14 from sys
import version_info
as _swig_python_version_info
18 import builtins
as __builtin__
24 strthis =
"proxy of " + self.this.__repr__()
25 except __builtin__.Exception:
27 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
30 def _swig_setattr_nondynamic_instance_variable(set):
31 def set_instance_attr(self, name, value):
33 set(self, name, value)
34 elif name ==
"thisown":
36 elif hasattr(self, name)
and isinstance(getattr(type(self), name), property):
37 set(self, name, value)
39 raise AttributeError(
"You cannot add instance attributes to %s" % self)
40 return set_instance_attr
43 def _swig_setattr_nondynamic_class_variable(set):
44 def set_class_attr(cls, name, value):
45 if hasattr(cls, name)
and not isinstance(getattr(cls, name), property):
48 raise AttributeError(
"You cannot add class attributes to %s" % cls)
52 def _swig_add_metaclass(metaclass):
53 """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
55 return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
59 class _SwigNonDynamicMeta(type):
60 """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
61 __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
66 class IMP_KERNEL_SwigPyIterator(object):
67 r"""Proxy of C++ swig::IMP_KERNEL_SwigPyIterator class."""
69 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
71 def __init__(self, *args, **kwargs):
72 raise AttributeError(
"No constructor defined - class is abstract")
74 __swig_destroy__ = _IMP_kernel.delete_IMP_KERNEL_SwigPyIterator
77 r"""value(IMP_KERNEL_SwigPyIterator self) -> PyObject *"""
78 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_value(self)
81 r"""incr(IMP_KERNEL_SwigPyIterator self, size_t n=1) -> IMP_KERNEL_SwigPyIterator"""
82 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_incr(self, n)
85 r"""decr(IMP_KERNEL_SwigPyIterator self, size_t n=1) -> IMP_KERNEL_SwigPyIterator"""
86 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_decr(self, n)
88 def distance(self, x):
89 r"""distance(IMP_KERNEL_SwigPyIterator self, IMP_KERNEL_SwigPyIterator x) -> ptrdiff_t"""
90 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_distance(self, x)
93 r"""equal(IMP_KERNEL_SwigPyIterator self, IMP_KERNEL_SwigPyIterator x) -> bool"""
94 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_equal(self, x)
97 r"""copy(IMP_KERNEL_SwigPyIterator self) -> IMP_KERNEL_SwigPyIterator"""
98 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_copy(self)
101 r"""next(IMP_KERNEL_SwigPyIterator self) -> PyObject *"""
102 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_next(self)
105 r"""__next__(IMP_KERNEL_SwigPyIterator self) -> PyObject *"""
106 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___next__(self)
109 r"""previous(IMP_KERNEL_SwigPyIterator self) -> PyObject *"""
110 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_previous(self)
112 def advance(self, n):
113 r"""advance(IMP_KERNEL_SwigPyIterator self, ptrdiff_t n) -> IMP_KERNEL_SwigPyIterator"""
114 return _IMP_kernel.IMP_KERNEL_SwigPyIterator_advance(self, n)
117 r"""__eq__(IMP_KERNEL_SwigPyIterator self, IMP_KERNEL_SwigPyIterator x) -> bool"""
118 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___eq__(self, x)
121 r"""__ne__(IMP_KERNEL_SwigPyIterator self, IMP_KERNEL_SwigPyIterator x) -> bool"""
122 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___ne__(self, x)
124 def __iadd__(self, n):
125 r"""__iadd__(IMP_KERNEL_SwigPyIterator self, ptrdiff_t n) -> IMP_KERNEL_SwigPyIterator"""
126 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___iadd__(self, n)
128 def __isub__(self, n):
129 r"""__isub__(IMP_KERNEL_SwigPyIterator self, ptrdiff_t n) -> IMP_KERNEL_SwigPyIterator"""
130 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___isub__(self, n)
132 def __add__(self, n):
133 r"""__add__(IMP_KERNEL_SwigPyIterator self, ptrdiff_t n) -> IMP_KERNEL_SwigPyIterator"""
134 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___add__(self, n)
136 def __sub__(self, *args):
138 __sub__(IMP_KERNEL_SwigPyIterator self, ptrdiff_t n) -> IMP_KERNEL_SwigPyIterator
139 __sub__(IMP_KERNEL_SwigPyIterator self, IMP_KERNEL_SwigPyIterator x) -> ptrdiff_t
141 return _IMP_kernel.IMP_KERNEL_SwigPyIterator___sub__(self, *args)
146 _IMP_kernel.IMP_KERNEL_SwigPyIterator_swigregister(IMP_KERNEL_SwigPyIterator)
153 IMP_DEBUG = _IMP_kernel.IMP_DEBUG
155 IMP_RELEASE = _IMP_kernel.IMP_RELEASE
157 IMP_SILENT = _IMP_kernel.IMP_SILENT
159 IMP_PROGRESS = _IMP_kernel.IMP_PROGRESS
161 IMP_TERSE = _IMP_kernel.IMP_TERSE
163 IMP_VERBOSE = _IMP_kernel.IMP_VERBOSE
165 IMP_MEMORY = _IMP_kernel.IMP_MEMORY
167 IMP_NONE = _IMP_kernel.IMP_NONE
169 IMP_USAGE = _IMP_kernel.IMP_USAGE
171 IMP_INTERNAL = _IMP_kernel.IMP_INTERNAL
173 IMP_KERNEL_HAS_LOG4CXX = _IMP_kernel.IMP_KERNEL_HAS_LOG4CXX
175 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_kernel.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_kernel.IMP_COMPILER_HAS_DEBUG_VECTOR
179 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_kernel.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 IMP_COMPILER_HAS_THREE_WAY = _IMP_kernel.IMP_COMPILER_HAS_THREE_WAY
183 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_kernel.IMP_KERNEL_HAS_BOOST_RANDOM
185 IMP_KERNEL_HAS_NUMPY = _IMP_kernel.IMP_KERNEL_HAS_NUMPY
187 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_kernel.IMP_KERNEL_HAS_BOOST_SYSTEM
189 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_kernel.IMP_KERNEL_HAS_GPERFTOOLS
191 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_kernel.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
193 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_kernel.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
195 IMPKERNEL_SHOW_WARNINGS = _IMP_kernel.IMPKERNEL_SHOW_WARNINGS
199 class _DirectorObjects:
200 """@internal Simple class to keep references to director objects
201 to prevent premature deletion."""
204 def register(self, obj):
205 """Take a reference to a director object; will only work for
206 refcounted C++ classes"""
207 if hasattr(obj,
'get_ref_count'):
208 self._objects.append(obj)
210 """Only drop our reference and allow cleanup by Python if no other
211 Python references exist (we hold 3 references: one in self._objects,
212 one in x, and one in the argument list for getrefcount) *and* no
213 other C++ references exist (the Python object always holds one)"""
214 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
215 or x.get_ref_count() > 1]
219 def get_object_count(self):
220 """Get number of director objects (useful for testing only)"""
221 return len(self._objects)
222 _director_objects = _DirectorObjects()
224 DEFAULT_CHECK = _IMP_kernel.DEFAULT_CHECK
226 NONE = _IMP_kernel.NONE
228 USAGE = _IMP_kernel.USAGE
230 USAGE_AND_INTERNAL = _IMP_kernel.USAGE_AND_INTERNAL
234 r"""set_check_level(IMP::CheckLevel tf)"""
235 return _IMP_kernel.set_check_level(tf)
238 r"""get_check_level() -> IMP::CheckLevel"""
239 return _IMP_kernel.get_check_level()
241 from _IMP_kernel
import Exception, InternalException, ModelException, EventException
242 from _IMP_kernel
import UsageException, IndexException, IOException, ValueException
243 from _IMP_kernel
import TypeException
245 class _ostream(object):
246 r"""Proxy of C++ std::ostream class."""
248 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
250 def __init__(self, *args, **kwargs):
251 raise AttributeError(
"No constructor defined")
252 __repr__ = _swig_repr
254 def write(self, osa_buf):
255 r"""write(_ostream self, char const * osa_buf)"""
256 return _IMP_kernel._ostream_write(self, osa_buf)
259 _IMP_kernel._ostream_swigregister(_ostream)
260 IMP_C_OPEN_BINARY = _IMP_kernel.IMP_C_OPEN_BINARY
263 from .
import _list_util
266 _models_set = weakref.WeakSet()
268 def _models_set_get(m):
269 for x
in _models_set:
274 _raii_types.append(
"SetLogState")
277 _raii_types.append(
"SetNumberOfThreads")
280 _raii_types.append(
"SetCheckState")
283 _object_types.append(
"Object")
286 def _object_cast_to_Object(o):
287 r"""_object_cast_to_Object(Object * o) -> Object"""
288 return _IMP_kernel._object_cast_to_Object(o)
290 _object_types.append(
"_TestObject")
293 def _object_cast_to__TestObject(o):
294 r"""_object_cast_to__TestObject(Object * o) -> _TestObject"""
295 return _IMP_kernel._object_cast_to__TestObject(o)
298 _plural_types.append(
"VersionInfos")
299 _value_types.append(
"VersionInfo")
302 _raii_types.append(
"CreateLogContext")
305 _raii_types.append(
"WarningContext")
308 _raii_types.append(
"SetLogTarget")
312 _plural_types.append(
"_TestValues")
313 _value_types.append(
"_TestValue")
317 _plural_types.append(
"Floats")
318 _value_types.append(
"Float")
322 _plural_types.append(
"Ints")
323 _value_types.append(
"Int")
327 _plural_types.append(
"Strings")
328 _value_types.append(
"String")
332 _plural_types.append(
"_Protections")
333 _value_types.append(
"_Protection")
335 class _GeometricPrimitive1D(object):
336 r"""Proxy of C++ IMP::GeometricPrimitiveD< 1 > class."""
338 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
340 def __init__(self, *args, **kwargs):
341 raise AttributeError(
"No constructor defined")
342 __repr__ = _swig_repr
343 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive1D
346 _IMP_kernel._GeometricPrimitive1D_swigregister(_GeometricPrimitive1D)
347 class _GeometricPrimitive2D(object):
348 r"""Proxy of C++ IMP::GeometricPrimitiveD< 2 > class."""
350 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
352 def __init__(self, *args, **kwargs):
353 raise AttributeError(
"No constructor defined")
354 __repr__ = _swig_repr
355 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive2D
358 _IMP_kernel._GeometricPrimitive2D_swigregister(_GeometricPrimitive2D)
359 class _GeometricPrimitive3D(object):
360 r"""Proxy of C++ IMP::GeometricPrimitiveD< 3 > class."""
362 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
364 def __init__(self, *args, **kwargs):
365 raise AttributeError(
"No constructor defined")
366 __repr__ = _swig_repr
367 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive3D
370 _IMP_kernel._GeometricPrimitive3D_swigregister(_GeometricPrimitive3D)
371 class _GeometricPrimitive4D(object):
372 r"""Proxy of C++ IMP::GeometricPrimitiveD< 4 > class."""
374 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
376 def __init__(self, *args, **kwargs):
377 raise AttributeError(
"No constructor defined")
378 __repr__ = _swig_repr
379 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive4D
382 _IMP_kernel._GeometricPrimitive4D_swigregister(_GeometricPrimitive4D)
383 class _GeometricPrimitive5D(object):
384 r"""Proxy of C++ IMP::GeometricPrimitiveD< 5 > class."""
386 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
388 def __init__(self, *args, **kwargs):
389 raise AttributeError(
"No constructor defined")
390 __repr__ = _swig_repr
391 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive5D
394 _IMP_kernel._GeometricPrimitive5D_swigregister(_GeometricPrimitive5D)
395 class _GeometricPrimitive6D(object):
396 r"""Proxy of C++ IMP::GeometricPrimitiveD< 6 > class."""
398 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
400 def __init__(self, *args, **kwargs):
401 raise AttributeError(
"No constructor defined")
402 __repr__ = _swig_repr
403 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitive6D
406 _IMP_kernel._GeometricPrimitive6D_swigregister(_GeometricPrimitive6D)
407 class _GeometricPrimitiveKD(object):
408 r"""Proxy of C++ IMP::GeometricPrimitiveD< -1 > class."""
410 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
412 def __init__(self, *args, **kwargs):
413 raise AttributeError(
"No constructor defined")
414 __repr__ = _swig_repr
415 __swig_destroy__ = _IMP_kernel.delete__GeometricPrimitiveKD
418 _IMP_kernel._GeometricPrimitiveKD_swigregister(_GeometricPrimitiveKD)
419 class _VectorBaseKD(_GeometricPrimitiveKD):
420 r"""Proxy of C++ IMP::internal::VectorBaseD< -1 > class."""
422 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
423 __repr__ = _swig_repr
426 r"""__init__(_VectorBaseKD self) -> _VectorBaseKD"""
427 _IMP_kernel._VectorBaseKD_swiginit(self, _IMP_kernel.new__VectorBaseKD())
429 def get_scalar_product(self, o):
430 r"""get_scalar_product(_VectorBaseKD self, _VectorBaseKD o) -> double"""
431 return _IMP_kernel._VectorBaseKD_get_scalar_product(self, o)
433 def get_squared_magnitude(self):
434 r"""get_squared_magnitude(_VectorBaseKD self) -> double"""
435 return _IMP_kernel._VectorBaseKD_get_squared_magnitude(self)
437 def get_magnitude(self):
438 r"""get_magnitude(_VectorBaseKD self) -> double"""
439 return _IMP_kernel._VectorBaseKD_get_magnitude(self)
442 r"""get_distance(_VectorBaseKD self, _VectorBaseKD o) -> double"""
443 return _IMP_kernel._VectorBaseKD_get_distance(self, o)
445 def __mul__(self, o):
446 r"""__mul__(_VectorBaseKD self, _VectorBaseKD o) -> double"""
447 return _IMP_kernel._VectorBaseKD___mul__(self, o)
449 def __iadd__(self, o):
450 r"""__iadd__(_VectorBaseKD self, _VectorBaseKD o) -> _VectorBaseKD"""
451 return _IMP_kernel._VectorBaseKD___iadd__(self, o)
453 def __isub__(self, o):
454 r"""__isub__(_VectorBaseKD self, _VectorBaseKD o) -> _VectorBaseKD"""
455 return _IMP_kernel._VectorBaseKD___isub__(self, o)
457 def __itruediv__(self, *args):
458 return _IMP_kernel._VectorBaseKD___itruediv__(self, *args)
459 __idiv__ = __itruediv__
463 def __imul__(self, f):
464 r"""__imul__(_VectorBaseKD self, double f) -> _VectorBaseKD"""
465 return _IMP_kernel._VectorBaseKD___imul__(self, f)
467 def show(self, *args):
469 show(_VectorBaseKD self, _ostream out, std::string delim, bool parens=True)
470 show(_VectorBaseKD self, _ostream out=std::cout)
472 return _IMP_kernel._VectorBaseKD_show(self, *args)
474 def get_dimension(self):
475 r"""get_dimension(_VectorBaseKD self) -> unsigned int"""
476 return _IMP_kernel._VectorBaseKD_get_dimension(self)
477 __swig_destroy__ = _IMP_kernel.delete__VectorBaseKD
480 _IMP_kernel._VectorBaseKD_swigregister(_VectorBaseKD)
481 class _VectorBase1D(_GeometricPrimitive1D):
482 r"""Proxy of C++ IMP::internal::VectorBaseD< 1 > class."""
484 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
485 __repr__ = _swig_repr
488 r"""__init__(_VectorBase1D self) -> _VectorBase1D"""
489 _IMP_kernel._VectorBase1D_swiginit(self, _IMP_kernel.new__VectorBase1D())
491 def get_scalar_product(self, o):
492 r"""get_scalar_product(_VectorBase1D self, _VectorBase1D o) -> double"""
493 return _IMP_kernel._VectorBase1D_get_scalar_product(self, o)
495 def get_squared_magnitude(self):
496 r"""get_squared_magnitude(_VectorBase1D self) -> double"""
497 return _IMP_kernel._VectorBase1D_get_squared_magnitude(self)
499 def get_magnitude(self):
500 r"""get_magnitude(_VectorBase1D self) -> double"""
501 return _IMP_kernel._VectorBase1D_get_magnitude(self)
504 r"""get_distance(_VectorBase1D self, _VectorBase1D o) -> double"""
505 return _IMP_kernel._VectorBase1D_get_distance(self, o)
507 def __mul__(self, o):
508 r"""__mul__(_VectorBase1D self, _VectorBase1D o) -> double"""
509 return _IMP_kernel._VectorBase1D___mul__(self, o)
511 def __iadd__(self, o):
512 r"""__iadd__(_VectorBase1D self, _VectorBase1D o) -> _VectorBase1D"""
513 return _IMP_kernel._VectorBase1D___iadd__(self, o)
515 def __isub__(self, o):
516 r"""__isub__(_VectorBase1D self, _VectorBase1D o) -> _VectorBase1D"""
517 return _IMP_kernel._VectorBase1D___isub__(self, o)
519 def __itruediv__(self, *args):
520 return _IMP_kernel._VectorBase1D___itruediv__(self, *args)
521 __idiv__ = __itruediv__
525 def __imul__(self, f):
526 r"""__imul__(_VectorBase1D self, double f) -> _VectorBase1D"""
527 return _IMP_kernel._VectorBase1D___imul__(self, f)
529 def show(self, *args):
531 show(_VectorBase1D self, _ostream out, std::string delim, bool parens=True)
532 show(_VectorBase1D self, _ostream out=std::cout)
534 return _IMP_kernel._VectorBase1D_show(self, *args)
536 def get_dimension(self):
537 r"""get_dimension(_VectorBase1D self) -> unsigned int"""
538 return _IMP_kernel._VectorBase1D_get_dimension(self)
539 __swig_destroy__ = _IMP_kernel.delete__VectorBase1D
542 _IMP_kernel._VectorBase1D_swigregister(_VectorBase1D)
543 class _VectorBase2D(_GeometricPrimitive2D):
544 r"""Proxy of C++ IMP::internal::VectorBaseD< 2 > class."""
546 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
547 __repr__ = _swig_repr
550 r"""__init__(_VectorBase2D self) -> _VectorBase2D"""
551 _IMP_kernel._VectorBase2D_swiginit(self, _IMP_kernel.new__VectorBase2D())
553 def get_scalar_product(self, o):
554 r"""get_scalar_product(_VectorBase2D self, _VectorBase2D o) -> double"""
555 return _IMP_kernel._VectorBase2D_get_scalar_product(self, o)
557 def get_squared_magnitude(self):
558 r"""get_squared_magnitude(_VectorBase2D self) -> double"""
559 return _IMP_kernel._VectorBase2D_get_squared_magnitude(self)
561 def get_magnitude(self):
562 r"""get_magnitude(_VectorBase2D self) -> double"""
563 return _IMP_kernel._VectorBase2D_get_magnitude(self)
566 r"""get_distance(_VectorBase2D self, _VectorBase2D o) -> double"""
567 return _IMP_kernel._VectorBase2D_get_distance(self, o)
569 def __mul__(self, o):
570 r"""__mul__(_VectorBase2D self, _VectorBase2D o) -> double"""
571 return _IMP_kernel._VectorBase2D___mul__(self, o)
573 def __iadd__(self, o):
574 r"""__iadd__(_VectorBase2D self, _VectorBase2D o) -> _VectorBase2D"""
575 return _IMP_kernel._VectorBase2D___iadd__(self, o)
577 def __isub__(self, o):
578 r"""__isub__(_VectorBase2D self, _VectorBase2D o) -> _VectorBase2D"""
579 return _IMP_kernel._VectorBase2D___isub__(self, o)
581 def __itruediv__(self, *args):
582 return _IMP_kernel._VectorBase2D___itruediv__(self, *args)
583 __idiv__ = __itruediv__
587 def __imul__(self, f):
588 r"""__imul__(_VectorBase2D self, double f) -> _VectorBase2D"""
589 return _IMP_kernel._VectorBase2D___imul__(self, f)
591 def show(self, *args):
593 show(_VectorBase2D self, _ostream out, std::string delim, bool parens=True)
594 show(_VectorBase2D self, _ostream out=std::cout)
596 return _IMP_kernel._VectorBase2D_show(self, *args)
598 def get_dimension(self):
599 r"""get_dimension(_VectorBase2D self) -> unsigned int"""
600 return _IMP_kernel._VectorBase2D_get_dimension(self)
601 __swig_destroy__ = _IMP_kernel.delete__VectorBase2D
604 _IMP_kernel._VectorBase2D_swigregister(_VectorBase2D)
605 class _VectorBase3D(_GeometricPrimitive3D):
606 r"""Proxy of C++ IMP::internal::VectorBaseD< 3 > class."""
608 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
609 __repr__ = _swig_repr
612 r"""__init__(_VectorBase3D self) -> _VectorBase3D"""
613 _IMP_kernel._VectorBase3D_swiginit(self, _IMP_kernel.new__VectorBase3D())
615 def get_scalar_product(self, o):
616 r"""get_scalar_product(_VectorBase3D self, _VectorBase3D o) -> double"""
617 return _IMP_kernel._VectorBase3D_get_scalar_product(self, o)
619 def get_squared_magnitude(self):
620 r"""get_squared_magnitude(_VectorBase3D self) -> double"""
621 return _IMP_kernel._VectorBase3D_get_squared_magnitude(self)
623 def get_magnitude(self):
624 r"""get_magnitude(_VectorBase3D self) -> double"""
625 return _IMP_kernel._VectorBase3D_get_magnitude(self)
628 r"""get_distance(_VectorBase3D self, _VectorBase3D o) -> double"""
629 return _IMP_kernel._VectorBase3D_get_distance(self, o)
631 def __mul__(self, o):
632 r"""__mul__(_VectorBase3D self, _VectorBase3D o) -> double"""
633 return _IMP_kernel._VectorBase3D___mul__(self, o)
635 def __iadd__(self, o):
636 r"""__iadd__(_VectorBase3D self, _VectorBase3D o) -> _VectorBase3D"""
637 return _IMP_kernel._VectorBase3D___iadd__(self, o)
639 def __isub__(self, o):
640 r"""__isub__(_VectorBase3D self, _VectorBase3D o) -> _VectorBase3D"""
641 return _IMP_kernel._VectorBase3D___isub__(self, o)
643 def __itruediv__(self, *args):
644 return _IMP_kernel._VectorBase3D___itruediv__(self, *args)
645 __idiv__ = __itruediv__
649 def __imul__(self, f):
650 r"""__imul__(_VectorBase3D self, double f) -> _VectorBase3D"""
651 return _IMP_kernel._VectorBase3D___imul__(self, f)
653 def show(self, *args):
655 show(_VectorBase3D self, _ostream out, std::string delim, bool parens=True)
656 show(_VectorBase3D self, _ostream out=std::cout)
658 return _IMP_kernel._VectorBase3D_show(self, *args)
660 def get_dimension(self):
661 r"""get_dimension(_VectorBase3D self) -> unsigned int"""
662 return _IMP_kernel._VectorBase3D_get_dimension(self)
663 __swig_destroy__ = _IMP_kernel.delete__VectorBase3D
666 _IMP_kernel._VectorBase3D_swigregister(_VectorBase3D)
667 class _VectorBase4D(_GeometricPrimitive4D):
668 r"""Proxy of C++ IMP::internal::VectorBaseD< 4 > class."""
670 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
671 __repr__ = _swig_repr
674 r"""__init__(_VectorBase4D self) -> _VectorBase4D"""
675 _IMP_kernel._VectorBase4D_swiginit(self, _IMP_kernel.new__VectorBase4D())
677 def get_scalar_product(self, o):
678 r"""get_scalar_product(_VectorBase4D self, _VectorBase4D o) -> double"""
679 return _IMP_kernel._VectorBase4D_get_scalar_product(self, o)
681 def get_squared_magnitude(self):
682 r"""get_squared_magnitude(_VectorBase4D self) -> double"""
683 return _IMP_kernel._VectorBase4D_get_squared_magnitude(self)
685 def get_magnitude(self):
686 r"""get_magnitude(_VectorBase4D self) -> double"""
687 return _IMP_kernel._VectorBase4D_get_magnitude(self)
690 r"""get_distance(_VectorBase4D self, _VectorBase4D o) -> double"""
691 return _IMP_kernel._VectorBase4D_get_distance(self, o)
693 def __mul__(self, o):
694 r"""__mul__(_VectorBase4D self, _VectorBase4D o) -> double"""
695 return _IMP_kernel._VectorBase4D___mul__(self, o)
697 def __iadd__(self, o):
698 r"""__iadd__(_VectorBase4D self, _VectorBase4D o) -> _VectorBase4D"""
699 return _IMP_kernel._VectorBase4D___iadd__(self, o)
701 def __isub__(self, o):
702 r"""__isub__(_VectorBase4D self, _VectorBase4D o) -> _VectorBase4D"""
703 return _IMP_kernel._VectorBase4D___isub__(self, o)
705 def __itruediv__(self, *args):
706 return _IMP_kernel._VectorBase4D___itruediv__(self, *args)
707 __idiv__ = __itruediv__
711 def __imul__(self, f):
712 r"""__imul__(_VectorBase4D self, double f) -> _VectorBase4D"""
713 return _IMP_kernel._VectorBase4D___imul__(self, f)
715 def show(self, *args):
717 show(_VectorBase4D self, _ostream out, std::string delim, bool parens=True)
718 show(_VectorBase4D self, _ostream out=std::cout)
720 return _IMP_kernel._VectorBase4D_show(self, *args)
722 def get_dimension(self):
723 r"""get_dimension(_VectorBase4D self) -> unsigned int"""
724 return _IMP_kernel._VectorBase4D_get_dimension(self)
725 __swig_destroy__ = _IMP_kernel.delete__VectorBase4D
728 _IMP_kernel._VectorBase4D_swigregister(_VectorBase4D)
729 class _VectorBase5D(_GeometricPrimitive5D):
730 r"""Proxy of C++ IMP::internal::VectorBaseD< 5 > class."""
732 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
733 __repr__ = _swig_repr
736 r"""__init__(_VectorBase5D self) -> _VectorBase5D"""
737 _IMP_kernel._VectorBase5D_swiginit(self, _IMP_kernel.new__VectorBase5D())
739 def get_scalar_product(self, o):
740 r"""get_scalar_product(_VectorBase5D self, _VectorBase5D o) -> double"""
741 return _IMP_kernel._VectorBase5D_get_scalar_product(self, o)
743 def get_squared_magnitude(self):
744 r"""get_squared_magnitude(_VectorBase5D self) -> double"""
745 return _IMP_kernel._VectorBase5D_get_squared_magnitude(self)
747 def get_magnitude(self):
748 r"""get_magnitude(_VectorBase5D self) -> double"""
749 return _IMP_kernel._VectorBase5D_get_magnitude(self)
752 r"""get_distance(_VectorBase5D self, _VectorBase5D o) -> double"""
753 return _IMP_kernel._VectorBase5D_get_distance(self, o)
755 def __mul__(self, o):
756 r"""__mul__(_VectorBase5D self, _VectorBase5D o) -> double"""
757 return _IMP_kernel._VectorBase5D___mul__(self, o)
759 def __iadd__(self, o):
760 r"""__iadd__(_VectorBase5D self, _VectorBase5D o) -> _VectorBase5D"""
761 return _IMP_kernel._VectorBase5D___iadd__(self, o)
763 def __isub__(self, o):
764 r"""__isub__(_VectorBase5D self, _VectorBase5D o) -> _VectorBase5D"""
765 return _IMP_kernel._VectorBase5D___isub__(self, o)
767 def __itruediv__(self, *args):
768 return _IMP_kernel._VectorBase5D___itruediv__(self, *args)
769 __idiv__ = __itruediv__
773 def __imul__(self, f):
774 r"""__imul__(_VectorBase5D self, double f) -> _VectorBase5D"""
775 return _IMP_kernel._VectorBase5D___imul__(self, f)
777 def show(self, *args):
779 show(_VectorBase5D self, _ostream out, std::string delim, bool parens=True)
780 show(_VectorBase5D self, _ostream out=std::cout)
782 return _IMP_kernel._VectorBase5D_show(self, *args)
784 def get_dimension(self):
785 r"""get_dimension(_VectorBase5D self) -> unsigned int"""
786 return _IMP_kernel._VectorBase5D_get_dimension(self)
787 __swig_destroy__ = _IMP_kernel.delete__VectorBase5D
790 _IMP_kernel._VectorBase5D_swigregister(_VectorBase5D)
791 class _VectorBase6D(_GeometricPrimitive6D):
792 r"""Proxy of C++ IMP::internal::VectorBaseD< 6 > class."""
794 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
795 __repr__ = _swig_repr
798 r"""__init__(_VectorBase6D self) -> _VectorBase6D"""
799 _IMP_kernel._VectorBase6D_swiginit(self, _IMP_kernel.new__VectorBase6D())
801 def get_scalar_product(self, o):
802 r"""get_scalar_product(_VectorBase6D self, _VectorBase6D o) -> double"""
803 return _IMP_kernel._VectorBase6D_get_scalar_product(self, o)
805 def get_squared_magnitude(self):
806 r"""get_squared_magnitude(_VectorBase6D self) -> double"""
807 return _IMP_kernel._VectorBase6D_get_squared_magnitude(self)
809 def get_magnitude(self):
810 r"""get_magnitude(_VectorBase6D self) -> double"""
811 return _IMP_kernel._VectorBase6D_get_magnitude(self)
814 r"""get_distance(_VectorBase6D self, _VectorBase6D o) -> double"""
815 return _IMP_kernel._VectorBase6D_get_distance(self, o)
817 def __mul__(self, o):
818 r"""__mul__(_VectorBase6D self, _VectorBase6D o) -> double"""
819 return _IMP_kernel._VectorBase6D___mul__(self, o)
821 def __iadd__(self, o):
822 r"""__iadd__(_VectorBase6D self, _VectorBase6D o) -> _VectorBase6D"""
823 return _IMP_kernel._VectorBase6D___iadd__(self, o)
825 def __isub__(self, o):
826 r"""__isub__(_VectorBase6D self, _VectorBase6D o) -> _VectorBase6D"""
827 return _IMP_kernel._VectorBase6D___isub__(self, o)
829 def __itruediv__(self, *args):
830 return _IMP_kernel._VectorBase6D___itruediv__(self, *args)
831 __idiv__ = __itruediv__
835 def __imul__(self, f):
836 r"""__imul__(_VectorBase6D self, double f) -> _VectorBase6D"""
837 return _IMP_kernel._VectorBase6D___imul__(self, f)
839 def show(self, *args):
841 show(_VectorBase6D self, _ostream out, std::string delim, bool parens=True)
842 show(_VectorBase6D self, _ostream out=std::cout)
844 return _IMP_kernel._VectorBase6D_show(self, *args)
846 def get_dimension(self):
847 r"""get_dimension(_VectorBase6D self) -> unsigned int"""
848 return _IMP_kernel._VectorBase6D_get_dimension(self)
849 __swig_destroy__ = _IMP_kernel.delete__VectorBase6D
852 _IMP_kernel._VectorBase6D_swigregister(_VectorBase6D)
853 class _InputAdaptor(object):
854 r"""Proxy of C++ IMP::InputAdaptor class."""
