator
9777 return _IMP_kernel._TrivialDecorator_setup_particle(*args)
9780 def get_is_setup(*args):
9782 get_is_setup(_ParticleAdaptor p) -> bool
9783 get_is_setup(Model m, ParticleIndex pi) -> bool
9785 return _IMP_kernel._TrivialDecorator_get_is_setup(*args)
9789 add_attribute(_TrivialDecorator self, FloatKey k, IMP::Float v, bool opt)
9790 add_attribute(_TrivialDecorator self, FloatKey a0, IMP::Float a1)
9791 add_attribute(_TrivialDecorator self, IntKey a0, IMP::Int a1)
9792 add_attribute(_TrivialDecorator self, FloatsKey a0, IMP::Floats a1)
9793 add_attribute(_TrivialDecorator self, IntsKey a0, IMP::Ints a1)
9794 add_attribute(_TrivialDecorator self, StringKey a0, IMP::String a1)
9795 add_attribute(_TrivialDecorator self, ParticleIndexKey a0, Particle a1)
9796 add_attribute(_TrivialDecorator self, ObjectKey a0, Object a1)
9797 add_attribute(_TrivialDecorator self, SparseFloatKey a0, IMP::Float a1)
9798 add_attribute(_TrivialDecorator self, SparseIntKey a0, IMP::Int a1)
9799 add_attribute(_TrivialDecorator self, SparseStringKey a0, IMP::String a1)
9800 add_attribute(_TrivialDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
9802 return _IMP_kernel._TrivialDecorator_add_attribute(self, *args)
9804 def get_value(self, *args):
9806 get_value(_TrivialDecorator self, FloatKey a0) -> IMP::Float
9807 get_value(_TrivialDecorator self, IntKey a0) -> IMP::Int
9808 get_value(_TrivialDecorator self, FloatsKey a0) -> IMP::Floats
9809 get_value(_TrivialDecorator self, IntsKey a0) -> IMP::Ints
9810 get_value(_TrivialDecorator self, StringKey a0) -> IMP::String
9811 get_value(_TrivialDecorator self, ParticleIndexKey a0) -> Particle
9812 get_value(_TrivialDecorator self, ObjectKey a0) -> Object
9813 get_value(_TrivialDecorator self, SparseFloatKey a0) -> IMP::Float
9814 get_value(_TrivialDecorator self, SparseIntKey a0) -> IMP::Int
9815 get_value(_TrivialDecorator self, SparseStringKey a0) -> IMP::String
9816 get_value(_TrivialDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
9818 return _IMP_kernel._TrivialDecorator_get_value(self, *args)
9820 def set_value(self, *args):
9822 set_value(_TrivialDecorator self, FloatKey a0, IMP::Float a1)
9823 set_value(_TrivialDecorator self, IntKey a0, IMP::Int a1)
9824 set_value(_TrivialDecorator self, FloatsKey a0, IMP::Floats a1)
9825 set_value(_TrivialDecorator self, IntsKey a0, IMP::Ints a1)
9826 set_value(_TrivialDecorator self, StringKey a0, IMP::String a1)
9827 set_value(_TrivialDecorator self, ParticleIndexKey a0, Particle a1)
9828 set_value(_TrivialDecorator self, ObjectKey a0, Object a1)
9829 set_value(_TrivialDecorator self, SparseFloatKey a0, IMP::Float a1)
9830 set_value(_TrivialDecorator self, SparseIntKey a0, IMP::Int a1)
9831 set_value(_TrivialDecorator self, SparseStringKey a0, IMP::String a1)
9832 set_value(_TrivialDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
9834 return _IMP_kernel._TrivialDecorator_set_value(self, *args)
9838 remove_attribute(_TrivialDecorator self, FloatKey a0)
9839 remove_attribute(_TrivialDecorator self, IntKey a0)
9840 remove_attribute(_TrivialDecorator self, FloatsKey a0)
9841 remove_attribute(_TrivialDecorator self, IntsKey a0)
9842 remove_attribute(_TrivialDecorator self, StringKey a0)
9843 remove_attribute(_TrivialDecorator self, ParticleIndexKey a0)
9844 remove_attribute(_TrivialDecorator self, ObjectKey a0)
9845 remove_attribute(_TrivialDecorator self, SparseFloatKey a0)
9846 remove_attribute(_TrivialDecorator self, SparseIntKey a0)
9847 remove_attribute(_TrivialDecorator self, SparseStringKey a0)
9848 remove_attribute(_TrivialDecorator self, SparseParticleIndexKey a0)
9850 return _IMP_kernel._TrivialDecorator_remove_attribute(self, *args)
9852 def has_attribute(self, *args):
9854 has_attribute(_TrivialDecorator self, FloatKey a0) -> bool
9855 has_attribute(_TrivialDecorator self, IntKey a0) -> bool
9856 has_attribute(_TrivialDecorator self, FloatsKey a0) -> bool
9857 has_attribute(_TrivialDecorator self, IntsKey a0) -> bool
9858 has_attribute(_TrivialDecorator self, StringKey a0) -> bool
9859 has_attribute(_TrivialDecorator self, ParticleIndexKey a0) -> bool
9860 has_attribute(_TrivialDecorator self, ObjectKey a0) -> bool
9861 has_attribute(_TrivialDecorator self, SparseFloatKey a0) -> bool
9862 has_attribute(_TrivialDecorator self, SparseIntKey a0) -> bool
9863 has_attribute(_TrivialDecorator self, SparseStringKey a0) -> bool
9864 has_attribute(_TrivialDecorator self, SparseParticleIndexKey a0) -> bool
9866 return _IMP_kernel._TrivialDecorator_has_attribute(self, *args)
9868 def get_derivative(self, a0):
9869 r"""get_derivative(_TrivialDecorator self, FloatKey a0) -> double"""
9870 return _IMP_kernel._TrivialDecorator_get_derivative(self, a0)
9873 r"""get_name(_TrivialDecorator self) -> std::string"""
9874 return _IMP_kernel._TrivialDecorator_get_name(self)
9877 r"""clear_caches(_TrivialDecorator self)"""
9878 return _IMP_kernel._TrivialDecorator_clear_caches(self)
9880 def set_name(self, a0):
9881 r"""set_name(_TrivialDecorator self, std::string a0)"""
9882 return _IMP_kernel._TrivialDecorator_set_name(self, a0)
9885 r"""set_check_level(_TrivialDecorator self, IMP::CheckLevel a0)"""
9886 return _IMP_kernel._TrivialDecorator_set_check_level(self, a0)
9888 def add_to_derivative(self, a0, a1, a2):
9889 r"""add_to_derivative(_TrivialDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9890 return _IMP_kernel._TrivialDecorator_add_to_derivative(self, a0, a1, a2)
9893 r"""set_is_optimized(_TrivialDecorator self, FloatKey a0, bool a1)"""
9894 return _IMP_kernel._TrivialDecorator_set_is_optimized(self, a0, a1)
9896 def get_is_optimized(self, a0):
9897 r"""get_is_optimized(_TrivialDecorator self, FloatKey a0) -> bool"""
9898 return _IMP_kernel._TrivialDecorator_get_is_optimized(self, a0)
9900 def get_check_level(self):
9901 r"""get_check_level(_TrivialDecorator self) -> IMP::CheckLevel"""
9902 return _IMP_kernel._TrivialDecorator_get_check_level(self)
9904 def __eq__(self, *args):
9906 __eq__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9907 __eq__(_TrivialDecorator self, Particle d) -> bool
9909 return _IMP_kernel._TrivialDecorator___eq__(self, *args)
9911 def __ne__(self, *args):
9913 __ne__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9914 __ne__(_TrivialDecorator self, Particle d) -> bool
9916 return _IMP_kernel._TrivialDecorator___ne__(self, *args)
9918 def __le__(self, *args):
9920 __le__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9921 __le__(_TrivialDecorator self, Particle d) -> bool
9923 return _IMP_kernel._TrivialDecorator___le__(self, *args)
9925 def __lt__(self, *args):
9927 __lt__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9928 __lt__(_TrivialDecorator self, Particle d) -> bool
9930 return _IMP_kernel._TrivialDecorator___lt__(self, *args)
9932 def __ge__(self, *args):
9934 __ge__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9935 __ge__(_TrivialDecorator self, Particle d) -> bool
9937 return _IMP_kernel._TrivialDecorator___ge__(self, *args)
9939 def __gt__(self, *args):
9941 __gt__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9942 __gt__(_TrivialDecorator self, Particle d) -> bool
9944 return _IMP_kernel._TrivialDecorator___gt__(self, *args)
9947 r"""__hash__(_TrivialDecorator self) -> std::size_t"""
9948 return _IMP_kernel._TrivialDecorator___hash__(self)
9951 r"""__str__(_TrivialDecorator self) -> std::string"""
9952 return _IMP_kernel._TrivialDecorator___str__(self)
9955 r"""__repr__(_TrivialDecorator self) -> std::string"""
9956 return _IMP_kernel._TrivialDecorator___repr__(self)
9958 def _get_as_binary(self):
9959 r"""_get_as_binary(_TrivialDecorator self) -> PyObject *"""
9960 return _IMP_kernel._TrivialDecorator__get_as_binary(self)
9962 def _set_from_binary(self, p):
9963 r"""_set_from_binary(_TrivialDecorator self, PyObject * p)"""
9964 return _IMP_kernel._TrivialDecorator__set_from_binary(self, p)
9966 def __getstate__(self):
9967 p = self._get_as_binary()
9968 if len(self.__dict__) > 1:
9969 d = self.__dict__.copy()
9974 def __setstate__(self, p):
9975 if not hasattr(self,
'this'):
9977 if isinstance(p, tuple):
9979 self.__dict__.update(d)
9980 return self._set_from_binary(p)
9982 __swig_destroy__ = _IMP_kernel.delete__TrivialDecorator
9985 _IMP_kernel._TrivialDecorator_swigregister(_TrivialDecorator)
9986 class _TrivialDerivedDecorator(_TrivialDecorator):
9987 r"""Proxy of C++ IMP::internal::_TrivialDerivedDecorator class."""