856 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
858 def __init__(self, *args, **kwargs):
859 raise AttributeError(
"No constructor defined")
860 __repr__ = _swig_repr
862 def __getstate__(self):
863 raise NotImplementedError(str(self.__class__)
864 +
" does not support serialization")
866 __swig_destroy__ = _IMP_kernel.delete__InputAdaptor
869 _IMP_kernel._InputAdaptor_swigregister(_InputAdaptor)
870 class _NonCopyable(object):
871 r"""Proxy of C++ IMP::NonCopyable class."""
873 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
875 def __init__(self, *args, **kwargs):
876 raise AttributeError(
"No constructor defined")
877 __repr__ = _swig_repr
878 __swig_destroy__ = _IMP_kernel.delete__NonCopyable
881 _IMP_kernel._NonCopyable_swigregister(_NonCopyable)
882 class _RAII(_NonCopyable):
883 r"""Proxy of C++ IMP::RAII class."""
885 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
887 def __init__(self, *args, **kwargs):
888 raise AttributeError(
"No constructor defined")
889 __repr__ = _swig_repr
890 __swig_destroy__ = _IMP_kernel.delete__RAII
893 _IMP_kernel._RAII_swigregister(_RAII)
894 class _Value(object):
895 r"""Proxy of C++ IMP::Value class."""
897 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
899 def __init__(self, *args, **kwargs):
900 raise AttributeError(
"No constructor defined")
901 __repr__ = _swig_repr
903 def __getstate__(self):
904 raise NotImplementedError(str(self.__class__)
905 +
" does not support serialization")
907 __swig_destroy__ = _IMP_kernel.delete__Value
910 _IMP_kernel._Value_swigregister(_Value)
913 r"""get_executable_name() -> std::string"""
914 return _IMP_kernel.get_executable_name()
918 setup_from_argv(IMP::Strings const & argv, std::string description)
919 setup_from_argv(IMP::Strings const & argv, std::string description, std::string positional_description, int num_positional) -> IMP::Strings
921 return _IMP_kernel.setup_from_argv(*args)
924 r"""add_string_flag(std::string name, std::string default_value, std::string description)"""
925 return _IMP_kernel.add_string_flag(name, default_value, description)
928 r"""get_string_flag(std::string name) -> std::string"""
929 return _IMP_kernel.get_string_flag(name)
932 r"""add_int_flag(std::string name, size_t default_value, std::string description)"""
933 return _IMP_kernel.add_int_flag(name, default_value, description)
936 r"""get_int_flag(std::string name) -> size_t"""
937 return _IMP_kernel.get_int_flag(name)
940 r"""add_bool_flag(std::string name, std::string description)"""
941 return _IMP_kernel.add_bool_flag(name, description)
944 r"""get_bool_flag(std::string name) -> bool"""
945 return _IMP_kernel.get_bool_flag(name)
948 r"""add_float_flag(std::string name, double default_value, std::string description)"""
949 return _IMP_kernel.add_float_flag(name, default_value, description)
952 r"""get_float_flag(std::string name) -> double"""
953 return _IMP_kernel.get_float_flag(name)
956 r"""write_help(_ostream out=std::cerr)"""
957 return _IMP_kernel.write_help(*args)
960 r"""get_is_quick_test() -> bool"""
961 return _IMP_kernel.get_is_quick_test()
962 DEFAULT = _IMP_kernel.DEFAULT
964 SILENT = _IMP_kernel.SILENT
966 WARNING = _IMP_kernel.WARNING
968 PROGRESS = _IMP_kernel.PROGRESS
970 TERSE = _IMP_kernel.TERSE
972 VERBOSE = _IMP_kernel.VERBOSE
974 MEMORY = _IMP_kernel.MEMORY
976 ALL_LOG = _IMP_kernel.ALL_LOG
978 class VersionInfo(_Value):
979 r"""Proxy of C++ IMP::VersionInfo class."""
981 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
983 def __init__(self, *args):
985 __init__(VersionInfo self, std::string module, std::string version) -> VersionInfo
986 __init__(VersionInfo self) -> VersionInfo
988 _IMP_kernel.VersionInfo_swiginit(self, _IMP_kernel.new_VersionInfo(*args))
990 def get_module(self):
991 r"""get_module(VersionInfo self) -> std::string"""
992 return _IMP_kernel.VersionInfo_get_module(self)
994 def get_version(self):
995 r"""get_version(VersionInfo self) -> std::string"""
996 return _IMP_kernel.VersionInfo_get_version(self)
998 def show(self, *args):
999 r"""show(VersionInfo self, _ostream out=std::cout)"""
1000 return _IMP_kernel.VersionInfo_show(self, *args)
1002 def __cmp__(self, o):
1003 r"""__cmp__(VersionInfo self, VersionInfo o) -> int"""
1004 return _IMP_kernel.VersionInfo___cmp__(self, o)
1006 def __eq__(self, o):
1007 r"""__eq__(VersionInfo self, VersionInfo o) -> bool"""
1008 return _IMP_kernel.VersionInfo___eq__(self, o)
1010 def __ne__(self, o):
1011 r"""__ne__(VersionInfo self, VersionInfo o) -> bool"""
1012 return _IMP_kernel.VersionInfo___ne__(self, o)
1014 def __lt__(self, o):
1015 r"""__lt__(VersionInfo self, VersionInfo o) -> bool"""
1016 return _IMP_kernel.VersionInfo___lt__(self, o)
1018 def __gt__(self, o):
1019 r"""__gt__(VersionInfo self, VersionInfo o) -> bool"""
1020 return _IMP_kernel.VersionInfo___gt__(self, o)
1022 def __ge__(self, o):
1023 r"""__ge__(VersionInfo self, VersionInfo o) -> bool"""
1024 return _IMP_kernel.VersionInfo___ge__(self, o)
1026 def __le__(self, o):
1027 r"""__le__(VersionInfo self, VersionInfo o) -> bool"""
1028 return _IMP_kernel.VersionInfo___le__(self, o)
1031 r"""__str__(VersionInfo self) -> std::string"""
1032 return _IMP_kernel.VersionInfo___str__(self)
1035 r"""__repr__(VersionInfo self) -> std::string"""
1036 return _IMP_kernel.VersionInfo___repr__(self)
1038 def _get_as_binary(self):
1039 r"""_get_as_binary(VersionInfo self) -> PyObject *"""
1040 return _IMP_kernel.VersionInfo__get_as_binary(self)
1042 def _set_from_binary(self, p):
1043 r"""_set_from_binary(VersionInfo self, PyObject * p)"""
1044 return _IMP_kernel.VersionInfo__set_from_binary(self, p)
1046 def __getstate__(self):
1047 p = self._get_as_binary()
1048 if len(self.__dict__) > 1:
1049 d = self.__dict__.copy()
1054 def __setstate__(self, p):
1055 if not hasattr(self,
'this'):
1057 if isinstance(p, tuple):
1059 self.__dict__.update(d)
1060 return self._set_from_binary(p)
1062 __swig_destroy__ = _IMP_kernel.delete_VersionInfo
1065 _IMP_kernel.VersionInfo_swigregister(VersionInfo)
1066 class TextOutput(_InputAdaptor):
1067 r"""Proxy of C++ IMP::TextOutput class."""
1069 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1070 __repr__ = _swig_repr
1072 def __init__(self, *args):
1074 __init__(TextOutput self, int arg2) -> TextOutput
1075 __init__(TextOutput self, double arg2) -> TextOutput
1076 __init__(TextOutput self, char const * c, bool append=False) -> TextOutput
1077 __init__(TextOutput self, IMP::TextProxy< std::ostream > p) -> TextOutput
1078 __init__(TextOutput self) -> TextOutput
1079 __init__(TextOutput self, std::string file_name, bool append=False) -> TextOutput
1081 _IMP_kernel.TextOutput_swiginit(self, _IMP_kernel.new_TextOutput(*args))
1083 def show(self, *args):
1084 r"""show(TextOutput self, _ostream out=std::cout)"""
1085 return _IMP_kernel.TextOutput_show(self, *args)
1088 r"""get_name(TextOutput self) -> std::string"""
1089 return _IMP_kernel.TextOutput_get_name(self)
1090 __swig_destroy__ = _IMP_kernel.delete_TextOutput
1093 _IMP_kernel.TextOutput_swigregister(TextOutput)
1094 class TextInput(_InputAdaptor):
1095 r"""Proxy of C++ IMP::TextInput class."""
1097 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1098 __repr__ = _swig_repr
1100 def __init__(self, *args):
1102 __init__(TextInput self, int arg2) -> TextInput
1103 __init__(TextInput self, double arg2) -> TextInput
1104 __init__(TextInput self, char const * c) -> TextInput
1105 __init__(TextInput self, IMP::TextProxy< std::istream > p) -> TextInput
1106 __init__(TextInput self) -> TextInput
1107 __init__(TextInput self, std::string file_name) -> TextInput
1109 _IMP_kernel.TextInput_swiginit(self, _IMP_kernel.new_TextInput(*args))
1111 def show(self, *args):
1112 r"""show(TextInput self, _ostream out=std::cout)"""
1113 return _IMP_kernel.TextInput_show(self, *args)
1116 r"""get_name(TextInput self) -> std::string"""
1117 return _IMP_kernel.TextInput_get_name(self)
1119 def set_binary_open_mode(self, binary):
1120 r"""set_binary_open_mode(TextInput self, bool binary)"""
1121 return _IMP_kernel.TextInput_set_binary_open_mode(self, binary)
1122 __swig_destroy__ = _IMP_kernel.delete_TextInput
1125 _IMP_kernel.TextInput_swigregister(TextInput)
1126 class SetLogTarget(_RAII):
1127 r"""Proxy of C++ IMP::SetLogTarget class."""
1129 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1131 def __init__(self, *args):
1133 __init__(SetLogTarget self) -> SetLogTarget
1134 __init__(SetLogTarget self, TextOutput to) -> SetLogTarget
1136 _IMP_kernel.SetLogTarget_swiginit(self, _IMP_kernel.new_SetLogTarget(*args))
1139 r"""set(SetLogTarget self, TextOutput to)"""
1140 return _IMP_kernel.SetLogTarget_set(self, to)
1143 r"""reset(SetLogTarget self)"""
1144 return _IMP_kernel.SetLogTarget_reset(self)
1145 __swig_destroy__ = _IMP_kernel.delete_SetLogTarget
1147 def show(self, *args):
1148 r"""show(SetLogTarget self, _ostream out=std::cout)"""
1149 return _IMP_kernel.SetLogTarget_show(self, *args)
1151 def __enter__(self):
1153 def __exit__(self, exc_type, exc_val, exc_tb):
1159 r"""__str__(SetLogTarget self) -> std::string"""
1160 return _IMP_kernel.SetLogTarget___str__(self)
1163 r"""__repr__(SetLogTarget self) -> std::string"""
1164 return _IMP_kernel.SetLogTarget___repr__(self)
1167 _IMP_kernel.SetLogTarget_swigregister(SetLogTarget)
1170 r"""create_temporary_file(std::string prefix="imp_temp", std::string suffix="") -> TextOutput"""
1171 return _IMP_kernel.create_temporary_file(*args)
1174 r"""create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="") -> std::string"""
1175 return _IMP_kernel.create_temporary_file_name(*args)
1178 r"""get_relative_path(std::string base, std::string relative) -> std::string"""
1179 return _IMP_kernel.get_relative_path(base, relative)
1182 r"""get_absolute_path(std::string file) -> std::string"""
1183 return _IMP_kernel.get_absolute_path(file)
1185 def push_log_context(functionname, object):
1186 r"""push_log_context(char const * functionname, void const * object)"""
1187 return _IMP_kernel.push_log_context(functionname, object)
1189 def pop_log_context():
1190 r"""pop_log_context()"""
1191 return _IMP_kernel.pop_log_context()
1195 add_to_log(std::string to_write)
1196 add_to_log(IMP::LogLevel level, std::string to_write)
1198 return _IMP_kernel.add_to_log(*args)
1201 r"""set_log_level(IMP::LogLevel l)"""
1202 return _IMP_kernel.set_log_level(l)
1205 r"""set_log_timer(bool tb)"""
1206 return _IMP_kernel.set_log_timer(tb)
1209 r"""reset_log_timer()"""
1210 return _IMP_kernel.reset_log_timer()
1213 r"""get_log_level() -> IMP::LogLevel"""
1214 return _IMP_kernel.get_log_level()
1217 r"""set_progress_display(std::string description, unsigned int steps)"""
1218 return _IMP_kernel.set_progress_display(description, steps)
1221 r"""add_to_progress_display(unsigned int step=1)"""
1222 return _IMP_kernel.add_to_progress_display(step)
1223 class Object(_NonCopyable):
1224 r"""Proxy of C++ IMP::Object class."""
1226 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1228 def __init__(self, name):
1229 r"""__init__(Object self, std::string name) -> Object"""
1230 if self.__class__ == Object:
1234 _IMP_kernel.Object_swiginit(self, _IMP_kernel.new_Object(_self, name))
1236 if self.__class__ != Object:
1237 _director_objects.register(self)
1241 __swig_destroy__ = _IMP_kernel.delete_Object
1244 r"""__hash__(Object self) -> std::size_t"""
1245 return _IMP_kernel.Object___hash__(self)
1248 r"""set_log_level(Object self, IMP::LogLevel l)"""
1249 return _IMP_kernel.Object_set_log_level(self, l)
1252 r"""set_check_level(Object self, IMP::CheckLevel l)"""
1253 return _IMP_kernel.Object_set_check_level(self, l)
1256 r"""get_log_level(Object self) -> IMP::LogLevel"""
1257 return _IMP_kernel.Object_get_log_level(self)
1260 r"""get_check_level(Object self) -> IMP::CheckLevel"""
1261 return _IMP_kernel.Object_get_check_level(self)
1263 def get_version_info(self):
1264 r"""get_version_info(Object self) -> VersionInfo"""
1265 val = _IMP_kernel.Object_get_version_info(self)
1266 if val.get_module() ==
'none':
1273 r"""get_name(Object self) -> std::string const &"""
1274 return _IMP_kernel.Object_get_name(self)
1276 def set_name(self, name):
1277 r"""set_name(Object self, std::string name)"""
1278 return _IMP_kernel.Object_set_name(self, name)
1280 def get_type_name(self):
1281 r"""get_type_name(Object self) -> std::string"""
1282 val = _IMP_kernel.Object_get_type_name(self)
1283 if val ==
'unknown object type':
1284 val = self.__class__.__name__
1287 def set_was_used(self, tf):
1288 r"""set_was_used(Object self, bool tf)"""
1289 return _IMP_kernel.Object_set_was_used(self, tf)
1291 def show(self, *args):
1292 r"""show(Object self, _ostream out=std::cout)"""
1293 return _IMP_kernel.Object_show(self, *args)
1295 def get_string(self):
1296 r"""get_string(Object self) -> std::string"""
1297 return _IMP_kernel.Object_get_string(self)
1299 def _on_destruction(self):
1300 r"""_on_destruction(Object self)"""
1301 return _IMP_kernel.Object__on_destruction(self)
1303 def get_is_valid(self):
1304 r"""get_is_valid(Object self) -> bool"""
1305 return _IMP_kernel.Object_get_is_valid(self)
1307 def get_ref_count(self):
1308 r"""get_ref_count(Object self) -> unsigned int"""
1309 return _IMP_kernel.Object_get_ref_count(self)
1312 def get_number_of_live_objects():
1313 r"""get_number_of_live_objects() -> unsigned int"""
1314 return _IMP_kernel.Object_get_number_of_live_objects()
1316 def get_is_shared(self):
1317 r"""get_is_shared(Object self) -> bool"""
1318 return _IMP_kernel.Object_get_is_shared(self)
1320 def clear_caches(self):
1321 r"""clear_caches(Object self)"""
1322 return _IMP_kernel.Object_clear_caches(self)
1324 def do_destroy(self):
1325 r"""do_destroy(Object self)"""
1326 return _IMP_kernel.Object_do_destroy(self)
1328 def __getstate__(self):
1329 raise NotImplementedError(str(self.__class__)
1330 +
" does not support serialization")
1333 def __eq__(self, o):
1334 r"""__eq__(Object self, Object o) -> bool"""
1335 return _IMP_kernel.Object___eq__(self, o)
1337 def __ne__(self, o):
1338 r"""__ne__(Object self, Object o) -> bool"""
1339 return _IMP_kernel.Object___ne__(self, o)
1341 def __le__(self, o):
1342 r"""__le__(Object self, Object o) -> bool"""
1343 return _IMP_kernel.Object___le__(self, o)
1345 def __lt__(self, o):
1346 r"""__lt__(Object self, Object o) -> bool"""
1347 return _IMP_kernel.Object___lt__(self, o)
1349 def __ge__(self, o):
1350 r"""__ge__(Object self, Object o) -> bool"""
1351 return _IMP_kernel.Object___ge__(self, o)
1353 def __gt__(self, o):
1354 r"""__gt__(Object self, Object o) -> bool"""
1355 return _IMP_kernel.Object___gt__(self, o)
1357 def _get_director_object(self):
1358 r"""_get_director_object(Object self) -> PyObject *"""
1359 return _IMP_kernel.Object__get_director_object(self)
1362 """Return this object cast to the most derived subclass."""
1364 pyobj = self._get_director_object()
1365 if pyobj
is not None:
1369 modname = self.get_version_info().get_module().replace(
'::',
'.')
1370 type_name = self.get_type_name()
1371 if (modname ==
'IMP.core'
1372 and type_name ==
'GenericBoundingBox3DSingletonScore'):
1373 type_name =
'BoundingBox3DSingletonScore'
1374 elif (modname ==
'IMP.core'
1375 and type_name ==
'GenericAttributeSingletonScore'):
1376 type_name =
'AttributeSingletonScore'
1377 elif (modname ==
'IMP.core'
1378 and type_name ==
'GenericBoundingSphere3DSingletonScore'):
1379 type_name =
'BoundingSphere3DSingletonScore'
1380 elif modname ==
'IMP' and type_name ==
'RestraintScoringFunction':
1384 elif modname ==
'IMP' and type_name ==
'GenericRestraintsScoringFunction':
1385 type_name =
'_RestraintsScoringFunction'
1386 modobj = sys.modules[modname]
1387 clsobj = getattr(modobj, type_name)
1388 return clsobj.get_from(self)
1392 r"""__str__(Object self) -> std::string"""
1393 return _IMP_kernel.Object___str__(self)
1396 r"""__repr__(Object self) -> std::string"""
1397 return _IMP_kernel.Object___repr__(self)
1401 return _object_cast_to_Object(o)
1403 def __disown__(self):
1405 _IMP_kernel.disown_Object(self)
1406 return weakref.proxy(self)
1409 _IMP_kernel.Object_swigregister(Object)
1410 class SetLogState(_RAII):
1411 r"""Proxy of C++ IMP::SetLogState class."""
1413 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1416 r"""reset(SetLogState self)"""
1417 return _IMP_kernel.SetLogState_reset(self)
1418 __swig_destroy__ = _IMP_kernel.delete_SetLogState
1420 def show(self, *args):
1421 r"""show(SetLogState self, _ostream out=std::cout)"""
1422 return _IMP_kernel.SetLogState_show(self, *args)
1424 def __init__(self, *args):
1426 __init__(SetLogState self) -> SetLogState
1427 __init__(SetLogState self, Object o, IMP::LogLevel l) -> SetLogState
1428 __init__(SetLogState self, IMP::LogLevel l) -> SetLogState
1430 _IMP_kernel.SetLogState_swiginit(self, _IMP_kernel.new_SetLogState(*args))
1432 def set(self, *args):
1434 set(SetLogState self, Object o, IMP::LogLevel l)
1435 set(SetLogState self, IMP::LogLevel l)
1437 return _IMP_kernel.SetLogState_set(self, *args)
1439 def __enter__(self):
1441 def __exit__(self, exc_type, exc_val, exc_tb):
1447 r"""__str__(SetLogState self) -> std::string"""
1448 return _IMP_kernel.SetLogState___str__(self)
1451 r"""__repr__(SetLogState self) -> std::string"""
1452 return _IMP_kernel.SetLogState___repr__(self)
1455 _IMP_kernel.SetLogState_swigregister(SetLogState)
1456 class WarningContext(object):
1457 r"""Proxy of C++ IMP::WarningContext class."""
1459 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1460 data_ = property(_IMP_kernel.WarningContext_data__get, _IMP_kernel.WarningContext_data__set, doc=
r"""data_ : boost::unordered_set<(std::string)>""")
1462 def add_warning(self, key, warning):
1463 r"""add_warning(WarningContext self, std::string key, std::string warning)"""
1464 return _IMP_kernel.WarningContext_add_warning(self, key, warning)
1466 def clear_warnings(self):
1467 r"""clear_warnings(WarningContext self)"""
1468 return _IMP_kernel.WarningContext_clear_warnings(self)
1470 def dump_warnings(self):
1471 r"""dump_warnings(WarningContext self)"""
1472 return _IMP_kernel.WarningContext_dump_warnings(self)
1473 __swig_destroy__ = _IMP_kernel.delete_WarningContext
1475 def show(self, *args):
1476 r"""show(WarningContext self, _ostream out=std::cout)"""
1477 return _IMP_kernel.WarningContext_show(self, *args)
1479 def __enter__(self):
1481 def __exit__(self, exc_type, exc_val, exc_tb):
1487 r"""__str__(WarningContext self) -> std::string"""
1488 return _IMP_kernel.WarningContext___str__(self)
1491 r"""__repr__(WarningContext self) -> std::string"""
1492 return _IMP_kernel.WarningContext___repr__(self)
1495 r"""__init__(WarningContext self) -> WarningContext"""
1496 _IMP_kernel.WarningContext_swiginit(self, _IMP_kernel.new_WarningContext())
1499 _IMP_kernel.WarningContext_swigregister(WarningContext)
1500 class CreateLogContext(_RAII):
1501 r"""Proxy of C++ IMP::CreateLogContext class."""
1503 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1505 def __init__(self, *args):
1507 __init__(CreateLogContext self, std::string fname, Object object=None) -> CreateLogContext
1508 __init__(CreateLogContext self) -> CreateLogContext
1509 __init__(CreateLogContext self, char const * fname, Object object=None) -> CreateLogContext
1511 _IMP_kernel.CreateLogContext_swiginit(self, _IMP_kernel.new_CreateLogContext(*args))
1513 def set(self, fname, object=None):
1514 r"""set(CreateLogContext self, char const * fname, Object object=None)"""
1515 return _IMP_kernel.CreateLogContext_set(self, fname, object)
1518 r"""reset(CreateLogContext self)"""
1519 return _IMP_kernel.CreateLogContext_reset(self)
1520 __swig_destroy__ = _IMP_kernel.delete_CreateLogContext
1522 def show(self, *args):
1523 r"""show(CreateLogContext self, _ostream out=std::cout)"""
1524 return _IMP_kernel.CreateLogContext_show(self, *args)
1526 def __enter__(self):
1528 def __exit__(self, exc_type, exc_val, exc_tb):
1534 r"""__str__(CreateLogContext self) -> std::string"""
1535 return _IMP_kernel.CreateLogContext___str__(self)
1538 r"""__repr__(CreateLogContext self) -> std::string"""
1539 return _IMP_kernel.CreateLogContext___repr__(self)
1542 _IMP_kernel.CreateLogContext_swigregister(CreateLogContext)
1543 class SetCheckState(_RAII):
1544 r"""Proxy of C++ IMP::SetCheckState class."""
1546 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1549 r"""reset(SetCheckState self)"""
1550 return _IMP_kernel.SetCheckState_reset(self)
1551 __swig_destroy__ = _IMP_kernel.delete_SetCheckState
1553 def show(self, *args):
1554 r"""show(SetCheckState self, _ostream out=std::cout)"""
1555 return _IMP_kernel.SetCheckState_show(self, *args)
1557 def __init__(self, *args):
1559 __init__(SetCheckState self) -> SetCheckState
1560 __init__(SetCheckState self, Object o, IMP::CheckLevel l) -> SetCheckState
1561 __init__(SetCheckState self, IMP::CheckLevel l) -> SetCheckState
1563 _IMP_kernel.SetCheckState_swiginit(self, _IMP_kernel.new_SetCheckState(*args))
1565 def set(self, *args):
1567 set(SetCheckState self, Object o, IMP::CheckLevel l)
1568 set(SetCheckState self, IMP::CheckLevel l)
1570 return _IMP_kernel.SetCheckState_set(self, *args)
1572 def __enter__(self):
1574 def __exit__(self, exc_type, exc_val, exc_tb):
1580 r"""__str__(SetCheckState self) -> std::string"""
1581 return _IMP_kernel.SetCheckState___str__(self)
1584 r"""__repr__(SetCheckState self) -> std::string"""
1585 return _IMP_kernel.SetCheckState___repr__(self)
1588 _IMP_kernel.SetCheckState_swigregister(SetCheckState)
1591 r"""get_unique_name(std::string templ) -> std::string"""
1592 return _IMP_kernel.get_unique_name(templ)
1595 r"""get_copyright() -> std::string"""
1596 return _IMP_kernel.get_copyright()
1597 class _Protection(object):
1598 r"""Proxy of C++ IMP::internal::_Protection class."""
1600 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1602 def __init__(self, *args, **kwargs):
1603 raise AttributeError(
"No constructor defined")
1605 def show(self, *args):
1606 r"""show(_Protection self, _ostream out=std::cout)"""
1607 return _IMP_kernel._Protection_show(self, *args)
1610 r"""__str__(_Protection self) -> std::string"""
1611 return _IMP_kernel._Protection___str__(self)
1614 r"""__repr__(_Protection self) -> std::string"""
1615 return _IMP_kernel._Protection___repr__(self)
1616 __swig_destroy__ = _IMP_kernel.delete__Protection
1619 _IMP_kernel._Protection_swigregister(_Protection)
1623 return _IMP_kernel._test_log()
1625 def _test_intranges(ips):
1626 r"""_test_intranges(IMP::IntRanges const & ips) -> int"""
1627 return _IMP_kernel._test_intranges(ips)
1629 def _test_intrange(*args):
1631 _test_intrange(IMP::IntRange const & ips) -> IMP::IntRange
1632 _test_intrange() -> IMP::IntRange
1634 return _IMP_kernel._test_intrange(*args)
1637 r"""_test_ifile(TextInput a) -> std::string"""
1638 return _IMP_kernel._test_ifile(a)
1641 r"""_test_ofile(TextOutput a) -> std::string"""
1642 return _IMP_kernel._test_ofile(a)
1644 def _test_ifile_overloaded(*args):
1646 _test_ifile_overloaded(TextInput a, int i) -> std::string
1647 _test_ifile_overloaded(TextInput a, std::string st) -> std::string
1649 return _IMP_kernel._test_ifile_overloaded(*args)
1651 def _test_ofile_overloaded(*args):
1653 _test_ofile_overloaded(TextOutput a, int i) -> std::string
1654 _test_ofile_overloaded(TextOutput a, std::string st) -> std::string
1656 return _IMP_kernel._test_ofile_overloaded(*args)
1657 class _TestValue(object):
1658 r"""Proxy of C++ IMP::internal::_TestValue class."""
1660 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1662 def __init__(self, i):
1663 r"""__init__(_TestValue self, int i) -> _TestValue"""
1664 _IMP_kernel._TestValue_swiginit(self, _IMP_kernel.new__TestValue(i))
1666 def show(self, *args):
1667 r"""show(_TestValue self, _ostream out=std::cout)"""
1668 return _IMP_kernel._TestValue_show(self, *args)
1670 def __cmp__(self, o):
1671 r"""__cmp__(_TestValue self, _TestValue o) -> int"""
1672 return _IMP_kernel._TestValue___cmp__(self, o)
1674 def __eq__(self, o):
1675 r"""__eq__(_TestValue self, _TestValue o) -> bool"""
1676 return _IMP_kernel._TestValue___eq__(self, o)
1678 def __ne__(self, o):
1679 r"""__ne__(_TestValue self, _TestValue o) -> bool"""
1680 return _IMP_kernel._TestValue___ne__(self, o)
1682 def __lt__(self, o):
1683 r"""__lt__(_TestValue self, _TestValue o) -> bool"""
1684 return _IMP_kernel._TestValue___lt__(self, o)
1686 def __gt__(self, o):
1687 r"""__gt__(_TestValue self, _TestValue o) -> bool"""
1688 return _IMP_kernel._TestValue___gt__(self, o)
1690 def __ge__(self, o):
1691 r"""__ge__(_TestValue self, _TestValue o) -> bool"""
1692 return _IMP_kernel._TestValue___ge__(self, o)
1694 def __le__(self, o):
1695 r"""__le__(_TestValue self, _TestValue o) -> bool"""
1696 return _IMP_kernel._TestValue___le__(self, o)
1699 r"""get(_TestValue self) -> int"""
1700 return _IMP_kernel._TestValue_get(self)
1702 def get_float(self):
1703 r"""get_float(_TestValue self) -> float const &"""
1704 return _IMP_kernel._TestValue_get_float(self)
1706 def get_double(self):
1707 r"""get_double(_TestValue self) -> double const &"""
1708 return _IMP_kernel._TestValue_get_double(self)
1710 def get_Float(self):
1711 r"""get_Float(_TestValue self) -> IMP::Float const &"""
1712 return _IMP_kernel._TestValue_get_Float(self)
1715 r"""get_int(_TestValue self) -> int const &"""
1716 return _IMP_kernel._TestValue_get_int(self)
1719 r"""get_Int(_TestValue self) -> IMP::Int const &"""
1720 return _IMP_kernel._TestValue_get_Int(self)
1722 def get_string(self):
1723 r"""get_string(_TestValue self) -> std::string const &"""
1724 return _IMP_kernel._TestValue_get_string(self)
1726 def get_String(self):
1727 r"""get_String(_TestValue self) -> IMP::String const &"""
1728 return _IMP_kernel._TestValue_get_String(self)
1731 r"""__str__(_TestValue self) -> std::string"""
1732 return _IMP_kernel._TestValue___str__(self)
1735 r"""__repr__(_TestValue self) -> std::string"""
1736 return _IMP_kernel._TestValue___repr__(self)
1737 __swig_destroy__ = _IMP_kernel.delete__TestValue
1740 _IMP_kernel._TestValue_swigregister(_TestValue)
1742 def _pass_plain_pair(p):
1743 r"""_pass_plain_pair(IMP::FloatPair p) -> IMP::FloatPair"""
1744 return _IMP_kernel._pass_plain_pair(p)
1746 def _pass_overloaded_strings(*args):
1748 _pass_overloaded_strings(IMP::Strings const & a, int arg2) -> IMP::Strings
1749 _pass_overloaded_strings(IMP::Strings const & a) -> IMP::Strings
1751 return _IMP_kernel._pass_overloaded_strings(*args)
1754 r"""_pass_pair(IMP::DerivativePair const & p) -> IMP::DerivativePair"""
1755 return _IMP_kernel._pass_pair(p)
1757 def _pass_floats(input):
1758 r"""_pass_floats(IMP::Floats const & input) -> IMP::Floats"""
1759 return _IMP_kernel._pass_floats(input)
1761 def _pass_ints(input):
1762 r"""_pass_ints(IMP::Ints input) -> IMP::Ints"""
1763 return _IMP_kernel._pass_ints(input)
1765 def _pass_ints_list(input):
1766 r"""_pass_ints_list(IMP::IntsList const & input) -> IMP::IntsList"""
1767 return _IMP_kernel._pass_ints_list(input)
1769 def _pass_ints_lists(input):
1770 r"""_pass_ints_lists(IMP::IntsLists const & input) -> IMP::IntsLists"""
1771 return _IMP_kernel._pass_ints_lists(input)
1773 def _pass_strings(input):
1774 r"""_pass_strings(IMP::Strings const & input) -> IMP::Strings const &"""
1775 return _IMP_kernel._pass_strings(input)
1776 class _TestObject(
Object):
1777 r"""Proxy of C++ IMP::internal::_TestObject class."""
1779 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1782 r"""__init__(_TestObject self) -> _TestObject"""
1783 _IMP_kernel._TestObject_swiginit(self, _IMP_kernel.new__TestObject())
1786 r"""get_version_info(_TestObject self) -> VersionInfo"""
1787 return _IMP_kernel._TestObject_get_version_info(self)
1788 __swig_destroy__ = _IMP_kernel.delete__TestObject
1791 r"""__str__(_TestObject self) -> std::string"""
1792 return _IMP_kernel._TestObject___str__(self)
1795 r"""__repr__(_TestObject self) -> std::string"""
1796 return _IMP_kernel._TestObject___repr__(self)
1800 return _object_cast_to__TestObject(o)
1804 _IMP_kernel._TestObject_swigregister(_TestObject)
1807 r"""get_live_object_names() -> IMP::Strings"""
1808 return _IMP_kernel.get_live_object_names()
1811 r"""get_live_objects() -> IMP::Objects"""
1812 return _IMP_kernel.get_live_objects()
1815 r"""set_show_leaked_objects(bool tf)"""
1816 return _IMP_kernel.set_show_leaked_objects(tf)
1819 r"""set_deprecation_warnings(bool tf)"""
1820 return _IMP_kernel.set_deprecation_warnings(tf)
1823 r"""set_deprecation_exceptions(bool tf)"""
1824 return _IMP_kernel.set_deprecation_exceptions(tf)
1827 r"""get_deprecation_exceptions() -> bool"""
1828 return _IMP_kernel.get_deprecation_exceptions()
1831 r"""handle_use_deprecated(std::string message)"""
1832 return _IMP_kernel.handle_use_deprecated(message)
1835 r"""get_number_of_threads() -> unsigned int"""
1836 return _IMP_kernel.get_number_of_threads()
1839 r"""set_number_of_threads(unsigned int n)"""
1840 return _IMP_kernel.set_number_of_threads(n)
1841 class SetNumberOfThreads(_RAII):
1842 r"""Proxy of C++ IMP::SetNumberOfThreads class."""
1844 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1846 def __init__(self, *args):
1848 __init__(SetNumberOfThreads self) -> SetNumberOfThreads
1849 __init__(SetNumberOfThreads self, unsigned int n) -> SetNumberOfThreads
1851 _IMP_kernel.SetNumberOfThreads_swiginit(self, _IMP_kernel.new_SetNumberOfThreads(*args))
1854 r"""set(SetNumberOfThreads self, unsigned int n)"""
1855 return _IMP_kernel.SetNumberOfThreads_set(self, n)
1858 r"""reset(SetNumberOfThreads self)"""
1859 return _IMP_kernel.SetNumberOfThreads_reset(self)
1860 __swig_destroy__ = _IMP_kernel.delete_SetNumberOfThreads
1862 def show(self, *args):
1863 r"""show(SetNumberOfThreads self, _ostream out=std::cout)"""
1864 return _IMP_kernel.SetNumberOfThreads_show(self, *args)
1866 def __enter__(self):
1868 def __exit__(self, exc_type, exc_val, exc_tb):
1874 r"""__str__(SetNumberOfThreads self) -> std::string"""
1875 return _IMP_kernel.SetNumberOfThreads___str__(self)
1878 r"""__repr__(SetNumberOfThreads self) -> std::string"""
1879 return _IMP_kernel.SetNumberOfThreads___repr__(self)
1882 _IMP_kernel.SetNumberOfThreads_swigregister(SetNumberOfThreads)
1885 i_m_p=
"IMP_MODULE_PATH"
1886 if i_m_p
in os.environ.keys():
1887 __path__.insert(0, os.environ[i_m_p])
1889 def _forward_add_attribute(self, name, value, opt=None):
1891 self.get_particle().add_attribute(name, value, opt)
1893 self.get_particle().add_attribute(name, value)
1894 def _forward_get_value(self, name):
1895 self.get_particle().get_value(name)
1896 def _forward_set_value(self, name, value):
1897 self.get_particle().set_value(name, value)
1903 _object_types.append(
"Constraint")
1906 def _object_cast_to_Constraint(o):
1907 r"""_object_cast_to_Constraint(Object o) -> Constraint"""
1908 return _IMP_kernel._object_cast_to_Constraint(o)
1910 _object_types.append(
"Undecorator")
1913 def _object_cast_to_Undecorator(o):
1914 r"""_object_cast_to_Undecorator(Object o) -> Undecorator"""
1915 return _IMP_kernel._object_cast_to_Undecorator(o)
1917 _object_types.append(
"Container")
1920 def _object_cast_to_Container(o):
1921 r"""_object_cast_to_Container(Object o) -> Container"""
1922 return _IMP_kernel._object_cast_to_Container(o)
1924 _object_types.append(
"Optimizer")
1927 def _object_cast_to_Optimizer(o):
1928 r"""_object_cast_to_Optimizer(Object o) -> Optimizer"""
1929 return _IMP_kernel._object_cast_to_Optimizer(o)
1931 _object_types.append(
"AttributeOptimizer")
1934 def _object_cast_to_AttributeOptimizer(o):
1935 r"""_object_cast_to_AttributeOptimizer(Object o) -> AttributeOptimizer"""
1936 return _IMP_kernel._object_cast_to_AttributeOptimizer(o)
1938 _object_types.append(
"OptimizerState")
1941 def _object_cast_to_OptimizerState(o):
1942 r"""_object_cast_to_OptimizerState(Object o) -> OptimizerState"""
1943 return _IMP_kernel._object_cast_to_OptimizerState(o)
1945 _object_types.append(
"PairContainer")
1948 def _object_cast_to_PairContainer(o):
1949 r"""_object_cast_to_PairContainer(Object o) -> PairContainer"""
1950 return _IMP_kernel._object_cast_to_PairContainer(o)
1952 _object_types.append(
"PairModifier")
1955 def _object_cast_to_PairModifier(o):
1956 r"""_object_cast_to_PairModifier(Object o) -> PairModifier"""
1957 return _IMP_kernel._object_cast_to_PairModifier(o)
1959 _object_types.append(
"PairScore")
1962 def _object_cast_to_PairScore(o):
1963 r"""_object_cast_to_PairScore(Object o) -> PairScore"""
1964 return _IMP_kernel._object_cast_to_PairScore(o)
1966 _object_types.append(
"QuadContainer")
1969 def _object_cast_to_QuadContainer(o):
1970 r"""_object_cast_to_QuadContainer(Object o) -> QuadContainer"""
1971 return _IMP_kernel._object_cast_to_QuadContainer(o)
1973 _object_types.append(
"QuadModifier")
1976 def _object_cast_to_QuadModifier(o):
1977 r"""_object_cast_to_QuadModifier(Object o) -> QuadModifier"""
1978 return _IMP_kernel._object_cast_to_QuadModifier(o)
1980 _object_types.append(
"QuadScore")
1983 def _object_cast_to_QuadScore(o):
1984 r"""_object_cast_to_QuadScore(Object o) -> QuadScore"""
1985 return _IMP_kernel._object_cast_to_QuadScore(o)
1987 _object_types.append(
"Refiner")
1990 def _object_cast_to_Refiner(o):
1991 r"""_object_cast_to_Refiner(Object o) -> Refiner"""
1992 return _IMP_kernel._object_cast_to_Refiner(o)
1994 _object_types.append(
"Restraint")
1997 def _object_cast_to_Restraint(o):
1998 r"""_object_cast_to_Restraint(Object o) -> Restraint"""
1999 return _IMP_kernel._object_cast_to_Restraint(o)
2001 _object_types.append(
"Sampler")
2004 def _object_cast_to_Sampler(o):
2005 r"""_object_cast_to_Sampler(Object o) -> Sampler"""
2006 return _IMP_kernel._object_cast_to_Sampler(o)
2008 _object_types.append(
"ScoreState")
2011 def _object_cast_to_ScoreState(o):
2012 r"""_object_cast_to_ScoreState(Object o) -> ScoreState"""
2013 return _IMP_kernel._object_cast_to_ScoreState(o)
2015 _object_types.append(
"SingletonContainer")
2018 def _object_cast_to_SingletonContainer(o):
2019 r"""_object_cast_to_SingletonContainer(Object o) -> SingletonContainer"""
2020 return _IMP_kernel._object_cast_to_SingletonContainer(o)
2022 _object_types.append(
"SingletonModifier")
2025 def _object_cast_to_SingletonModifier(o):
2026 r"""_object_cast_to_SingletonModifier(Object o) -> SingletonModifier"""
2027 return _IMP_kernel._object_cast_to_SingletonModifier(o)
2029 _object_types.append(
"SingletonScore")
2032 def _object_cast_to_SingletonScore(o):
2033 r"""_object_cast_to_SingletonScore(Object o) -> SingletonScore"""
2034 return _IMP_kernel._object_cast_to_SingletonScore(o)
2036 _object_types.append(
"TripletContainer")
2039 def _object_cast_to_TripletContainer(o):
2040 r"""_object_cast_to_TripletContainer(Object o) -> TripletContainer"""
2041 return _IMP_kernel._object_cast_to_TripletContainer(o)
2043 _object_types.append(
"TripletModifier")
2046 def _object_cast_to_TripletModifier(o):
2047 r"""_object_cast_to_TripletModifier(Object o) -> TripletModifier"""
2048 return _IMP_kernel._object_cast_to_TripletModifier(o)
2050 _object_types.append(
"TripletScore")
2053 def _object_cast_to_TripletScore(o):
2054 r"""_object_cast_to_TripletScore(Object o) -> TripletScore"""
2055 return _IMP_kernel._object_cast_to_TripletScore(o)
2057 _object_types.append(
"UnaryFunction")
2060 def _object_cast_to_UnaryFunction(o):
2061 r"""_object_cast_to_UnaryFunction(Object o) -> UnaryFunction"""
2062 return _IMP_kernel._object_cast_to_UnaryFunction(o)
2064 _object_types.append(
"RestraintInfo")
2067 def _object_cast_to_RestraintInfo(o):
2068 r"""_object_cast_to_RestraintInfo(Object o) -> RestraintInfo"""
2069 return _IMP_kernel._object_cast_to_RestraintInfo(o)
2071 _object_types.append(
"ConfigurationSet")
2074 def _object_cast_to_ConfigurationSet(o):
2075 r"""_object_cast_to_ConfigurationSet(Object o) -> ConfigurationSet"""
2076 return _IMP_kernel._object_cast_to_ConfigurationSet(o)
2078 _object_types.append(
"Configuration")
2081 def _object_cast_to_Configuration(o):
2082 r"""_object_cast_to_Configuration(Object o) -> Configuration"""
2083 return _IMP_kernel._object_cast_to_Configuration(o)
2085 _object_types.append(
"Model")
2088 def _object_cast_to_Model(o):
2089 r"""_object_cast_to_Model(Object o) -> Model"""
2090 return _IMP_kernel._object_cast_to_Model(o)
2092 _object_types.append(
"Particle")
2095 def _object_cast_to_Particle(o):
2096 r"""_object_cast_to_Particle(Object o) -> Particle"""
2097 return _IMP_kernel._object_cast_to_Particle(o)
2099 _object_types.append(
"RestraintSet")
2102 def _object_cast_to_RestraintSet(o):
2103 r"""_object_cast_to_RestraintSet(Object o) -> RestraintSet"""
2104 return _IMP_kernel._object_cast_to_RestraintSet(o)
2106 ParticlePairsTemp=list
2107 _plural_types.append(
"ParticlePairsTemp")
2108 _value_types.append(
"ParticlePair")
2111 ParticleTripletsTemp=list
2112 _plural_types.append(
"ParticleTripletsTemp")
2113 _value_types.append(
"ParticleTriplet")
2116 ParticleQuadsTemp=list
2117 _plural_types.append(
"ParticleQuadsTemp")
2118 _value_types.append(
"ParticleQuad")
2121 ParticleIndexPairs=list
2122 _plural_types.append(
"ParticleIndexPairs")
2123 _value_types.append(
"ParticleIndexPair")
2126 ParticleIndexTriplets=list
2127 _plural_types.append(
"ParticleIndexTriplets")
2128 _value_types.append(
"ParticleIndexTriplet")
2131 ParticleIndexQuads=list
2132 _plural_types.append(
"ParticleIndexQuads")
2133 _value_types.append(
"ParticleIndexQuad")
2136 _object_types.append(
"SingletonPredicate")
2139 def _object_cast_to_SingletonPredicate(o):
2140 r"""_object_cast_to_SingletonPredicate(Object o) -> SingletonPredicate"""
2141 return _IMP_kernel._object_cast_to_SingletonPredicate(o)
2143 _object_types.append(
"PairPredicate")
2146 def _object_cast_to_PairPredicate(o):
2147 r"""_object_cast_to_PairPredicate(Object o) -> PairPredicate"""
2148 return _IMP_kernel._object_cast_to_PairPredicate(o)
2150 _object_types.append(
"TripletPredicate")
2153 def _object_cast_to_TripletPredicate(o):
2154 r"""_object_cast_to_TripletPredicate(Object o) -> TripletPredicate"""
2155 return _IMP_kernel._object_cast_to_TripletPredicate(o)
2157 _object_types.append(
"QuadPredicate")
2160 def _object_cast_to_QuadPredicate(o):
2161 r"""_object_cast_to_QuadPredicate(Object o) -> QuadPredicate"""
2162 return _IMP_kernel._object_cast_to_QuadPredicate(o)
2164 _object_types.append(
"SaveToConfigurationSetOptimizerState")
2167 def _object_cast_to_SaveToConfigurationSetOptimizerState(o):
2168 r"""_object_cast_to_SaveToConfigurationSetOptimizerState(Object o) -> SaveToConfigurationSetOptimizerState"""
2169 return _IMP_kernel._object_cast_to_SaveToConfigurationSetOptimizerState(o)
2171 EvaluationStates=list
2172 _plural_types.append(
"EvaluationStates")
2173 _value_types.append(
"EvaluationState")
2176 ScoreAccumulators=list
2177 _plural_types.append(
"ScoreAccumulators")
2178 _value_types.append(
"ScoreAccumulator")
2181 ParticleIndexes=list
2182 _plural_types.append(
"ParticleIndexes")
2183 _value_types.append(
"ParticleIndex")
2187 _plural_types.append(
"FloatIndexes")
2188 _value_types.append(
"FloatIndex")
2192 _plural_types.append(
"FloatKeys")
2193 _value_types.append(
"FloatKey")
2197 _plural_types.append(
"FloatsKeys")
2198 _value_types.append(
"FloatsKey")
2202 _plural_types.append(
"IntKeys")
2203 _value_types.append(
"IntKey")
2207 _plural_types.append(
"IntsKeys")
2208 _value_types.append(
"IntsKey")
2212 _plural_types.append(
"StringKeys")
2213 _value_types.append(
"StringKey")
2216 ParticleIndexKeys=list
2217 _plural_types.append(
"ParticleIndexKeys")
2218 _value_types.append(
"ParticleIndexKey")
2221 ParticleIndexesKeys=list
2222 _plural_types.append(
"ParticleIndexesKeys")
2223 _value_types.append(
"ParticleIndexesKey")
2227 _plural_types.append(
"ObjectKeys")
2228 _value_types.append(
"ObjectKey")
2232 _plural_types.append(
"ModelKeys")
2233 _value_types.append(
"ModelKey")
2237 _plural_types.append(
"TriggerKeys")
2238 _value_types.append(
"TriggerKey")
2241 SparseFloatKeys=list
2242 _plural_types.append(
"SparseFloatKeys")
2243 _value_types.append(
"SparseFloatKey")
2247 _plural_types.append(
"SparseIntKeys")
2248 _value_types.append(
"SparseIntKey")
2251 SparseStringKeys=list
2252 _plural_types.append(
"SparseStringKeys")
2253 _value_types.append(
"SparseStringKey")
2256 SparseParticleIndexKeys=list
2257 _plural_types.append(
"SparseParticleIndexKeys")
2258 _value_types.append(
"SparseParticleIndexKey")
2262 _plural_types.append(
"Vector3DKeys")
2263 _value_types.append(
"Vector3DKey")
2267 _plural_types.append(
"Vector4DKeys")
2268 _value_types.append(
"Vector4DKey")
2271 Vector3DDerivKeys=list
2272 _plural_types.append(
"Vector3DDerivKeys")
2273 _value_types.append(
"Vector3DDerivKey")
2276 Vector4DDerivKeys=list
2277 _plural_types.append(
"Vector4DDerivKeys")
2278 _value_types.append(
"Vector4DDerivKey")
2281 _raii_types.append(
"ScopedSetFloatAttribute")
2284 _object_types.append(
"ScoringFunction")
2287 def _object_cast_to_ScoringFunction(o):
2288 r"""_object_cast_to_ScoringFunction(Object o) -> ScoringFunction"""
2289 return _IMP_kernel._object_cast_to_ScoringFunction(o)
2291 _object_types.append(
"ModelObject")
2294 def _object_cast_to_ModelObject(o):
2295 r"""_object_cast_to_ModelObject(Object o) -> ModelObject"""
2296 return _IMP_kernel._object_cast_to_ModelObject(o)
2298 _object_types.append(
"_RestraintsScoringFunction")
2301 def _object_cast_to__RestraintsScoringFunction(o):
2302 r"""_object_cast_to__RestraintsScoringFunction(Object o) -> _RestraintsScoringFunction"""
2303 return _IMP_kernel._object_cast_to__RestraintsScoringFunction(o)
2305 def _TrivialDecorators(l=[]):
2306 return [_TrivialDecorator(x)
for x
in l]
2307 _plural_types.append(
"_TrivialDecorators")
2310 _value_types.append(
"_TrivialDecorator")
2313 def _TrivialDerivedDecorators(l=[]):
2314 return [_TrivialDerivedDecorator(x)
for x
in l]
2315 _plural_types.append(
"_TrivialDerivedDecorators")
2318 _value_types.append(
"_TrivialDerivedDecorator")
2321 def _TrivialTraitsDecorators(l=[]):
2322 return [_TrivialTraitsDecorator(x)
for x
in l]
2323 _plural_types.append(
"_TrivialTraitsDecorators")
2326 _value_types.append(
"_TrivialTraitsDecorator")
2329 _object_types.append(
"_ConstRestraint")
2332 def _object_cast_to__ConstRestraint(o):
2333 r"""_object_cast_to__ConstRestraint(Object o) -> _ConstRestraint"""
2334 return _IMP_kernel._object_cast_to__ConstRestraint(o)
2336 _object_types.append(
"_ConstOptimizer")
2339 def _object_cast_to__ConstOptimizer(o):
2340 r"""_object_cast_to__ConstOptimizer(Object o) -> _ConstOptimizer"""
2341 return _IMP_kernel._object_cast_to__ConstOptimizer(o)
2343 _object_types.append(
"_ConstSingletonScore")
2346 def _object_cast_to__ConstSingletonScore(o):
2347 r"""_object_cast_to__ConstSingletonScore(Object o) -> _ConstSingletonScore"""
2348 return _IMP_kernel._object_cast_to__ConstSingletonScore(o)
2350 _object_types.append(
"_ConstPairScore")
2353 def _object_cast_to__ConstPairScore(o):
2354 r"""_object_cast_to__ConstPairScore(Object o) -> _ConstPairScore"""
2355 return _IMP_kernel._object_cast_to__ConstPairScore(o)
2357 r"""Proxy of C++ IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex > class."""
2359 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2360 __repr__ = _swig_repr
2363 r"""__init__(DependencyGraph self) -> DependencyGraph"""
2364 _IMP_kernel.DependencyGraph_swiginit(self, _IMP_kernel.new_DependencyGraph())
2366 def get_graph(self):
2367 r"""get_graph(DependencyGraph self) -> IMP::DependencyGraph const &"""
2368 return _IMP_kernel.DependencyGraph_get_graph(self)
2371 r"""get_vertices(DependencyGraph self) -> IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptors"""
2372 return _IMP_kernel.DependencyGraph_get_vertices(self)
2374 def get_vertex_name(self, i):
2375 r"""get_vertex_name(DependencyGraph self, IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor i) -> ModelObject"""
2376 return _IMP_kernel.DependencyGraph_get_vertex_name(self, i)
2378 def get_in_neighbors(self, v):
2379 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"""
2380 return _IMP_kernel.DependencyGraph_get_in_neighbors(self, v)
2382 def get_out_neighbors(self, v):
2383 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"""
2384 return _IMP_kernel.DependencyGraph_get_out_neighbors(self, v)
2387 r"""show_graphviz(DependencyGraph self, _ostream out=std::cout)"""
2388 return _IMP_kernel.DependencyGraph_show_graphviz(self, *args)
2390 def get_graphviz_string(self):
2391 r"""get_graphviz_string(DependencyGraph self) -> std::string"""
2392 return _IMP_kernel.DependencyGraph_get_graphviz_string(self)
2394 def add_edge(self, v0, v1):
2395 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)"""
2396 return _IMP_kernel.DependencyGraph_add_edge(self, v0, v1)
2398 def add_vertex(self, l):
2399 r"""add_vertex(DependencyGraph self, ModelObject l) -> IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor"""
2400 return _IMP_kernel.DependencyGraph_add_vertex(self, l)
2402 def remove_vertex(self, l):
2403 r"""remove_vertex(DependencyGraph self, IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor l)"""
2404 return _IMP_kernel.DependencyGraph_remove_vertex(self, l)
2405 __swig_destroy__ = _IMP_kernel.delete_DependencyGraph
2408 _IMP_kernel.DependencyGraph_swigregister(DependencyGraph)
2410 _value_types.append(
"DependencyGraph")
2413 r"""Proxy of C++ IMP::Key< 0 > class."""
2415 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2417 def __init__(self, *args):
2419 __init__(FloatKey self) -> FloatKey
2420 __init__(FloatKey self, std::string const & c, bool is_implicit_add_permitted=True) -> FloatKey
2421 __init__(FloatKey self, unsigned int i) -> FloatKey
2423 _IMP_kernel.FloatKey_swiginit(self, _IMP_kernel.new_FloatKey(*args))
2427 r"""add_key(std::string sc) -> unsigned int"""
2428 return _IMP_kernel.FloatKey_add_key(sc)
2431 def get_key_exists(sc):
2432 r"""get_key_exists(std::string sc) -> bool"""
2433 return _IMP_kernel.FloatKey_get_key_exists(sc)
2435 def get_string(self):
2436 r"""get_string(FloatKey self) -> std::string const"""
2437 return _IMP_kernel.FloatKey_get_string(self)
2439 def __cmp__(self, o):
2440 r"""__cmp__(FloatKey self, FloatKey o) -> int"""
2441 return _IMP_kernel.FloatKey___cmp__(self, o)
2443 def __eq__(self, o):
2444 r"""__eq__(FloatKey self, FloatKey o) -> bool"""
2445 return _IMP_kernel.FloatKey___eq__(self, o)
2447 def __ne__(self, o):
2448 r"""__ne__(FloatKey self, FloatKey o) -> bool"""
2449 return _IMP_kernel.FloatKey___ne__(self, o)
2451 def __lt__(self, o):
2452 r"""__lt__(FloatKey self, FloatKey o) -> bool"""
2453 return _IMP_kernel.FloatKey___lt__(self, o)
2455 def __gt__(self, o):
2456 r"""__gt__(FloatKey self, FloatKey o) -> bool"""
2457 return _IMP_kernel.FloatKey___gt__(self, o)
2459 def __ge__(self, o):
2460 r"""__ge__(FloatKey self, FloatKey o) -> bool"""
2461 return _IMP_kernel.FloatKey___ge__(self, o)
2463 def __le__(self, o):
2464 r"""__le__(FloatKey self, FloatKey o) -> bool"""
2465 return _IMP_kernel.FloatKey___le__(self, o)
2468 r"""__hash__(FloatKey self) -> std::size_t"""
2469 return _IMP_kernel.FloatKey___hash__(self)
2471 def show(self, *args):
2472 r"""show(FloatKey self, _ostream out=std::cout)"""
2473 return _IMP_kernel.FloatKey_show(self, *args)
2476 def add_alias(old_key, new_name):
2477 r"""add_alias(FloatKey old_key, std::string new_name) -> FloatKey"""
2478 return _IMP_kernel.FloatKey_add_alias(old_key, new_name)
2481 def get_number_of_keys():
2482 r"""get_number_of_keys() -> unsigned int"""
2483 return _IMP_kernel.FloatKey_get_number_of_keys()
2486 r"""get_index(FloatKey self) -> unsigned int"""
2487 return _IMP_kernel.FloatKey_get_index(self)
2491 r"""show_all(_ostream out)"""
2492 return _IMP_kernel.FloatKey_show_all(out)
2495 def get_all_strings():
2496 r"""get_all_strings() -> IMP::Vector< std::string >"""
2497 return _IMP_kernel.FloatKey_get_all_strings()
2500 def get_number_unique():
2501 r"""get_number_unique() -> unsigned int"""
2502 return _IMP_kernel.FloatKey_get_number_unique()
2505 r"""__str__(FloatKey self) -> std::string"""
2506 return _IMP_kernel.FloatKey___str__(self)
2509 r"""__repr__(FloatKey self) -> std::string"""
2510 return _IMP_kernel.FloatKey___repr__(self)
2511 __swig_destroy__ = _IMP_kernel.delete_FloatKey
2514 _IMP_kernel.FloatKey_swigregister(FloatKey)
2516 r"""Proxy of C++ IMP::Key< 1 > class."""
2518 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2520 def __init__(self, *args):
2522 __init__(IntKey self) -> IntKey
2523 __init__(IntKey self, std::string const & c, bool is_implicit_add_permitted=True) -> IntKey
2524 __init__(IntKey self, unsigned int i) -> IntKey
2526 _IMP_kernel.IntKey_swiginit(self, _IMP_kernel.new_IntKey(*args))
2530 r"""add_key(std::string sc) -> unsigned int"""
2531 return _IMP_kernel.IntKey_add_key(sc)
2534 def get_key_exists(sc):
2535 r"""get_key_exists(std::string sc) -> bool"""
2536 return _IMP_kernel.IntKey_get_key_exists(sc)
2538 def get_string(self):
2539 r"""get_string(IntKey self) -> std::string const"""
2540 return _IMP_kernel.IntKey_get_string(self)
2542 def __cmp__(self, o):
2543 r"""__cmp__(IntKey self, IntKey o) -> int"""
2544 return _IMP_kernel.IntKey___cmp__(self, o)
2546 def __eq__(self, o):
2547 r"""__eq__(IntKey self, IntKey o) -> bool"""
2548 return _IMP_kernel.IntKey___eq__(self, o)
2550 def __ne__(self, o):
2551 r"""__ne__(IntKey self, IntKey o) -> bool"""
2552 return _IMP_kernel.IntKey___ne__(self, o)
2554 def __lt__(self, o):
2555 r"""__lt__(IntKey self, IntKey o) -> bool"""
2556 return _IMP_kernel.IntKey___lt__(self, o)
2558 def __gt__(self, o):
2559 r"""__gt__(IntKey self, IntKey o) -> bool"""
2560 return _IMP_kernel.IntKey___gt__(self, o)
2562 def __ge__(self, o):
2563 r"""__ge__(IntKey self, IntKey o) -> bool"""
2564 return _IMP_kernel.IntKey___ge__(self, o)
2566 def __le__(self, o):
2567 r"""__le__(IntKey self, IntKey o) -> bool"""
2568 return _IMP_kernel.IntKey___le__(self, o)
2571 r"""__hash__(IntKey self) -> std::size_t"""
2572 return _IMP_kernel.IntKey___hash__(self)
2574 def show(self, *args):
2575 r"""show(IntKey self, _ostream out=std::cout)"""
2576 return _IMP_kernel.IntKey_show(self, *args)
2579 def add_alias(old_key, new_name):
2580 r"""add_alias(IntKey old_key, std::string new_name) -> IntKey"""
2581 return _IMP_kernel.IntKey_add_alias(old_key, new_name)
2584 def get_number_of_keys():
2585 r"""get_number_of_keys() -> unsigned int"""
2586 return _IMP_kernel.IntKey_get_number_of_keys()
2589 r"""get_index(IntKey self) -> unsigned int"""
2590 return _IMP_kernel.IntKey_get_index(self)
2594 r"""show_all(_ostream out)"""
2595 return _IMP_kernel.IntKey_show_all(out)
2598 def get_all_strings():
2599 r"""get_all_strings() -> IMP::Vector< std::string >"""
2600 return _IMP_kernel.IntKey_get_all_strings()
2603 def get_number_unique():
2604 r"""get_number_unique() -> unsigned int"""
2605 return _IMP_kernel.IntKey_get_number_unique()
2608 r"""__str__(IntKey self) -> std::string"""
2609 return _IMP_kernel.IntKey___str__(self)
2612 r"""__repr__(IntKey self) -> std::string"""
2613 return _IMP_kernel.IntKey___repr__(self)
2614 __swig_destroy__ = _IMP_kernel.delete_IntKey
2617 _IMP_kernel.IntKey_swigregister(IntKey)
2619 r"""Proxy of C++ IMP::Key< 2 > class."""