9989 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9991 def __init__(self, *args):
9993 __init__(_TrivialDerivedDecorator self) -> _TrivialDerivedDecorator
9994 __init__(_TrivialDerivedDecorator self, Model m, ParticleIndex id) -> _TrivialDerivedDecorator
9995 __init__(_TrivialDerivedDecorator self, _ParticleAdaptor d) -> _TrivialDerivedDecorator
9997 _IMP_kernel._TrivialDerivedDecorator_swiginit(self, _IMP_kernel.new__TrivialDerivedDecorator(*args))
9999 def show(self, *args):
10000 r"""show(_TrivialDerivedDecorator self, _ostream out=std::cout)"""
10001 return _IMP_kernel._TrivialDerivedDecorator_show(self, *args)
10004 def setup_particle(*args):
10006 setup_particle(Model m, ParticleIndex pi) -> _TrivialDerivedDecorator
10007 setup_particle(_ParticleAdaptor pa) -> _TrivialDerivedDecorator
10009 return _IMP_kernel._TrivialDerivedDecorator_setup_particle(*args)
10012 def get_is_setup(*args):
10014 get_is_setup(_ParticleAdaptor p) -> bool
10015 get_is_setup(Model m, ParticleIndex pi) -> bool
10017 return _IMP_kernel._TrivialDerivedDecorator_get_is_setup(*args)
10021 add_attribute(_TrivialDerivedDecorator self, FloatKey k, IMP::Float v, bool opt)
10022 add_attribute(_TrivialDerivedDecorator self, FloatKey a0, IMP::Float a1)
10023 add_attribute(_TrivialDerivedDecorator self, IntKey a0, IMP::Int a1)
10024 add_attribute(_TrivialDerivedDecorator self, FloatsKey a0, IMP::Floats a1)
10025 add_attribute(_TrivialDerivedDecorator self, IntsKey a0, IMP::Ints a1)
10026 add_attribute(_TrivialDerivedDecorator self, StringKey a0, IMP::String a1)
10027 add_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0, Particle a1)
10028 add_attribute(_TrivialDerivedDecorator self, ObjectKey a0, Object a1)
10029 add_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0, IMP::Float a1)
10030 add_attribute(_TrivialDerivedDecorator self, SparseIntKey a0, IMP::Int a1)
10031 add_attribute(_TrivialDerivedDecorator self, SparseStringKey a0, IMP::String a1)
10032 add_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
10034 return _IMP_kernel._TrivialDerivedDecorator_add_attribute(self, *args)
10036 def get_value(self, *args):
10038 get_value(_TrivialDerivedDecorator self, FloatKey a0) -> IMP::Float
10039 get_value(_TrivialDerivedDecorator self, IntKey a0) -> IMP::Int
10040 get_value(_TrivialDerivedDecorator self, FloatsKey a0) -> IMP::Floats
10041 get_value(_TrivialDerivedDecorator self, IntsKey a0) -> IMP::Ints
10042 get_value(_TrivialDerivedDecorator self, StringKey a0) -> IMP::String
10043 get_value(_TrivialDerivedDecorator self, ParticleIndexKey a0) -> Particle
10044 get_value(_TrivialDerivedDecorator self, ObjectKey a0) -> Object
10045 get_value(_TrivialDerivedDecorator self, SparseFloatKey a0) -> IMP::Float
10046 get_value(_TrivialDerivedDecorator self, SparseIntKey a0) -> IMP::Int
10047 get_value(_TrivialDerivedDecorator self, SparseStringKey a0) -> IMP::String
10048 get_value(_TrivialDerivedDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
10050 return _IMP_kernel._TrivialDerivedDecorator_get_value(self, *args)
10052 def set_value(self, *args):
10054 set_value(_TrivialDerivedDecorator self, FloatKey a0, IMP::Float a1)
10055 set_value(_TrivialDerivedDecorator self, IntKey a0, IMP::Int a1)
10056 set_value(_TrivialDerivedDecorator self, FloatsKey a0, IMP::Floats a1)
10057 set_value(_TrivialDerivedDecorator self, IntsKey a0, IMP::Ints a1)
10058 set_value(_TrivialDerivedDecorator self, StringKey a0, IMP::String a1)
10059 set_value(_TrivialDerivedDecorator self, ParticleIndexKey a0, Particle a1)
10060 set_value(_TrivialDerivedDecorator self, ObjectKey a0, Object a1)
10061 set_value(_TrivialDerivedDecorator self, SparseFloatKey a0, IMP::Float a1)
10062 set_value(_TrivialDerivedDecorator self, SparseIntKey a0, IMP::Int a1)
10063 set_value(_TrivialDerivedDecorator self, SparseStringKey a0, IMP::String a1)
10064 set_value(_TrivialDerivedDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
10066 return _IMP_kernel._TrivialDerivedDecorator_set_value(self, *args)
10070 remove_attribute(_TrivialDerivedDecorator self, FloatKey a0)
10071 remove_attribute(_TrivialDerivedDecorator self, IntKey a0)
10072 remove_attribute(_TrivialDerivedDecorator self, FloatsKey a0)
10073 remove_attribute(_TrivialDerivedDecorator self, IntsKey a0)
10074 remove_attribute(_TrivialDerivedDecorator self, StringKey a0)
10075 remove_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0)
10076 remove_attribute(_TrivialDerivedDecorator self, ObjectKey a0)
10077 remove_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0)
10078 remove_attribute(_TrivialDerivedDecorator self, SparseIntKey a0)
10079 remove_attribute(_TrivialDerivedDecorator self, SparseStringKey a0)
10080 remove_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0)
10082 return _IMP_kernel._TrivialDerivedDecorator_remove_attribute(self, *args)
10084 def has_attribute(self, *args):
10086 has_attribute(_TrivialDerivedDecorator self, FloatKey a0) -> bool
10087 has_attribute(_TrivialDerivedDecorator self, IntKey a0) -> bool
10088 has_attribute(_TrivialDerivedDecorator self, FloatsKey a0) -> bool
10089 has_attribute(_TrivialDerivedDecorator self, IntsKey a0) -> bool
10090 has_attribute(_TrivialDerivedDecorator self, StringKey a0) -> bool
10091 has_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0) -> bool
10092 has_attribute(_TrivialDerivedDecorator self, ObjectKey a0) -> bool
10093 has_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0) -> bool
10094 has_attribute(_TrivialDerivedDecorator self, SparseIntKey a0) -> bool
10095 has_attribute(_TrivialDerivedDecorator self, SparseStringKey a0) -> bool
10096 has_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0) -> bool
10098 return _IMP_kernel._TrivialDerivedDecorator_has_attribute(self, *args)
10100 def get_derivative(self, a0):
10101 r"""get_derivative(_TrivialDerivedDecorator self, FloatKey a0) -> double"""
10102 return _IMP_kernel._TrivialDerivedDecorator_get_derivative(self, a0)
10104 def get_name(self):
10105 r"""get_name(_TrivialDerivedDecorator self) -> std::string"""
10106 return _IMP_kernel._TrivialDerivedDecorator_get_name(self)
10109 r"""clear_caches(_TrivialDerivedDecorator self)"""
10110 return _IMP_kernel._TrivialDerivedDecorator_clear_caches(self)
10112 def set_name(self, a0):
10113 r"""set_name(_TrivialDerivedDecorator self, std::string a0)"""
10114 return _IMP_kernel._TrivialDerivedDecorator_set_name(self, a0)
10117 r"""set_check_level(_TrivialDerivedDecorator self, IMP::CheckLevel a0)"""
10118 return _IMP_kernel._TrivialDerivedDecorator_set_check_level(self, a0)
10120 def add_to_derivative(self, a0, a1, a2):
10121 r"""add_to_derivative(_TrivialDerivedDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10122 return _IMP_kernel._TrivialDerivedDecorator_add_to_derivative(self, a0, a1, a2)
10125 r"""set_is_optimized(_TrivialDerivedDecorator self, FloatKey a0, bool a1)"""
10126 return _IMP_kernel._TrivialDerivedDecorator_set_is_optimized(self, a0, a1)
10128 def get_is_optimized(self, a0):
10129 r"""get_is_optimized(_TrivialDerivedDecorator self, FloatKey a0) -> bool"""
10130 return _IMP_kernel._TrivialDerivedDecorator_get_is_optimized(self, a0)
10132 def get_check_level(self):
10133 r"""get_check_level(_TrivialDerivedDecorator self) -> IMP::CheckLevel"""
10134 return _IMP_kernel._TrivialDerivedDecorator_get_check_level(self)
10136 def __eq__(self, *args):
10138 __eq__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
10139 __eq__(_TrivialDerivedDecorator self, Particle d) -> bool
10141 return _IMP_kernel._TrivialDerivedDecorator___eq__(self, *args)
10143 def __ne__(self, *args):
10145 __ne__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
10146 __ne__(_TrivialDerivedDecorator self, Particle d) -> bool
10148 return _IMP_kernel._TrivialDerivedDecorator___ne__(self, *args)
10150 def __le__(self, *args):
10152 __le__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
10153 __le__(_TrivialDerivedDecorator self, Particle d) -> bool
10155 return _IMP_kernel._TrivialDerivedDecorator___le__(self, *args)
10157 def __lt__(self, *args):
10159 __lt__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
10160 __lt__(_TrivialDerivedDecorator self, Particle d) -> bool
10162 return _IMP_kernel._TrivialDerivedDecorator___lt__(self, *args)
10164 def __ge__(self, *args):
10166 __ge__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
10167 __ge__(_TrivialDerivedDecorator self, Particle d) -> bool
10169 return _IMP_kernel._TrivialDerivedDecorator___ge__(self, *args)
10171 def __gt__(self, *args):
10173 __gt__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
10174 __gt__(_TrivialDerivedDecorator self, Particle d) -> bool
10176 return _IMP_kernel._TrivialDerivedDecorator___gt__(self, *args)
10178 def __hash__(self):
10179 r"""__hash__(_TrivialDerivedDecorator self) -> std::size_t"""
10180 return _IMP_kernel._TrivialDerivedDecorator___hash__(self)
10183 r"""__str__(_TrivialDerivedDecorator self) -> std::string"""
10184 return _IMP_kernel._TrivialDerivedDecorator___str__(self)
10186 def __repr__(self):
10187 r"""__repr__(_TrivialDerivedDecorator self) -> std::string"""
10188 return _IMP_kernel._TrivialDerivedDecorator___repr__(self)
10190 def _get_as_binary(self):
10191 r"""_get_as_binary(_TrivialDerivedDecorator self) -> PyObject *"""
10192 return _IMP_kernel._TrivialDerivedDecorator__get_as_binary(self)
10194 def _set_from_binary(self, p):
10195 r"""_set_from_binary(_TrivialDerivedDecorator self, PyObject * p)"""
10196 return _IMP_kernel._TrivialDerivedDecorator__set_from_binary(self, p)
10198 def __getstate__(self):
10199 p = self._get_as_binary()
10200 if len(self.__dict__) > 1:
10201 d = self.__dict__.copy()
10206 def __setstate__(self, p):
10207 if not hasattr(self,
'this'):
10209 if isinstance(p, tuple):
10211 self.__dict__.update(d)
10212 return self._set_from_binary(p)
10214 __swig_destroy__ = _IMP_kernel.delete__TrivialDerivedDecorator
10217 _IMP_kernel._TrivialDerivedDecorator_swigregister(_TrivialDerivedDecorator)
10218 class _TrivialTraitsDecorator(
Decorator):
10219 r"""Proxy of C++ IMP::internal::_TrivialTraitsDecorator class."""
10221 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10223 def get_decorator_traits(self):
10224 r"""get_decorator_traits(_TrivialTraitsDecorator self) -> StringKey"""
10225 return _IMP_kernel._TrivialTraitsDecorator_get_decorator_traits(self)
10228 def get_default_decorator_traits():
10229 r"""get_default_decorator_traits() -> StringKey"""
10230 return _IMP_kernel._TrivialTraitsDecorator_get_default_decorator_traits()
10232 def __init__(self, *args):
10234 __init__(_TrivialTraitsDecorator self) -> _TrivialTraitsDecorator
10235 __init__(_TrivialTraitsDecorator self, Model m, ParticleIndex id, StringKey tr=get_default_key()) -> _TrivialTraitsDecorator
10236 __init__(_TrivialTraitsDecorator self, _ParticleAdaptor d, StringKey tr=get_default_key()) -> _TrivialTraitsDecorator
10238 _IMP_kernel._TrivialTraitsDecorator_swiginit(self, _IMP_kernel.new__TrivialTraitsDecorator(*args))
10240 def show(self, *args):
10241 r"""show(_TrivialTraitsDecorator self, _ostream out=std::cout)"""
10242 return _IMP_kernel._TrivialTraitsDecorator_show(self, *args)
10245 def setup_particle(*args):
10247 setup_particle(Model m, ParticleIndex pi, StringKey tr=IMP::internal::_TrivialTraitsDecorator::get_default_decorator_traits()) -> _TrivialTraitsDecorator
10248 setup_particle(_ParticleAdaptor d, StringKey tr=IMP::internal::_TrivialTraitsDecorator::get_default_decorator_traits()) -> _TrivialTraitsDecorator
10250 return _IMP_kernel._TrivialTraitsDecorator_setup_particle(*args)
10253 def get_is_setup(*args):
10255 get_is_setup(_ParticleAdaptor p, StringKey tr=get_default_key()) -> bool
10256 get_is_setup(Model m, ParticleIndex pi, StringKey k=get_default_key()) -> bool
10258 return _IMP_kernel._TrivialTraitsDecorator_get_is_setup(*args)
10261 def get_default_key():
10262 r"""get_default_key() -> StringKey"""
10263 return _IMP_kernel._TrivialTraitsDecorator_get_default_key()
10267 add_attribute(_TrivialTraitsDecorator self, FloatKey k, IMP::Float v, bool opt)
10268 add_attribute(_TrivialTraitsDecorator self, FloatKey a0, IMP::Float a1)
10269 add_attribute(_TrivialTraitsDecorator self, IntKey a0, IMP::Int a1)
10270 add_attribute(_TrivialTraitsDecorator self, FloatsKey a0, IMP::Floats a1)
10271 add_attribute(_TrivialTraitsDecorator self, IntsKey a0, IMP::Ints a1)
10272 add_attribute(_TrivialTraitsDecorator self, StringKey a0, IMP::String a1)
10273 add_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0, Particle a1)
10274 add_attribute(_TrivialTraitsDecorator self, ObjectKey a0, Object a1)
10275 add_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0, IMP::Float a1)
10276 add_attribute(_TrivialTraitsDecorator self, SparseIntKey a0, IMP::Int a1)
10277 add_attribute(_TrivialTraitsDecorator self, SparseStringKey a0, IMP::String a1)
10278 add_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
10280 return _IMP_kernel._TrivialTraitsDecorator_add_attribute(self, *args)
10282 def get_value(self, *args):
10284 get_value(_TrivialTraitsDecorator self, FloatKey a0) -> IMP::Float
10285 get_value(_TrivialTraitsDecorator self, IntKey a0) -> IMP::Int
10286 get_value(_TrivialTraitsDecorator self, FloatsKey a0) -> IMP::Floats
10287 get_value(_TrivialTraitsDecorator self, IntsKey a0) -> IMP::Ints
10288 get_value(_TrivialTraitsDecorator self, StringKey a0) -> IMP::String
10289 get_value(_TrivialTraitsDecorator self, ParticleIndexKey a0) -> Particle
10290 get_value(_TrivialTraitsDecorator self, ObjectKey a0) -> Object
10291 get_value(_TrivialTraitsDecorator self, SparseFloatKey a0) -> IMP::Float
10292 get_value(_TrivialTraitsDecorator self, SparseIntKey a0) -> IMP::Int
10293 get_value(_TrivialTraitsDecorator self, SparseStringKey a0) -> IMP::String
10294 get_value(_TrivialTraitsDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
10296 return _IMP_kernel._TrivialTraitsDecorator_get_value(self, *args)
10298 def set_value(self, *args):
10300 set_value(_TrivialTraitsDecorator self, FloatKey a0, IMP::Float a1)
10301 set_value(_TrivialTraitsDecorator self, IntKey a0, IMP::Int a1)
10302 set_value(_TrivialTraitsDecorator self, FloatsKey a0, IMP::Floats a1)
10303 set_value(_TrivialTraitsDecorator self, IntsKey a0, IMP::Ints a1)
10304 set_value(_TrivialTraitsDecorator self, StringKey a0, IMP::String a1)