2621 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2623 def __init__(self, *args):
2625 __init__(StringKey self) -> StringKey
2626 __init__(StringKey self, std::string const & c, bool is_implicit_add_permitted=True) -> StringKey
2627 __init__(StringKey self, unsigned int i) -> StringKey
2629 _IMP_kernel.StringKey_swiginit(self, _IMP_kernel.new_StringKey(*args))
2633 r"""add_key(std::string sc) -> unsigned int"""
2634 return _IMP_kernel.StringKey_add_key(sc)
2637 def get_key_exists(sc):
2638 r"""get_key_exists(std::string sc) -> bool"""
2639 return _IMP_kernel.StringKey_get_key_exists(sc)
2641 def get_string(self):
2642 r"""get_string(StringKey self) -> std::string const"""
2643 return _IMP_kernel.StringKey_get_string(self)
2645 def __cmp__(self, o):
2646 r"""__cmp__(StringKey self, StringKey o) -> int"""
2647 return _IMP_kernel.StringKey___cmp__(self, o)
2649 def __eq__(self, o):
2650 r"""__eq__(StringKey self, StringKey o) -> bool"""
2651 return _IMP_kernel.StringKey___eq__(self, o)
2653 def __ne__(self, o):
2654 r"""__ne__(StringKey self, StringKey o) -> bool"""
2655 return _IMP_kernel.StringKey___ne__(self, o)
2657 def __lt__(self, o):
2658 r"""__lt__(StringKey self, StringKey o) -> bool"""
2659 return _IMP_kernel.StringKey___lt__(self, o)
2661 def __gt__(self, o):
2662 r"""__gt__(StringKey self, StringKey o) -> bool"""
2663 return _IMP_kernel.StringKey___gt__(self, o)
2665 def __ge__(self, o):
2666 r"""__ge__(StringKey self, StringKey o) -> bool"""
2667 return _IMP_kernel.StringKey___ge__(self, o)
2669 def __le__(self, o):
2670 r"""__le__(StringKey self, StringKey o) -> bool"""
2671 return _IMP_kernel.StringKey___le__(self, o)
2674 r"""__hash__(StringKey self) -> std::size_t"""
2675 return _IMP_kernel.StringKey___hash__(self)
2677 def show(self, *args):
2678 r"""show(StringKey self, _ostream out=std::cout)"""
2679 return _IMP_kernel.StringKey_show(self, *args)
2682 def add_alias(old_key, new_name):
2683 r"""add_alias(StringKey old_key, std::string new_name) -> StringKey"""
2684 return _IMP_kernel.StringKey_add_alias(old_key, new_name)
2687 def get_number_of_keys():
2688 r"""get_number_of_keys() -> unsigned int"""
2689 return _IMP_kernel.StringKey_get_number_of_keys()
2692 r"""get_index(StringKey self) -> unsigned int"""
2693 return _IMP_kernel.StringKey_get_index(self)
2697 r"""show_all(_ostream out)"""
2698 return _IMP_kernel.StringKey_show_all(out)
2701 def get_all_strings():
2702 r"""get_all_strings() -> IMP::Vector< std::string >"""
2703 return _IMP_kernel.StringKey_get_all_strings()
2706 def get_number_unique():
2707 r"""get_number_unique() -> unsigned int"""
2708 return _IMP_kernel.StringKey_get_number_unique()
2711 r"""__str__(StringKey self) -> std::string"""
2712 return _IMP_kernel.StringKey___str__(self)
2715 r"""__repr__(StringKey self) -> std::string"""
2716 return _IMP_kernel.StringKey___repr__(self)
2717 __swig_destroy__ = _IMP_kernel.delete_StringKey
2720 _IMP_kernel.StringKey_swigregister(StringKey)
2722 r"""Proxy of C++ IMP::Key< 3 > class."""
2724 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2726 def __init__(self, *args):
2728 __init__(ParticleIndexKey self) -> ParticleIndexKey
2729 __init__(ParticleIndexKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ParticleIndexKey
2730 __init__(ParticleIndexKey self, unsigned int i) -> ParticleIndexKey
2732 _IMP_kernel.ParticleIndexKey_swiginit(self, _IMP_kernel.new_ParticleIndexKey(*args))
2736 r"""add_key(std::string sc) -> unsigned int"""
2737 return _IMP_kernel.ParticleIndexKey_add_key(sc)
2740 def get_key_exists(sc):
2741 r"""get_key_exists(std::string sc) -> bool"""
2742 return _IMP_kernel.ParticleIndexKey_get_key_exists(sc)
2744 def get_string(self):
2745 r"""get_string(ParticleIndexKey self) -> std::string const"""
2746 return _IMP_kernel.ParticleIndexKey_get_string(self)
2748 def __cmp__(self, o):
2749 r"""__cmp__(ParticleIndexKey self, ParticleIndexKey o) -> int"""
2750 return _IMP_kernel.ParticleIndexKey___cmp__(self, o)
2752 def __eq__(self, o):
2753 r"""__eq__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2754 return _IMP_kernel.ParticleIndexKey___eq__(self, o)
2756 def __ne__(self, o):
2757 r"""__ne__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2758 return _IMP_kernel.ParticleIndexKey___ne__(self, o)
2760 def __lt__(self, o):
2761 r"""__lt__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2762 return _IMP_kernel.ParticleIndexKey___lt__(self, o)
2764 def __gt__(self, o):
2765 r"""__gt__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2766 return _IMP_kernel.ParticleIndexKey___gt__(self, o)
2768 def __ge__(self, o):
2769 r"""__ge__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2770 return _IMP_kernel.ParticleIndexKey___ge__(self, o)
2772 def __le__(self, o):
2773 r"""__le__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2774 return _IMP_kernel.ParticleIndexKey___le__(self, o)
2777 r"""__hash__(ParticleIndexKey self) -> std::size_t"""
2778 return _IMP_kernel.ParticleIndexKey___hash__(self)
2780 def show(self, *args):
2781 r"""show(ParticleIndexKey self, _ostream out=std::cout)"""
2782 return _IMP_kernel.ParticleIndexKey_show(self, *args)
2785 def add_alias(old_key, new_name):
2786 r"""add_alias(ParticleIndexKey old_key, std::string new_name) -> ParticleIndexKey"""
2787 return _IMP_kernel.ParticleIndexKey_add_alias(old_key, new_name)
2790 def get_number_of_keys():
2791 r"""get_number_of_keys() -> unsigned int"""
2792 return _IMP_kernel.ParticleIndexKey_get_number_of_keys()
2795 r"""get_index(ParticleIndexKey self) -> unsigned int"""
2796 return _IMP_kernel.ParticleIndexKey_get_index(self)
2800 r"""show_all(_ostream out)"""
2801 return _IMP_kernel.ParticleIndexKey_show_all(out)
2804 def get_all_strings():
2805 r"""get_all_strings() -> IMP::Vector< std::string >"""
2806 return _IMP_kernel.ParticleIndexKey_get_all_strings()
2809 def get_number_unique():
2810 r"""get_number_unique() -> unsigned int"""
2811 return _IMP_kernel.ParticleIndexKey_get_number_unique()
2814 r"""__str__(ParticleIndexKey self) -> std::string"""
2815 return _IMP_kernel.ParticleIndexKey___str__(self)
2818 r"""__repr__(ParticleIndexKey self) -> std::string"""
2819 return _IMP_kernel.ParticleIndexKey___repr__(self)
2820 __swig_destroy__ = _IMP_kernel.delete_ParticleIndexKey
2823 _IMP_kernel.ParticleIndexKey_swigregister(ParticleIndexKey)
2825 r"""Proxy of C++ IMP::Key< 4 > class."""
2827 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2829 def __init__(self, *args):
2831 __init__(ObjectKey self) -> ObjectKey
2832 __init__(ObjectKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ObjectKey
2833 __init__(ObjectKey self, unsigned int i) -> ObjectKey
2835 _IMP_kernel.ObjectKey_swiginit(self, _IMP_kernel.new_ObjectKey(*args))
2839 r"""add_key(std::string sc) -> unsigned int"""
2840 return _IMP_kernel.ObjectKey_add_key(sc)
2843 def get_key_exists(sc):
2844 r"""get_key_exists(std::string sc) -> bool"""
2845 return _IMP_kernel.ObjectKey_get_key_exists(sc)
2847 def get_string(self):
2848 r"""get_string(ObjectKey self) -> std::string const"""
2849 return _IMP_kernel.ObjectKey_get_string(self)
2851 def __cmp__(self, o):
2852 r"""__cmp__(ObjectKey self, ObjectKey o) -> int"""
2853 return _IMP_kernel.ObjectKey___cmp__(self, o)
2855 def __eq__(self, o):
2856 r"""__eq__(ObjectKey self, ObjectKey o) -> bool"""
2857 return _IMP_kernel.ObjectKey___eq__(self, o)
2859 def __ne__(self, o):
2860 r"""__ne__(ObjectKey self, ObjectKey o) -> bool"""
2861 return _IMP_kernel.ObjectKey___ne__(self, o)
2863 def __lt__(self, o):
2864 r"""__lt__(ObjectKey self, ObjectKey o) -> bool"""
2865 return _IMP_kernel.ObjectKey___lt__(self, o)
2867 def __gt__(self, o):
2868 r"""__gt__(ObjectKey self, ObjectKey o) -> bool"""
2869 return _IMP_kernel.ObjectKey___gt__(self, o)
2871 def __ge__(self, o):
2872 r"""__ge__(ObjectKey self, ObjectKey o) -> bool"""
2873 return _IMP_kernel.ObjectKey___ge__(self, o)
2875 def __le__(self, o):
2876 r"""__le__(ObjectKey self, ObjectKey o) -> bool"""
2877 return _IMP_kernel.ObjectKey___le__(self, o)
2880 r"""__hash__(ObjectKey self) -> std::size_t"""
2881 return _IMP_kernel.ObjectKey___hash__(self)
2883 def show(self, *args):
2884 r"""show(ObjectKey self, _ostream out=std::cout)"""
2885 return _IMP_kernel.ObjectKey_show(self, *args)
2888 def add_alias(old_key, new_name):
2889 r"""add_alias(ObjectKey old_key, std::string new_name) -> ObjectKey"""
2890 return _IMP_kernel.ObjectKey_add_alias(old_key, new_name)
2893 def get_number_of_keys():
2894 r"""get_number_of_keys() -> unsigned int"""
2895 return _IMP_kernel.ObjectKey_get_number_of_keys()
2898 r"""get_index(ObjectKey self) -> unsigned int"""
2899 return _IMP_kernel.ObjectKey_get_index(self)
2903 r"""show_all(_ostream out)"""
2904 return _IMP_kernel.ObjectKey_show_all(out)
2907 def get_all_strings():
2908 r"""get_all_strings() -> IMP::Vector< std::string >"""
2909 return _IMP_kernel.ObjectKey_get_all_strings()
2912 def get_number_unique():
2913 r"""get_number_unique() -> unsigned int"""
2914 return _IMP_kernel.ObjectKey_get_number_unique()
2917 r"""__str__(ObjectKey self) -> std::string"""
2918 return _IMP_kernel.ObjectKey___str__(self)
2921 r"""__repr__(ObjectKey self) -> std::string"""
2922 return _IMP_kernel.ObjectKey___repr__(self)
2923 __swig_destroy__ = _IMP_kernel.delete_ObjectKey
2926 _IMP_kernel.ObjectKey_swigregister(ObjectKey)
2928 r"""Proxy of C++ IMP::Key< 5 > class."""
2930 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2932 def __init__(self, *args):
2934 __init__(IntsKey self) -> IntsKey
2935 __init__(IntsKey self, std::string const & c, bool is_implicit_add_permitted=True) -> IntsKey
2936 __init__(IntsKey self, unsigned int i) -> IntsKey
2938 _IMP_kernel.IntsKey_swiginit(self, _IMP_kernel.new_IntsKey(*args))
2942 r"""add_key(std::string sc) -> unsigned int"""
2943 return _IMP_kernel.IntsKey_add_key(sc)
2946 def get_key_exists(sc):
2947 r"""get_key_exists(std::string sc) -> bool"""
2948 return _IMP_kernel.IntsKey_get_key_exists(sc)
2950 def get_string(self):
2951 r"""get_string(IntsKey self) -> std::string const"""
2952 return _IMP_kernel.IntsKey_get_string(self)
2954 def __cmp__(self, o):
2955 r"""__cmp__(IntsKey self, IntsKey o) -> int"""
2956 return _IMP_kernel.IntsKey___cmp__(self, o)
2958 def __eq__(self, o):
2959 r"""__eq__(IntsKey self, IntsKey o) -> bool"""
2960 return _IMP_kernel.IntsKey___eq__(self, o)
2962 def __ne__(self, o):
2963 r"""__ne__(IntsKey self, IntsKey o) -> bool"""
2964 return _IMP_kernel.IntsKey___ne__(self, o)
2966 def __lt__(self, o):
2967 r"""__lt__(IntsKey self, IntsKey o) -> bool"""
2968 return _IMP_kernel.IntsKey___lt__(self, o)
2970 def __gt__(self, o):
2971 r"""__gt__(IntsKey self, IntsKey o) -> bool"""
2972 return _IMP_kernel.IntsKey___gt__(self, o)
2974 def __ge__(self, o):
2975 r"""__ge__(IntsKey self, IntsKey o) -> bool"""
2976 return _IMP_kernel.IntsKey___ge__(self, o)
2978 def __le__(self, o):
2979 r"""__le__(IntsKey self, IntsKey o) -> bool"""
2980 return _IMP_kernel.IntsKey___le__(self, o)
2983 r"""__hash__(IntsKey self) -> std::size_t"""
2984 return _IMP_kernel.IntsKey___hash__(self)
2986 def show(self, *args):
2987 r"""show(IntsKey self, _ostream out=std::cout)"""
2988 return _IMP_kernel.IntsKey_show(self, *args)
2991 def add_alias(old_key, new_name):
2992 r"""add_alias(IntsKey old_key, std::string new_name) -> IntsKey"""
2993 return _IMP_kernel.IntsKey_add_alias(old_key, new_name)
2996 def get_number_of_keys():
2997 r"""get_number_of_keys() -> unsigned int"""
2998 return _IMP_kernel.IntsKey_get_number_of_keys()
3001 r"""get_index(IntsKey self) -> unsigned int"""
3002 return _IMP_kernel.IntsKey_get_index(self)
3006 r"""show_all(_ostream out)"""
3007 return _IMP_kernel.IntsKey_show_all(out)
3010 def get_all_strings():
3011 r"""get_all_strings() -> IMP::Vector< std::string >"""
3012 return _IMP_kernel.IntsKey_get_all_strings()
3015 def get_number_unique():
3016 r"""get_number_unique() -> unsigned int"""
3017 return _IMP_kernel.IntsKey_get_number_unique()
3020 r"""__str__(IntsKey self) -> std::string"""
3021 return _IMP_kernel.IntsKey___str__(self)
3024 r"""__repr__(IntsKey self) -> std::string"""
3025 return _IMP_kernel.IntsKey___repr__(self)
3026 __swig_destroy__ = _IMP_kernel.delete_IntsKey
3029 _IMP_kernel.IntsKey_swigregister(IntsKey)
3031 r"""Proxy of C++ IMP::Key< 6 > class."""
3033 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3035 def __init__(self, *args):
3037 __init__(ParticleIndexesKey self) -> ParticleIndexesKey
3038 __init__(ParticleIndexesKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ParticleIndexesKey
3039 __init__(ParticleIndexesKey self, unsigned int i) -> ParticleIndexesKey
3041 _IMP_kernel.ParticleIndexesKey_swiginit(self, _IMP_kernel.new_ParticleIndexesKey(*args))
3045 r"""add_key(std::string sc) -> unsigned int"""
3046 return _IMP_kernel.ParticleIndexesKey_add_key(sc)
3049 def get_key_exists(sc):
3050 r"""get_key_exists(std::string sc) -> bool"""
3051 return _IMP_kernel.ParticleIndexesKey_get_key_exists(sc)
3053 def get_string(self):
3054 r"""get_string(ParticleIndexesKey self) -> std::string const"""
3055 return _IMP_kernel.ParticleIndexesKey_get_string(self)
3057 def __cmp__(self, o):
3058 r"""__cmp__(ParticleIndexesKey self, ParticleIndexesKey o) -> int"""
3059 return _IMP_kernel.ParticleIndexesKey___cmp__(self, o)
3061 def __eq__(self, o):
3062 r"""__eq__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3063 return _IMP_kernel.ParticleIndexesKey___eq__(self, o)
3065 def __ne__(self, o):
3066 r"""__ne__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3067 return _IMP_kernel.ParticleIndexesKey___ne__(self, o)
3069 def __lt__(self, o):
3070 r"""__lt__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3071 return _IMP_kernel.ParticleIndexesKey___lt__(self, o)
3073 def __gt__(self, o):
3074 r"""__gt__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3075 return _IMP_kernel.ParticleIndexesKey___gt__(self, o)
3077 def __ge__(self, o):
3078 r"""__ge__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3079 return _IMP_kernel.ParticleIndexesKey___ge__(self, o)
3081 def __le__(self, o):
3082 r"""__le__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
3083 return _IMP_kernel.ParticleIndexesKey___le__(self, o)
3086 r"""__hash__(ParticleIndexesKey self) -> std::size_t"""
3087 return _IMP_kernel.ParticleIndexesKey___hash__(self)
3089 def show(self, *args):
3090 r"""show(ParticleIndexesKey self, _ostream out=std::cout)"""
3091 return _IMP_kernel.ParticleIndexesKey_show(self, *args)
3094 def add_alias(old_key, new_name):
3095 r"""add_alias(ParticleIndexesKey old_key, std::string new_name) -> ParticleIndexesKey"""
3096 return _IMP_kernel.ParticleIndexesKey_add_alias(old_key, new_name)
3099 def get_number_of_keys():
3100 r"""get_number_of_keys() -> unsigned int"""
3101 return _IMP_kernel.ParticleIndexesKey_get_number_of_keys()
3104 r"""get_index(ParticleIndexesKey self) -> unsigned int"""
3105 return _IMP_kernel.ParticleIndexesKey_get_index(self)
3109 r"""show_all(_ostream out)"""
3110 return _IMP_kernel.ParticleIndexesKey_show_all(out)
3113 def get_all_strings():
3114 r"""get_all_strings() -> IMP::Vector< std::string >"""
3115 return _IMP_kernel.ParticleIndexesKey_get_all_strings()
3118 def get_number_unique():
3119 r"""get_number_unique() -> unsigned int"""
3120 return _IMP_kernel.ParticleIndexesKey_get_number_unique()
3123 r"""__str__(ParticleIndexesKey self) -> std::string"""
3124 return _IMP_kernel.ParticleIndexesKey___str__(self)
3127 r"""__repr__(ParticleIndexesKey self) -> std::string"""
3128 return _IMP_kernel.ParticleIndexesKey___repr__(self)
3129 __swig_destroy__ = _IMP_kernel.delete_ParticleIndexesKey
3132 _IMP_kernel.ParticleIndexesKey_swigregister(ParticleIndexesKey)
3134 r"""Proxy of C++ IMP::Key< 8 > class."""
3136 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3138 def __init__(self, *args):
3140 __init__(ModelKey self) -> ModelKey
3141 __init__(ModelKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ModelKey
3142 __init__(ModelKey self, unsigned int i) -> ModelKey
3144 _IMP_kernel.ModelKey_swiginit(self, _IMP_kernel.new_ModelKey(*args))
3148 r"""add_key(std::string sc) -> unsigned int"""
3149 return _IMP_kernel.ModelKey_add_key(sc)
3152 def get_key_exists(sc):
3153 r"""get_key_exists(std::string sc) -> bool"""
3154 return _IMP_kernel.ModelKey_get_key_exists(sc)
3156 def get_string(self):
3157 r"""get_string(ModelKey self) -> std::string const"""
3158 return _IMP_kernel.ModelKey_get_string(self)
3160 def __cmp__(self, o):
3161 r"""__cmp__(ModelKey self, ModelKey o) -> int"""
3162 return _IMP_kernel.ModelKey___cmp__(self, o)
3164 def __eq__(self, o):
3165 r"""__eq__(ModelKey self, ModelKey o) -> bool"""
3166 return _IMP_kernel.ModelKey___eq__(self, o)
3168 def __ne__(self, o):
3169 r"""__ne__(ModelKey self, ModelKey o) -> bool"""
3170 return _IMP_kernel.ModelKey___ne__(self, o)
3172 def __lt__(self, o):
3173 r"""__lt__(ModelKey self, ModelKey o) -> bool"""
3174 return _IMP_kernel.ModelKey___lt__(self, o)
3176 def __gt__(self, o):
3177 r"""__gt__(ModelKey self, ModelKey o) -> bool"""
3178 return _IMP_kernel.ModelKey___gt__(self, o)
3180 def __ge__(self, o):
3181 r"""__ge__(ModelKey self, ModelKey o) -> bool"""
3182 return _IMP_kernel.ModelKey___ge__(self, o)
3184 def __le__(self, o):
3185 r"""__le__(ModelKey self, ModelKey o) -> bool"""
3186 return _IMP_kernel.ModelKey___le__(self, o)
3189 r"""__hash__(ModelKey self) -> std::size_t"""
3190 return _IMP_kernel.ModelKey___hash__(self)
3192 def show(self, *args):
3193 r"""show(ModelKey self, _ostream out=std::cout)"""
3194 return _IMP_kernel.ModelKey_show(self, *args)
3197 def add_alias(old_key, new_name):
3198 r"""add_alias(ModelKey old_key, std::string new_name) -> ModelKey"""
3199 return _IMP_kernel.ModelKey_add_alias(old_key, new_name)
3202 def get_number_of_keys():
3203 r"""get_number_of_keys() -> unsigned int"""
3204 return _IMP_kernel.ModelKey_get_number_of_keys()
3207 r"""get_index(ModelKey self) -> unsigned int"""
3208 return _IMP_kernel.ModelKey_get_index(self)
3212 r"""show_all(_ostream out)"""
3213 return _IMP_kernel.ModelKey_show_all(out)
3216 def get_all_strings():
3217 r"""get_all_strings() -> IMP::Vector< std::string >"""
3218 return _IMP_kernel.ModelKey_get_all_strings()
3221 def get_number_unique():
3222 r"""get_number_unique() -> unsigned int"""
3223 return _IMP_kernel.ModelKey_get_number_unique()
3226 r"""__str__(ModelKey self) -> std::string"""
3227 return _IMP_kernel.ModelKey___str__(self)
3230 r"""__repr__(ModelKey self) -> std::string"""
3231 return _IMP_kernel.ModelKey___repr__(self)
3232 __swig_destroy__ = _IMP_kernel.delete_ModelKey
3235 _IMP_kernel.ModelKey_swigregister(ModelKey)
3237 r"""Proxy of C++ IMP::Key< 11 > class."""
3239 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3241 def __init__(self, *args):
3243 __init__(TriggerKey self) -> TriggerKey
3244 __init__(TriggerKey self, std::string const & c, bool is_implicit_add_permitted=True) -> TriggerKey
3245 __init__(TriggerKey self, unsigned int i) -> TriggerKey
3247 _IMP_kernel.TriggerKey_swiginit(self, _IMP_kernel.new_TriggerKey(*args))
3251 r"""add_key(std::string sc) -> unsigned int"""
3252 return _IMP_kernel.TriggerKey_add_key(sc)
3255 def get_key_exists(sc):
3256 r"""get_key_exists(std::string sc) -> bool"""
3257 return _IMP_kernel.TriggerKey_get_key_exists(sc)
3259 def get_string(self):
3260 r"""get_string(TriggerKey self) -> std::string const"""
3261 return _IMP_kernel.TriggerKey_get_string(self)
3263 def __cmp__(self, o):
3264 r"""__cmp__(TriggerKey self, TriggerKey o) -> int"""
3265 return _IMP_kernel.TriggerKey___cmp__(self, o)
3267 def __eq__(self, o):
3268 r"""__eq__(TriggerKey self, TriggerKey o) -> bool"""
3269 return _IMP_kernel.TriggerKey___eq__(self, o)
3271 def __ne__(self, o):
3272 r"""__ne__(TriggerKey self, TriggerKey o) -> bool"""
3273 return _IMP_kernel.TriggerKey___ne__(self, o)
3275 def __lt__(self, o):
3276 r"""__lt__(TriggerKey self, TriggerKey o) -> bool"""
3277 return _IMP_kernel.TriggerKey___lt__(self, o)
3279 def __gt__(self, o):
3280 r"""__gt__(TriggerKey self, TriggerKey o) -> bool"""
3281 return _IMP_kernel.TriggerKey___gt__(self, o)
3283 def __ge__(self, o):
3284 r"""__ge__(TriggerKey self, TriggerKey o) -> bool"""
3285 return _IMP_kernel.TriggerKey___ge__(self, o)
3287 def __le__(self, o):
3288 r"""__le__(TriggerKey self, TriggerKey o) -> bool"""
3289 return _IMP_kernel.TriggerKey___le__(self, o)
3292 r"""__hash__(TriggerKey self) -> std::size_t"""
3293 return _IMP_kernel.TriggerKey___hash__(self)
3295 def show(self, *args):
3296 r"""show(TriggerKey self, _ostream out=std::cout)"""
3297 return _IMP_kernel.TriggerKey_show(self, *args)
3300 def add_alias(old_key, new_name):
3301 r"""add_alias(TriggerKey old_key, std::string new_name) -> TriggerKey"""
3302 return _IMP_kernel.TriggerKey_add_alias(old_key, new_name)
3305 def get_number_of_keys():
3306 r"""get_number_of_keys() -> unsigned int"""
3307 return _IMP_kernel.TriggerKey_get_number_of_keys()
3310 r"""get_index(TriggerKey self) -> unsigned int"""
3311 return _IMP_kernel.TriggerKey_get_index(self)
3315 r"""show_all(_ostream out)"""
3316 return _IMP_kernel.TriggerKey_show_all(out)
3319 def get_all_strings():
3320 r"""get_all_strings() -> IMP::Vector< std::string >"""
3321 return _IMP_kernel.TriggerKey_get_all_strings()
3324 def get_number_unique():
3325 r"""get_number_unique() -> unsigned int"""
3326 return _IMP_kernel.TriggerKey_get_number_unique()
3329 r"""__str__(TriggerKey self) -> std::string"""
3330 return _IMP_kernel.TriggerKey___str__(self)
3333 r"""__repr__(TriggerKey self) -> std::string"""
3334 return _IMP_kernel.TriggerKey___repr__(self)
3335 __swig_destroy__ = _IMP_kernel.delete_TriggerKey
3338 _IMP_kernel.TriggerKey_swigregister(TriggerKey)
3340 r"""Proxy of C++ IMP::Index< IMP::ParticleIndexTag > class."""
3342 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3344 def __init__(self, *args):
3346 __init__(ParticleIndex self, int i) -> ParticleIndex
3347 __init__(ParticleIndex self) -> ParticleIndex
3349 _IMP_kernel.ParticleIndex_swiginit(self, _IMP_kernel.new_ParticleIndex(*args))
3352 r"""get_index(ParticleIndex self) -> int"""
3353 return _IMP_kernel.ParticleIndex_get_index(self)
3355 def __cmp__(self, o):
3356 r"""__cmp__(ParticleIndex self, ParticleIndex o) -> int"""
3357 return _IMP_kernel.ParticleIndex___cmp__(self, o)
3359 def __eq__(self, o):
3360 r"""__eq__(ParticleIndex self, ParticleIndex o) -> bool"""
3361 return _IMP_kernel.ParticleIndex___eq__(self, o)
3363 def __ne__(self, o):
3364 r"""__ne__(ParticleIndex self, ParticleIndex o) -> bool"""
3365 return _IMP_kernel.ParticleIndex___ne__(self, o)
3367 def __lt__(self, o):
3368 r"""__lt__(ParticleIndex self, ParticleIndex o) -> bool"""
3369 return _IMP_kernel.ParticleIndex___lt__(self, o)
3371 def __gt__(self, o):
3372 r"""__gt__(ParticleIndex self, ParticleIndex o) -> bool"""
3373 return _IMP_kernel.ParticleIndex___gt__(self, o)
3375 def __ge__(self, o):
3376 r"""__ge__(ParticleIndex self, ParticleIndex o) -> bool"""
3377 return _IMP_kernel.ParticleIndex___ge__(self, o)
3379 def __le__(self, o):
3380 r"""__le__(ParticleIndex self, ParticleIndex o) -> bool"""
3381 return _IMP_kernel.ParticleIndex___le__(self, o)
3383 def show(self, *args):
3384 r"""show(ParticleIndex self, _ostream out=std::cout)"""
3385 return _IMP_kernel.ParticleIndex_show(self, *args)
3388 r"""__hash__(ParticleIndex self) -> std::size_t"""
3389 return _IMP_kernel.ParticleIndex___hash__(self)
3392 r"""__str__(ParticleIndex self) -> std::string"""
3393 return _IMP_kernel.ParticleIndex___str__(self)
3396 r"""__repr__(ParticleIndex self) -> std::string"""
3397 return _IMP_kernel.ParticleIndex___repr__(self)
3398 __swig_destroy__ = _IMP_kernel.delete_ParticleIndex
3401 _IMP_kernel.ParticleIndex_swigregister(ParticleIndex)
3403 r"""Proxy of C++ IMP::Key< 10 > class."""
3405 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3407 def __init__(self, *args):
3409 __init__(FloatsKey self) -> FloatsKey
3410 __init__(FloatsKey self, std::string const & c, bool is_implicit_add_permitted=True) -> FloatsKey
3411 __init__(FloatsKey self, unsigned int i) -> FloatsKey
3413 _IMP_kernel.FloatsKey_swiginit(self, _IMP_kernel.new_FloatsKey(*args))
3417 r"""add_key(std::string sc) -> unsigned int"""
3418 return _IMP_kernel.FloatsKey_add_key(sc)
3421 def get_key_exists(sc):
3422 r"""get_key_exists(std::string sc) -> bool"""
3423 return _IMP_kernel.FloatsKey_get_key_exists(sc)
3425 def get_string(self):
3426 r"""get_string(FloatsKey self) -> std::string const"""
3427 return _IMP_kernel.FloatsKey_get_string(self)
3429 def __cmp__(self, o):
3430 r"""__cmp__(FloatsKey self, FloatsKey o) -> int"""
3431 return _IMP_kernel.FloatsKey___cmp__(self, o)
3433 def __eq__(self, o):
3434 r"""__eq__(FloatsKey self, FloatsKey o) -> bool"""
3435 return _IMP_kernel.FloatsKey___eq__(self, o)
3437 def __ne__(self, o):
3438 r"""__ne__(FloatsKey self, FloatsKey o) -> bool"""
3439 return _IMP_kernel.FloatsKey___ne__(self, o)
3441 def __lt__(self, o):
3442 r"""__lt__(FloatsKey self, FloatsKey o) -> bool"""
3443 return _IMP_kernel.FloatsKey___lt__(self, o)
3445 def __gt__(self, o):
3446 r"""__gt__(FloatsKey self, FloatsKey o) -> bool"""
3447 return _IMP_kernel.FloatsKey___gt__(self, o)
3449 def __ge__(self, o):
3450 r"""__ge__(FloatsKey self, FloatsKey o) -> bool"""
3451 return _IMP_kernel.FloatsKey___ge__(self, o)
3453 def __le__(self, o):
3454 r"""__le__(FloatsKey self, FloatsKey o) -> bool"""
3455 return _IMP_kernel.FloatsKey___le__(self, o)
3458 r"""__hash__(FloatsKey self) -> std::size_t"""
3459 return _IMP_kernel.FloatsKey___hash__(self)
3461 def show(self, *args):
3462 r"""show(FloatsKey self, _ostream out=std::cout)"""
3463 return _IMP_kernel.FloatsKey_show(self, *args)
3466 def add_alias(old_key, new_name):
3467 r"""add_alias(FloatsKey old_key, std::string new_name) -> FloatsKey"""
3468 return _IMP_kernel.FloatsKey_add_alias(old_key, new_name)
3471 def get_number_of_keys():
3472 r"""get_number_of_keys() -> unsigned int"""
3473 return _IMP_kernel.FloatsKey_get_number_of_keys()
3476 r"""get_index(FloatsKey self) -> unsigned int"""
3477 return _IMP_kernel.FloatsKey_get_index(self)
3481 r"""show_all(_ostream out)"""
3482 return _IMP_kernel.FloatsKey_show_all(out)
3485 def get_all_strings():
3486 r"""get_all_strings() -> IMP::Vector< std::string >"""
3487 return _IMP_kernel.FloatsKey_get_all_strings()
3490 def get_number_unique():
3491 r"""get_number_unique() -> unsigned int"""
3492 return _IMP_kernel.FloatsKey_get_number_unique()
3495 r"""__str__(FloatsKey self) -> std::string"""
3496 return _IMP_kernel.FloatsKey___str__(self)
3499 r"""__repr__(FloatsKey self) -> std::string"""
3500 return _IMP_kernel.FloatsKey___repr__(self)
3501 __swig_destroy__ = _IMP_kernel.delete_FloatsKey
3504 _IMP_kernel.FloatsKey_swigregister(FloatsKey)
3506 r"""Proxy of C++ IMP::Key< 12 > class."""
3508 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3510 def __init__(self, *args):
3512 __init__(SparseStringKey self) -> SparseStringKey
3513 __init__(SparseStringKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseStringKey
3514 __init__(SparseStringKey self, unsigned int i) -> SparseStringKey
3516 _IMP_kernel.SparseStringKey_swiginit(self, _IMP_kernel.new_SparseStringKey(*args))
3520 r"""add_key(std::string sc) -> unsigned int"""
3521 return _IMP_kernel.SparseStringKey_add_key(sc)
3524 def get_key_exists(sc):
3525 r"""get_key_exists(std::string sc) -> bool"""
3526 return _IMP_kernel.SparseStringKey_get_key_exists(sc)
3528 def get_string(self):
3529 r"""get_string(SparseStringKey self) -> std::string const"""
3530 return _IMP_kernel.SparseStringKey_get_string(self)
3532 def __cmp__(self, o):
3533 r"""__cmp__(SparseStringKey self, SparseStringKey o) -> int"""
3534 return _IMP_kernel.SparseStringKey___cmp__(self, o)
3536 def __eq__(self, o):
3537 r"""__eq__(SparseStringKey self, SparseStringKey o) -> bool"""
3538 return _IMP_kernel.SparseStringKey___eq__(self, o)
3540 def __ne__(self, o):
3541 r"""__ne__(SparseStringKey self, SparseStringKey o) -> bool"""
3542 return _IMP_kernel.SparseStringKey___ne__(self, o)
3544 def __lt__(self, o):
3545 r"""__lt__(SparseStringKey self, SparseStringKey o) -> bool"""
3546 return _IMP_kernel.SparseStringKey___lt__(self, o)
3548 def __gt__(self, o):
3549 r"""__gt__(SparseStringKey self, SparseStringKey o) -> bool"""
3550 return _IMP_kernel.SparseStringKey___gt__(self, o)
3552 def __ge__(self, o):
3553 r"""__ge__(SparseStringKey self, SparseStringKey o) -> bool"""
3554 return _IMP_kernel.SparseStringKey___ge__(self, o)
3556 def __le__(self, o):
3557 r"""__le__(SparseStringKey self, SparseStringKey o) -> bool"""
3558 return _IMP_kernel.SparseStringKey___le__(self, o)
3561 r"""__hash__(SparseStringKey self) -> std::size_t"""
3562 return _IMP_kernel.SparseStringKey___hash__(self)
3564 def show(self, *args):
3565 r"""show(SparseStringKey self, _ostream out=std::cout)"""
3566 return _IMP_kernel.SparseStringKey_show(self, *args)
3569 def add_alias(old_key, new_name):
3570 r"""add_alias(SparseStringKey old_key, std::string new_name) -> SparseStringKey"""
3571 return _IMP_kernel.SparseStringKey_add_alias(old_key, new_name)
3574 def get_number_of_keys():
3575 r"""get_number_of_keys() -> unsigned int"""
3576 return _IMP_kernel.SparseStringKey_get_number_of_keys()
3579 r"""get_index(SparseStringKey self) -> unsigned int"""
3580 return _IMP_kernel.SparseStringKey_get_index(self)
3584 r"""show_all(_ostream out)"""
3585 return _IMP_kernel.SparseStringKey_show_all(out)
3588 def get_all_strings():
3589 r"""get_all_strings() -> IMP::Vector< std::string >"""
3590 return _IMP_kernel.SparseStringKey_get_all_strings()
3593 def get_number_unique():
3594 r"""get_number_unique() -> unsigned int"""
3595 return _IMP_kernel.SparseStringKey_get_number_unique()
3598 r"""__str__(SparseStringKey self) -> std::string"""
3599 return _IMP_kernel.SparseStringKey___str__(self)
3602 r"""__repr__(SparseStringKey self) -> std::string"""
3603 return _IMP_kernel.SparseStringKey___repr__(self)
3604 __swig_destroy__ = _IMP_kernel.delete_SparseStringKey
3607 _IMP_kernel.SparseStringKey_swigregister(SparseStringKey)
3609 r"""Proxy of C++ IMP::Key< 13 > class."""
3611 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3613 def __init__(self, *args):
3615 __init__(SparseIntKey self) -> SparseIntKey
3616 __init__(SparseIntKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseIntKey
3617 __init__(SparseIntKey self, unsigned int i) -> SparseIntKey
3619 _IMP_kernel.SparseIntKey_swiginit(self, _IMP_kernel.new_SparseIntKey(*args))
3623 r"""add_key(std::string sc) -> unsigned int"""
3624 return _IMP_kernel.SparseIntKey_add_key(sc)
3627 def get_key_exists(sc):
3628 r"""get_key_exists(std::string sc) -> bool"""
3629 return _IMP_kernel.SparseIntKey_get_key_exists(sc)
3631 def get_string(self):
3632 r"""get_string(SparseIntKey self) -> std::string const"""
3633 return _IMP_kernel.SparseIntKey_get_string(self)
3635 def __cmp__(self, o):
3636 r"""__cmp__(SparseIntKey self, SparseIntKey o) -> int"""
3637 return _IMP_kernel.SparseIntKey___cmp__(self, o)
3639 def __eq__(self, o):
3640 r"""__eq__(SparseIntKey self, SparseIntKey o) -> bool"""
3641 return _IMP_kernel.SparseIntKey___eq__(self, o)
3643 def __ne__(self, o):
3644 r"""__ne__(SparseIntKey self, SparseIntKey o) -> bool"""
3645 return _IMP_kernel.SparseIntKey___ne__(self, o)
3647 def __lt__(self, o):
3648 r"""__lt__(SparseIntKey self, SparseIntKey o) -> bool"""
3649 return _IMP_kernel.SparseIntKey___lt__(self, o)
3651 def __gt__(self, o):
3652 r"""__gt__(SparseIntKey self, SparseIntKey o) -> bool"""
3653 return _IMP_kernel.SparseIntKey___gt__(self, o)
3655 def __ge__(self, o):
3656 r"""__ge__(SparseIntKey self, SparseIntKey o) -> bool"""
3657 return _IMP_kernel.SparseIntKey___ge__(self, o)
3659 def __le__(self, o):
3660 r"""__le__(SparseIntKey self, SparseIntKey o) -> bool"""
3661 return _IMP_kernel.SparseIntKey___le__(self, o)
3664 r"""__hash__(SparseIntKey self) -> std::size_t"""
3665 return _IMP_kernel.SparseIntKey___hash__(self)
3667 def show(self, *args):
3668 r"""show(SparseIntKey self, _ostream out=std::cout)"""
3669 return _IMP_kernel.SparseIntKey_show(self, *args)
3672 def add_alias(old_key, new_name):
3673 r"""add_alias(SparseIntKey old_key, std::string new_name) -> SparseIntKey"""
3674 return _IMP_kernel.SparseIntKey_add_alias(old_key, new_name)
3677 def get_number_of_keys():
3678 r"""get_number_of_keys() -> unsigned int"""
3679 return _IMP_kernel.SparseIntKey_get_number_of_keys()
3682 r"""get_index(SparseIntKey self) -> unsigned int"""
3683 return _IMP_kernel.SparseIntKey_get_index(self)
3687 r"""show_all(_ostream out)"""
3688 return _IMP_kernel.SparseIntKey_show_all(out)
3691 def get_all_strings():
3692 r"""get_all_strings() -> IMP::Vector< std::string >"""
3693 return _IMP_kernel.SparseIntKey_get_all_strings()
3696 def get_number_unique():
3697 r"""get_number_unique() -> unsigned int"""
3698 return _IMP_kernel.SparseIntKey_get_number_unique()
3701 r"""__str__(SparseIntKey self) -> std::string"""
3702 return _IMP_kernel.SparseIntKey___str__(self)
3705 r"""__repr__(SparseIntKey self) -> std::string"""
3706 return _IMP_kernel.SparseIntKey___repr__(self)
3707 __swig_destroy__ = _IMP_kernel.delete_SparseIntKey
3710 _IMP_kernel.SparseIntKey_swigregister(SparseIntKey)
3712 r"""Proxy of C++ IMP::Key< 14 > class."""
3714 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3716 def __init__(self, *args):
3718 __init__(SparseFloatKey self) -> SparseFloatKey
3719 __init__(SparseFloatKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseFloatKey
3720 __init__(SparseFloatKey self, unsigned int i) -> SparseFloatKey
3722 _IMP_kernel.SparseFloatKey_swiginit(self, _IMP_kernel.new_SparseFloatKey(*args))
3726 r"""add_key(std::string sc) -> unsigned int"""
3727 return _IMP_kernel.SparseFloatKey_add_key(sc)
3730 def get_key_exists(sc):
3731 r"""get_key_exists(std::string sc) -> bool"""
3732 return _IMP_kernel.SparseFloatKey_get_key_exists(sc)
3734 def get_string(self):
3735 r"""get_string(SparseFloatKey self) -> std::string const"""
3736 return _IMP_kernel.SparseFloatKey_get_string(self)
3738 def __cmp__(self, o):
3739 r"""__cmp__(SparseFloatKey self, SparseFloatKey o) -> int"""
3740 return _IMP_kernel.SparseFloatKey___cmp__(self, o)
3742 def __eq__(self, o):
3743 r"""__eq__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3744 return _IMP_kernel.SparseFloatKey___eq__(self, o)
3746 def __ne__(self, o):
3747 r"""__ne__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3748 return _IMP_kernel.SparseFloatKey___ne__(self, o)
3750 def __lt__(self, o):
3751 r"""__lt__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3752 return _IMP_kernel.SparseFloatKey___lt__(self, o)
3754 def __gt__(self, o):
3755 r"""__gt__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3756 return _IMP_kernel.SparseFloatKey___gt__(self, o)
3758 def __ge__(self, o):
3759 r"""__ge__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3760 return _IMP_kernel.SparseFloatKey___ge__(self, o)
3762 def __le__(self, o):
3763 r"""__le__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3764 return _IMP_kernel.SparseFloatKey___le__(self, o)
3767 r"""__hash__(SparseFloatKey self) -> std::size_t"""
3768 return _IMP_kernel.SparseFloatKey___hash__(self)
3770 def show(self, *args):
3771 r"""show(SparseFloatKey self, _ostream out=std::cout)"""
3772 return _IMP_kernel.SparseFloatKey_show(self, *args)
3775 def add_alias(old_key, new_name):
3776 r"""add_alias(SparseFloatKey old_key, std::string new_name) -> SparseFloatKey"""
3777 return _IMP_kernel.SparseFloatKey_add_alias(old_key, new_name)
3780 def get_number_of_keys():
3781 r"""get_number_of_keys() -> unsigned int"""
3782 return _IMP_kernel.SparseFloatKey_get_number_of_keys()
3785 r"""get_index(SparseFloatKey self) -> unsigned int"""
3786 return _IMP_kernel.SparseFloatKey_get_index(self)
3790 r"""show_all(_ostream out)"""
3791 return _IMP_kernel.SparseFloatKey_show_all(out)
3794 def get_all_strings():
3795 r"""get_all_strings() -> IMP::Vector< std::string >"""
3796 return _IMP_kernel.SparseFloatKey_get_all_strings()
3799 def get_number_unique():
3800 r"""get_number_unique() -> unsigned int"""
3801 return _IMP_kernel.SparseFloatKey_get_number_unique()
3804 r"""__str__(SparseFloatKey self) -> std::string"""
3805 return _IMP_kernel.SparseFloatKey___str__(self)
3808 r"""__repr__(SparseFloatKey self) -> std::string"""
3809 return _IMP_kernel.SparseFloatKey___repr__(self)
3810 __swig_destroy__ = _IMP_kernel.delete_SparseFloatKey
3813 _IMP_kernel.SparseFloatKey_swigregister(SparseFloatKey)
3815 r"""Proxy of C++ IMP::Key< 15 > class."""
3817 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3819 def __init__(self, *args):
3821 __init__(SparseParticleIndexKey self) -> SparseParticleIndexKey
3822 __init__(SparseParticleIndexKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseParticleIndexKey
3823 __init__(SparseParticleIndexKey self, unsigned int i) -> SparseParticleIndexKey
3825 _IMP_kernel.SparseParticleIndexKey_swiginit(self, _IMP_kernel.new_SparseParticleIndexKey(*args))
3829 r"""add_key(std::string sc) -> unsigned int"""
3830 return _IMP_kernel.SparseParticleIndexKey_add_key(sc)
3833 def get_key_exists(sc):
3834 r"""get_key_exists(std::string sc) -> bool"""
3835 return _IMP_kernel.SparseParticleIndexKey_get_key_exists(sc)
3837 def get_string(self):
3838 r"""get_string(SparseParticleIndexKey self) -> std::string const"""
3839 return _IMP_kernel.SparseParticleIndexKey_get_string(self)
3841 def __cmp__(self, o):
3842 r"""__cmp__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> int"""
3843 return _IMP_kernel.SparseParticleIndexKey___cmp__(self, o)
3845 def __eq__(self, o):
3846 r"""__eq__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3847 return _IMP_kernel.SparseParticleIndexKey___eq__(self, o)
3849 def __ne__(self, o):
3850 r"""__ne__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3851 return _IMP_kernel.SparseParticleIndexKey___ne__(self, o)
3853 def __lt__(self, o):
3854 r"""__lt__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3855 return _IMP_kernel.SparseParticleIndexKey___lt__(self, o)
3857 def __gt__(self, o):
3858 r"""__gt__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3859 return _IMP_kernel.SparseParticleIndexKey___gt__(self, o)
3861 def __ge__(self, o):
3862 r"""__ge__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3863 return _IMP_kernel.SparseParticleIndexKey___ge__(self, o)
3865 def __le__(self, o):
3866 r"""__le__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3867 return _IMP_kernel.SparseParticleIndexKey___le__(self, o)
3870 r"""__hash__(SparseParticleIndexKey self) -> std::size_t"""
3871 return _IMP_kernel.SparseParticleIndexKey___hash__(self)
3873 def show(self, *args):
3874 r"""show(SparseParticleIndexKey self, _ostream out=std::cout)"""
3875 return _IMP_kernel.SparseParticleIndexKey_show(self, *args)
3878 def add_alias(old_key, new_name):
3879 r"""add_alias(SparseParticleIndexKey old_key, std::string new_name) -> SparseParticleIndexKey"""
3880 return _IMP_kernel.SparseParticleIndexKey_add_alias(old_key, new_name)
3883 def get_number_of_keys():
3884 r"""get_number_of_keys() -> unsigned int"""
3885 return _IMP_kernel.SparseParticleIndexKey_get_number_of_keys()
3888 r"""get_index(SparseParticleIndexKey self) -> unsigned int"""
3889 return _IMP_kernel.SparseParticleIndexKey_get_index(self)
3893 r"""show_all(_ostream out)"""
3894 return _IMP_kernel.SparseParticleIndexKey_show_all(out)
3897 def get_all_strings():
3898 r"""get_all_strings() -> IMP::Vector< std::string >"""
3899 return _IMP_kernel.SparseParticleIndexKey_get_all_strings()
3902 def get_number_unique():
3903 r"""get_number_unique() -> unsigned int"""
3904 return _IMP_kernel.SparseParticleIndexKey_get_number_unique()
3907 r"""__str__(SparseParticleIndexKey self) -> std::string"""
3908 return _IMP_kernel.SparseParticleIndexKey___str__(self)
3911 r"""__repr__(SparseParticleIndexKey self) -> std::string"""
3912 return _IMP_kernel.SparseParticleIndexKey___repr__(self)
3913 __swig_destroy__ = _IMP_kernel.delete_SparseParticleIndexKey
3916 _IMP_kernel.SparseParticleIndexKey_swigregister(SparseParticleIndexKey)
3918 r"""Proxy of C++ IMP::Key< 16 > class."""
3920 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3922 def __init__(self, *args):
3924 __init__(Vector3DKey self) -> Vector3DKey
3925 __init__(Vector3DKey self, std::string const & c, bool is_implicit_add_permitted=True) -> Vector3DKey
3926 __init__(Vector3DKey self, unsigned int i) -> Vector3DKey
3928 _IMP_kernel.Vector3DKey_swiginit(self, _IMP_kernel.new_Vector3DKey(*args))
3932 r"""add_key(std::string sc) -> unsigned int"""
3933 return _IMP_kernel.Vector3DKey_add_key(sc)
3936 def get_key_exists(sc):
3937 r"""get_key_exists(std::string sc) -> bool"""
3938 return _IMP_kernel.Vector3DKey_get_key_exists(sc)
3940 def get_string(self):
3941 r"""get_string(Vector3DKey self) -> std::string const"""
3942 return _IMP_kernel.Vector3DKey_get_string(self)
3944 def __cmp__(self, o):
3945 r"""__cmp__(Vector3DKey self, Vector3DKey o) -> int"""
3946 return _IMP_kernel.Vector3DKey___cmp__(self, o)
3948 def __eq__(self, o):
3949 r"""__eq__(Vector3DKey self, Vector3DKey o) -> bool"""
3950 return _IMP_kernel.Vector3DKey___eq__(self, o)
3952 def __ne__(self, o):
3953 r"""__ne__(Vector3DKey self, Vector3DKey o) -> bool"""
3954 return _IMP_kernel.Vector3DKey___ne__(self, o)
3956 def __lt__(self, o):
3957 r"""__lt__(Vector3DKey self, Vector3DKey o) -> bool"""
3958 return _IMP_kernel.Vector3DKey___lt__(self, o)
3960 def __gt__(self, o):
3961 r"""__gt__(Vector3DKey self, Vector3DKey o) -> bool"""
3962 return _IMP_kernel.Vector3DKey___gt__(self, o)
3964 def __ge__(self, o):
3965 r"""__ge__(Vector3DKey self, Vector3DKey o) -> bool"""
3966 return _IMP_kernel.Vector3DKey___ge__(self, o)
3968 def __le__(self, o):
3969 r"""__le__(Vector3DKey self, Vector3DKey o) -> bool"""
3970 return _IMP_kernel.Vector3DKey___le__(self, o)
3973 r"""__hash__(Vector3DKey self) -> std::size_t"""
3974 return _IMP_kernel.Vector3DKey___hash__(self)
3976 def show(self, *args):
3977 r"""show(Vector3DKey self, _ostream out=std::cout)"""
3978 return _IMP_kernel.Vector3DKey_show(self, *args)
3981 def add_alias(old_key, new_name):
3982 r"""add_alias(Vector3DKey old_key, std::string new_name) -> Vector3DKey"""
3983 return _IMP_kernel.Vector3DKey_add_alias(old_key, new_name)
3986 def get_number_of_keys():
3987 r"""get_number_of_keys() -> unsigned int"""
3988 return _IMP_kernel.Vector3DKey_get_number_of_keys()
3991 r"""get_index(Vector3DKey self) -> unsigned int"""
3992 return _IMP_kernel.Vector3DKey_get_index(self)
3996 r"""show_all(_ostream out)"""
3997 return _IMP_kernel.Vector3DKey_show_all(out)
4000 def get_all_strings():
4001 r"""get_all_strings() -> IMP::Vector< std::string >"""
4002 return _IMP_kernel.Vector3DKey_get_all_strings()
4005 def get_number_unique():
4006 r"""get_number_unique() -> unsigned int"""
4007 return _IMP_kernel.Vector3DKey_get_number_unique()
4010 r"""__str__(Vector3DKey self) -> std::string"""
4011 return _IMP_kernel.Vector3DKey___str__(self)
4014 r"""__repr__(Vector3DKey self) -> std::string"""
4015 return _IMP_kernel.Vector3DKey___repr__(self)
4016 __swig_destroy__ = _IMP_kernel.delete_Vector3DKey
4019 _IMP_kernel.Vector3DKey_swigregister(Vector3DKey)
4021 r"""Proxy of C++ IMP::Key< 17 > class."""
4023 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4025 def __init__(self, *args):
4027 __init__(Vector3DDerivKey self) -> Vector3DDerivKey
4028 __init__(Vector3DDerivKey self, std::string const & c, bool is_implicit_add_permitted=True) -> Vector3DDerivKey
4029 __init__(Vector3DDerivKey self, unsigned int i) -> Vector3DDerivKey
4031 _IMP_kernel.Vector3DDerivKey_swiginit(self, _IMP_kernel.new_Vector3DDerivKey(*args))
4035 r"""add_key(std::string sc) -> unsigned int"""
4036 return _IMP_kernel.Vector3DDerivKey_add_key(sc)
4039 def get_key_exists(sc):
4040 r"""get_key_exists(std::string sc) -> bool"""
4041 return _IMP_kernel.Vector3DDerivKey_get_key_exists(sc)
4043 def get_string(self):
4044 r"""get_string(Vector3DDerivKey self) -> std::string const"""
4045 return _IMP_kernel.Vector3DDerivKey_get_string(self)
4047 def __cmp__(self, o):
4048 r"""__cmp__(Vector3DDerivKey self, Vector3DDerivKey o) -> int"""
4049 return _IMP_kernel.Vector3DDerivKey___cmp__(self, o)
4051 def __eq__(self, o):
4052 r"""__eq__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4053 return _IMP_kernel.Vector3DDerivKey___eq__(self, o)
4055 def __ne__(self, o):
4056 r"""__ne__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4057 return _IMP_kernel.Vector3DDerivKey___ne__(self, o)
4059 def __lt__(self, o):
4060 r"""__lt__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4061 return _IMP_kernel.Vector3DDerivKey___lt__(self, o)
4063 def __gt__(self, o):
4064 r"""__gt__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4065 return _IMP_kernel.Vector3DDerivKey___gt__(self, o)
4067 def __ge__(self, o):
4068 r"""__ge__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4069 return _IMP_kernel.Vector3DDerivKey___ge__(self, o)
4071 def __le__(self, o):
4072 r"""__le__(Vector3DDerivKey self, Vector3DDerivKey o) -> bool"""
4073 return _IMP_kernel.Vector3DDerivKey___le__(self, o)
4076 r"""__hash__(Vector3DDerivKey self) -> std::size_t"""
4077 return _IMP_kernel.Vector3DDerivKey___hash__(self)
4079 def show(self, *args):
4080 r"""show(Vector3DDerivKey self, _ostream out=std::cout)"""
4081 return _IMP_kernel.Vector3DDerivKey_show(self, *args)
4084 def add_alias(old_key, new_name):
4085 r"""add_alias(Vector3DDerivKey old_key, std::string new_name) -> Vector3DDerivKey"""
4086 return _IMP_kernel.Vector3DDerivKey_add_alias(old_key, new_name)
4089 def get_number_of_keys():
4090 r"""get_number_of_keys() -> unsigned int"""
4091 return _IMP_kernel.Vector3DDerivKey_get_number_of_keys()
4094 r"""get_index(Vector3DDerivKey self) -> unsigned int"""
4095 return _IMP_kernel.Vector3DDerivKey_get_index(self)
4099 r"""show_all(_ostream out)"""
4100 return _IMP_kernel.Vector3DDerivKey_show_all(out)
4103 def get_all_strings():
4104 r"""get_all_strings() -> IMP::Vector< std::string >"""
4105 return _IMP_kernel.Vector3DDerivKey_get_all_strings()
4108 def get_number_unique():
4109 r"""get_number_unique() -> unsigned int"""
4110 return _IMP_kernel.Vector3DDerivKey_get_number_unique()
4113 r"""__str__(Vector3DDerivKey self) -> std::string"""
4114 return _IMP_kernel.Vector3DDerivKey___str__(self)
4117 r"""__repr__(Vector3DDerivKey self) -> std::string"""
4118 return _IMP_kernel.Vector3DDerivKey___repr__(self)
4119 __swig_destroy__ = _IMP_kernel.delete_Vector3DDerivKey
4122 _IMP_kernel.Vector3DDerivKey_swigregister(Vector3DDerivKey)
4124 r"""Proxy of C++ IMP::Key< 18 > class."""
4126 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4128 def __init__(self, *args):
4130 __init__(Vector4DKey self) -> Vector4DKey
4131 __init__(Vector4DKey self, std::string const & c, bool is_implicit_add_permitted=True) -> Vector4DKey
4132 __init__(Vector4DKey self, unsigned int i) -> Vector4DKey
4134 _IMP_kernel.Vector4DKey_swiginit(self, _IMP_kernel.new_Vector4DKey(*args))
4138 r"""add_key(std::string sc) -> unsigned int"""
4139 return _IMP_kernel.Vector4DKey_add_key(sc)
4142 def get_key_exists(sc):
4143 r"""get_key_exists(std::string sc) -> bool"""
4144 return _IMP_kernel.Vector4DKey_get_key_exists(sc)
4146 def get_string(self):
4147 r"""get_string(Vector4DKey self) -> std::string const"""
4148 return _IMP_kernel.Vector4DKey_get_string(self)
4150 def __cmp__(self, o):
4151 r"""__cmp__(Vector4DKey self, Vector4DKey o) -> int"""
4152 return _IMP_kernel.Vector4DKey___cmp__(self, o)
4154 def __eq__(self, o):
4155 r"""__eq__(Vector4DKey self, Vector4DKey o) -> bool"""
4156 return _IMP_kernel.Vector4DKey___eq__(self, o)
4158 def __ne__(self, o):
4159 r"""__ne__(Vector4DKey self, Vector4DKey o) -> bool"""
4160 return _IMP_kernel.Vector4DKey___ne__(self, o)
4162 def __lt__(self, o):
4163 r"""__lt__(Vector4DKey self, Vector4DKey o) -> bool"""
4164 return _IMP_kernel.Vector4DKey___lt__(self, o)
4166 def __gt__(self, o):
4167 r"""__gt__(Vector4DKey self, Vector4DKey o) -> bool"""
4168 return _IMP_kernel.Vector4DKey___gt__(self, o)
4170 def __ge__(self, o):
4171 r"""__ge__(Vector4DKey self, Vector4DKey o) -> bool"""
4172 return _IMP_kernel.Vector4DKey___ge__(self, o)
4174 def __le__(self, o):
4175 r"""__le__(Vector4DKey self, Vector4DKey o) -> bool"""
4176 return _IMP_kernel.Vector4DKey___le__(self, o)
4179 r"""__hash__(Vector4DKey self) -> std::size_t"""
4180 return _IMP_kernel.Vector4DKey___hash__(self)
4182 def show(self, *args):
4183 r"""show(Vector4DKey self, _ostream out=std::cout)"""
4184 return _IMP_kernel.Vector4DKey_show(self, *args)
4187 def add_alias(old_key, new_name):
4188 r"""add_alias(Vector4DKey old_key, std::string new_name) -> Vector4DKey"""
4189 return _IMP_kernel.Vector4DKey_add_alias(old_key, new_name)
4192 def get_number_of_keys():
4193 r"""get_number_of_keys() -> unsigned int"""
4194 return _IMP_kernel.Vector4DKey_get_number_of_keys()
4197 r"""get_index(Vector4DKey self) -> unsigned int"""
4198 return _IMP_kernel.Vector4DKey_get_index(self)
4202 r"""show_all(_ostream out)"""
4203 return _IMP_kernel.Vector4DKey_show_all(out)
4206 def get_all_strings():
4207 r"""get_all_strings() -> IMP::Vector< std::string >"""
4208 return _IMP_kernel.Vector4DKey_get_all_strings()
4211 def get_number_unique():
4212 r"""get_number_unique() -> unsigned int"""
4213 return _IMP_kernel.Vector4DKey_get_number_unique()
4216 r"""__str__(Vector4DKey self) -> std::string"""
4217 return _IMP_kernel.Vector4DKey___str__(self)
4220 r"""__repr__(Vector4DKey self) -> std::string"""
4221 return _IMP_kernel.Vector4DKey___repr__(self)
4222 __swig_destroy__ = _IMP_kernel.delete_Vector4DKey
4225 _IMP_kernel.Vector4DKey_swigregister(Vector4DKey)
4227 r"""Proxy of C++ IMP::Key< 19 > class."""