10305 set_value(_TrivialTraitsDecorator self, ParticleIndexKey a0, Particle a1)
10306 set_value(_TrivialTraitsDecorator self, ObjectKey a0, Object a1)
10307 set_value(_TrivialTraitsDecorator self, SparseFloatKey a0, IMP::Float a1)
10308 set_value(_TrivialTraitsDecorator self, SparseIntKey a0, IMP::Int a1)
10309 set_value(_TrivialTraitsDecorator self, SparseStringKey a0, IMP::String a1)
10310 set_value(_TrivialTraitsDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
10312 return _IMP_kernel._TrivialTraitsDecorator_set_value(self, *args)
10316 remove_attribute(_TrivialTraitsDecorator self, FloatKey a0)
10317 remove_attribute(_TrivialTraitsDecorator self, IntKey a0)
10318 remove_attribute(_TrivialTraitsDecorator self, FloatsKey a0)
10319 remove_attribute(_TrivialTraitsDecorator self, IntsKey a0)
10320 remove_attribute(_TrivialTraitsDecorator self, StringKey a0)
10321 remove_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0)
10322 remove_attribute(_TrivialTraitsDecorator self, ObjectKey a0)
10323 remove_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0)
10324 remove_attribute(_TrivialTraitsDecorator self, SparseIntKey a0)
10325 remove_attribute(_TrivialTraitsDecorator self, SparseStringKey a0)
10326 remove_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0)
10328 return _IMP_kernel._TrivialTraitsDecorator_remove_attribute(self, *args)
10330 def has_attribute(self, *args):
10332 has_attribute(_TrivialTraitsDecorator self, FloatKey a0) -> bool
10333 has_attribute(_TrivialTraitsDecorator self, IntKey a0) -> bool
10334 has_attribute(_TrivialTraitsDecorator self, FloatsKey a0) -> bool
10335 has_attribute(_TrivialTraitsDecorator self, IntsKey a0) -> bool
10336 has_attribute(_TrivialTraitsDecorator self, StringKey a0) -> bool
10337 has_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0) -> bool
10338 has_attribute(_TrivialTraitsDecorator self, ObjectKey a0) -> bool
10339 has_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0) -> bool
10340 has_attribute(_TrivialTraitsDecorator self, SparseIntKey a0) -> bool
10341 has_attribute(_TrivialTraitsDecorator self, SparseStringKey a0) -> bool
10342 has_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0) -> bool
10344 return _IMP_kernel._TrivialTraitsDecorator_has_attribute(self, *args)
10346 def get_derivative(self, a0):
10347 r"""get_derivative(_TrivialTraitsDecorator self, FloatKey a0) -> double"""
10348 return _IMP_kernel._TrivialTraitsDecorator_get_derivative(self, a0)
10350 def get_name(self):
10351 r"""get_name(_TrivialTraitsDecorator self) -> std::string"""
10352 return _IMP_kernel._TrivialTraitsDecorator_get_name(self)
10355 r"""clear_caches(_TrivialTraitsDecorator self)"""
10356 return _IMP_kernel._TrivialTraitsDecorator_clear_caches(self)
10358 def set_name(self, a0):
10359 r"""set_name(_TrivialTraitsDecorator self, std::string a0)"""
10360 return _IMP_kernel._TrivialTraitsDecorator_set_name(self, a0)
10363 r"""set_check_level(_TrivialTraitsDecorator self, IMP::CheckLevel a0)"""
10364 return _IMP_kernel._TrivialTraitsDecorator_set_check_level(self, a0)
10366 def add_to_derivative(self, a0, a1, a2):
10367 r"""add_to_derivative(_TrivialTraitsDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10368 return _IMP_kernel._TrivialTraitsDecorator_add_to_derivative(self, a0, a1, a2)
10371 r"""set_is_optimized(_TrivialTraitsDecorator self, FloatKey a0, bool a1)"""
10372 return _IMP_kernel._TrivialTraitsDecorator_set_is_optimized(self, a0, a1)
10374 def get_is_optimized(self, a0):
10375 r"""get_is_optimized(_TrivialTraitsDecorator self, FloatKey a0) -> bool"""
10376 return _IMP_kernel._TrivialTraitsDecorator_get_is_optimized(self, a0)
10378 def get_check_level(self):
10379 r"""get_check_level(_TrivialTraitsDecorator self) -> IMP::CheckLevel"""
10380 return _IMP_kernel._TrivialTraitsDecorator_get_check_level(self)
10382 def __eq__(self, *args):
10384 __eq__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10385 __eq__(_TrivialTraitsDecorator self, Particle d) -> bool
10387 return _IMP_kernel._TrivialTraitsDecorator___eq__(self, *args)
10389 def __ne__(self, *args):
10391 __ne__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10392 __ne__(_TrivialTraitsDecorator self, Particle d) -> bool
10394 return _IMP_kernel._TrivialTraitsDecorator___ne__(self, *args)
10396 def __le__(self, *args):
10398 __le__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10399 __le__(_TrivialTraitsDecorator self, Particle d) -> bool
10401 return _IMP_kernel._TrivialTraitsDecorator___le__(self, *args)
10403 def __lt__(self, *args):
10405 __lt__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10406 __lt__(_TrivialTraitsDecorator self, Particle d) -> bool
10408 return _IMP_kernel._TrivialTraitsDecorator___lt__(self, *args)
10410 def __ge__(self, *args):
10412 __ge__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10413 __ge__(_TrivialTraitsDecorator self, Particle d) -> bool
10415 return _IMP_kernel._TrivialTraitsDecorator___ge__(self, *args)
10417 def __gt__(self, *args):
10419 __gt__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10420 __gt__(_TrivialTraitsDecorator self, Particle d) -> bool
10422 return _IMP_kernel._TrivialTraitsDecorator___gt__(self, *args)
10424 def __hash__(self):
10425 r"""__hash__(_TrivialTraitsDecorator self) -> std::size_t"""
10426 return _IMP_kernel._TrivialTraitsDecorator___hash__(self)
10429 r"""__str__(_TrivialTraitsDecorator self) -> std::string"""
10430 return _IMP_kernel._TrivialTraitsDecorator___str__(self)
10432 def __repr__(self):
10433 r"""__repr__(_TrivialTraitsDecorator self) -> std::string"""
10434 return _IMP_kernel._TrivialTraitsDecorator___repr__(self)
10435 __swig_destroy__ = _IMP_kernel.delete__TrivialTraitsDecorator
10438 _IMP_kernel._TrivialTraitsDecorator_swigregister(_TrivialTraitsDecorator)
10440 def __lshift__(*args):
10442 __lshift__(_ostream out, _TrivialDecorator n) -> _ostream
10443 __lshift__(_ostream out, _TrivialDerivedDecorator n) -> _ostream
10444 __lshift__(_ostream out, _TrivialTraitsDecorator n) -> _ostream
10446 return _IMP_kernel.__lshift__(*args)
10448 r"""Proxy of C++ IMP::internal::_ConstOptimizer class."""
10450 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10452 def __init__(self, *args):
10454 __init__(_ConstOptimizer self, Model m) -> _ConstOptimizer
10455 __init__(_ConstOptimizer self) -> _ConstOptimizer
10457 _IMP_kernel._ConstOptimizer_swiginit(self, _IMP_kernel.new__ConstOptimizer(*args))
10459 def do_optimize(self, max_steps):
10460 r"""do_optimize(_ConstOptimizer self, unsigned int max_steps) -> IMP::Float"""
10461 return _IMP_kernel._ConstOptimizer_do_optimize(self, max_steps)
10464 r"""get_version_info(_ConstOptimizer self) -> VersionInfo"""
10465 return _IMP_kernel._ConstOptimizer_get_version_info(self)
10466 __swig_destroy__ = _IMP_kernel.delete__ConstOptimizer
10469 r"""__str__(_ConstOptimizer self) -> std::string"""
10470 return _IMP_kernel._ConstOptimizer___str__(self)
10472 def __repr__(self):
10473 r"""__repr__(_ConstOptimizer self) -> std::string"""
10474 return _IMP_kernel._ConstOptimizer___repr__(self)
10478 return _object_cast_to__ConstOptimizer(o)
10481 def _get_as_binary(self):
10482 r"""_get_as_binary(_ConstOptimizer self) -> PyObject *"""
10483 return _IMP_kernel._ConstOptimizer__get_as_binary(self)
10485 def _set_from_binary(self, p):
10486 r"""_set_from_binary(_ConstOptimizer self, PyObject * p)"""
10487 return _IMP_kernel._ConstOptimizer__set_from_binary(self, p)
10489 def __getstate__(self):
10490 p = self._get_as_binary()
10491 if len(self.__dict__) > 1:
10492 d = self.__dict__.copy()
10497 def __setstate__(self, p):
10498 if not hasattr(self,
'this'):
10500 if isinstance(p, tuple):
10502 self.__dict__.update(d)
10503 return self._set_from_binary(p)
10507 _IMP_kernel._ConstOptimizer_swigregister(_ConstOptimizer)
10510 r"""get_particle(Particle p) -> Particle"""
10511 return _IMP_kernel.get_particle(p)
10513 def _decorator_test(p):
10514 r"""_decorator_test(Particle p)"""
10515 return _IMP_kernel._decorator_test(p)
10517 def _overloaded_decorator(*args):
10519 _overloaded_decorator(_TrivialDecorator a) -> int
10520 _overloaded_decorator(_TrivialDerivedDecorator a) -> int
10522 return _IMP_kernel._overloaded_decorator(*args)
10524 def _take_particles(*args):
10526 _take_particles(IMP::Particles const & ps) -> unsigned int
10527 _take_particles(Model m, IMP::Particles const & ps) -> unsigned int
10528 _take_particles(Model m, IMP::Particles const & ps, TextOutput out) -> unsigned int
10530 return _IMP_kernel._take_particles(*args)
10532 def _give_particles(m):
10533 r"""_give_particles(Model m) -> IMP::Particles const &"""
10534 return _IMP_kernel._give_particles(m)
10536 def _pass_particles(ps):
10537 r"""_pass_particles(IMP::Particles const & ps) -> IMP::Particles const &"""
10538 return _IMP_kernel._pass_particles(ps)
10540 def _pass_particle(ps):
10541 r"""_pass_particle(Particle ps) -> Particle"""
10542 return _IMP_kernel._pass_particle(ps)
10544 def _pass_particle_pair(pp):
10545 r"""_pass_particle_pair(IMP::ParticlePair const & pp) -> IMP::ParticlePair const &"""
10546 return _IMP_kernel._pass_particle_pair(pp)
10548 def _give_particles_copy(m):
10549 r"""_give_particles_copy(Model m) -> IMP::Particles"""
10550 return _IMP_kernel._give_particles_copy(m)
10552 def _pass_float_keys(input):
10553 r"""_pass_float_keys(IMP::FloatKeys const & input) -> IMP::FloatKeys"""
10554 return _IMP_kernel._pass_float_keys(input)
10558 _pass(IMP::Particles const & p) -> IMP::Particles const
10559 _pass(IMP::Restraints const & p) -> IMP::Restraints const &
10561 return _IMP_kernel._pass(*args)
10563 def _pass_decorators(p):
10564 r"""_pass_decorators(IMP::internal::_TrivialDecorators const & p) -> IMP::internal::_TrivialDecorators const &"""
10565 return _IMP_kernel._pass_decorators(p)
10567 def _pass_decorator_traits(p):
10568 r"""_pass_decorator_traits(IMP::internal::_TrivialTraitsDecorators const & p) -> IMP::internal::_TrivialTraitsDecorators const &"""
10569 return _IMP_kernel._pass_decorator_traits(p)
10571 def _pass_particle_pairs(p):
10572 r"""_pass_particle_pairs(IMP::ParticlePairsTemp const & p) -> IMP::ParticlePairsTemp"""
10573 return _IMP_kernel._pass_particle_pairs(p)
10575 def _pass_particle_index_pairs(p):
10576 r"""_pass_particle_index_pairs(IMP::ParticleIndexPairs const & p) -> IMP::ParticleIndexPairs"""
10577 return _IMP_kernel._pass_particle_index_pairs(p)
10579 def _pass_model_objects(p):
10580 r"""_pass_model_objects(IMP::ModelObjectsTemp const & p) -> IMP::ModelObjectsTemp"""
10581 return _IMP_kernel._pass_model_objects(p)
10583 def _pass_particles_temps(ps):
10584 r"""_pass_particles_temps(IMP::ParticlesTemps const & ps) -> IMP::ParticlesTemps"""
10585 return _IMP_kernel._pass_particles_temps(ps)
10587 def _test_overload(*args):
10589 _test_overload(IMP::Particles const & ps) -> int
10590 _test_overload(IMP::Restraints const & ps) -> int
10592 return _IMP_kernel._test_overload(*args)
10594 def _get_range(m, k):
10595 r"""_get_range(Model m, FloatKey k) -> IMP::FloatRange"""
10596 return _IMP_kernel._get_range(m, k)
10598 def _create_particles_from_pdb(name, m):
10599 r"""_create_particles_from_pdb(std::string name, Model m) -> IMP::ParticleIndexes"""
10600 return _IMP_kernel._create_particles_from_pdb(name, m)
10602 r"""Proxy of C++ IMP::internal::_LogPairScore class."""
10604 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10605 __repr__ = _swig_repr
10607 def __init__(self):
10608 r"""__init__(_LogPairScore self) -> _LogPairScore"""
10609 _IMP_kernel._LogPairScore_swiginit(self, _IMP_kernel.new__LogPairScore())
10611 def do_get_inputs(self, arg2, arg3):
10612 r"""do_get_inputs(_LogPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
10613 return _IMP_kernel._LogPairScore_do_get_inputs(self, arg2, arg3)
10615 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
10616 r"""evaluate_indexes(_LogPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
10617 return _IMP_kernel._LogPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
10619 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
10620 r"""evaluate_indexes_scores(_LogPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, unsigned int lower_bound, unsigned int upper_bound, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
10621 return _IMP_kernel._LogPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
10623 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
10624 r"""evaluate_indexes_delta(_LogPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, std::vector< unsigned int,std::allocator< unsigned int > > const & indexes, std::vector< double,std::allocator< double > > & score, bool all_indexes_checked=False) -> double"""
10625 return _IMP_kernel._LogPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
10627 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
10628 r"""evaluate_if_good_indexes(_LogPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound, bool all_indexes_checked=False) -> double"""
10629 return _IMP_kernel._LogPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
10632 r"""get_version_info(_LogPairScore self) -> VersionInfo"""
10633 return _IMP_kernel._LogPairScore_get_version_info(self)
10634 __swig_destroy__ = _IMP_kernel.delete__LogPairScore
10636 def get_particle_pairs(self):
10637 r"""get_particle_pairs(_LogPairScore self) -> IMP::ParticlePairsTemp"""
10638 return _IMP_kernel._LogPairScore_get_particle_pairs(self)
10641 r"""clear(_LogPairScore self)"""
10642 return _IMP_kernel._LogPairScore_clear(self)
10644 def get_contains(self, pp):
10645 r"""get_contains(_LogPairScore self, IMP::ParticlePair const & pp) -> bool"""
10646 return _IMP_kernel._LogPairScore_get_contains(self, pp)
10649 _IMP_kernel._LogPairScore_swigregister(_LogPairScore)
10651 def _overloaded_particles(*args):
10653 _overloaded_particles(Particle arg1)
10654 _overloaded_particles(IMP::Particles const & arg1)
10655 _overloaded_particles(IMP::ParticlesTemp const & arg1)
10656 _overloaded_particles(Model arg1, IMP::ParticleIndexes const & arg2)
10657 _overloaded_particles(IMP::internal::_TrivialDecorators const & arg1)
10658 _overloaded_particles(_TrivialDecorator arg1)
10660 return _IMP_kernel._overloaded_particles(*args)
10661 class _ImplicitParticles(object):
10662 r"""Proxy of C++ IMP::internal::_ImplicitParticles class."""