4229 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4231 def __init__(self, *args):
4233 __init__(Vector4DDerivKey self) -> Vector4DDerivKey
4234 __init__(Vector4DDerivKey self, std::string const & c, bool is_implicit_add_permitted=True) -> Vector4DDerivKey
4235 __init__(Vector4DDerivKey self, unsigned int i) -> Vector4DDerivKey
4237 _IMP_kernel.Vector4DDerivKey_swiginit(self, _IMP_kernel.new_Vector4DDerivKey(*args))
4241 r"""add_key(std::string sc) -> unsigned int"""
4242 return _IMP_kernel.Vector4DDerivKey_add_key(sc)
4245 def get_key_exists(sc):
4246 r"""get_key_exists(std::string 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 __cmp__(self, o):
4254 r"""__cmp__(Vector4DDerivKey self, Vector4DDerivKey o) -> int"""
4255 return _IMP_kernel.Vector4DDerivKey___cmp__(self, o)
4257 def __eq__(self, o):
4258 r"""__eq__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4259 return _IMP_kernel.Vector4DDerivKey___eq__(self, o)
4261 def __ne__(self, o):
4262 r"""__ne__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4263 return _IMP_kernel.Vector4DDerivKey___ne__(self, o)
4265 def __lt__(self, o):
4266 r"""__lt__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4267 return _IMP_kernel.Vector4DDerivKey___lt__(self, o)
4269 def __gt__(self, o):
4270 r"""__gt__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4271 return _IMP_kernel.Vector4DDerivKey___gt__(self, o)
4273 def __ge__(self, o):
4274 r"""__ge__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4275 return _IMP_kernel.Vector4DDerivKey___ge__(self, o)
4277 def __le__(self, o):
4278 r"""__le__(Vector4DDerivKey self, Vector4DDerivKey o) -> bool"""
4279 return _IMP_kernel.Vector4DDerivKey___le__(self, o)
4282 r"""__hash__(Vector4DDerivKey self) -> std::size_t"""
4283 return _IMP_kernel.Vector4DDerivKey___hash__(self)
4285 def show(self, *args):
4286 r"""show(Vector4DDerivKey self, _ostream out=std::cout)"""
4287 return _IMP_kernel.Vector4DDerivKey_show(self, *args)
4290 def add_alias(old_key, new_name):
4291 r"""add_alias(Vector4DDerivKey old_key, std::string new_name) -> Vector4DDerivKey"""
4292 return _IMP_kernel.Vector4DDerivKey_add_alias(old_key, new_name)
4295 def get_number_of_keys():
4296 r"""get_number_of_keys() -> unsigned int"""
4297 return _IMP_kernel.Vector4DDerivKey_get_number_of_keys()
4300 r"""get_index(Vector4DDerivKey self) -> unsigned int"""
4301 return _IMP_kernel.Vector4DDerivKey_get_index(self)
4305 r"""show_all(_ostream out)"""
4306 return _IMP_kernel.Vector4DDerivKey_show_all(out)
4309 def get_all_strings():
4310 r"""get_all_strings() -> IMP::Vector< std::string >"""
4311 return _IMP_kernel.Vector4DDerivKey_get_all_strings()
4314 def get_number_unique():
4315 r"""get_number_unique() -> unsigned int"""
4316 return _IMP_kernel.Vector4DDerivKey_get_number_unique()
4319 r"""__str__(Vector4DDerivKey self) -> std::string"""
4320 return _IMP_kernel.Vector4DDerivKey___str__(self)
4323 r"""__repr__(Vector4DDerivKey self) -> std::string"""
4324 return _IMP_kernel.Vector4DDerivKey___repr__(self)
4325 __swig_destroy__ = _IMP_kernel.delete_Vector4DDerivKey
4328 _IMP_kernel.Vector4DDerivKey_swigregister(Vector4DDerivKey)
4337 class FloatIndex(_Value):
4338 r"""Proxy of C++ IMP::FloatIndex class."""
4340 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4342 def __init__(self, *args):
4344 __init__(FloatIndex self, ParticleIndex pi, FloatKey k) -> FloatIndex
4345 __init__(FloatIndex self, ParticleIndex pi, Vector3DDerivKey k, int index) -> FloatIndex
4346 __init__(FloatIndex self, ParticleIndex pi, Vector4DDerivKey k, int index) -> FloatIndex
4348 _IMP_kernel.FloatIndex_swiginit(self, _IMP_kernel.new_FloatIndex(*args))
4350 def get_float_key(self):
4351 r"""get_float_key(FloatIndex self) -> FloatKey"""
4352 return _IMP_kernel.FloatIndex_get_float_key(self)
4354 def set_value(self, m, v):
4355 r"""set_value(FloatIndex self, Model m, IMP::Float v)"""
4356 return _IMP_kernel.FloatIndex_set_value(self, m, v)
4358 def get_value(self, m):
4359 r"""get_value(FloatIndex self, Model m) -> IMP::Float"""
4360 return _IMP_kernel.FloatIndex_get_value(self, m)
4362 def get_derivative(self, m):
4363 r"""get_derivative(FloatIndex self, Model m) -> IMP::Float"""
4364 return _IMP_kernel.FloatIndex_get_derivative(self, m)
4366 def show(self, *args):
4367 r"""show(FloatIndex self, _ostream out=std::cout)"""
4368 return _IMP_kernel.FloatIndex_show(self, *args)
4371 r"""__str__(FloatIndex self) -> std::string"""
4372 return _IMP_kernel.FloatIndex___str__(self)
4375 r"""__repr__(FloatIndex self) -> std::string"""
4376 return _IMP_kernel.FloatIndex___repr__(self)
4377 __swig_destroy__ = _IMP_kernel.delete_FloatIndex
4380 _IMP_kernel.FloatIndex_swigregister(FloatIndex)
4381 class _ParticleIndexTag(object):
4382 r"""Proxy of C++ IMP::ParticleIndexTag class."""
4384 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4385 __repr__ = _swig_repr
4388 r"""__init__(_ParticleIndexTag self) -> _ParticleIndexTag"""
4389 _IMP_kernel._ParticleIndexTag_swiginit(self, _IMP_kernel.new__ParticleIndexTag())
4390 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexTag
4393 _IMP_kernel._ParticleIndexTag_swigregister(_ParticleIndexTag)
4394 class ModelObject(
Object):
4395 r"""Proxy of C++ IMP::ModelObject class."""
4397 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4399 def __init__(self, *args):
4401 __init__(ModelObject self, Model m, std::string name) -> ModelObject
4402 __init__(ModelObject self) -> ModelObject
4404 if self.__class__ == ModelObject:
4408 _IMP_kernel.ModelObject_swiginit(self, _IMP_kernel.new_ModelObject(_self, *args))
4410 if self.__class__ != ModelObject:
4411 _director_objects.register(self)
4415 __swig_destroy__ = _IMP_kernel.delete_ModelObject
4417 def get_model(self):
4418 m = _IMP_kernel.ModelObject_get_model(self)
4419 if m
in _models_set:
4420 m = _models_set_get(m)
4425 def get_inputs(self):
4426 r"""get_inputs(ModelObject self) -> IMP::ModelObjectsTemp"""
4427 return _IMP_kernel.ModelObject_get_inputs(self)
4429 def get_outputs(self):
4430 r"""get_outputs(ModelObject self) -> IMP::ModelObjectsTemp"""
4431 return _IMP_kernel.ModelObject_get_outputs(self)
4433 def get_interactions(self):
4434 r"""get_interactions(ModelObject self) -> IMP::ModelObjectsTemps"""
4435 return _IMP_kernel.ModelObject_get_interactions(self)
4437 def get_has_dependencies(self):
4438 r"""get_has_dependencies(ModelObject self) -> bool"""
4439 return _IMP_kernel.ModelObject_get_has_dependencies(self)
4441 def set_has_dependencies(self, tf):
4442 r"""set_has_dependencies(ModelObject self, bool tf)"""
4443 return _IMP_kernel.ModelObject_set_has_dependencies(self, tf)
4445 def set_has_required_score_states(self, tf):
4446 r"""set_has_required_score_states(ModelObject self, bool tf)"""
4447 return _IMP_kernel.ModelObject_set_has_required_score_states(self, tf)
4449 def get_has_required_score_states(self):
4450 r"""get_has_required_score_states(ModelObject self) -> bool"""
4451 return _IMP_kernel.ModelObject_get_has_required_score_states(self)
4453 def get_required_score_states(self):
4454 r"""get_required_score_states(ModelObject self) -> IMP::ScoreStatesTemp const &"""
4455 return _IMP_kernel.ModelObject_get_required_score_states(self)
4457 def handle_set_has_required_score_states(self, arg0):
4458 r"""handle_set_has_required_score_states(ModelObject self, bool arg0)"""
4459 return _IMP_kernel.ModelObject_handle_set_has_required_score_states(self, arg0)
4461 def do_get_inputs(self):
4462 r"""do_get_inputs(ModelObject self) -> IMP::ModelObjectsTemp"""
4463 return _IMP_kernel.ModelObject_do_get_inputs(self)
4465 def do_get_outputs(self):
4466 r"""do_get_outputs(ModelObject self) -> IMP::ModelObjectsTemp"""
4467 return _IMP_kernel.ModelObject_do_get_outputs(self)
4469 def do_get_interactions(self):
4470 r"""do_get_interactions(ModelObject self) -> IMP::ModelObjectsTemps"""
4471 return _IMP_kernel.ModelObject_do_get_interactions(self)
4474 r"""__str__(ModelObject self) -> std::string"""
4475 return _IMP_kernel.ModelObject___str__(self)
4478 r"""__repr__(ModelObject self) -> std::string"""
4479 return _IMP_kernel.ModelObject___repr__(self)
4483 return _object_cast_to_ModelObject(o)
4486 def do_show(self, out):
4491 return _object_cast_to_ModelObject(o)
4493 def __disown__(self):
4495 _IMP_kernel.disown_ModelObject(self)
4496 return weakref.proxy(self)
4499 r"""do_destroy(ModelObject self)"""
4500 return _IMP_kernel.ModelObject_do_destroy(self)
4503 _IMP_kernel.ModelObject_swigregister(ModelObject)
4504 cvar = _IMP_kernel.cvar
4505 NO_MAX = cvar.NO_MAX
4506 BAD_SCORE = cvar.BAD_SCORE
4508 class _ParticleInputs(object):
4509 r"""Proxy of C++ IMP::ParticleInputs class."""
4511 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4513 def __init__(self, *args, **kwargs):
4514 raise AttributeError(
"No constructor defined - class is abstract")
4515 __repr__ = _swig_repr
4517 def get_inputs(self, m, pis):
4518 r"""get_inputs(_ParticleInputs self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4519 return _IMP_kernel._ParticleInputs_get_inputs(self, m, pis)
4522 _IMP_kernel._ParticleInputs_swigregister(_ParticleInputs)
4523 class _ParticleOutputs(object):
4524 r"""Proxy of C++ IMP::ParticleOutputs class."""
4526 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4528 def __init__(self, *args, **kwargs):
4529 raise AttributeError(
"No constructor defined - class is abstract")
4530 __repr__ = _swig_repr
4532 def get_outputs(self, m, pis):
4533 r"""get_outputs(_ParticleOutputs self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4534 return _IMP_kernel._ParticleOutputs_get_outputs(self, m, pis)
4537 _IMP_kernel._ParticleOutputs_swigregister(_ParticleOutputs)
4540 r"""get_input_particles(IMP::ModelObjectsTemp const & mos) -> IMP::ParticlesTemp"""
4541 return _IMP_kernel.get_input_particles(mos)
4544 r"""get_input_containers(IMP::ModelObjectsTemp const & mos) -> IMP::ContainersTemp"""
4545 return _IMP_kernel.get_input_containers(mos)
4548 r"""get_output_particles(IMP::ModelObjectsTemp const & mos) -> IMP::ParticlesTemp"""
4549 return _IMP_kernel.get_output_particles(mos)
4552 r"""get_output_containers(IMP::ModelObjectsTemp const & mos) -> IMP::ContainersTemp"""
4553 return _IMP_kernel.get_output_containers(mos)
4556 _plural_types.append(
"Vector1Ds")
4557 _value_types.append(
"Vector1D")
4561 _plural_types.append(
"Vector2Ds")
4562 _value_types.append(
"Vector2D")
4566 _plural_types.append(
"Vector3Ds")
4567 _value_types.append(
"Vector3D")
4571 _plural_types.append(
"Vector4Ds")
4572 _value_types.append(
"Vector4D")
4576 _plural_types.append(
"Vector5Ds")
4577 _value_types.append(
"Vector5D")
4581 _plural_types.append(
"Vector6Ds")
4582 _value_types.append(
"Vector6D")
4586 _plural_types.append(
"Vector1Ds")
4587 _value_types.append(
"VectorD<1>")
4591 _plural_types.append(
"Vector2Ds")
4592 _value_types.append(
"VectorD<2>")
4596 _plural_types.append(
"Vector3Ds")
4597 _value_types.append(
"VectorD<3>")
4601 _plural_types.append(
"Vector4Ds")
4602 _value_types.append(
"VectorD<4>")
4606 _plural_types.append(
"Vector5Ds")
4607 _value_types.append(
"VectorD<5>")
4611 _plural_types.append(
"Vector6Ds")
4612 _value_types.append(
"VectorD<6>")
4616 _plural_types.append(
"VectorKDs")
4617 _value_types.append(
"VectorKD")
4621 _plural_types.append(
"VectorKDs")
4622 _value_types.append(
"VectorD<-1>")
4626 r"""get_basis_vector_kd(int D, unsigned int coordinate) -> VectorKD"""
4627 return _IMP_kernel.get_basis_vector_kd(D, coordinate)
4630 r"""get_zero_vector_kd(int D) -> VectorKD"""
4631 return _IMP_kernel.get_zero_vector_kd(D)
4634 r"""get_ones_vector_kd(unsigned int D, double v=1) -> VectorKD"""
4635 return _IMP_kernel.get_ones_vector_kd(D, v)
4638 r"""get_vector_product(Vector3D p1, Vector3D p2) -> Vector3D"""
4639 return _IMP_kernel.get_vector_product(p1, p2)
4642 r"""get_orthogonal_vector(Vector3D v) -> Vector3D"""
4643 return _IMP_kernel.get_orthogonal_vector(v)
4646 r"""get_centroid(IMP::Vector3Ds const & ps) -> Vector3D"""
4647 return _IMP_kernel.get_centroid(ps)
4650 r"""get_radius_of_gyration(IMP::Vector3Ds const & ps) -> double"""
4651 return _IMP_kernel.get_radius_of_gyration(ps)
4652 class DerivativeAccumulator(object):
4653 r"""Proxy of C++ IMP::DerivativeAccumulator class."""
4655 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4656 __repr__ = _swig_repr
4658 def __init__(self, *args):
4660 __init__(DerivativeAccumulator self, DerivativeAccumulator arg2) -> DerivativeAccumulator
4661 __init__(DerivativeAccumulator self, double weight=1.0) -> DerivativeAccumulator
4662 __init__(DerivativeAccumulator self, DerivativeAccumulator copy, double weight) -> DerivativeAccumulator
4664 _IMP_kernel.DerivativeAccumulator_swiginit(self, _IMP_kernel.new_DerivativeAccumulator(*args))
4666 def __call__(self, *args):
4668 __call__(DerivativeAccumulator self, double const value) -> double
4669 __call__(DerivativeAccumulator self, Vector3D value) -> Vector3D
4670 __call__(DerivativeAccumulator self, Vector4D value) -> Vector4D
4672 return _IMP_kernel.DerivativeAccumulator___call__(self, *args)
4674 def get_weight(self):
4675 r"""get_weight(DerivativeAccumulator self) -> double"""
4676 return _IMP_kernel.DerivativeAccumulator_get_weight(self)
4678 def show(self, *args):
4679 r"""show(DerivativeAccumulator self, _ostream out=std::cout)"""
4680 return _IMP_kernel.DerivativeAccumulator_show(self, *args)
4681 __swig_destroy__ = _IMP_kernel.delete_DerivativeAccumulator
4684 _IMP_kernel.DerivativeAccumulator_swigregister(DerivativeAccumulator)
4685 class EvaluationState(object):
4686 r"""Proxy of C++ IMP::EvaluationState class."""
4688 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4689 score = property(_IMP_kernel.EvaluationState_score_get, _IMP_kernel.EvaluationState_score_set, doc=
r"""score : double""")
4690 good = property(_IMP_kernel.EvaluationState_good_get, _IMP_kernel.EvaluationState_good_set, doc=
r"""good : bool""")
4692 def __init__(self, *args):
4694 __init__(EvaluationState self, double oscore, bool ogood) -> EvaluationState
4695 __init__(EvaluationState self) -> EvaluationState
4697 _IMP_kernel.EvaluationState_swiginit(self, _IMP_kernel.new_EvaluationState(*args))
4699 def show(self, *args):
4700 r"""show(EvaluationState self, _ostream out=std::cout)"""
4701 return _IMP_kernel.EvaluationState_show(self, *args)
4704 r"""__str__(EvaluationState self) -> std::string"""
4705 return _IMP_kernel.EvaluationState___str__(self)
4708 r"""__repr__(EvaluationState self) -> std::string"""
4709 return _IMP_kernel.EvaluationState___repr__(self)
4710 __swig_destroy__ = _IMP_kernel.delete_EvaluationState
4713 _IMP_kernel.EvaluationState_swigregister(EvaluationState)
4714 class ScoreAccumulator(_Value):
4715 r"""Proxy of C++ IMP::ScoreAccumulator class."""
4717 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4719 def __init__(self, *args):
4721 __init__(ScoreAccumulator self, ScoreAccumulator arg2) -> ScoreAccumulator
4722 __init__(ScoreAccumulator self) -> ScoreAccumulator
4723 __init__(ScoreAccumulator self, ScoreAccumulator o, Restraint r) -> ScoreAccumulator
4724 __init__(ScoreAccumulator self, ScoreAccumulator o, double weight, double local_max) -> ScoreAccumulator
4726 _IMP_kernel.ScoreAccumulator_swiginit(self, _IMP_kernel.new_ScoreAccumulator(*args))
4728 def add_score(self, score):
4729 r"""add_score(ScoreAccumulator self, double score)"""
4730 return _IMP_kernel.ScoreAccumulator_add_score(self, score)
4732 def get_abort_evaluation(self):
4733 r"""get_abort_evaluation(ScoreAccumulator self) -> bool"""
4734 return _IMP_kernel.ScoreAccumulator_get_abort_evaluation(self)
4736 def get_is_evaluate_if_below(self):
4737 r"""get_is_evaluate_if_below(ScoreAccumulator self) -> bool"""
4738 return _IMP_kernel.ScoreAccumulator_get_is_evaluate_if_below(self)
4740 def get_is_evaluate_if_good(self):
4741 r"""get_is_evaluate_if_good(ScoreAccumulator self) -> bool"""
4742 return _IMP_kernel.ScoreAccumulator_get_is_evaluate_if_good(self)
4744 def get_maximum(self):
4745 r"""get_maximum(ScoreAccumulator self) -> double"""
4746 return _IMP_kernel.ScoreAccumulator_get_maximum(self)
4748 def get_derivative_accumulator(self):
4749 r"""get_derivative_accumulator(ScoreAccumulator self) -> DerivativeAccumulator"""
4750 return _IMP_kernel.ScoreAccumulator_get_derivative_accumulator(self)
4752 def show(self, *args):
4753 r"""show(ScoreAccumulator self, _ostream out=std::cout)"""
4754 return _IMP_kernel.ScoreAccumulator_show(self, *args)
4757 r"""__str__(ScoreAccumulator self) -> std::string"""
4758 return _IMP_kernel.ScoreAccumulator___str__(self)
4761 r"""__repr__(ScoreAccumulator self) -> std::string"""
4762 return _IMP_kernel.ScoreAccumulator___repr__(self)
4763 __swig_destroy__ = _IMP_kernel.delete_ScoreAccumulator
4766 _IMP_kernel.ScoreAccumulator_swigregister(ScoreAccumulator)
4767 class ScoreState(ModelObject):
4768 r"""Proxy of C++ IMP::ScoreState class."""
4770 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4772 def set_can_skip(self, can_skip):
4773 r"""set_can_skip(ScoreState self, bool can_skip)"""
4774 return _IMP_kernel.ScoreState_set_can_skip(self, can_skip)
4776 def __init__(self, *args):
4778 __init__(ScoreState self, Model m, std::string name) -> ScoreState
4779 __init__(ScoreState self) -> ScoreState
4781 if self.__class__ == ScoreState:
4785 _IMP_kernel.ScoreState_swiginit(self, _IMP_kernel.new_ScoreState(_self, *args))
4787 if self.__class__ != ScoreState:
4788 _director_objects.register(self)
4793 def before_evaluate(self):
4794 r"""before_evaluate(ScoreState self)"""
4795 return _IMP_kernel.ScoreState_before_evaluate(self)
4797 def after_evaluate(self, accpt):
4798 r"""after_evaluate(ScoreState self, DerivativeAccumulator accpt)"""
4799 return _IMP_kernel.ScoreState_after_evaluate(self, accpt)
4801 def get_can_skip(self):
4802 r"""get_can_skip(ScoreState self) -> bool"""
4803 return _IMP_kernel.ScoreState_get_can_skip(self)
4805 def get_has_update_order(self):
4806 r"""get_has_update_order(ScoreState self) -> bool"""
4807 return _IMP_kernel.ScoreState_get_has_update_order(self)
4810 r"""get_update_order(ScoreState self) -> unsigned int"""
4811 return _IMP_kernel.ScoreState_get_update_order(self)
4813 def handle_set_has_required_score_states(self, tf):
4814 r"""handle_set_has_required_score_states(ScoreState self, bool tf)"""
4815 return _IMP_kernel.ScoreState_handle_set_has_required_score_states(self, tf)
4817 def do_before_evaluate(self):
4818 r"""do_before_evaluate(ScoreState self)"""
4819 return _IMP_kernel.ScoreState_do_before_evaluate(self)
4821 def do_after_evaluate(self, accpt):
4822 r"""do_after_evaluate(ScoreState self, DerivativeAccumulator accpt)"""
4823 return _IMP_kernel.ScoreState_do_after_evaluate(self, accpt)
4824 __swig_destroy__ = _IMP_kernel.delete_ScoreState
4827 r"""__str__(ScoreState self) -> std::string"""
4828 return _IMP_kernel.ScoreState___str__(self)
4831 r"""__repr__(ScoreState self) -> std::string"""
4832 return _IMP_kernel.ScoreState___repr__(self)
4836 return _object_cast_to_ScoreState(o)
4839 def do_show(self, out):
4844 return _object_cast_to_ScoreState(o)
4847 def _wrap_jax(self, apply_func, keys=None):
4848 """Create the return value for _get_jax.
4849 Use this method in _get_jax() to wrap the JAX apply function
4850 with other model- and ScoreState-specific information.
4852 @param apply_func A function implemented using JAX that takes
4853 a single argument (the current JAX Model) and returns
4854 a new JAX Model with the ScoreState's transformation
4856 @param keys If given, a set of IMP::Key objects describing Model
4857 attributes (other than xyz and radius) that the ScoreState
4860 from IMP._jax_util
import JAXScoreStateInfo
4861 return JAXScoreStateInfo(m=self.get_model(), apply_func=apply_func,
4865 """Return a JAX implementation of this ScoreState.
4866 Implement this method in a ScoreState subclass to provide
4867 an equivalent function using [JAX](https://docs.jax.dev/)
4868 that modifies the JAX Model. See also _wrap_jax.
4870 raise NotImplementedError(
4871 f
"No JAX implementation for {self} ({type(self)})")
4873 def __disown__(self):
4875 _IMP_kernel.disown_ScoreState(self)
4876 return weakref.proxy(self)
4879 r"""do_destroy(ScoreState self)"""
4880 return _IMP_kernel.ScoreState_do_destroy(self)
4882 def do_get_inputs(self):
4883 r"""do_get_inputs(ScoreState self) -> IMP::ModelObjectsTemp"""
4884 return _IMP_kernel.ScoreState_do_get_inputs(self)
4886 def do_get_outputs(self):
4887 r"""do_get_outputs(ScoreState self) -> IMP::ModelObjectsTemp"""
4888 return _IMP_kernel.ScoreState_do_get_outputs(self)
4890 def do_get_interactions(self):
4891 r"""do_get_interactions(ScoreState self) -> IMP::ModelObjectsTemps"""
4892 return _IMP_kernel.ScoreState_do_get_interactions(self)
4895 _IMP_kernel.ScoreState_swigregister(ScoreState)
4898 r"""get_update_order(IMP::ScoreStatesTemp input) -> IMP::ScoreStatesTemp"""
4899 return _IMP_kernel.get_update_order(input)
4900 class Constraint(ScoreState):
4901 r"""Proxy of C++ IMP::Constraint class."""
4903 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4905 def __init__(self, *args):
4907 __init__(Constraint self, Model m, std::string name="Constraint %1%") -> Constraint
4908 __init__(Constraint self) -> Constraint
4910 if self.__class__ == Constraint:
4914 _IMP_kernel.Constraint_swiginit(self, _IMP_kernel.new_Constraint(_self, *args))
4916 if self.__class__ != Constraint:
4917 _director_objects.register(self)
4922 def do_update_attributes(self):
4923 r"""do_update_attributes(Constraint self)"""
4924 return _IMP_kernel.Constraint_do_update_attributes(self)
4926 def do_update_derivatives(self, da):
4927 r"""do_update_derivatives(Constraint self, DerivativeAccumulator da)"""
4928 return _IMP_kernel.Constraint_do_update_derivatives(self, da)
4930 def do_before_evaluate(self):
4931 r"""do_before_evaluate(Constraint self)"""
4932 return _IMP_kernel.Constraint_do_before_evaluate(self)
4934 def do_after_evaluate(self, da):
4935 r"""do_after_evaluate(Constraint self, DerivativeAccumulator da)"""
4936 return _IMP_kernel.Constraint_do_after_evaluate(self, da)
4937 __swig_destroy__ = _IMP_kernel.delete_Constraint
4940 r"""__str__(Constraint self) -> std::string"""
4941 return _IMP_kernel.Constraint___str__(self)
4944 r"""__repr__(Constraint self) -> std::string"""
4945 return _IMP_kernel.Constraint___repr__(self)
4949 return _object_cast_to_Constraint(o)
4952 def do_show(self, out):
4957 return _object_cast_to_Constraint(o)
4959 def __disown__(self):
4961 _IMP_kernel.disown_Constraint(self)
4962 return weakref.proxy(self)
4965 r"""do_destroy(Constraint self)"""
4966 return _IMP_kernel.Constraint_do_destroy(self)
4968 def do_get_inputs(self):
4969 r"""do_get_inputs(Constraint self) -> IMP::ModelObjectsTemp"""
4970 return _IMP_kernel.Constraint_do_get_inputs(self)
4972 def do_get_outputs(self):
4973 r"""do_get_outputs(Constraint self) -> IMP::ModelObjectsTemp"""
4974 return _IMP_kernel.Constraint_do_get_outputs(self)
4976 def do_get_interactions(self):
4977 r"""do_get_interactions(Constraint self) -> IMP::ModelObjectsTemps"""
4978 return _IMP_kernel.Constraint_do_get_interactions(self)
4981 _IMP_kernel.Constraint_swigregister(Constraint)
4982 class Container(ModelObject):
4983 r"""Proxy of C++ IMP::Container class."""
4985 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4987 def __init__(self, *args):
4989 __init__(Container self, Model m, std::string name="Container %1%") -> Container
4990 __init__(Container self) -> Container
4992 if self.__class__ == Container:
4996 _IMP_kernel.Container_swiginit(self, _IMP_kernel.new_Container(_self, *args))
4998 if self.__class__ != Container:
4999 _director_objects.register(self)
5004 def do_get_contents_hash(self):
5005 r"""do_get_contents_hash(Container self) -> std::size_t"""
5006 return _IMP_kernel.Container_do_get_contents_hash(self)
5008 def get_all_possible_indexes(self):
5009 r"""get_all_possible_indexes(Container self) -> IMP::ParticleIndexes"""
5010 return _IMP_kernel.Container_get_all_possible_indexes(self)
5012 def get_contents_hash(self):
5013 r"""get_contents_hash(Container self) -> std::size_t"""
5014 return _IMP_kernel.Container_get_contents_hash(self)
5016 def do_get_outputs(self):
5017 r"""do_get_outputs(Container self) -> IMP::ModelObjectsTemp"""
5018 return _IMP_kernel.Container_do_get_outputs(self)
5020 def get_is_decomposable(self):
5021 r"""get_is_decomposable(Container self) -> bool"""
5022 return _IMP_kernel.Container_get_is_decomposable(self)
5024 def validate_readable(self):
5025 r"""validate_readable(Container self)"""
5026 return _IMP_kernel.Container_validate_readable(self)
5028 def validate_writable(self):
5029 r"""validate_writable(Container self)"""
5030 return _IMP_kernel.Container_validate_writable(self)
5032 def set_is_readable(self, tf):
5033 r"""set_is_readable(Container self, bool tf)"""
5034 return _IMP_kernel.Container_set_is_readable(self, tf)
5036 def set_is_writable(self, tf):
5037 r"""set_is_writable(Container self, bool tf)"""
5038 return _IMP_kernel.Container_set_is_writable(self, tf)
5039 __swig_destroy__ = _IMP_kernel.delete_Container
5042 r"""__str__(Container self) -> std::string"""
5043 return _IMP_kernel.Container___str__(self)
5046 r"""__repr__(Container self) -> std::string"""
5047 return _IMP_kernel.Container___repr__(self)
5051 return _object_cast_to_Container(o)
5054 def do_show(self, out):
5059 return _object_cast_to_Container(o)
5061 def __disown__(self):
5063 _IMP_kernel.disown_Container(self)
5064 return weakref.proxy(self)
5067 r"""do_destroy(Container self)"""
5068 return _IMP_kernel.Container_do_destroy(self)
5070 def handle_set_has_required_score_states(self, arg0):
5071 r"""handle_set_has_required_score_states(Container self, bool arg0)"""
5072 return _IMP_kernel.Container_handle_set_has_required_score_states(self, arg0)
5074 def do_get_inputs(self):
5075 r"""do_get_inputs(Container self) -> IMP::ModelObjectsTemp"""
5076 return _IMP_kernel.Container_do_get_inputs(self)
5078 def do_get_interactions(self):
5079 r"""do_get_interactions(Container self) -> IMP::ModelObjectsTemps"""
5080 return _IMP_kernel.Container_do_get_interactions(self)
5083 _IMP_kernel.Container_swigregister(Container)
5084 class RestraintInfo(
Object):
5085 r"""Proxy of C++ IMP::RestraintInfo class."""