10664 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10665 __repr__ = _swig_repr
10667 def __init__(self, *args):
10669 __init__(_ImplicitParticles self, Particle arg2) -> _ImplicitParticles
10670 __init__(_ImplicitParticles self, IMP::Particles const & arg2) -> _ImplicitParticles
10671 __init__(_ImplicitParticles self, IMP::ParticlesTemp const & arg2) -> _ImplicitParticles
10672 __init__(_ImplicitParticles self, Model arg2, IMP::ParticleIndexes const & arg3) -> _ImplicitParticles
10673 __init__(_ImplicitParticles self, IMP::internal::_TrivialDecorators const & arg2) -> _ImplicitParticles
10674 __init__(_ImplicitParticles self, _TrivialDecorator arg2) -> _ImplicitParticles
10676 _IMP_kernel._ImplicitParticles_swiginit(self, _IMP_kernel.new__ImplicitParticles(*args))
10677 __swig_destroy__ = _IMP_kernel.delete__ImplicitParticles
10680 _IMP_kernel._ImplicitParticles_swigregister(_ImplicitParticles)
10682 def _implicit_particles(arg1):
10683 r"""_implicit_particles(_ImplicitParticles arg1)"""
10684 return _IMP_kernel._implicit_particles(arg1)
10686 def _take_particle_adaptor(pa):
10687 r"""_take_particle_adaptor(_ParticleAdaptor pa) -> ParticleIndex"""
10688 return _IMP_kernel._take_particle_adaptor(pa)
10690 def _take_particle_indexes_adaptor(pa):
10691 r"""_take_particle_indexes_adaptor(_ParticleIndexesAdaptor pa) -> IMP::ParticleIndexes"""
10692 return _IMP_kernel._take_particle_indexes_adaptor(pa)
10693 class Vector1D(_VectorBase1D):
10694 r"""Proxy of C++ IMP::VectorD< 1 > class."""
10696 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10698 def get_unit_vector(self):
10699 r"""get_unit_vector(Vector1D self) -> Vector1D"""
10700 return _IMP_kernel.Vector1D_get_unit_vector(self)
10702 def __truediv__(self, *args):
10703 return _IMP_kernel.Vector1D___truediv__(self, *args)
10708 r"""__neg__(Vector1D self) -> Vector1D"""
10709 return _IMP_kernel.Vector1D___neg__(self)
10711 def __sub__(self, o):
10712 r"""__sub__(Vector1D self, Vector1D o) -> Vector1D"""
10713 return _IMP_kernel.Vector1D___sub__(self, o)
10715 def __add__(self, ret):
10716 r"""__add__(Vector1D self, Vector1D ret) -> Vector1D"""
10717 return _IMP_kernel.Vector1D___add__(self, ret)
10719 def __mul__(self, *args):
10721 __mul__(Vector1D self, double s) -> Vector1D
10722 __mul__(Vector1D self, Vector1D o) -> double
10724 return _IMP_kernel.Vector1D___mul__(self, *args)
10726 def __init__(self, *args):
10728 __init__(Vector1D self, IMP::Floats const & f) -> Vector1D
10729 __init__(Vector1D self) -> Vector1D
10730 __init__(Vector1D self, double x) -> Vector1D
10732 _IMP_kernel.Vector1D_swiginit(self, _IMP_kernel.new_Vector1D(*args))
10734 def __iadd__(self, *args):
10735 _IMP_kernel.Vector1D___iadd__(self, *args)
10740 def __imul__(self, *args):
10741 _IMP_kernel.Vector1D___imul__(self, *args)
10746 def __itruediv__(self, *args):
10747 _IMP_kernel.Vector1D___itruediv__(self, *args)
10752 def __isub__(self, *args):
10753 _IMP_kernel.Vector1D___isub__(self, *args)
10759 r"""__len__(Vector1D self) -> unsigned int"""
10760 return _IMP_kernel.Vector1D___len__(self)
10762 def __rmul__(self, f):
10763 r"""__rmul__(Vector1D self, double f) -> Vector1D"""
10764 return _IMP_kernel.Vector1D___rmul__(self, f)
10767 r"""__str__(Vector1D self) -> std::string"""
10768 return _IMP_kernel.Vector1D___str__(self)
10770 def __repr__(self):
10771 r"""__repr__(Vector1D self) -> std::string"""
10772 return _IMP_kernel.Vector1D___repr__(self)
10774 def __eq__(self, arg2):
10775 r"""__eq__(Vector1D self, Vector1D arg2) -> bool"""
10776 return _IMP_kernel.Vector1D___eq__(self, arg2)
10778 def _get_as_binary(self):
10779 r"""_get_as_binary(Vector1D self) -> PyObject *"""
10780 return _IMP_kernel.Vector1D__get_as_binary(self)
10782 def _set_from_binary(self, p):
10783 r"""_set_from_binary(Vector1D self, PyObject * p)"""
10784 return _IMP_kernel.Vector1D__set_from_binary(self, p)
10786 def __getstate__(self):
10787 p = self._get_as_binary()
10788 if len(self.__dict__) > 1:
10789 d = self.__dict__.copy()
10794 def __setstate__(self, p):
10795 if not hasattr(self,
'this'):
10797 if isinstance(p, tuple):
10799 self.__dict__.update(d)
10800 return self._set_from_binary(p)
10803 def __getitem__(self, index):
10804 if isinstance(index, slice):
10805 return [self[i]
for i
in range(*index.indices(len(self)))]
10807 return _IMP_kernel.Vector1D___getitem__(self, index)
10811 def __setitem__(self, index, val):
10812 if isinstance(index, slice):
10813 if not hasattr(val,
'__iter__'):
10814 raise TypeError(
"must assign iterable to extended slice")
10815 inds = range(*index.indices(len(self)))
10816 if len(inds) != len(val):
10818 "attempt to assign sequence of size %d "
10819 "to extended slice of size %d" % (len(val), len(inds)))
10820 for ind, v
in zip(inds, val):
10823 return _IMP_kernel.Vector1D___setitem__(self, index, val)
10826 __swig_destroy__ = _IMP_kernel.delete_Vector1D
10829 _IMP_kernel.Vector1D_swigregister(Vector1D)
10830 class Vector2D(_VectorBase2D):
10831 r"""Proxy of C++ IMP::VectorD< 2 > class."""
10833 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10835 def get_unit_vector(self):
10836 r"""get_unit_vector(Vector2D self) -> Vector2D"""
10837 return _IMP_kernel.Vector2D_get_unit_vector(self)
10839 def __truediv__(self, *args):
10840 return _IMP_kernel.Vector2D___truediv__(self, *args)
10845 r"""__neg__(Vector2D self) -> Vector2D"""
10846 return _IMP_kernel.Vector2D___neg__(self)
10848 def __sub__(self, o):
10849 r"""__sub__(Vector2D self, Vector2D o) -> Vector2D"""
10850 return _IMP_kernel.Vector2D___sub__(self, o)
10852 def __add__(self, ret):
10853 r"""__add__(Vector2D self, Vector2D ret) -> Vector2D"""
10854 return _IMP_kernel.Vector2D___add__(self, ret)
10856 def __mul__(self, *args):
10858 __mul__(Vector2D self, double s) -> Vector2D
10859 __mul__(Vector2D self, Vector2D o) -> double
10861 return _IMP_kernel.Vector2D___mul__(self, *args)
10863 def __init__(self, *args):
10865 __init__(Vector2D self, IMP::Floats const & f) -> Vector2D
10866 __init__(Vector2D self) -> Vector2D
10867 __init__(Vector2D self, double x, double y) -> Vector2D
10869 _IMP_kernel.Vector2D_swiginit(self, _IMP_kernel.new_Vector2D(*args))
10871 def __iadd__(self, *args):
10872 _IMP_kernel.Vector2D___iadd__(self, *args)
10877 def __imul__(self, *args):
10878 _IMP_kernel.Vector2D___imul__(self, *args)
10883 def __itruediv__(self, *args):
10884 _IMP_kernel.Vector2D___itruediv__(self, *args)
10889 def __isub__(self, *args):
10890 _IMP_kernel.Vector2D___isub__(self, *args)
10896 r"""__len__(Vector2D self) -> unsigned int"""
10897 return _IMP_kernel.Vector2D___len__(self)
10899 def __rmul__(self, f):
10900 r"""__rmul__(Vector2D self, double f) -> Vector2D"""
10901 return _IMP_kernel.Vector2D___rmul__(self, f)
10904 r"""__str__(Vector2D self) -> std::string"""
10905 return _IMP_kernel.Vector2D___str__(self)
10907 def __repr__(self):
10908 r"""__repr__(Vector2D self) -> std::string"""
10909 return _IMP_kernel.Vector2D___repr__(self)
10911 def __eq__(self, arg2):
10912 r"""__eq__(Vector2D self, Vector2D arg2) -> bool"""
10913 return _IMP_kernel.Vector2D___eq__(self, arg2)
10915 def _get_as_binary(self):
10916 r"""_get_as_binary(Vector2D self) -> PyObject *"""
10917 return _IMP_kernel.Vector2D__get_as_binary(self)
10919 def _set_from_binary(self, p):
10920 r"""_set_from_binary(Vector2D self, PyObject * p)"""
10921 return _IMP_kernel.Vector2D__set_from_binary(self, p)
10923 def __getstate__(self):
10924 p = self._get_as_binary()
10925 if len(self.__dict__) > 1:
10926 d = self.__dict__.copy()
10931 def __setstate__(self, p):
10932 if not hasattr(self,
'this'):
10934 if isinstance(p, tuple):
10936 self.__dict__.update(d)
10937 return self._set_from_binary(p)
10940 def __getitem__(self, index):
10941 if isinstance(index, slice):
10942 return [self[i]
for i
in range(*index.indices(len(self)))]
10944 return _IMP_kernel.Vector2D___getitem__(self, index)
10948 def __setitem__(self, index, val):
10949 if isinstance(index, slice):
10950 if not hasattr(val,
'__iter__'):
10951 raise TypeError(
"must assign iterable to extended slice")
10952 inds = range(*index.indices(len(self)))
10953 if len(inds) != len(val):
10955 "attempt to assign sequence of size %d "
10956 "to extended slice of size %d" % (len(val), len(inds)))
10957 for ind, v
in zip(inds, val):
10960 return _IMP_kernel.Vector2D___setitem__(self, index, val)
10963 __swig_destroy__ = _IMP_kernel.delete_Vector2D
10966 _IMP_kernel.Vector2D_swigregister(Vector2D)
10967 class Vector3D(_VectorBase3D):
10968 r"""Proxy of C++ IMP::VectorD< 3 > class."""
10970 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10972 def get_unit_vector(self):
10973 r"""get_unit_vector(Vector3D self) -> Vector3D"""
10974 return _IMP_kernel.Vector3D_get_unit_vector(self)
10976 def __truediv__(self, *args):
10977 return _IMP_kernel.Vector3D___truediv__(self, *args)
10982 r"""__neg__(Vector3D self) -> Vector3D"""
10983 return _IMP_kernel.Vector3D___neg__(self)
10985 def __sub__(self, o):
10986 r"""__sub__(Vector3D self, Vector3D o) -> Vector3D"""
10987 return _IMP_kernel.Vector3D___sub__(self, o)
10989 def __add__(self, ret):
10990 r"""__add__(Vector3D self, Vector3D ret) -> Vector3D"""
10991 return _IMP_kernel.Vector3D___add__(self, ret)
10993 def __mul__(self, *args):
10995 __mul__(Vector3D self, double s) -> Vector3D
10996 __mul__(Vector3D self, Vector3D o) -> double
10998 return _IMP_kernel.Vector3D___mul__(self, *args)
11000 def __init__(self, *args):
11002 __init__(Vector3D self, IMP::Floats const & f) -> Vector3D
11003 __init__(Vector3D self) -> Vector3D
11004 __init__(Vector3D self, double x, double y, double z) -> Vector3D
11006 _IMP_kernel.Vector3D_swiginit(self, _IMP_kernel.new_Vector3D(*args))
11008 def __iadd__(self, *args):
11009 _IMP_kernel.Vector3D___iadd__(self, *args)
11014 def __imul__(self, *args):
11015 _IMP_kernel.Vector3D___imul__(self, *args)
11020 def __itruediv__(self, *args):
11021 _IMP_kernel.Vector3D___itruediv__(self, *args)
11026 def __isub__(self, *args):
11027 _IMP_kernel.Vector3D___isub__(self, *args)
11033 r"""__len__(Vector3D self) -> unsigned int"""
11034 return _IMP_kernel.Vector3D___len__(self)
11036 def __rmul__(self, f):
11037 r"""__rmul__(Vector3D self, double f) -> Vector3D"""
11038 return _IMP_kernel.Vector3D___rmul__(self, f)
11041 r"""__str__(Vector3D self) -> std::string"""
11042 return _IMP_kernel.Vector3D___str__(self)
11044 def __repr__(self):
11045 r"""__repr__(Vector3D self) -> std::string"""
11046 return _IMP_kernel.Vector3D___repr__(self)
11048 def __eq__(self, arg2):
11049 r"""__eq__(Vector3D self, Vector3D arg2) -> bool"""
11050 return _IMP_kernel.Vector3D___eq__(self, arg2)
11052 def _get_as_binary(self):
11053 r"""_get_as_binary(Vector3D self) -> PyObject *"""
11054 return _IMP_kernel.Vector3D__get_as_binary(self)
11056 def _set_from_binary(self, p):
11057 r"""_set_from_binary(Vector3D self, PyObject * p)"""
11058 return _IMP_kernel.Vector3D__set_from_binary(self, p)
11060 def __getstate__(self):
11061 p = self._get_as_binary()
11062 if len(self.__dict__) > 1:
11063 d = self.__dict__.copy()
11068 def __setstate__(self, p):
11069 if not hasattr(self,
'this'):
11071 if isinstance(p, tuple):
11073 self.__dict__.update(d)
11074 return self._set_from_binary(p)
11077 def __getitem__(self, index):
11078 if isinstance(index, slice):
11079 return [self[i]
for i
in range(*index.indices(len(self)))]
11081 return _IMP_kernel.Vector3D___getitem__(self, index)
11085 def __setitem__(self, index, val):
11086 if isinstance(index, slice):
11087 if not hasattr(val,
'__iter__'):
11088 raise TypeError(
"must assign iterable to extended slice")
11089 inds = range(*index.indices(len(self)))
11090 if len(inds) != len(val):
11092 "attempt to assign sequence of size %d "
11093 "to extended slice of size %d" % (len(val), len(inds)))
11094 for ind, v
in zip(inds, val):
11097 return _IMP_kernel.Vector3D___setitem__(self, index, val)
11100 __swig_destroy__ = _IMP_kernel.delete_Vector3D
11103 _IMP_kernel.Vector3D_swigregister(Vector3D)
11104 class Vector4D(_VectorBase4D):
11105 r"""Proxy of C++ IMP::VectorD< 4 > class."""
11107 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11109 def get_unit_vector(self):
11110 r"""get_unit_vector(Vector4D self) -> Vector4D"""
11111 return _IMP_kernel.Vector4D_get_unit_vector(self)
11113 def __truediv__(self, *args):
11114 return _IMP_kernel.Vector4D___truediv__(self, *args)
11119 r"""__neg__(Vector4D self) -> Vector4D"""
11120 return _IMP_kernel.Vector4D___neg__(self)
11122 def __sub__(self, o):
11123 r"""__sub__(Vector4D self, Vector4D o) -> Vector4D"""
11124 return _IMP_kernel.Vector4D___sub__(self, o)
11126 def __add__(self, ret):
11127 r"""__add__(Vector4D self, Vector4D ret) -> Vector4D"""
11128 return _IMP_kernel.Vector4D___add__(self, ret)
11130 def __mul__(self, *args):
11132 __mul__(Vector4D self, double s) -> Vector4D
11133 __mul__(Vector4D self, Vector4D o) -> double
11135 return _IMP_kernel.Vector4D___mul__(self, *args)
11137 def __init__(self, *args):
11139 __init__(Vector4D self, IMP::Floats const & f) -> Vector4D
11140 __init__(Vector4D self) -> Vector4D
11141 __init__(Vector4D self, double x0, double x1, double x2, double x3) -> Vector4D
11143 _IMP_kernel.Vector4D_swiginit(self, _IMP_kernel.new_Vector4D(*args))
11145 def __iadd__(self, *args):
11146 _IMP_kernel.Vector4D___iadd__(self, *args)
11151 def __imul__(self, *args):
11152 _IMP_kernel.Vector4D___imul__(self, *args)
11157 def __itruediv__(self, *args):
11158 _IMP_kernel.Vector4D___itruediv__(self, *args)
11163 def __isub__(self, *args):
11164 _IMP_kernel.Vector4D___isub__(self, *args)
11170 r"""__len__(Vector4D self) -> unsigned int"""
11171 return _IMP_kernel.Vector4D___len__(self)
11173 def __rmul__(self, f):
11174 r"""__rmul__(Vector4D self, double f) -> Vector4D"""
11175 return _IMP_kernel.Vector4D___rmul__(self, f)
11178 r"""__str__(Vector4D self) -> std::string"""
11179 return _IMP_kernel.Vector4D___str__(self)
11181 def __repr__(self):
11182 r"""__repr__(Vector4D self) -> std::string"""
11183 return _IMP_kernel.Vector4D___repr__(self)
11185 def __eq__(self, arg2):
11186 r"""__eq__(Vector4D self, Vector4D arg2) -> bool"""
11187 return _IMP_kernel.Vector4D___eq__(self, arg2)
11189 def _get_as_binary(self):
11190 r"""_get_as_binary(Vector4D self) -> PyObject *"""
11191 return _IMP_kernel.Vector4D__get_as_binary(self)
11193 def _set_from_binary(self, p):
11194 r"""_set_from_binary(Vector4D self, PyObject * p)"""
11195 return _IMP_kernel.Vector4D__set_from_binary(self, p)
11197 def __getstate__(self):
11198 p = self._get_as_binary()
11199 if len(self.__dict__) > 1:
11200 d = self.__dict__.copy()
11205 def __setstate__(self, p):
11206 if not hasattr(self,
'this'):
11208 if isinstance(p, tuple):
11210 self.__dict__.update(d)
11211 return self._set_from_binary(p)
11214 def __getitem__(self, index):
11215 if isinstance(index, slice):
11216 return [self[i]
for i
in range(*index.indices(len(self)))]
11218 return _IMP_kernel.Vector4D___getitem__(self, index)
11222 def __setitem__(self, index, val):
11223 if isinstance(index, slice):
11224 if not hasattr(val,
'__iter__'):
11225 raise TypeError(
"must assign iterable to extended slice")
11226 inds = range(*index.indices(len(self)))
11227 if len(inds) != len(val):
11229 "attempt to assign sequence of size %d "
11230 "to extended slice of size %d" % (len(val), len(inds)))
11231 for ind, v
in zip(inds, val):
11234 return _IMP_kernel.Vector4D___setitem__(self, index, val)
11237 __swig_destroy__ = _IMP_kernel.delete_Vector4D
11240 _IMP_kernel.Vector4D_swigregister(Vector4D)
11241 class Vector5D(_VectorBase5D):
11242 r"""Proxy of C++ IMP::VectorD< 5 > class."""
11244 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11246 def get_unit_vector(self):
11247 r"""get_unit_vector(Vector5D self) -> Vector5D"""
11248 return _IMP_kernel.Vector5D_get_unit_vector(self)
11250 def __truediv__(self, *args):
11251 return _IMP_kernel.Vector5D___truediv__(self, *args)
11256 r"""__neg__(Vector5D self) -> Vector5D"""
11257 return _IMP_kernel.Vector5D___neg__(self)
11259 def __sub__(self, o):
11260 r"""__sub__(Vector5D self, Vector5D o) -> Vector5D"""
11261 return _IMP_kernel.Vector5D___sub__(self, o)
11263 def __add__(self, ret):
11264 r"""__add__(Vector5D self, Vector5D ret) -> Vector5D"""
11265 return _IMP_kernel.Vector5D___add__(self, ret)
11267 def __mul__(self, *args):
11269 __mul__(Vector5D self, double s) -> Vector5D
11270 __mul__(Vector5D self, Vector5D o) -> double
11272 return _IMP_kernel.Vector5D___mul__(self, *args)
11274 def __init__(self, *args):
11276 __init__(Vector5D self, IMP::Floats const & f) -> Vector5D
11277 __init__(Vector5D self) -> Vector5D
11278 __init__(Vector5D self, double x0, double x1, double x2, double x3, double x4) -> Vector5D
11280 _IMP_kernel.Vector5D_swiginit(self, _IMP_kernel.new_Vector5D(*args))
11282 def __iadd__(self, *args):
11283 _IMP_kernel.Vector5D___iadd__(self, *args)
11288 def __imul__(self, *args):
11289 _IMP_kernel.Vector5D___imul__(self, *args)
11294 def __itruediv__(self, *args):
11295 _IMP_kernel.Vector5D___itruediv__(self, *args)
11300 def __isub__(self, *args):
11301 _IMP_kernel.Vector5D___isub__(self, *args)
11307 r"""__len__(Vector5D self) -> unsigned int"""
11308 return _IMP_kernel.Vector5D___len__(self)
11310 def __rmul__(self, f):
11311 r"""__rmul__(Vector5D self, double f) -> Vector5D"""
11312 return _IMP_kernel.Vector5D___rmul__(self, f)
11315 r"""__str__(Vector5D self) -> std::string"""
11316 return _IMP_kernel.Vector5D___str__(self)
11318 def __repr__(self):
11319 r"""__repr__(Vector5D self) -> std::string"""
11320 return _IMP_kernel.Vector5D___repr__(self)
11322 def __eq__(self, arg2):
11323 r"""__eq__(Vector5D self, Vector5D arg2) -> bool"""
11324 return _IMP_kernel.Vector5D___eq__(self, arg2)
11326 def _get_as_binary(self):
11327 r"""_get_as_binary(Vector5D self) -> PyObject *"""
11328 return _IMP_kernel.Vector5D__get_as_binary(self)
11330 def _set_from_binary(self, p):
11331 r"""_set_from_binary(Vector5D self, PyObject * p)"""
11332 return _IMP_kernel.Vector5D__set_from_binary(self, p)
11334 def __getstate__(self):
11335 p = self._get_as_binary()
11336 if len(self.__dict__) > 1:
11337 d = self.__dict__.copy()
11342 def __setstate__(self, p):
11343 if not hasattr(self,
'this'):
11345 if isinstance(p, tuple):
11347 self.__dict__.update(d)
11348 return self._set_from_binary(p)
11351 def __getitem__(self, index):
11352 if isinstance(index, slice):
11353 return [self[i]
for i
in range(*index.indices(len(self)))]
11355 return _IMP_kernel.Vector5D___getitem__(self, index)
11359 def __setitem__(self, index, val):
11360 if isinstance(index, slice):
11361 if not hasattr(val,
'__iter__'):
11362 raise TypeError(
"must assign iterable to extended slice")
11363 inds = range(*index.indices(len(self)))
11364 if len(inds) != len(val):
11366 "attempt to assign sequence of size %d "
11367 "to extended slice of size %d" % (len(val), len(inds)))
11368 for ind, v
in zip(inds, val):
11371 return _IMP_kernel.Vector5D___setitem__(self, index, val)
11374 __swig_destroy__ = _IMP_kernel.delete_Vector5D
11377 _IMP_kernel.Vector5D_swigregister(Vector5D)
11378 class Vector6D(_VectorBase6D):
11379 r"""Proxy of C++ IMP::VectorD< 6 > class."""
11381 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11383 def get_unit_vector(self):
11384 r"""get_unit_vector(Vector6D self) -> Vector6D"""
11385 return _IMP_kernel.Vector6D_get_unit_vector(self)
11387 def __truediv__(self, *args):
11388 return _IMP_kernel.Vector6D___truediv__(self, *args)
11393 r"""__neg__(Vector6D self) -> Vector6D"""
11394 return _IMP_kernel.Vector6D___neg__(self)
11396 def __sub__(self, o):
11397 r"""__sub__(Vector6D self, Vector6D o) -> Vector6D"""
11398 return _IMP_kernel.Vector6D___sub__(self, o)
11400 def __add__(self, ret):
11401 r"""__add__(Vector6D self, Vector6D ret) -> Vector6D"""
11402 return _IMP_kernel.Vector6D___add__(self, ret)
11404 def __mul__(self, *args):
11406 __mul__(Vector6D self, double s) -> Vector6D
11407 __mul__(Vector6D self, Vector6D o) -> double
11409 return _IMP_kernel.Vector6D___mul__(self, *args)
11411 def __init__(self, *args):
11413 __init__(Vector6D self, IMP::Floats const & f) -> Vector6D
11414 __init__(Vector6D self) -> Vector6D
11415 __init__(Vector6D self, double x0, double x1, double x2, double x3, double x4, double x5) -> Vector6D
11417 _IMP_kernel.Vector6D_swiginit(self, _IMP_kernel.new_Vector6D(*args))
11419 def __iadd__(self, *args):
11420 _IMP_kernel.Vector6D___iadd__(self, *args)
11425 def __imul__(self, *args):
11426 _IMP_kernel.Vector6D___imul__(self, *args)
11431 def __itruediv__(self, *args):
11432 _IMP_kernel.Vector6D___itruediv__(self, *args)
11437 def __isub__(self, *args):
11438 _IMP_kernel.Vector6D___isub__(self, *args)
11444 r"""__len__(Vector6D self) -> unsigned int"""
11445 return _IMP_kernel.Vector6D___len__(self)
11447 def __rmul__(self, f):
11448 r"""__rmul__(Vector6D self, double f) -> Vector6D"""
11449 return _IMP_kernel.Vector6D___rmul__(self, f)
11452 r"""__str__(Vector6D self) -> std::string"""
11453 return _IMP_kernel.Vector6D___str__(self)
11455 def __repr__(self):
11456 r"""__repr__(Vector6D self) -> std::string"""
11457 return _IMP_kernel.Vector6D___repr__(self)
11459 def __eq__(self, arg2):
11460 r"""__eq__(Vector6D self, Vector6D arg2) -> bool"""
11461 return _IMP_kernel.Vector6D___eq__(self, arg2)
11463 def _get_as_binary(self):
11464 r"""_get_as_binary(Vector6D self) -> PyObject *"""
11465 return _IMP_kernel.Vector6D__get_as_binary(self)
11467 def _set_from_binary(self, p):
11468 r"""_set_from_binary(Vector6D self, PyObject * p)"""
11469 return _IMP_kernel.Vector6D__set_from_binary(self, p)
11471 def __getstate__(self):
11472 p = self._get_as_binary()
11473 if len(self.__dict__) > 1:
11474 d = self.__dict__.copy()
11479 def __setstate__(self, p):
11480 if not hasattr(self,
'this'):
11482 if isinstance(p, tuple):
11484 self.__dict__.update(d)
11485 return self._set_from_binary(p)
11488 def __getitem__(self, index):
11489 if isinstance(index, slice):
11490 return [self[i]
for i
in range(*index.indices(len(self)))]
11492 return _IMP_kernel.Vector6D___getitem__(self, index)
11496 def __setitem__(self, index, val):
11497 if isinstance(index, slice):
11498 if not hasattr(val,
'__iter__'):
11499 raise TypeError(
"must assign iterable to extended slice")
11500 inds = range(*index.indices(len(self)))
11501 if len(inds) != len(val):
11503 "attempt to assign sequence of size %d "
11504 "to extended slice of size %d" % (len(val), len(inds)))
11505 for ind, v
in zip(inds, val):
11508 return _IMP_kernel.Vector6D___setitem__(self, index, val)
11511 __swig_destroy__ = _IMP_kernel.delete_Vector6D
11514 _IMP_kernel.Vector6D_swigregister(Vector6D)
11515 class VectorKD(_VectorBaseKD):
11516 r"""Proxy of C++ IMP::VectorD< -1 > class."""