5087 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5089 def __init__(self, *args):
5090 r"""__init__(RestraintInfo self, std::string name="RestraintInfo %1%") -> RestraintInfo"""
5091 _IMP_kernel.RestraintInfo_swiginit(self, _IMP_kernel.new_RestraintInfo(*args))
5094 r"""clear(RestraintInfo self)"""
5095 return _IMP_kernel.RestraintInfo_clear(self)
5097 def add_int(self, key, value):
5098 r"""add_int(RestraintInfo self, std::string key, int value)"""
5099 return _IMP_kernel.RestraintInfo_add_int(self, key, value)
5101 def get_number_of_int(self):
5102 r"""get_number_of_int(RestraintInfo self) -> unsigned int"""
5103 return _IMP_kernel.RestraintInfo_get_number_of_int(self)
5105 def get_int_key(self, i):
5106 r"""get_int_key(RestraintInfo self, unsigned int i) -> std::string"""
5107 return _IMP_kernel.RestraintInfo_get_int_key(self, i)
5109 def get_int_value(self, i):
5110 r"""get_int_value(RestraintInfo self, unsigned int i) -> int"""
5111 return _IMP_kernel.RestraintInfo_get_int_value(self, i)
5113 def add_float(self, key, value):
5114 r"""add_float(RestraintInfo self, std::string key, double value)"""
5115 return _IMP_kernel.RestraintInfo_add_float(self, key, value)
5117 def get_number_of_float(self):
5118 r"""get_number_of_float(RestraintInfo self) -> unsigned int"""
5119 return _IMP_kernel.RestraintInfo_get_number_of_float(self)
5121 def get_float_key(self, i):
5122 r"""get_float_key(RestraintInfo self, unsigned int i) -> std::string"""
5123 return _IMP_kernel.RestraintInfo_get_float_key(self, i)
5125 def get_float_value(self, i):
5126 r"""get_float_value(RestraintInfo self, unsigned int i) -> double"""
5127 return _IMP_kernel.RestraintInfo_get_float_value(self, i)
5129 def add_string(self, key, value):
5130 r"""add_string(RestraintInfo self, std::string key, std::string value)"""
5131 return _IMP_kernel.RestraintInfo_add_string(self, key, value)
5133 def get_number_of_string(self):
5134 r"""get_number_of_string(RestraintInfo self) -> unsigned int"""
5135 return _IMP_kernel.RestraintInfo_get_number_of_string(self)
5137 def get_string_key(self, i):
5138 r"""get_string_key(RestraintInfo self, unsigned int i) -> std::string"""
5139 return _IMP_kernel.RestraintInfo_get_string_key(self, i)
5141 def get_string_value(self, i):
5142 r"""get_string_value(RestraintInfo self, unsigned int i) -> std::string"""
5143 return _IMP_kernel.RestraintInfo_get_string_value(self, i)
5145 def add_filename(self, key, value):
5146 r"""add_filename(RestraintInfo self, std::string key, std::string value)"""
5147 return _IMP_kernel.RestraintInfo_add_filename(self, key, value)
5149 def get_number_of_filename(self):
5150 r"""get_number_of_filename(RestraintInfo self) -> unsigned int"""
5151 return _IMP_kernel.RestraintInfo_get_number_of_filename(self)
5153 def get_filename_key(self, i):
5154 r"""get_filename_key(RestraintInfo self, unsigned int i) -> std::string"""
5155 return _IMP_kernel.RestraintInfo_get_filename_key(self, i)
5157 def get_filename_value(self, i):
5158 r"""get_filename_value(RestraintInfo self, unsigned int i) -> std::string"""
5159 return _IMP_kernel.RestraintInfo_get_filename_value(self, i)
5161 def add_floats(self, key, value):
5162 r"""add_floats(RestraintInfo self, std::string key, IMP::Floats value)"""
5163 return _IMP_kernel.RestraintInfo_add_floats(self, key, value)
5165 def get_number_of_floats(self):
5166 r"""get_number_of_floats(RestraintInfo self) -> unsigned int"""
5167 return _IMP_kernel.RestraintInfo_get_number_of_floats(self)
5169 def get_floats_key(self, i):
5170 r"""get_floats_key(RestraintInfo self, unsigned int i) -> std::string"""
5171 return _IMP_kernel.RestraintInfo_get_floats_key(self, i)
5173 def get_floats_value(self, i):
5174 r"""get_floats_value(RestraintInfo self, unsigned int i) -> IMP::Floats"""
5175 return _IMP_kernel.RestraintInfo_get_floats_value(self, i)
5177 def add_ints(self, key, value):
5178 r"""add_ints(RestraintInfo self, std::string key, IMP::Ints value)"""
5179 return _IMP_kernel.RestraintInfo_add_ints(self, key, value)
5181 def get_number_of_ints(self):
5182 r"""get_number_of_ints(RestraintInfo self) -> unsigned int"""
5183 return _IMP_kernel.RestraintInfo_get_number_of_ints(self)
5185 def get_ints_key(self, i):
5186 r"""get_ints_key(RestraintInfo self, unsigned int i) -> std::string"""
5187 return _IMP_kernel.RestraintInfo_get_ints_key(self, i)
5189 def get_ints_value(self, i):
5190 r"""get_ints_value(RestraintInfo self, unsigned int i) -> IMP::Ints"""
5191 return _IMP_kernel.RestraintInfo_get_ints_value(self, i)
5193 def add_strings(self, key, value):
5194 r"""add_strings(RestraintInfo self, std::string key, IMP::Strings value)"""
5195 return _IMP_kernel.RestraintInfo_add_strings(self, key, value)
5197 def get_number_of_strings(self):
5198 r"""get_number_of_strings(RestraintInfo self) -> unsigned int"""
5199 return _IMP_kernel.RestraintInfo_get_number_of_strings(self)
5201 def get_strings_key(self, i):
5202 r"""get_strings_key(RestraintInfo self, unsigned int i) -> std::string"""
5203 return _IMP_kernel.RestraintInfo_get_strings_key(self, i)
5205 def get_strings_value(self, i):
5206 r"""get_strings_value(RestraintInfo self, unsigned int i) -> IMP::Strings"""
5207 return _IMP_kernel.RestraintInfo_get_strings_value(self, i)
5209 def add_filenames(self, key, value):
5210 r"""add_filenames(RestraintInfo self, std::string key, IMP::Strings value)"""
5211 return _IMP_kernel.RestraintInfo_add_filenames(self, key, value)
5213 def get_number_of_filenames(self):
5214 r"""get_number_of_filenames(RestraintInfo self) -> unsigned int"""
5215 return _IMP_kernel.RestraintInfo_get_number_of_filenames(self)
5217 def get_filenames_key(self, i):
5218 r"""get_filenames_key(RestraintInfo self, unsigned int i) -> std::string"""
5219 return _IMP_kernel.RestraintInfo_get_filenames_key(self, i)
5221 def get_filenames_value(self, i):
5222 r"""get_filenames_value(RestraintInfo self, unsigned int i) -> IMP::Strings"""
5223 return _IMP_kernel.RestraintInfo_get_filenames_value(self, i)
5225 def add_particle_indexes(self, key, value):
5226 r"""add_particle_indexes(RestraintInfo self, std::string key, IMP::ParticleIndexes value)"""
5227 return _IMP_kernel.RestraintInfo_add_particle_indexes(self, key, value)
5229 def get_number_of_particle_indexes(self):
5230 r"""get_number_of_particle_indexes(RestraintInfo self) -> unsigned int"""
5231 return _IMP_kernel.RestraintInfo_get_number_of_particle_indexes(self)
5233 def get_particle_indexes_key(self, i):
5234 r"""get_particle_indexes_key(RestraintInfo self, unsigned int i) -> std::string"""
5235 return _IMP_kernel.RestraintInfo_get_particle_indexes_key(self, i)
5237 def get_particle_indexes_value(self, i):
5238 r"""get_particle_indexes_value(RestraintInfo self, unsigned int i) -> IMP::ParticleIndexes"""
5239 return _IMP_kernel.RestraintInfo_get_particle_indexes_value(self, i)
5242 r"""get_version_info(RestraintInfo self) -> VersionInfo"""
5243 return _IMP_kernel.RestraintInfo_get_version_info(self)
5244 __swig_destroy__ = _IMP_kernel.delete_RestraintInfo
5247 r"""__str__(RestraintInfo self) -> std::string"""
5248 return _IMP_kernel.RestraintInfo___str__(self)
5251 r"""__repr__(RestraintInfo self) -> std::string"""
5252 return _IMP_kernel.RestraintInfo___repr__(self)
5256 return _object_cast_to_RestraintInfo(o)
5260 _IMP_kernel.RestraintInfo_swigregister(RestraintInfo)
5261 class Restraint(ModelObject):
5262 r"""Proxy of C++ IMP::Restraint class."""
5264 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5266 def __init__(self, *args):
5268 __init__(Restraint self, Model m, std::string name) -> Restraint
5269 __init__(Restraint self) -> Restraint
5271 if self.__class__ == Restraint:
5275 _IMP_kernel.Restraint_swiginit(self, _IMP_kernel.new_Restraint(_self, *args))
5277 if self.__class__ != Restraint:
5278 _director_objects.register(self)
5283 def get_score(self):
5284 r"""get_score(Restraint self) -> double"""
5285 return _IMP_kernel.Restraint_get_score(self)
5287 def evaluate(self, calc_derivs):
5288 r"""evaluate(Restraint self, bool calc_derivs) -> double"""
5289 return _IMP_kernel.Restraint_evaluate(self, calc_derivs)
5291 def evaluate_moved(self, calc_derivs, moved_pis, reset_pis):
5292 r"""evaluate_moved(Restraint self, bool calc_derivs, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
5293 return _IMP_kernel.Restraint_evaluate_moved(self, calc_derivs, moved_pis, reset_pis)
5295 def evaluate_moved_if_below(self, calc_derivatives, moved_pis, reset_pis, max):
5296 r"""evaluate_moved_if_below(Restraint self, bool calc_derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
5297 return _IMP_kernel.Restraint_evaluate_moved_if_below(self, calc_derivatives, moved_pis, reset_pis, max)
5299 def evaluate_moved_if_good(self, calc_derivatives, moved_pis, reset_pis):
5300 r"""evaluate_moved_if_good(Restraint self, bool calc_derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
5301 return _IMP_kernel.Restraint_evaluate_moved_if_good(self, calc_derivatives, moved_pis, reset_pis)
5303 def evaluate_if_good(self, calc_derivatives):
5304 r"""evaluate_if_good(Restraint self, bool calc_derivatives) -> double"""
5305 return _IMP_kernel.Restraint_evaluate_if_good(self, calc_derivatives)
5307 def evaluate_if_below(self, calc_derivatives, max):
5308 r"""evaluate_if_below(Restraint self, bool calc_derivatives, double max) -> double"""
5309 return _IMP_kernel.Restraint_evaluate_if_below(self, calc_derivatives, max)
5311 def unprotected_evaluate(self, da):
5312 r"""unprotected_evaluate(Restraint self, DerivativeAccumulator da) -> double"""
5313 return _IMP_kernel.Restraint_unprotected_evaluate(self, da)
5315 def unprotected_evaluate_moved(self, da, moved_pis, reset_pis):
5316 r"""unprotected_evaluate_moved(Restraint self, DerivativeAccumulator da, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
5317 return _IMP_kernel.Restraint_unprotected_evaluate_moved(self, da, moved_pis, reset_pis)
5319 def unprotected_evaluate_if_good(self, da, max):
5320 r"""unprotected_evaluate_if_good(Restraint self, DerivativeAccumulator da, double max) -> double"""
5321 return _IMP_kernel.Restraint_unprotected_evaluate_if_good(self, da, max)
5323 def unprotected_evaluate_if_below(self, da, max):
5324 r"""unprotected_evaluate_if_below(Restraint self, DerivativeAccumulator da, double max) -> double"""
5325 return _IMP_kernel.Restraint_unprotected_evaluate_if_below(self, da, max)
5327 def unprotected_evaluate_moved_if_below(self, da, moved_pis, reset_pis, max):
5328 r"""unprotected_evaluate_moved_if_below(Restraint self, DerivativeAccumulator da, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
5329 return _IMP_kernel.Restraint_unprotected_evaluate_moved_if_below(self, da, moved_pis, reset_pis, max)
5331 def unprotected_evaluate_moved_if_good(self, da, moved_pis, reset_pis, max):
5332 r"""unprotected_evaluate_moved_if_good(Restraint self, DerivativeAccumulator da, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
5333 return _IMP_kernel.Restraint_unprotected_evaluate_moved_if_good(self, da, moved_pis, reset_pis, max)
5335 def get_static_info(self):
5336 r"""get_static_info(Restraint self) -> RestraintInfo"""
5337 return _IMP_kernel.Restraint_get_static_info(self)
5339 def get_dynamic_info(self):
5340 r"""get_dynamic_info(Restraint self) -> RestraintInfo"""
5341 return _IMP_kernel.Restraint_get_dynamic_info(self)
5343 def add_score_and_derivatives(self, sa):
5344 r"""add_score_and_derivatives(Restraint self, ScoreAccumulator sa)"""
5345 return _IMP_kernel.Restraint_add_score_and_derivatives(self, sa)
5347 def add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
5348 r"""add_score_and_derivatives_moved(Restraint self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
5349 return _IMP_kernel.Restraint_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
5352 r"""create_decomposition(Restraint self) -> Restraint"""
5353 return _IMP_kernel.Restraint_create_decomposition(self)
5355 def create_current_decomposition(self):
5356 r"""create_current_decomposition(Restraint self) -> Restraint"""
5357 return _IMP_kernel.Restraint_create_current_decomposition(self)
5359 def set_weight(self, weight):
5360 r"""set_weight(Restraint self, IMP::Float weight)"""
5361 return _IMP_kernel.Restraint_set_weight(self, weight)
5363 def get_weight(self):
5364 r"""get_weight(Restraint self) -> IMP::Float"""
5365 return _IMP_kernel.Restraint_get_weight(self)
5367 def get_maximum_score(self):
5368 r"""get_maximum_score(Restraint self) -> double"""
5369 return _IMP_kernel.Restraint_get_maximum_score(self)
5371 def set_maximum_score(self, s):
5372 r"""set_maximum_score(Restraint self, double s)"""
5373 return _IMP_kernel.Restraint_set_maximum_score(self, s)
5376 r"""create_scoring_function(Restraint self, double weight=1.0, double max=NO_MAX) -> ScoringFunction"""
5377 return _IMP_kernel.Restraint_create_scoring_function(self, *args)
5379 def set_last_score(self, s):
5380 r"""set_last_score(Restraint self, double s)"""
5381 return _IMP_kernel.Restraint_set_last_score(self, s)
5383 def set_last_last_score(self, s):
5384 r"""set_last_last_score(Restraint self, double s)"""
5385 return _IMP_kernel.Restraint_set_last_last_score(self, s)
5387 def get_last_score(self):
5388 r"""get_last_score(Restraint self) -> double"""
5389 return _IMP_kernel.Restraint_get_last_score(self)
5391 def get_last_last_score(self):
5392 r"""get_last_last_score(Restraint self) -> double"""
5393 return _IMP_kernel.Restraint_get_last_last_score(self)
5395 def get_is_aggregate(self):
5396 r"""get_is_aggregate(Restraint self) -> bool"""
5397 return _IMP_kernel.Restraint_get_is_aggregate(self)
5399 def get_was_good(self):
5400 r"""get_was_good(Restraint self) -> bool"""
5401 return _IMP_kernel.Restraint_get_was_good(self)
5402 __swig_destroy__ = _IMP_kernel.delete_Restraint
5404 def do_create_decomposition(self):
5405 r"""do_create_decomposition(Restraint self) -> IMP::Restraints"""
5406 return _IMP_kernel.Restraint_do_create_decomposition(self)
5408 def do_create_current_decomposition(self):
5409 r"""do_create_current_decomposition(Restraint self) -> IMP::Restraints"""
5410 return _IMP_kernel.Restraint_do_create_current_decomposition(self)
5412 def do_add_score_and_derivatives(self, sa):
5413 r"""do_add_score_and_derivatives(Restraint self, ScoreAccumulator sa)"""
5414 return _IMP_kernel.Restraint_do_add_score_and_derivatives(self, sa)
5416 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
5417 r"""do_add_score_and_derivatives_moved(Restraint self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
5418 return _IMP_kernel.Restraint_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
5420 def do_get_outputs(self):
5421 r"""do_get_outputs(Restraint self) -> IMP::ModelObjectsTemp"""
5422 return _IMP_kernel.Restraint_do_get_outputs(self)
5423 is_aggregate_ = property(_IMP_kernel.Restraint_is_aggregate__get, _IMP_kernel.Restraint_is_aggregate__set, doc=
r"""is_aggregate_ : bool""")
5426 r"""__str__(Restraint self) -> std::string"""
5427 return _IMP_kernel.Restraint___str__(self)
5430 r"""__repr__(Restraint self) -> std::string"""
5431 return _IMP_kernel.Restraint___repr__(self)
5435 return _object_cast_to_Restraint(o)
5438 def do_show(self, out):
5443 return _object_cast_to_Restraint(o)
5446 def _wrap_jax(self, score_func, keys=None):
5447 """Create the return value for _get_jax.
5448 Use this method in _get_jax() to wrap the JAX scoring function
5449 with other model- and restraint-specific information.
5451 @param score_func A function implemented using JAX that takes
5452 a single argument (the current JAX Model) and returns
5453 the score of the restraint.
5454 @param keys If given, a set of IMP::Key objects describing Model
5455 attributes (other than xyz and radius) that the restraint
5456 uses. For example, a restraint that uses electrostatic charge
5457 would pass IMP::atom::Charged::get_charge_key() here.
5459 from IMP._jax_util
import JAXRestraintInfo
5460 return JAXRestraintInfo(m=self.get_model(), score_func=score_func,
5461 weight=self.get_weight(), keys=keys)
5464 """Return a JAX implementation of this Restraint.
5465 Implement this method in a Restraint subclass to provide
5466 an equivalent function using [JAX](https://docs.jax.dev/)
5467 that scores the current JAX Model. See also _wrap_jax.
5469 raise NotImplementedError(
5470 f
"No JAX implementation for {self} ({type(self)})")
5472 def _evaluate_jax(self):
5473 """Similar to evaluate(False), but using JAX.
5474 This is intended to be useful for testing purposes. It will likely
5475 not be particularly fast as it will copy the IMP Model and
5476 jax.jit-compile the scoring function each time."""
5478 ji = self._get_jax()
5479 jm = ji.get_jax_model()
5480 j = jax.jit(ji.score_func)
5483 def __disown__(self):
5485 _IMP_kernel.disown_Restraint(self)
5486 return weakref.proxy(self)
5489 r"""do_destroy(Restraint self)"""
5490 return _IMP_kernel.Restraint_do_destroy(self)
5492 def handle_set_has_required_score_states(self, arg0):
5493 r"""handle_set_has_required_score_states(Restraint self, bool arg0)"""
5494 return _IMP_kernel.Restraint_handle_set_has_required_score_states(self, arg0)
5496 def do_get_inputs(self):
5497 r"""do_get_inputs(Restraint self) -> IMP::ModelObjectsTemp"""
5498 return _IMP_kernel.Restraint_do_get_inputs(self)
5500 def do_get_interactions(self):
5501 r"""do_get_interactions(Restraint self) -> IMP::ModelObjectsTemps"""
5502 return _IMP_kernel.Restraint_do_get_interactions(self)
5505 _IMP_kernel.Restraint_swigregister(Restraint)
5506 class _RestraintsAdaptor(_InputAdaptor):
5507 r"""Proxy of C++ IMP::RestraintsAdaptor class."""
5509 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5510 __repr__ = _swig_repr
5512 def __init__(self, *args):
5514 __init__(_RestraintsAdaptor self) -> _RestraintsAdaptor
5515 __init__(_RestraintsAdaptor self, IMP::Restraints const & sf) -> _RestraintsAdaptor
5516 __init__(_RestraintsAdaptor self, IMP::RestraintsTemp const & sf) -> _RestraintsAdaptor
5517 __init__(_RestraintsAdaptor self, Restraint sf) -> _RestraintsAdaptor
5519 _IMP_kernel._RestraintsAdaptor_swiginit(self, _IMP_kernel.new__RestraintsAdaptor(*args))
5520 __swig_destroy__ = _IMP_kernel.delete__RestraintsAdaptor
5523 _IMP_kernel._RestraintsAdaptor_swigregister(_RestraintsAdaptor)
5524 class RestraintSet(Restraint):
5525 r"""Proxy of C++ IMP::RestraintSet class."""
5527 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5529 def __init__(self, *args):
5531 __init__(RestraintSet self, Model m, double weight, std::string const & name="RestraintSet %1%") -> RestraintSet
5532 __init__(RestraintSet self, Model m, std::string const & name="RestraintSet %1%") -> RestraintSet
5533 __init__(RestraintSet self, IMP::RestraintsTemp const & rs, double weight, std::string const & name="RestraintSet %1%") -> RestraintSet
5534 __init__(RestraintSet self) -> RestraintSet
5536 if self.__class__ == RestraintSet:
5540 _IMP_kernel.RestraintSet_swiginit(self, _IMP_kernel.new_RestraintSet(_self, *args))
5542 if self.__class__ != RestraintSet:
5543 _director_objects.register(self)
5548 def unprotected_evaluate(self, da):
5549 r"""unprotected_evaluate(RestraintSet self, DerivativeAccumulator da) -> double"""
5550 return _IMP_kernel.RestraintSet_unprotected_evaluate(self, da)
5552 def get_type_name(self):
5553 r"""get_type_name(RestraintSet self) -> std::string"""
5554 return _IMP_kernel.RestraintSet_get_type_name(self)
5557 r"""get_version_info(RestraintSet self) -> VersionInfo"""
5558 return _IMP_kernel.RestraintSet_get_version_info(self)
5559 __swig_destroy__ = _IMP_kernel.delete_RestraintSet
5560 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)
5561 def __set_restraints(self, obj): _list_util.set_varlist(self.restraints, obj)
5562 def __del_restraints(self): _list_util.del_varlist(self.restraints)
5563 restraints = property(__get_restraints, __set_restraints, __del_restraints, doc=
"List of ##ucnames")
5565 def remove_restraint(self, d):
5566 r"""remove_restraint(RestraintSet self, Restraint d)"""
5567 return _IMP_kernel.RestraintSet_remove_restraint(self, d)
5569 def _python_index_restraint(self, d, start, stop):
5570 r"""_python_index_restraint(RestraintSet self, Restraint d, unsigned int start, unsigned int stop) -> unsigned int"""
5571 return _IMP_kernel.RestraintSet__python_index_restraint(self, d, start, stop)
5573 def remove_restraints(self, d):
5574 r"""remove_restraints(RestraintSet self, IMP::Restraints const & d)"""
5575 return _IMP_kernel.RestraintSet_remove_restraints(self, d)
5577 def set_restraints(self, ps):
5578 r"""set_restraints(RestraintSet self, IMP::Restraints const & ps)"""
5579 return _IMP_kernel.RestraintSet_set_restraints(self, ps)
5581 def set_restraints_order(self, objs):
5582 r"""set_restraints_order(RestraintSet self, IMP::Restraints const & objs)"""
5583 return _IMP_kernel.RestraintSet_set_restraints_order(self, objs)
5586 r"""add_restraint(RestraintSet self, Restraint obj) -> unsigned int"""
5587 return _IMP_kernel.RestraintSet_add_restraint(self, obj)
5590 r"""add_restraints(RestraintSet self, IMP::Restraints const & objs)"""
5591 return _IMP_kernel.RestraintSet_add_restraints(self, objs)
5593 def clear_restraints(self):
5594 r"""clear_restraints(RestraintSet self)"""
5595 return _IMP_kernel.RestraintSet_clear_restraints(self)
5597 def get_number_of_restraints(self):
5598 r"""get_number_of_restraints(RestraintSet self) -> unsigned int"""
5599 return _IMP_kernel.RestraintSet_get_number_of_restraints(self)
5601 def get_has_restraints(self):
5602 r"""get_has_restraints(RestraintSet self) -> bool"""
5603 return _IMP_kernel.RestraintSet_get_has_restraints(self)
5605 def get_restraint(self, i):
5606 r"""get_restraint(RestraintSet self, unsigned int i) -> Restraint"""
5607 return _IMP_kernel.RestraintSet_get_restraint(self, i)
5609 def get_restraints(self):
5610 r"""get_restraints(RestraintSet self) -> IMP::Restraints"""
5611 return _IMP_kernel.RestraintSet_get_restraints(self)
5613 def erase_restraint(self, i):
5614 r"""erase_restraint(RestraintSet self, unsigned int i)"""
5615 return _IMP_kernel.RestraintSet_erase_restraint(self, i)
5617 def reserve_restraints(self, sz):
5618 r"""reserve_restraints(RestraintSet self, unsigned int sz)"""
5619 return _IMP_kernel.RestraintSet_reserve_restraints(self, sz)
5621 def get_non_sets_and_sets(self):
5622 r"""get_non_sets_and_sets(RestraintSet self) -> std::pair< IMP::RestraintsTemp,IMP::RestraintSetsTemp >"""
5623 return _IMP_kernel.RestraintSet_get_non_sets_and_sets(self)
5625 def do_get_inputs(self):
5626 r"""do_get_inputs(RestraintSet self) -> IMP::ModelObjectsTemp"""
5627 return _IMP_kernel.RestraintSet_do_get_inputs(self)
5630 r"""create_scoring_function(RestraintSet self, double weight=1.0, double max=std::numeric_limits< double >::max()) -> ScoringFunction"""
5631 return _IMP_kernel.RestraintSet_create_scoring_function(self, *args)
5633 def get_last_score(self):
5634 r"""get_last_score(RestraintSet self) -> double"""
5635 return _IMP_kernel.RestraintSet_get_last_score(self)
5638 r"""__str__(RestraintSet self) -> std::string"""
5639 return _IMP_kernel.RestraintSet___str__(self)
5642 r"""__repr__(RestraintSet self) -> std::string"""
5643 return _IMP_kernel.RestraintSet___repr__(self)
5647 return _object_cast_to_RestraintSet(o)
5650 def do_show(self, out):
5655 return _object_cast_to_RestraintSet(o)
5658 def _get_as_binary(self):
5659 r"""_get_as_binary(RestraintSet self) -> PyObject *"""
5660 return _IMP_kernel.RestraintSet__get_as_binary(self)
5662 def _set_from_binary(self, p):
5663 r"""_set_from_binary(RestraintSet self, PyObject * p)"""
5664 return _IMP_kernel.RestraintSet__set_from_binary(self, p)
5666 def __getstate__(self):
5667 p = self._get_as_binary()
5668 if len(self.__dict__) > 1:
5669 d = self.__dict__.copy()
5674 def __setstate__(self, p):
5675 if not hasattr(self,
'this'):
5677 if isinstance(p, tuple):
5679 self.__dict__.update(d)
5680 return self._set_from_binary(p)
5684 jis = [r.get_derived_object()._get_jax()
for r
in self.restraints]
5685 funcs = [j.score_func
for j
in jis]
5686 keys = frozenset(x
for j
in jis
for x
in j._keys)
5689 return sum(f(jm)
for f
in funcs)
5693 return self._wrap_jax(jax_sf, keys=keys)
5695 def __disown__(self):
5697 _IMP_kernel.disown_RestraintSet(self)
5698 return weakref.proxy(self)
5701 r"""do_destroy(RestraintSet self)"""
5702 return _IMP_kernel.RestraintSet_do_destroy(self)
5704 def handle_set_has_required_score_states(self, arg0):
5705 r"""handle_set_has_required_score_states(RestraintSet self, bool arg0)"""
5706 return _IMP_kernel.RestraintSet_handle_set_has_required_score_states(self, arg0)
5708 def do_get_outputs(self):
5709 r"""do_get_outputs(RestraintSet self) -> IMP::ModelObjectsTemp"""
5710 return _IMP_kernel.RestraintSet_do_get_outputs(self)
5712 def do_get_interactions(self):
5713 r"""do_get_interactions(RestraintSet self) -> IMP::ModelObjectsTemps"""
5714 return _IMP_kernel.RestraintSet_do_get_interactions(self)
5716 def do_create_decomposition(self):
5717 r"""do_create_decomposition(RestraintSet self) -> IMP::Restraints"""
5718 return _IMP_kernel.RestraintSet_do_create_decomposition(self)
5720 def do_create_current_decomposition(self):
5721 r"""do_create_current_decomposition(RestraintSet self) -> IMP::Restraints"""
5722 return _IMP_kernel.RestraintSet_do_create_current_decomposition(self)
5724 def do_add_score_and_derivatives(self, sa):
5725 r"""do_add_score_and_derivatives(RestraintSet self, ScoreAccumulator sa)"""
5726 return _IMP_kernel.RestraintSet_do_add_score_and_derivatives(self, sa)
5728 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
5729 r"""do_add_score_and_derivatives_moved(RestraintSet self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
5730 return _IMP_kernel.RestraintSet_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
5733 _IMP_kernel.RestraintSet_swigregister(RestraintSet)
5735 def get_restraints(rs):
5736 r"""get_restraints(IMP::RestraintsTemp const & rs) -> IMP::RestraintsTemp"""
5737 return _IMP_kernel.get_restraints(rs)
5739 def _check_particle(p, a):
5740 if (
not p.get_is_active()):
5741 raise ValueError(
"Inactive Particle")
5742 if (type(a)() == a):
5743 raise IndexError(
"Cannot use default Index")
5744 if (
not p.has_attribute(a)):
5745 raise IndexError(
"Particle does not have attribute")
5747 class Particle(ModelObject):
5748 r"""Proxy of C++ IMP::Particle class."""