11518 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11520 def get_unit_vector(self):
11521 r"""get_unit_vector(VectorKD self) -> VectorKD"""
11522 return _IMP_kernel.VectorKD_get_unit_vector(self)
11524 def __truediv__(self, *args):
11525 return _IMP_kernel.VectorKD___truediv__(self, *args)
11530 r"""__neg__(VectorKD self) -> VectorKD"""
11531 return _IMP_kernel.VectorKD___neg__(self)
11533 def __sub__(self, o):
11534 r"""__sub__(VectorKD self, VectorKD o) -> VectorKD"""
11535 return _IMP_kernel.VectorKD___sub__(self, o)
11537 def __add__(self, ret):
11538 r"""__add__(VectorKD self, VectorKD ret) -> VectorKD"""
11539 return _IMP_kernel.VectorKD___add__(self, ret)
11541 def __mul__(self, *args):
11543 __mul__(VectorKD self, double s) -> VectorKD
11544 __mul__(VectorKD self, VectorKD o) -> double
11546 return _IMP_kernel.VectorKD___mul__(self, *args)
11548 def __init__(self, *args):
11550 __init__(VectorKD self, IMP::Floats const & f) -> VectorKD
11551 __init__(VectorKD self) -> VectorKD
11552 __init__(VectorKD self, double x0, double x1=std::numeric_limits< double >::max(), double x2=std::numeric_limits< double >::max(), double x3=std::numeric_limits< double >::max(), double x4=std::numeric_limits< double >::max(), double x5=std::numeric_limits< double >::max()) -> VectorKD
11554 _IMP_kernel.VectorKD_swiginit(self, _IMP_kernel.new_VectorKD(*args))
11556 def __iadd__(self, *args):
11557 _IMP_kernel.VectorKD___iadd__(self, *args)
11562 def __imul__(self, *args):
11563 _IMP_kernel.VectorKD___imul__(self, *args)
11568 def __itruediv__(self, *args):
11569 _IMP_kernel.VectorKD___itruediv__(self, *args)
11574 def __isub__(self, *args):
11575 _IMP_kernel.VectorKD___isub__(self, *args)
11581 r"""__len__(VectorKD self) -> unsigned int"""
11582 return _IMP_kernel.VectorKD___len__(self)
11584 def __rmul__(self, f):
11585 r"""__rmul__(VectorKD self, double f) -> VectorKD"""
11586 return _IMP_kernel.VectorKD___rmul__(self, f)
11589 r"""__str__(VectorKD self) -> std::string"""
11590 return _IMP_kernel.VectorKD___str__(self)
11592 def __repr__(self):
11593 r"""__repr__(VectorKD self) -> std::string"""
11594 return _IMP_kernel.VectorKD___repr__(self)
11596 def __eq__(self, arg2):
11597 r"""__eq__(VectorKD self, VectorKD arg2) -> bool"""
11598 return _IMP_kernel.VectorKD___eq__(self, arg2)
11600 def _get_as_binary(self):
11601 r"""_get_as_binary(VectorKD self) -> PyObject *"""
11602 return _IMP_kernel.VectorKD__get_as_binary(self)
11604 def _set_from_binary(self, p):
11605 r"""_set_from_binary(VectorKD self, PyObject * p)"""
11606 return _IMP_kernel.VectorKD__set_from_binary(self, p)
11608 def __getstate__(self):
11609 p = self._get_as_binary()
11610 if len(self.__dict__) > 1:
11611 d = self.__dict__.copy()
11616 def __setstate__(self, p):
11617 if not hasattr(self,
'this'):
11619 if isinstance(p, tuple):
11621 self.__dict__.update(d)
11622 return self._set_from_binary(p)
11625 def __getitem__(self, index):
11626 if isinstance(index, slice):
11627 return [self[i]
for i
in range(*index.indices(len(self)))]
11629 return _IMP_kernel.VectorKD___getitem__(self, index)
11633 def __setitem__(self, index, val):
11634 if isinstance(index, slice):
11635 if not hasattr(val,
'__iter__'):
11636 raise TypeError(
"must assign iterable to extended slice")
11637 inds = range(*index.indices(len(self)))
11638 if len(inds) != len(val):
11640 "attempt to assign sequence of size %d "
11641 "to extended slice of size %d" % (len(val), len(inds)))
11642 for ind, v
in zip(inds, val):
11645 return _IMP_kernel.VectorKD___setitem__(self, index, val)
11648 __swig_destroy__ = _IMP_kernel.delete_VectorKD
11651 _IMP_kernel.VectorKD_swigregister(VectorKD)
11653 def get_basis_vector_1d(coordinate):
11654 r"""get_basis_vector_1d(unsigned int coordinate) -> Vector1D"""
11655 return _IMP_kernel.get_basis_vector_1d(coordinate)
11657 def get_basis_vector_2d(coordinate):
11658 r"""get_basis_vector_2d(unsigned int coordinate) -> Vector2D"""
11659 return _IMP_kernel.get_basis_vector_2d(coordinate)
11661 def get_basis_vector_3d(coordinate):
11662 r"""get_basis_vector_3d(unsigned int coordinate) -> Vector3D"""
11663 return _IMP_kernel.get_basis_vector_3d(coordinate)
11665 def get_basis_vector_4d(coordinate):
11666 r"""get_basis_vector_4d(unsigned int coordinate) -> Vector4D"""
11667 return _IMP_kernel.get_basis_vector_4d(coordinate)
11669 def get_basis_vector_5d(coordinate):
11670 r"""get_basis_vector_5d(unsigned int coordinate) -> Vector5D"""
11671 return _IMP_kernel.get_basis_vector_5d(coordinate)
11673 def get_basis_vector_6d(coordinate):
11674 r"""get_basis_vector_6d(unsigned int coordinate) -> Vector6D"""
11675 return _IMP_kernel.get_basis_vector_6d(coordinate)
11677 def get_zero_vector_1d():
11678 r"""get_zero_vector_1d() -> Vector1D"""
11679 return _IMP_kernel.get_zero_vector_1d()
11681 def get_zero_vector_2d():
11682 r"""get_zero_vector_2d() -> Vector2D"""
11683 return _IMP_kernel.get_zero_vector_2d()
11685 def get_zero_vector_3d():
11686 r"""get_zero_vector_3d() -> Vector3D"""
11687 return _IMP_kernel.get_zero_vector_3d()
11689 def get_zero_vector_4d():
11690 r"""get_zero_vector_4d() -> Vector4D"""
11691 return _IMP_kernel.get_zero_vector_4d()
11693 def get_zero_vector_5d():
11694 r"""get_zero_vector_5d() -> Vector5D"""
11695 return _IMP_kernel.get_zero_vector_5d()
11697 def get_zero_vector_6d():
11698 r"""get_zero_vector_6d() -> Vector6D"""
11699 return _IMP_kernel.get_zero_vector_6d()
11701 def get_ones_vector_1d(v=1):
11702 r"""get_ones_vector_1d(double v=1) -> Vector1D"""
11703 return _IMP_kernel.get_ones_vector_1d(v)
11705 def get_ones_vector_2d(v=1):
11706 r"""get_ones_vector_2d(double v=1) -> Vector2D"""
11707 return _IMP_kernel.get_ones_vector_2d(v)
11709 def get_ones_vector_3d(v=1):
11710 r"""get_ones_vector_3d(double v=1) -> Vector3D"""
11711 return _IMP_kernel.get_ones_vector_3d(v)
11713 def get_ones_vector_4d(v=1):
11714 r"""get_ones_vector_4d(double v=1) -> Vector4D"""
11715 return _IMP_kernel.get_ones_vector_4d(v)
11717 def get_ones_vector_5d(v=1):
11718 r"""get_ones_vector_5d(double v=1) -> Vector5D"""
11719 return _IMP_kernel.get_ones_vector_5d(v)
11721 def get_ones_vector_6d(v=1):
11722 r"""get_ones_vector_6d(double v=1) -> Vector6D"""
11723 return _IMP_kernel.get_ones_vector_6d(v)
11725 r"""Proxy of C++ IMP::internal::GenericRestraintsScoringFunction< ::IMP::Restraints > class."""
11727 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11728 __repr__ = _swig_repr
11730 def __init__(self, *args):
11732 __init__(_RestraintsScoringFunction self, IMP::RestraintsTemp const & rs, double weight=1.0, double max=NO_MAX, std::string name="RestraintsScoringFunction%1%") -> _RestraintsScoringFunction
11733 __init__(_RestraintsScoringFunction self) -> _RestraintsScoringFunction
11735 _IMP_kernel._RestraintsScoringFunction_swiginit(self, _IMP_kernel.new__RestraintsScoringFunction(*args))
11737 def do_add_score_and_derivatives(self, sa, ss):
11738 r"""do_add_score_and_derivatives(_RestraintsScoringFunction self, ScoreAccumulator sa, IMP::ScoreStatesTemp const & ss)"""
11739 return _IMP_kernel._RestraintsScoringFunction_do_add_score_and_derivatives(self, sa, ss)
11741 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss):
11742 r"""do_add_score_and_derivatives_moved(_RestraintsScoringFunction self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, IMP::ScoreStatesTemp const & ss)"""
11743 return _IMP_kernel._RestraintsScoringFunction_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss)
11745 def do_get_inputs(self):
11746 r"""do_get_inputs(_RestraintsScoringFunction self) -> IMP::ModelObjectsTemp"""
11747 return _IMP_kernel._RestraintsScoringFunction_do_get_inputs(self)
11749 def get_restraints(self):
11750 r"""get_restraints(_RestraintsScoringFunction self) -> IMP::Vector< IMP::Pointer< IMP::Restraint >,std::allocator< IMP::Pointer< IMP::Restraint > > > const &"""
11751 return _IMP_kernel._RestraintsScoringFunction_get_restraints(self)
11753 def set_restraints(self, s):
11754 r"""set_restraints(_RestraintsScoringFunction self, IMP::RestraintsTemp const & s)"""
11755 return _IMP_kernel._RestraintsScoringFunction_set_restraints(self, s)
11757 def get_number_of_restraints(self):
11758 r"""get_number_of_restraints(_RestraintsScoringFunction self) -> unsigned int"""
11759 return _IMP_kernel._RestraintsScoringFunction_get_number_of_restraints(self)
11761 def clear_restraints(self):
11762 r"""clear_restraints(_RestraintsScoringFunction self)"""
11763 return _IMP_kernel._RestraintsScoringFunction_clear_restraints(self)
11765 def get_restraint(self, i):
11766 r"""get_restraint(_RestraintsScoringFunction self, unsigned int i) -> Restraint"""
11767 return _IMP_kernel._RestraintsScoringFunction_get_restraint(self, i)
11769 def erase_restraint(self, i):
11770 r"""erase_restraint(_RestraintsScoringFunction self, unsigned int i)"""
11771 return _IMP_kernel._RestraintsScoringFunction_erase_restraint(self, i)
11774 r"""add_restraint(_RestraintsScoringFunction self, Restraint r) -> unsigned int"""
11775 return _IMP_kernel._RestraintsScoringFunction_add_restraint(self, r)
11778 r"""add_restraints(_RestraintsScoringFunction self, IMP::Vector< IMP::Pointer< IMP::Restraint >,std::allocator< IMP::Pointer< IMP::Restraint > > > const & r)"""
11779 return _IMP_kernel._RestraintsScoringFunction_add_restraints(self, r)
11781 def _python_index_restraint(self, r, start, stop):
11782 r"""_python_index_restraint(_RestraintsScoringFunction self, Restraint r, unsigned int start, unsigned int stop) -> unsigned int"""
11783 return _IMP_kernel._RestraintsScoringFunction__python_index_restraint(self, r, start, stop)
11786 r"""get_version_info(_RestraintsScoringFunction self) -> VersionInfo"""
11787 return _IMP_kernel._RestraintsScoringFunction_get_version_info(self)
11788 __swig_destroy__ = _IMP_kernel.delete__RestraintsScoringFunction
11792 return _object_cast_to__RestraintsScoringFunction(o)
11795 def __get_restraints(self):
11796 return _list_util.VarList(
11797 getdimfunc=self.get_number_of_restraints,
11798 getfunc=self.get_restraint, erasefunc=self.erase_restraint,
11799 appendfunc=self.add_restraint, extendfunc=self.add_restraints,
11800 clearfunc=self.clear_restraints,
11801 indexfunc=self._python_index_restraint)
11803 def __set_restraints(self, obj):
11804 _list_util.set_varlist(self.restraints, obj)
11806 def __del_restraints(self):
11807 _list_util.del_varlist(self.restraints)
11809 restraints = property(__get_restraints, __set_restraints,
11810 __del_restraints, doc=
"List of Restraints")
11813 def _get_jax(self, space=None):
11816 jis = [r.get_derived_object()._get_jax(space)
for r
in self.restraints]
11817 funcs = [j.score_func
for j
in jis]
11818 keys = frozenset(x
for j
in jis
for x
in j._keys)
11820 return sum(f(jm)
for f
in funcs)
11821 return IMP._jax_util.JAXRestraintInfo(
11822 m=self.get_model(), score_func=jax_sf, weight=1.0, keys=keys)
11826 _IMP_kernel._RestraintsScoringFunction_swigregister(_RestraintsScoringFunction)
11828 r"""Proxy of C++ IMP::ScopedSetAttribute< IMP::FloatKey,IMP::Float > class."""
11830 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11832 def __init__(self, *args):
11834 __init__(ScopedSetFloatAttribute self) -> ScopedSetFloatAttribute
11835 __init__(ScopedSetFloatAttribute self, Particle p, FloatKey key, double const & value) -> ScopedSetFloatAttribute
11837 _IMP_kernel.ScopedSetFloatAttribute_swiginit(self, _IMP_kernel.new_ScopedSetFloatAttribute(*args))
11839 def set(self, p, key, value):
11840 r"""set(ScopedSetFloatAttribute self, Particle p, FloatKey key, double const & value)"""
11841 return _IMP_kernel.ScopedSetFloatAttribute_set(self, p, key, value)
11844 r"""reset(ScopedSetFloatAttribute self)"""
11845 return _IMP_kernel.ScopedSetFloatAttribute_reset(self)
11846 __swig_destroy__ = _IMP_kernel.delete_ScopedSetFloatAttribute
11848 def show(self, *args):
11849 r"""show(ScopedSetFloatAttribute self, _ostream out=std::cout)"""
11850 return _IMP_kernel.ScopedSetFloatAttribute_show(self, *args)
11853 r"""__str__(ScopedSetFloatAttribute self) -> std::string"""
11854 return _IMP_kernel.ScopedSetFloatAttribute___str__(self)
11856 def __repr__(self):
11857 r"""__repr__(ScopedSetFloatAttribute self) -> std::string"""
11858 return _IMP_kernel.ScopedSetFloatAttribute___repr__(self)
11861 _IMP_kernel.ScopedSetFloatAttribute_swigregister(ScopedSetFloatAttribute)
11863 def _get_module_data_path(module, file_name):
11864 r"""_get_module_data_path(std::string module, std::string file_name) -> std::string"""
11865 return _IMP_kernel._get_module_data_path(module, file_name)
11867 def _get_module_example_path(module, file_name):
11868 r"""_get_module_example_path(std::string module, std::string file_name) -> std::string"""
11869 return _IMP_kernel._get_module_example_path(module, file_name)
11878 if sys.platform ==
'win32' and 'IMP_LD_PATH' in os.environ:
11879 dirs = os.environ[
'IMP_LD_PATH'].split(
":")
11880 pathcomps = os.environ[
'PATH'].split(
";")
11882 if d
not in pathcomps:
11883 os.environ[
'PATH'] = d +
';' + os.environ[
'PATH']
11891 """Allow command line tools to easily implement multiple commands.
11892 Typically, an IMP command line tool will use an instance of this class
11893 to provide a consistent interface to multiple distinct commands
11894 from a single binary, rather than providing a potentially large
11895 number of binaries. This is similar to the way a number of common
11896 command line tools outside of IMP function (e.g. Git provides a single
11897 `git` tool which implements multiple commands - `git add`, `git commit`,
11898 `git push` and so on).
11900 Each command is implemented with a Python module of the same name
11901 that can be imported from the module (for example, if `module_name`
11902 is `IMP.foo`, the `bar` command is provided by the `IMP.foo.bar` Python
11903 module, which would usually be found as `modules/foo/pyext/src/bar.py`).
11904 Each such module should have a docstring and a `%main()` method
11905 that takes no arguments (the module should also call its `%main()` method
11906 if it is run directly, i.e. with something like
11907 `if __name__=="__main__": %main()`). The encompassing module
11908 (`IMP.foo` in the example) should define `_all_commands` as a Python
11909 list of all valid commands.
11911 See the `multifit` and `cnmultifit` command line tools for example
11917 @param short_help A few words that describe the command line tool.
11918 @param long_help Longer text, used in the `help` command.
11919 @param module_name Name of the module (e.g. `IMP.foo`) that
11920 implements the commands.
11922 self.short_help = short_help
11923 self.long_help = long_help
11924 self.module_name = module_name
11925 self._all_commands = self.import_module()._all_commands
11926 self._progname = os.path.basename(sys.argv[0])
11929 """Call this method to act upon the user-provided command line"""
11930 if len(sys.argv) <= 1:
11931 print(self.short_help +
" Use '%s help' for help." % self._progname)
11933 command = sys.argv[1]
11934 if command
in (
'help',
'--help',
'-h'):
11935 if len(sys.argv) == 3:
11936 self.show_command_help(sys.argv[2])
11939 elif command ==
'--version':
11940 self.show_version()
11941 elif command
in self._all_commands:
11942 self.do_command(command)
11944 self.unknown_command(command)
11946 def import_module(self, mod=None):
11947 modname = self.module_name
11948 if mod
is not None:
11949 modname +=
"." + mod
11950 return __import__(modname, {}, {}, [
''])
11952 def unknown_command(self, command):
11953 print(
"Unknown command: '%s'" % command)
11954 print(
"Use '%s help' for help." % self._progname)
11957 def _get_version(self):
11960 def show_version(self):
11961 print(self._progname +
' ' + self._get_version())
11963 def show_help(self):
11964 ver = self._get_version()
11965 print(
"%s, version %s." % (self._progname, ver))
11966 print(self.long_help +
"""
11968 This program is part of IMP, the Integrative Modeling Platform,
11970 For additional information about IMP, see <https://integrativemodeling.org>.
11972 Usage: %s <command> [options] [args]
11975 commands = self._all_commands[:] + [
'help']
11977 cmdlen = max([len(c)
for c
in commands])
11980 doc =
'Get help on using %s.' % self._progname
11982 doc = self.import_module(c).__doc__
or "<no help>"
11983 c +=
' ' * (cmdlen - len(c))
11984 print(
' ' + c +
' ' + doc)
11986 Use "%s help <command>" for detailed help on any command
11987 or "%s --version" to see the version number.""" % (self._progname,
11990 def do_command(self, command):
11991 mod = self.import_module(command)
11992 sys.argv[0] = self._progname +
' ' + command
11996 def show_command_help(self, command):
11997 if command ==
'help':
11999 elif command
in self._all_commands
or command ==
'help':
12000 mod = self.import_module(command)
12001 sys.argv = [self._progname +
' ' + command,
'--help']
12004 self.unknown_command(command)
12011 g = networkx.DiGraph()
12012 if len(ig.get_vertices()) == 0:
12021 return self.p.get_name()
12023 def __call__(self, name):
12024 return self.p.__call__(name)
12026 for vi
in ig.get_vertices():
12027 n = ig.get_vertex_name(vi)
12028 g.add_node(NodeWrapper(n))
12029 for vi
in ig.get_vertices():
12030 n = ig.get_vertex_name(vi)
12031 for ni
in ig.get_out_neighbors(vi):
12032 nn = ig.get_vertex_name(ni)
12033 g.add_edge(NodeWrapper(n), NodeWrapper(nn))
12040 n0 = name.get_name()
12043 n1 = str(n0).replace(
'"',
'')
12044 n2 = n1.replace(
"\n",
'')
12047 from altgraph
import Graph, Dot
12048 graph = Graph.Graph()
12049 for i, v
in enumerate(g.get_vertices()):
12051 for i, v
in enumerate(g.get_vertices()):
12052 for n
in g.get_out_neighbors(v):
12053 graph.add_edge(v, n)
12054 dot = Dot.Dot(graph)
12055 for i, v
in enumerate(g.get_vertices()):
12056 dot.node_style(i, label=clean(g.get_vertex_name(v)))
12064 st = g.get_graphviz_string()
12065 with open(tfn,
"w")
as fh:
12068 print(
"running dot")
12069 sp = subprocess.Popen([
"dot",
"-Tpdf", tfn,
"-o" + tfon])
12073 sys.stderr.write(
"The dot command from the graphviz package was not found. Please make sure it is in the PATH passed to IMP.\n")
12076 if platform.system() ==
"Darwin":
12079 cmd = [
"gv",
"acroread",
"xpdf"]
12082 print(
"launching viewer " + c)
12084 subprocess.check_call([c, tfon])
12090 print(
"Could not display file. It is saved at " + tfon)
12100 """Mark a Python module as deprecated.
12101 @note The `module` argument would normally be `__name__`.
12102 @see [deprecation support](@ref deprecation)."""
12104 "Module %s is deprecated. %s\n" % (module, help_message))
12107 """Python decorator to mark a class as deprecated.
12108 @see [deprecation support](@ref deprecation)."""
12110 orig_init = obj.__init__
12113 @functools.wraps(orig_init, (
'__name__',
'__doc__'))
12114 def __init__(obj, *args, **keys):
12116 % (type(obj), help_message))
12117 orig_init(obj, *args, **keys)
12118 obj.__init__ = __init__
12123 """Python decorator to mark a method as deprecated.
12124 @see [deprecation support](@ref deprecation)."""
12125 def out_wrapper(obj):
12126 @functools.wraps(obj)
12127 def wrapper(cls, *args, **keys):
12129 % (obj.__name__, type(cls), help_message))
12130 return obj(cls, *args, **keys)
12135 """Python decorator to mark a function as deprecated.
12136 @see [deprecation support](@ref deprecation)."""
12137 def out_wrapper(obj):
12138 @functools.wraps(obj)
12139 def wrapper(*args, **keys):
12141 % (obj.__name__, help_message))
12142 return obj(*args, **keys)
12146 @contextlib.contextmanager
12148 """Context manager to temporarily allow (or disallow) deprecated code.
12149 @see [deprecation support](@ref deprecation)."""
12156 def _get_all_flags(ntokens):
12157 r"""_get_all_flags(unsigned int ntokens) -> IMP::Strings"""
12158 return _IMP_kernel._get_all_flags(ntokens)
12160 def _print_internal_help(out, description):
12161 r"""_print_internal_help(_ostream out, std::string description)"""
12162 return _IMP_kernel._print_internal_help(out, description)
12168 class _PassThroughAction(argparse.Action):
12169 """Pass an argument through to the IMP Boost parser"""
12170 def __call__(self, parser, namespace, values, option_string=None):
12171 parser._boost_command_line.append(option_string)
12173 parser._boost_command_line.append(values)
12176 if option_string
in (
'-h',
'--help',
'--help_advanced',
'--version'):
12177 parser._handle_boost()
12181 """IMP-specific subclass of argparse.ArgumentParser.
12182 This adds options common to all IMP applications
12183 (see IMP::setup_from_argv()).
12186 def __init__(self, *args, **kwargs):
12188 kwargs[
'add_help'] =
False
12189 super().__init__(*args, **kwargs)
12190 for ntoken
in (0, 1):
12191 flags = _get_all_flags(ntoken)
12193 arg = [
'-h',
'--help']
if f ==
'help' else [
'--' + f]
12194 self.add_argument(*arg, help=argparse.SUPPRESS,
12195 nargs=
None if ntoken
else 0,
12196 action=_PassThroughAction,
12197 default=argparse.SUPPRESS)
12200 """Parse the command line and return optional and positional arguments.
12201 This functions in the same way as the method in the base class
12202 argparse.ArgumentParser, except that it also processes optional
12203 arguments common to all IMP applications (these are not returned
12204 in `args`, but can be obtained in the usual way, e.g. by calling
12205 IMP::get_string_flag()).
12208 self._boost_command_line = [sys.argv[0]]
12210 if len(self._boost_command_line) > 1:
12211 self._handle_boost()
12214 def _get_description(self):
12215 return self.format_help() +
"\nOptions common to all IMP applications:"
12217 def print_help(self, file=None):
12218 _print_internal_help(file
if file
else sys.stdout,
12219 self._get_description())
12221 def _handle_boost(self):
12223 self._get_description(),
12226 class RandomNumberGenerator(object):
12227 r"""Proxy of C++ IMP::RandomNumberGenerator class."""
12229 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12230 __repr__ = _swig_repr
12233 r"""seed(RandomNumberGenerator self, int x)"""
12234 return _IMP_kernel.RandomNumberGenerator_seed(self, x)
12236 def __call__(self):
12237 r"""__call__(RandomNumberGenerator self) -> int"""
12238 return _IMP_kernel.RandomNumberGenerator___call__(self)
12240 def get_state(self):
12241 r"""get_state(RandomNumberGenerator self) -> PyObject *"""
12242 return _IMP_kernel.RandomNumberGenerator_get_state(self)
12244 def set_state(self, p):
12245 r"""set_state(RandomNumberGenerator self, PyObject * p)"""
12246 return _IMP_kernel.RandomNumberGenerator_set_state(self, p)
12248 def __init__(self):
12249 r"""__init__(RandomNumberGenerator self) -> RandomNumberGenerator"""
12250 _IMP_kernel.RandomNumberGenerator_swiginit(self, _IMP_kernel.new_RandomNumberGenerator())
12251 __swig_destroy__ = _IMP_kernel.delete_RandomNumberGenerator
12254 _IMP_kernel.RandomNumberGenerator_swigregister(RandomNumberGenerator)
12258 get_random_float_uniform() -> float
12259 get_random_float_uniform(float min, float max) -> float
12261 return _IMP_kernel.get_random_float_uniform(*args)
12265 get_random_double_uniform() -> double
12266 get_random_double_uniform(double min, double max) -> double
12268 return _IMP_kernel.get_random_double_uniform(*args)
12270 def get_random_floats_normal(n, mean=0.0, stddev=1.0):
12271 r"""get_random_floats_normal(unsigned int n, float mean=0.0, float stddev=1.0) -> IMP::Vector< float,std::allocator< float > >"""
12272 return _IMP_kernel.get_random_floats_normal(n, mean, stddev)
12274 def get_random_doubles_normal(n, mean=0.0, stddev=1.0):
12275 r"""get_random_doubles_normal(unsigned int n, double mean=0.0, double stddev=1.0) -> IMP::Vector< double,std::allocator< double > >"""
12276 return _IMP_kernel.get_random_doubles_normal(n, mean, stddev)
12278 def get_random_floats_uniform(n):
12279 r"""get_random_floats_uniform(unsigned int n) -> IMP::Vector< float,std::allocator< float > >"""
12280 return _IMP_kernel.get_random_floats_uniform(n)
12282 def get_random_doubles_uniform(n):
12283 r"""get_random_doubles_uniform(unsigned int n) -> IMP::Vector< double,std::allocator< double > >"""
12284 return _IMP_kernel.get_random_doubles_uniform(n)
12287 r"""get_random_seed() -> boost::uint64_t"""
12288 return _IMP_kernel.get_random_seed()
12290 def _get_derivatives_numpy(m, k, m_pyobj, read_only):
12291 r"""_get_derivatives_numpy(Model m, FloatKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12292 return _IMP_kernel._get_derivatives_numpy(m, k, m_pyobj, read_only)
12294 def _get_floats_numpy(m, k, m_pyobj, read_only):
12295 r"""_get_floats_numpy(Model m, FloatKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12296 return _IMP_kernel._get_floats_numpy(m, k, m_pyobj, read_only)
12298 def _get_ints_numpy(m, k, m_pyobj, read_only):
12299 r"""_get_ints_numpy(Model m, IntKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12300 return _IMP_kernel._get_ints_numpy(m, k, m_pyobj, read_only)
12302 def _get_particle_indexes_numpy(m, k, m_pyobj, read_only):
12303 r"""_get_particle_indexes_numpy(Model m, ParticleIndexKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12304 return _IMP_kernel._get_particle_indexes_numpy(m, k, m_pyobj, read_only)
12306 def _get_vector3ds_numpy(m, k, m_pyobj, read_only):
12307 r"""_get_vector3ds_numpy(Model m, Vector3DKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12308 return _IMP_kernel._get_vector3ds_numpy(m, k, m_pyobj, read_only)
12310 def _get_vector3dderiv_numpy(m, k, m_pyobj, read_only):
12311 r"""_get_vector3dderiv_numpy(Model m, Vector3DDerivKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12312 return _IMP_kernel._get_vector3dderiv_numpy(m, k, m_pyobj, read_only)
12314 def _get_vector3dderiv_derivatives_numpy(m, k, m_pyobj, read_only):
12315 r"""_get_vector3dderiv_derivatives_numpy(Model m, Vector3DDerivKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12316 return _IMP_kernel._get_vector3dderiv_derivatives_numpy(m, k, m_pyobj, read_only)
12318 def _get_vector4ds_numpy(m, k, m_pyobj, read_only):
12319 r"""_get_vector4ds_numpy(Model m, Vector4DKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12320 return _IMP_kernel._get_vector4ds_numpy(m, k, m_pyobj, read_only)
12322 def _get_vector4dderiv_numpy(m, k, m_pyobj, read_only):
12323 r"""_get_vector4dderiv_numpy(Model m, Vector4DDerivKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12324 return _IMP_kernel._get_vector4dderiv_numpy(m, k, m_pyobj, read_only)
12326 def _get_vector4dderiv_derivatives_numpy(m, k, m_pyobj, read_only):
12327 r"""_get_vector4dderiv_derivatives_numpy(Model m, Vector4DDerivKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12328 return _IMP_kernel._get_vector4dderiv_derivatives_numpy(m, k, m_pyobj, read_only)
12330 def _get_spheres_numpy(m, m_pyobj, read_only):
12331 r"""_get_spheres_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12332 return _IMP_kernel._get_spheres_numpy(m, m_pyobj, read_only)
12334 def _get_sphere_derivatives_numpy(m, m_pyobj, read_only):
12335 r"""_get_sphere_derivatives_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12336 return _IMP_kernel._get_sphere_derivatives_numpy(m, m_pyobj, read_only)
12338 def _get_internal_coordinates_numpy(m, m_pyobj, read_only):
12339 r"""_get_internal_coordinates_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12340 return _IMP_kernel._get_internal_coordinates_numpy(m, m_pyobj, read_only)
12342 def _get_internal_coordinate_derivatives_numpy(m, m_pyobj, read_only):
12343 r"""_get_internal_coordinate_derivatives_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12344 return _IMP_kernel._get_internal_coordinate_derivatives_numpy(m, m_pyobj, read_only)
12348 ParticleIndex = numpy.intc
12349 except ImportError:
12354 """Warning for incomplete JAX support or different behavior of JAX code"""
12358 def get_module_name():
12359 r"""get_module_name() -> std::string const"""
12360 return _IMP_kernel.get_module_name()
12363 r"""get_module_version() -> std::string const"""
12364 return _IMP_kernel.get_module_version()
12367 r"""get_example_path(std::string fname) -> std::string"""
12368 return _IMP_kernel.get_example_path(fname)
12371 r"""get_data_path(std::string fname) -> std::string"""
12372 return _IMP_kernel.get_data_path(fname)
12374 from .
import _version_check
12379 random_number_generator = cvar.random_number_generator
Particle * get_particle(ParticleIndex p) const
Get the particle from an index.
A base class for modifiers of ParticlesTemp.
A class to store a configuration of a model.
def get_ints_numpy
Get the model's attribute array for IntKey k as a NumPy array.
VectorD< D > get_basis_vector_kd(int Di, unsigned int coordinate)
Return the basis vector for the given coordinate.
Abstract class for scoring object(s) of type ParticleIndexPair.
A shared container for Pairs.
void add_int_flag(std::string name, size_t default_value, std::string description)
Allow command line tools to easily implement multiple commands.
CheckLevel get_check_level()
Get the current audit mode.
VectorD< D > get_ones_vector_kd(unsigned int Di, double v=1)
Return a vector of ones (or another constant)
Key< 11 > TriggerKey
The type used to identify changed model properties.
Abstract predicate function.
Key< 0 > FloatKey
The type used to identify float attributes in the Particles.
def allow_deprecated
Context manager to temporarily allow (or disallow) deprecated code.
std::string get_unique_name(std::string templ)
Return a unique name produced from the string.
DependencyGraph get_dependency_graph(Model *m)
def get_floats_numpy
Get the model's attribute array for FloatKey k as a NumPy array.
Objects get_live_objects()
Return pointers to all live objects.
def get_derived_object
Return this object cast to the most derived subclass.
Vector< char > write_particles_to_buffer(const ParticlesTemp &particles, const FloatKeys &keys)
return a binary buffer with the data
Key< 13 > SparseIntKey
The type used to identify sparse int attributes in the Particles.
def main
Call this method to act upon the user-provided command line.
Key< 15 > SparseParticleIndexKey
The type used to identify sparse particle attributes in the Particles.
Vector3D get_orthogonal_vector(const Vector3D &v)
Return a vector that is perpendicular to the given vector.
boost::graph DependencyGraph
Directed graph on the interactions between the various objects in the model.
ContainersTemp get_input_containers(const ModelObjectsTemp &mos)
Return all the input particles for a given ModelObject.
def deprecated_module
Mark a Python module as deprecated.
Key< 16 > Vector3DKey
The type used to identify 3D vector attributes in the Particles.
Vector< VectorD< D > > get_vertices(const BoundingBoxD< D > &bb)
Return a list of the 2^D bounding points for the bounding box.
Array< 4, WeakPointer< Particle >, Particle * > ParticleQuad
bool get_bool_flag(std::string name)
VectorD< D > get_zero_vector_kd(int Di)
Return a dynamically sized vector of zeros.
void handle_use_deprecated(std::string message)
Break in this method in gdb to find deprecated uses at runtime.
void set_progress_display(std::string description, unsigned int steps)
Set up the progress bar with the passed description.
def deprecated_function
Python decorator to mark a function as deprecated.
virtual ::IMP::VersionInfo get_version_info() const override
Get information about the module and version of the object.
void remove_attribute(TypeKey attribute_key, ParticleIndex particle)
remove particle attribute with the specified key
Index< ParticleIndexTag > ParticleIndex
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Get the particles from a list of indexes.
An unbounded space with no periodic boundary conditions.
Key< 19 > Vector4DDerivKey
The type used to identify 4D vector attributes&derivatives in the Particles.
Key< 6 > ParticleIndexesKey
The type used to identify a particle attribute in the Particles.
Array< 3, WeakPointer< Particle >, Particle * > ParticleTriplet
ContainersTemp get_output_containers(const ModelObjectsTemp &mos)
Return all the output particles for a given ModelObject.
Base class for all samplers.
void add_particle(RMF::FileHandle fh, Particle *hs)
virtual void clear_caches()
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
void add_string_flag(std::string name, std::string default_value, std::string description)
LogLevel get_log_level()
Get the currently active global log level.
def get_sphere_derivatives_numpy
Get the model's XYZR attribute derivatives arrays as NumPy arrays.
void set_deprecation_warnings(bool tf)
Toggle printing of warnings on using deprecated classes.
Vector3D get_centroid(const Vector3Ds &ps)
Return the centroid of a set of vectors.
def get_numpy
Get the model's attribute array for any type of Key k as a NumPy array.
TextOutput create_temporary_file(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file. The path can be extracted from the TextOutput.
ParticlesTemp get_output_particles(const ModelObjectsTemp &mos)
Return all the output particles for a given ModelObject.
ScoringFunction * create_scoring_function(RestraintType *rs, double weight=1.0, double max=NO_MAX, std::string name=std::string())
Create a ScoringFunction on a single restraint.
A base class for modifiers of ParticlePairsTemp.
void write_help(std::ostream &out=std::cerr)
Key< 2 > StringKey
The type used to identify string attributes in the Particles.
size_t get_int_flag(std::string name)
Key< 10 > FloatsKey
The type used to identify float vector attributes in the Particles.
void add_restraint(RMF::FileHandle fh, Restraint *hs)
Key< 17 > Vector3DDerivKey
The type used to identify 3D vector attributes&derivatives in the Particles.
Abstract class for scoring object(s) of type ParticleIndexQuad.
Base class for objects in a Model that depend on other objects.
boost::uint64_t get_random_seed()
Return the initial random seed.
Abstract predicate function.
Key< 3 > ParticleIndexKey
The type used to identify a particle attribute in the Particles.
Strings get_live_object_names()
Return the names of all live objects.
void add_to_progress_display(unsigned int step=1)
Set the current progress.
void add_attribute(TypeKey attribute_key, ParticleIndex particle, Type value)
add particle attribute with the specified key and initial value
void add_float_flag(std::string name, double default_value, std::string description)
virtual void do_destroy()
Ints get_index(const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded)
double get_radius_of_gyration(const Vector3Ds &ps)
Return the radius of gyration of a set of points.
Common base class for heavy weight IMP objects.
ParticleIndexes get_particle_indexes(ParticlesTemp const &particles)
def deprecated_method
Python decorator to mark a method as deprecated.
Abstract class for scoring object(s) of type ParticleIndex.
Base class for all optimizers.
void reset_log_timer()
Reset the log timer.
void add_restraints(RMF::FileHandle fh, const Restraints &hs)
void add_to_log(LogLevel level, std::string to_write)
Write a string to the log, for Python.
def parse_args
Parse the command line and return optional and positional arguments.
def get_internal_coordinates_numpy
Get the model's internal coordinate array as a NumPy array.
double get_distance(const VectorD< D > &v1, const VectorD< D > &v2)
Compute the distance between two vectors.
void set_is_optimized(TypeKey attribute_key, ParticleIndex particle, bool true_or_false)
Key< 1 > IntKey
The type used to identify int attributes in the Particles.
Restraints create_decomposition(const RestraintsTemp &rs)
Return the decomposition of a list of restraints.
std::string get_relative_path(std::string base, std::string relative)
Return a path to a file relative to another file.
A class to store a set of configurations of a model.
A shared container for Quads.
def get_internal_coordinate_derivatives_numpy
Get the model's internal coordinate derivative array as a NumPy array.
A shared container for Singletons.
void set_deprecation_exceptions(bool tf)
Toggle whether an exception is thrown when a deprecated method is used.
Support for the JAX Python library.
def get_spheres_numpy
Get the model's XYZR attribute arrays as NumPy arrays.
Key< 4 > ObjectKey
The type used to identify an Object attribute.
Interface to specialized Particle types (e.g. atoms)
IMP-specific subclass of argparse.ArgumentParser.
def get_derivatives_numpy
Get the model's attribute derivatives array for key k as a NumPy array.
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
std::string get_absolute_path(std::string file)
Convert a possibly relative path to an absolute path.
std::string get_executable_name()
Return the name of the current executable.
void set_log_level(LogLevel l)
Set the current global log level.
unsigned int get_number_of_threads()
float get_random_float_uniform()
Return a uniformly distributed float number in range [0..1)
def deprecated_object
Python decorator to mark a class as deprecated.
ParticlesTemp get_input_particles(const ModelObjectsTemp &mos)
Return all the input particles for a given ModelObject.
Base class for optimizers that act on individual attributes.
void set_show_leaked_objects(bool tf)
Set whether to complain about objects not being properly cleaned up.
Abstract predicate function.
bool get_deprecation_exceptions()
Get whether an exception is thrown when a deprecated method is used.
Represents a scoring function on the model.
void set_log_timer(bool tb)
Set whether log messages are tagged with the current log time.
void show_restraint_hierarchy(ScoringFunctionAdaptor rs, std::ostream &out=std::cout)
Print the hierarchy of restraints.
DependencyGraph get_pruned_dependency_graph(Model *m)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Warning for incomplete JAX support or different behavior of JAX code.
Object(std::string name)
Construct an object with the given name.
Array< 2, WeakPointer< Particle >, Particle * > ParticlePair
Key< 5 > IntsKey
The type used to identify int attributes in the Particles.
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Restraints create_restraints(RMF::FileConstHandle fh, Model *m)
Shared optimizer state that is invoked upon commitment of new coordinates.
Abstract predicate function.
Abstract class to implement hierarchical methods.
A base class for modifiers of ParticleTripletsTemp.
std::string show_graphviz(Graph g)
void set_check_level(CheckLevel l)
std::string get_string_flag(std::string name)
networkx::DiGraph get_networkx_graph(Graph g)
Key< 18 > Vector4DKey
The type used to identify 4D vector attributes in the Particles.
double get_random_double_uniform()
Return a uniformly distributed double number in range [0..1)
Key< 8 > ModelKey
The type used to identify data stored directly in the model.
A base class for modifiers of ParticleQuadsTemp.
Key< 14 > SparseFloatKey
The type used to identify sparse float attributes in the Particles.
A shared container for Triplets.
def get_vector3ds_numpy
Get the model's attribute array for Vector3DKey k as a NumPy array.
Vector3D get_vector_product(const Vector3D &p1, const Vector3D &p2)
Return the vector product (cross product) of two vectors.
Abstract class for scoring object(s) of type ParticleIndexTriplet.
void show_altgraph(Graph g)
void update()
Sometimes it is useful to be able to make sure the model is up to date.
void setup_from_argv(int argc, char **argv, std::string description)
Parse the command line flags and return the positional arguments.
void add_bool_flag(std::string name, std::string description)
ParticleIndexes get_indexes(const ParticlesTemp &ps)
Get the indexes from a list of particles.
Abstract class for containers of particles.
void read_particles_from_buffer(const Vector< char > &buffer, const ParticlesTemp &particles, const FloatKeys &keys)
load found attributes into the particles
Abstract single variable functor class for score functions.
void set_number_of_threads(unsigned int n)
double get_float_flag(std::string name)
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
ScoreStatesTemp get_update_order(ScoreStatesTemp input)
std::string get_module_version()
Return the version of this module, as a string.
std::string create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="")
Create a temporary file.
A restraint is a term in an IMP ScoringFunction.
Key< 12 > SparseStringKey
The type used to identify sparse string attributes in the Particles.
std::string get_copyright()
Get the IMP copyright notice.