5750 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5753 r"""get_version_info(Particle self) -> VersionInfo"""
5754 return _IMP_kernel.Particle_get_version_info(self)
5755 __swig_destroy__ = _IMP_kernel.delete_Particle
5757 def __init__(self, *args):
5759 __init__(Particle self, Model m, std::string name) -> Particle
5760 __init__(Particle self, Model m) -> Particle
5761 __init__(Particle self) -> Particle
5763 _IMP_kernel.Particle_swiginit(self, _IMP_kernel.new_Particle(*args))
5765 def get_float_keys(self):
5766 r"""get_float_keys(Particle self) -> IMP::FloatKeys"""
5767 return _IMP_kernel.Particle_get_float_keys(self)
5769 def get_floats_keys(self):
5770 r"""get_floats_keys(Particle self) -> IMP::FloatsKeys"""
5771 return _IMP_kernel.Particle_get_floats_keys(self)
5773 def get_int_keys(self):
5774 r"""get_int_keys(Particle self) -> IMP::IntKeys"""
5775 return _IMP_kernel.Particle_get_int_keys(self)
5777 def get_ints_keys(self):
5778 r"""get_ints_keys(Particle self) -> IMP::IntsKeys"""
5779 return _IMP_kernel.Particle_get_ints_keys(self)
5781 def get_string_keys(self):
5782 r"""get_string_keys(Particle self) -> IMP::StringKeys"""
5783 return _IMP_kernel.Particle_get_string_keys(self)
5785 def get_object_keys(self):
5786 r"""get_object_keys(Particle self) -> IMP::ObjectKeys"""
5787 return _IMP_kernel.Particle_get_object_keys(self)
5789 def add_cache_attribute(self, *args):
5791 add_cache_attribute(Particle self, FloatKey name, IMP::Float value)
5792 add_cache_attribute(Particle self, FloatsKey name, IMP::Floats value)
5793 add_cache_attribute(Particle self, IntKey name, IMP::Int value)
5794 add_cache_attribute(Particle self, IntsKey name, IMP::Ints value)
5795 add_cache_attribute(Particle self, StringKey name, IMP::String value)
5796 add_cache_attribute(Particle self, ObjectKey name, Object value)
5797 add_cache_attribute(Particle self, IMP::WeakObjectKey name, Object value)
5799 return _IMP_kernel.Particle_add_cache_attribute(self, *args)
5801 def get_weak_object_keys(self):
5802 r"""get_weak_object_keys(Particle self) -> IMP::WeakObjectKeys"""
5803 return _IMP_kernel.Particle_get_weak_object_keys(self)
5805 def add_to_derivative(self, *args):
5807 add_to_derivative(Particle self, FloatKey key, IMP::Float value, DerivativeAccumulator da)
5808 add_to_derivative(Particle self, Vector3DDerivKey key, Vector3D value, DerivativeAccumulator da)
5809 add_to_derivative(Particle self, Vector4DDerivKey key, Vector4D value, DerivativeAccumulator da)
5811 return _IMP_kernel.Particle_add_to_derivative(self, *args)
5813 def set_is_optimized(self, *args):
5815 set_is_optimized(Particle self, FloatKey k, bool tf)
5816 set_is_optimized(Particle self, Vector3DDerivKey k, bool tf)
5817 set_is_optimized(Particle self, Vector4DDerivKey k, bool tf)
5819 return _IMP_kernel.Particle_set_is_optimized(self, *args)
5821 def get_is_optimized(self, *args):
5823 get_is_optimized(Particle self, FloatKey k) -> bool
5824 get_is_optimized(Particle self, Vector3DDerivKey k) -> bool
5825 get_is_optimized(Particle self, Vector4DDerivKey k) -> bool
5827 return _IMP_kernel.Particle_get_is_optimized(self, *args)
5829 def get_derivative(self, *args):
5831 get_derivative(Particle self, FloatKey k) -> IMP::Float
5832 get_derivative(Particle self, Vector3DDerivKey k) -> Vector3D
5833 get_derivative(Particle self, Vector4DDerivKey k) -> Vector4D
5835 return _IMP_kernel.Particle_get_derivative(self, *args)
5837 def add_attribute(self, *args):
5839 add_attribute(Particle self, FloatKey name, IMP::Float initial_value)
5840 add_attribute(Particle self, FloatsKey name, IMP::Floats initial_value)
5841 add_attribute(Particle self, IntKey name, IMP::Int initial_value)
5842 add_attribute(Particle self, IntsKey name, IMP::Ints initial_value)
5843 add_attribute(Particle self, StringKey name, IMP::String initial_value)
5844 add_attribute(Particle self, ObjectKey name, Object initial_value)
5845 add_attribute(Particle self, IMP::WeakObjectKey name, Object initial_value)
5846 add_attribute(Particle self, SparseStringKey name, IMP::String initial_value)
5847 add_attribute(Particle self, SparseIntKey name, IMP::Int initial_value)
5848 add_attribute(Particle self, SparseFloatKey name, IMP::Float initial_value)
5849 add_attribute(Particle self, SparseParticleIndexKey name, ParticleIndex initial_value)
5850 add_attribute(Particle self, FloatKey name, IMP::Float const initial_value, bool optimized)
5851 add_attribute(Particle self, ParticleIndexKey k, Particle v)
5853 return _IMP_kernel.Particle_add_attribute(self, *args)
5855 def has_attribute(self, *args):
5857 has_attribute(Particle self, FloatKey name) -> bool
5858 has_attribute(Particle self, FloatsKey name) -> bool
5859 has_attribute(Particle self, IntKey name) -> bool
5860 has_attribute(Particle self, IntsKey name) -> bool
5861 has_attribute(Particle self, StringKey name) -> bool
5862 has_attribute(Particle self, ObjectKey name) -> bool
5863 has_attribute(Particle self, IMP::WeakObjectKey name) -> bool
5864 has_attribute(Particle self, SparseStringKey name) -> bool
5865 has_attribute(Particle self, SparseIntKey name) -> bool
5866 has_attribute(Particle self, SparseFloatKey name) -> bool
5867 has_attribute(Particle self, SparseParticleIndexKey name) -> bool
5868 has_attribute(Particle self, ParticleIndexKey k) -> bool
5870 return _IMP_kernel.Particle_has_attribute(self, *args)
5872 def set_value(self, *args):
5874 set_value(Particle self, FloatKey name, IMP::Float value)
5875 set_value(Particle self, FloatsKey name, IMP::Floats value)
5876 set_value(Particle self, IntKey name, IMP::Int value)
5877 set_value(Particle self, IntsKey name, IMP::Ints value)
5878 set_value(Particle self, StringKey name, IMP::String value)
5879 set_value(Particle self, ObjectKey name, Object value)
5880 set_value(Particle self, IMP::WeakObjectKey name, Object value)
5881 set_value(Particle self, SparseStringKey name, IMP::String value)
5882 set_value(Particle self, SparseIntKey name, IMP::Int value)
5883 set_value(Particle self, SparseFloatKey name, IMP::Float value)
5884 set_value(Particle self, SparseParticleIndexKey name, ParticleIndex value)
5885 set_value(Particle self, ParticleIndexKey k, Particle v)
5887 return _IMP_kernel.Particle_set_value(self, *args)
5889 def get_value(self, *args):
5891 get_value(Particle self, FloatKey name) -> IMP::Float
5892 get_value(Particle self, FloatsKey name) -> IMP::Floats
5893 get_value(Particle self, IntKey name) -> IMP::Int
5894 get_value(Particle self, IntsKey name) -> IMP::Ints
5895 get_value(Particle self, StringKey name) -> IMP::String
5896 get_value(Particle self, ObjectKey name) -> Object
5897 get_value(Particle self, IMP::WeakObjectKey name) -> Object
5898 get_value(Particle self, SparseStringKey name) -> IMP::String
5899 get_value(Particle self, SparseIntKey name) -> IMP::Int
5900 get_value(Particle self, SparseFloatKey name) -> IMP::Float
5901 get_value(Particle self, SparseParticleIndexKey name) -> ParticleIndex
5902 get_value(Particle self, ParticleIndexKey k) -> Particle
5904 return _IMP_kernel.Particle_get_value(self, *args)
5906 def remove_attribute(self, *args):
5908 remove_attribute(Particle self, FloatKey name)
5909 remove_attribute(Particle self, FloatsKey name)
5910 remove_attribute(Particle self, IntKey name)
5911 remove_attribute(Particle self, IntsKey name)
5912 remove_attribute(Particle self, StringKey name)
5913 remove_attribute(Particle self, ObjectKey name)
5914 remove_attribute(Particle self, IMP::WeakObjectKey name)
5915 remove_attribute(Particle self, SparseStringKey name)
5916 remove_attribute(Particle self, SparseIntKey name)
5917 remove_attribute(Particle self, SparseFloatKey name)
5918 remove_attribute(Particle self, SparseParticleIndexKey name)
5919 remove_attribute(Particle self, ParticleIndexKey k)
5921 return _IMP_kernel.Particle_remove_attribute(self, *args)
5923 def get_particle_keys(self):
5924 r"""get_particle_keys(Particle self) -> IMP::ParticleIndexKeys"""
5925 return _IMP_kernel.Particle_get_particle_keys(self)
5927 def show(self, *args):
5928 r"""show(Particle self, _ostream out=std::cout)"""
5929 return _IMP_kernel.Particle_show(self, *args)
5931 def get_is_active(self):
5932 r"""get_is_active(Particle self) -> bool"""
5933 return _IMP_kernel.Particle_get_is_active(self)
5936 r"""get_index(Particle self) -> ParticleIndex"""
5937 return _IMP_kernel.Particle_get_index(self)
5939 def __eq__(self, *args):
5941 __eq__(Particle self, Particle o) -> bool
5942 __eq__(Particle self, Decorator d) -> bool
5944 return _IMP_kernel.Particle___eq__(self, *args)
5946 def __ne__(self, *args):
5948 __ne__(Particle self, Particle o) -> bool
5949 __ne__(Particle self, Decorator d) -> bool
5951 return _IMP_kernel.Particle___ne__(self, *args)
5953 def __le__(self, *args):
5955 __le__(Particle self, Particle o) -> bool
5956 __le__(Particle self, Decorator d) -> bool
5958 return _IMP_kernel.Particle___le__(self, *args)
5960 def __lt__(self, *args):
5962 __lt__(Particle self, Particle o) -> bool
5963 __lt__(Particle self, Decorator d) -> bool
5965 return _IMP_kernel.Particle___lt__(self, *args)
5967 def __ge__(self, *args):
5969 __ge__(Particle self, Particle o) -> bool
5970 __ge__(Particle self, Decorator d) -> bool
5972 return _IMP_kernel.Particle___ge__(self, *args)
5974 def __gt__(self, *args):
5976 __gt__(Particle self, Particle o) -> bool
5977 __gt__(Particle self, Decorator d) -> bool
5979 return _IMP_kernel.Particle___gt__(self, *args)
5981 __hash__ = ModelObject.__hash__
5985 r"""__str__(Particle self) -> std::string"""
5986 return _IMP_kernel.Particle___str__(self)
5989 r"""__repr__(Particle self) -> std::string"""
5990 return _IMP_kernel.Particle___repr__(self)
5994 return _object_cast_to_Particle(o)
5997 def _get_as_binary(self):
5998 r"""_get_as_binary(Particle self) -> PyObject *"""
5999 return _IMP_kernel.Particle__get_as_binary(self)
6001 def _set_from_binary(self, p):
6002 r"""_set_from_binary(Particle self, PyObject * p)"""
6003 return _IMP_kernel.Particle__set_from_binary(self, p)
6005 def __getstate__(self):
6006 p = self._get_as_binary()
6007 if len(self.__dict__) > 1:
6008 d = self.__dict__.copy()
6013 def __setstate__(self, p):
6014 if not hasattr(self,
'this'):
6016 if isinstance(p, tuple):
6018 self.__dict__.update(d)
6019 return self._set_from_binary(p)
6023 _IMP_kernel.Particle_swigregister(Particle)
6024 class _ParticleAdaptor(_InputAdaptor):
6025 r"""Proxy of C++ IMP::ParticleAdaptor class."""
6027 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6028 __repr__ = _swig_repr
6030 def __init__(self, *args):
6032 __init__(_ParticleAdaptor self) -> _ParticleAdaptor
6033 __init__(_ParticleAdaptor self, Particle p) -> _ParticleAdaptor
6034 __init__(_ParticleAdaptor self, Decorator d) -> _ParticleAdaptor
6036 _IMP_kernel._ParticleAdaptor_swiginit(self, _IMP_kernel.new__ParticleAdaptor(*args))
6038 def get_model(self):
6039 r"""get_model(_ParticleAdaptor self) -> Model"""
6040 return _IMP_kernel._ParticleAdaptor_get_model(self)
6042 def get_particle_index(self):
6043 r"""get_particle_index(_ParticleAdaptor self) -> ParticleIndex"""
6044 return _IMP_kernel._ParticleAdaptor_get_particle_index(self)
6045 __swig_destroy__ = _IMP_kernel.delete__ParticleAdaptor
6048 _IMP_kernel._ParticleAdaptor_swigregister(_ParticleAdaptor)
6049 class _DependencyGraphVertexIndex(object):
6050 r"""Proxy of C++ IMP::DependencyGraphVertexIndex class."""
6052 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6053 __repr__ = _swig_repr
6056 r"""__init__(_DependencyGraphVertexIndex self) -> _DependencyGraphVertexIndex"""
6057 _IMP_kernel._DependencyGraphVertexIndex_swiginit(self, _IMP_kernel.new__DependencyGraphVertexIndex())
6058 __swig_destroy__ = _IMP_kernel.delete__DependencyGraphVertexIndex
6061 _IMP_kernel._DependencyGraphVertexIndex_swigregister(_DependencyGraphVertexIndex)
6063 def show_as_graphviz(name, out):
6064 r"""show_as_graphviz(IMP::DependencyGraph const & name, TextOutput out)"""
6065 return _IMP_kernel.show_as_graphviz(name, out)
6067 def get_vertex_index(g):
6068 r"""get_vertex_index(IMP::DependencyGraph const & g) -> _DependencyGraphVertexIndex"""
6069 return _IMP_kernel.get_vertex_index(g)
6072 r"""get_dependency_graph(Model m) -> IMP::DependencyGraph"""
6073 return _IMP_kernel.get_dependency_graph(m)
6076 r"""get_pruned_dependency_graph(Model m) -> IMP::DependencyGraph"""
6077 return _IMP_kernel.get_pruned_dependency_graph(m)
6079 def get_dependent_particles(p, all, dg, index):
6080 r"""get_dependent_particles(ModelObject p, IMP::ModelObjectsTemp const & all, IMP::DependencyGraph const & dg, _DependencyGraphVertexIndex index) -> IMP::ParticlesTemp"""
6081 return _IMP_kernel.get_dependent_particles(p, all, dg, index)
6083 def get_required_score_states(*args):
6085 get_required_score_states(IMP::ModelObjectsTemp const & mos, IMP::ScoreStatesTemp exclude=IMP::ScoreStatesTemp()) -> IMP::ScoreStatesTemp
6086 get_required_score_states(ModelObject p, IMP::ModelObjectsTemp const & all, IMP::DependencyGraph const & dg, _DependencyGraphVertexIndex index) -> IMP::ScoreStatesTemp
6087 get_required_score_states(Model m, ParticleIndex pi) -> IMP::ScoreStatesTemp
6089 return _IMP_kernel.get_required_score_states(*args)
6090 class ScoringFunction(ModelObject):
6091 r"""Proxy of C++ IMP::ScoringFunction class."""
6093 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6095 def do_add_score_and_derivatives(self, sa, ss):
6096 r"""do_add_score_and_derivatives(ScoringFunction self, ScoreAccumulator sa, IMP::ScoreStatesTemp const & ss)"""
6097 return _IMP_kernel.ScoringFunction_do_add_score_and_derivatives(self, sa, ss)
6099 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss):
6100 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)"""
6101 return _IMP_kernel.ScoringFunction_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss)
6103 def get_score_accumulator_if_below(self, deriv, max):
6104 r"""get_score_accumulator_if_below(ScoringFunction self, bool deriv, double max) -> ScoreAccumulator"""
6105 return _IMP_kernel.ScoringFunction_get_score_accumulator_if_below(self, deriv, max)
6107 def get_score_accumulator_if_good(self, deriv):
6108 r"""get_score_accumulator_if_good(ScoringFunction self, bool deriv) -> ScoreAccumulator"""
6109 return _IMP_kernel.ScoringFunction_get_score_accumulator_if_good(self, deriv)
6111 def get_score_accumulator(self, deriv):
6112 r"""get_score_accumulator(ScoringFunction self, bool deriv) -> ScoreAccumulator"""
6113 return _IMP_kernel.ScoringFunction_get_score_accumulator(self, deriv)
6115 def __init__(self, *args):
6117 __init__(ScoringFunction self, Model m, std::string name) -> ScoringFunction
6118 __init__(ScoringFunction self) -> ScoringFunction
6120 if self.__class__ == ScoringFunction:
6124 _IMP_kernel.ScoringFunction_swiginit(self, _IMP_kernel.new_ScoringFunction(_self, *args))
6126 if self.__class__ != ScoringFunction:
6127 _director_objects.register(self)
6132 def do_get_outputs(self):
6133 r"""do_get_outputs(ScoringFunction self) -> IMP::ModelObjectsTemp"""
6134 return _IMP_kernel.ScoringFunction_do_get_outputs(self)
6136 def evaluate(self, derivatives):
6137 r"""evaluate(ScoringFunction self, bool derivatives) -> double"""
6138 return _IMP_kernel.ScoringFunction_evaluate(self, derivatives)
6140 def evaluate_if_good(self, derivatives):
6141 r"""evaluate_if_good(ScoringFunction self, bool derivatives) -> double"""
6142 return _IMP_kernel.ScoringFunction_evaluate_if_good(self, derivatives)
6144 def evaluate_if_below(self, derivatives, max):
6145 r"""evaluate_if_below(ScoringFunction self, bool derivatives, double max) -> double"""
6146 return _IMP_kernel.ScoringFunction_evaluate_if_below(self, derivatives, max)
6148 def evaluate_moved(self, derivatives, moved_pis, reset_pis):
6149 r"""evaluate_moved(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
6150 return _IMP_kernel.ScoringFunction_evaluate_moved(self, derivatives, moved_pis, reset_pis)
6152 def evaluate_moved_if_below(self, derivatives, moved_pis, reset_pis, max):
6153 r"""evaluate_moved_if_below(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
6154 return _IMP_kernel.ScoringFunction_evaluate_moved_if_below(self, derivatives, moved_pis, reset_pis, max)
6156 def evaluate_moved_if_good(self, derivatives, moved_pis, reset_pis):
6157 r"""evaluate_moved_if_good(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
6158 return _IMP_kernel.ScoringFunction_evaluate_moved_if_good(self, derivatives, moved_pis, reset_pis)
6160 def get_had_good_score(self):
6161 r"""get_had_good_score(ScoringFunction self) -> bool"""
6162 return _IMP_kernel.ScoringFunction_get_had_good_score(self)
6164 def get_last_score(self):
6165 r"""get_last_score(ScoringFunction self) -> double"""
6166 return _IMP_kernel.ScoringFunction_get_last_score(self)
6169 r"""create_restraints(ScoringFunction self) -> IMP::Restraints"""
6170 return _IMP_kernel.ScoringFunction_create_restraints(self)
6172 def get_single_restraint(self):
6173 r"""get_single_restraint(ScoringFunction self) -> Restraint"""
6174 return _IMP_kernel.ScoringFunction_get_single_restraint(self)
6177 r"""__str__(ScoringFunction self) -> std::string"""
6178 return _IMP_kernel.ScoringFunction___str__(self)
6181 r"""__repr__(ScoringFunction self) -> std::string"""
6182 return _IMP_kernel.ScoringFunction___repr__(self)
6186 return _object_cast_to_ScoringFunction(o)
6189 def do_show(self, out):
6194 return _object_cast_to_ScoringFunction(o)
6198 r = self.get_single_restraint()
6200 raise NotImplementedError(
6201 f
"No JAX implementation for {self} ({type(self)})")
6203 return r.get_derived_object()._get_jax()
6205 def _evaluate_jax(self):
6206 """Similar to evaluate(False), but using JAX.
6207 This is intended to be useful for testing purposes. It will likely
6208 not be particularly fast as it will copy the IMP Model and
6209 jax.jit-compile the scoring function each time."""
6211 ji = self._get_jax()
6212 jm = ji.get_jax_model()
6213 j = jax.jit(ji.score_func)
6216 __swig_destroy__ = _IMP_kernel.delete_ScoringFunction
6217 def __disown__(self):
6219 _IMP_kernel.disown_ScoringFunction(self)
6220 return weakref.proxy(self)
6223 r"""do_destroy(ScoringFunction self)"""
6224 return _IMP_kernel.ScoringFunction_do_destroy(self)
6226 def handle_set_has_required_score_states(self, arg0):
6227 r"""handle_set_has_required_score_states(ScoringFunction self, bool arg0)"""
6228 return _IMP_kernel.ScoringFunction_handle_set_has_required_score_states(self, arg0)
6230 def do_get_inputs(self):
6231 r"""do_get_inputs(ScoringFunction self) -> IMP::ModelObjectsTemp"""
6232 return _IMP_kernel.ScoringFunction_do_get_inputs(self)
6234 def do_get_interactions(self):
6235 r"""do_get_interactions(ScoringFunction self) -> IMP::ModelObjectsTemps"""
6236 return _IMP_kernel.ScoringFunction_do_get_interactions(self)
6239 _IMP_kernel.ScoringFunction_swigregister(ScoringFunction)
6243 create_decomposition(IMP::RestraintsTemp const & rs) -> IMP::Restraints
6244 create_decomposition(ScoringFunction sf) -> IMP::ScoringFunctions
6246 return _IMP_kernel.create_decomposition(*args)
6247 class _ScoringFunctionAdaptor(_InputAdaptor):
6248 r"""Proxy of C++ IMP::ScoringFunctionAdaptor class."""
6250 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6251 __repr__ = _swig_repr
6253 def __init__(self, *args):
6255 __init__(_ScoringFunctionAdaptor self) -> _ScoringFunctionAdaptor
6256 __init__(_ScoringFunctionAdaptor self, ScoringFunction sf) -> _ScoringFunctionAdaptor
6257 __init__(_ScoringFunctionAdaptor self, IMP::RestraintsTemp const & sf) -> _ScoringFunctionAdaptor
6258 __init__(_ScoringFunctionAdaptor self, IMP::Restraints const & sf) -> _ScoringFunctionAdaptor
6259 __init__(_ScoringFunctionAdaptor self, Restraint sf) -> _ScoringFunctionAdaptor
6261 _IMP_kernel._ScoringFunctionAdaptor_swiginit(self, _IMP_kernel.new__ScoringFunctionAdaptor(*args))
6262 __swig_destroy__ = _IMP_kernel.delete__ScoringFunctionAdaptor
6265 _IMP_kernel._ScoringFunctionAdaptor_swigregister(_ScoringFunctionAdaptor)
6268 r"""show_restraint_hierarchy(_ScoringFunctionAdaptor rs, _ostream out=std::cout)"""
6269 return _IMP_kernel.show_restraint_hierarchy(*args)
6270 class Undecorator(
Object):
6271 r"""Proxy of C++ IMP::Undecorator class."""
6273 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6275 def __init__(self, m, name):
6276 r"""__init__(Undecorator self, Model m, std::string name) -> Undecorator"""
6277 if self.__class__ == Undecorator:
6281 _IMP_kernel.Undecorator_swiginit(self, _IMP_kernel.new_Undecorator(_self, m, name))
6283 if self.__class__ != Undecorator:
6284 _director_objects.register(self)
6289 def teardown(self, pi):
6290 r"""teardown(Undecorator self, ParticleIndex pi)"""
6291 return _IMP_kernel.Undecorator_teardown(self, pi)
6294 r"""__str__(Undecorator self) -> std::string"""
6295 return _IMP_kernel.Undecorator___str__(self)
6298 r"""__repr__(Undecorator self) -> std::string"""
6299 return _IMP_kernel.Undecorator___repr__(self)
6303 return _object_cast_to_Undecorator(o)
6306 def do_show(self, out):
6311 return _object_cast_to_Undecorator(o)
6313 __swig_destroy__ = _IMP_kernel.delete_Undecorator
6314 def __disown__(self):
6316 _IMP_kernel.disown_Undecorator(self)
6317 return weakref.proxy(self)
6320 r"""do_destroy(Undecorator self)"""
6321 return _IMP_kernel.Undecorator_do_destroy(self)
6324 _IMP_kernel.Undecorator_swigregister(Undecorator)
6326 r"""Proxy of C++ IMP::Model class."""
6328 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6330 def __init__(self, *args):
6331 r"""__init__(Model self, std::string name="Model %1%") -> Model"""
6332 _IMP_kernel.Model_swiginit(self, _IMP_kernel.new_Model(*args))
6334 if self
not in _models_set:
6335 _models_set.add(self)
6340 def clear_particle_caches(self, pi):
6341 r"""clear_particle_caches(Model self, ParticleIndex pi)"""
6342 return _IMP_kernel.Model_clear_particle_caches(self, pi)
6345 r"""add_particle(Model self, std::string name) -> ParticleIndex"""
6346 return _IMP_kernel.Model_add_particle(self, name)
6348 def get_particle_name(self, pi):
6349 r"""get_particle_name(Model self, ParticleIndex pi) -> std::string"""
6350 return _IMP_kernel.Model_get_particle_name(self, pi)
6352 def add_undecorator(self, pi, d):
6353 r"""add_undecorator(Model self, ParticleIndex pi, Undecorator d)"""
6354 return _IMP_kernel.Model_add_undecorator(self, pi, d)
6356 def get_dependent_restraints_uncached(self, pi):
6357 r"""get_dependent_restraints_uncached(Model self, ParticleIndex pi) -> IMP::RestraintsTemp"""
6358 return _IMP_kernel.Model_get_dependent_restraints_uncached(self, pi)
6360 def get_dependent_particles_uncached(self, pi):
6361 r"""get_dependent_particles_uncached(Model self, ParticleIndex pi) -> IMP::ParticlesTemp"""
6362 return _IMP_kernel.Model_get_dependent_particles_uncached(self, pi)
6364 def get_dependent_score_states_uncached(self, pi):
6365 r"""get_dependent_score_states_uncached(Model self, ParticleIndex pi) -> IMP::ScoreStatesTemp"""
6366 return _IMP_kernel.Model_get_dependent_score_states_uncached(self, pi)
6367 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)
6368 def __set_score_states(self, obj): _list_util.set_varlist(self.score_states, obj)
6369 def __del_score_states(self): _list_util.del_varlist(self.score_states)
6370 score_states = property(__get_score_states, __set_score_states, __del_score_states, doc=
"List of ##ucnames")
6372 def remove_score_state(self, d):
6373 r"""remove_score_state(Model self, ScoreState d)"""
6374 return _IMP_kernel.Model_remove_score_state(self, d)
6376 def _python_index_score_state(self, d, start, stop):
6377 r"""_python_index_score_state(Model self, ScoreState d, unsigned int start, unsigned int stop) -> unsigned int"""
6378 return _IMP_kernel.Model__python_index_score_state(self, d, start, stop)
6380 def remove_score_states(self, d):
6381 r"""remove_score_states(Model self, IMP::ScoreStates const & d)"""
6382 return _IMP_kernel.Model_remove_score_states(self, d)
6384 def set_score_states(self, ps):
6385 r"""set_score_states(Model self, IMP::ScoreStates const & ps)"""
6386 return _IMP_kernel.Model_set_score_states(self, ps)
6388 def set_score_states_order(self, objs):
6389 r"""set_score_states_order(Model self, IMP::ScoreStates const & objs)"""
6390 return _IMP_kernel.Model_set_score_states_order(self, objs)
6392 def add_score_state(self, obj):
6393 r"""add_score_state(Model self, ScoreState obj) -> unsigned int"""
6394 return _IMP_kernel.Model_add_score_state(self, obj)
6396 def add_score_states(self, objs):
6397 r"""add_score_states(Model self, IMP::ScoreStates const & objs)"""
6398 return _IMP_kernel.Model_add_score_states(self, objs)
6400 def clear_score_states(self):
6401 r"""clear_score_states(Model self)"""
6402 return _IMP_kernel.Model_clear_score_states(self)
6404 def get_number_of_score_states(self):
6405 r"""get_number_of_score_states(Model self) -> unsigned int"""
6406 return _IMP_kernel.Model_get_number_of_score_states(self)
6408 def get_has_score_states(self):
6409 r"""get_has_score_states(Model self) -> bool"""
6410 return _IMP_kernel.Model_get_has_score_states(self)
6412 def get_score_state(self, i):
6413 r"""get_score_state(Model self, unsigned int i) -> ScoreState"""
6414 return _IMP_kernel.Model_get_score_state(self, i)
6416 def get_score_states(self):
6417 r"""get_score_states(Model self) -> IMP::ScoreStates"""
6418 return _IMP_kernel.Model_get_score_states(self)
6420 def erase_score_state(self, i):
6421 r"""erase_score_state(Model self, unsigned int i)"""
6422 return _IMP_kernel.Model_erase_score_state(self, i)
6424 def reserve_score_states(self, sz):
6425 r"""reserve_score_states(Model self, unsigned int sz)"""
6426 return _IMP_kernel.Model_reserve_score_states(self, sz)
6429 r"""update(Model self)"""
6430 return _IMP_kernel.Model_update(self)
6432 def get_ordered_score_states(self):
6433 r"""get_ordered_score_states(Model self) -> IMP::ScoreStatesTemp"""
6434 return _IMP_kernel.Model_get_ordered_score_states(self)
6436 def add_cache_attribute(self, *args):
6438 add_cache_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
6439 add_cache_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
6440 add_cache_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
6441 add_cache_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, Vector3D value)
6442 add_cache_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle, Vector4D value)
6443 add_cache_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle, Vector3D value)
6444 add_cache_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle, Vector4D value)
6445 add_cache_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
6446 add_cache_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
6447 add_cache_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
6448 add_cache_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
6449 add_cache_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
6450 add_cache_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
6452 return _IMP_kernel.Model_add_cache_attribute(self, *args)
6454 def add_attribute(self, *args):
6456 add_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
6457 add_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
6458 add_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
6459 add_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, Vector3D value)
6460 add_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle, Vector4D value)
6461 add_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle, Vector3D value)
6462 add_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle, Vector4D value)
6463 add_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
6464 add_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
6465 add_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
6466 add_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
6467 add_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
6468 add_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
6469 add_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle, IMP::String value)
6470 add_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle, IMP::Int value)
6471 add_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle, IMP::Float value)
6472 add_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
6474 return _IMP_kernel.Model_add_attribute(self, *args)
6476 def remove_attribute(self, *args):
6478 remove_attribute(Model self, FloatKey attribute_key, ParticleIndex particle)
6479 remove_attribute(Model self, IntKey attribute_key, ParticleIndex particle)
6480 remove_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle)
6481 remove_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle)
6482 remove_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle)
6483 remove_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle)
6484 remove_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle)
6485 remove_attribute(Model self, IntsKey attribute_key, ParticleIndex particle)
6486 remove_attribute(Model self, StringKey attribute_key, ParticleIndex particle)
6487 remove_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle)
6488 remove_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle)
6489 remove_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle)
6490 remove_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle)
6491 remove_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle)
6492 remove_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle)
6493 remove_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle)
6494 remove_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle)
6496 return _IMP_kernel.Model_remove_attribute(self, *args)
6498 def get_has_attribute(self, *args):
6500 get_has_attribute(Model self, FloatKey attribute_key, ParticleIndex particle) -> bool
6501 get_has_attribute(Model self, IntKey attribute_key, ParticleIndex particle) -> bool
6502 get_has_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle) -> bool
6503 get_has_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle) -> bool
6504 get_has_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle) -> bool
6505 get_has_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle) -> bool
6506 get_has_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle) -> bool
6507 get_has_attribute(Model self, IntsKey attribute_key, ParticleIndex particle) -> bool
6508 get_has_attribute(Model self, StringKey attribute_key, ParticleIndex particle) -> bool
6509 get_has_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle) -> bool
6510 get_has_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle) -> bool
6511 get_has_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle) -> bool
6512 get_has_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle) -> bool
6513 get_has_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle) -> bool
6514 get_has_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle) -> bool
6515 get_has_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle) -> bool
6516 get_has_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle) -> bool
6518 return _IMP_kernel.Model_get_has_attribute(self, *args)
6520 def set_attribute(self, *args):
6522 set_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
6523 set_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
6524 set_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
6525 set_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, Vector3D value)
6526 set_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle, Vector4D value)
6527 set_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle, Vector3D value)
6528 set_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle, Vector4D value)
6529 set_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
6530 set_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
6531 set_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
6532 set_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
6533 set_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
6534 set_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
6535 set_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle, IMP::String value)
6536 set_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle, IMP::Int value)
6537 set_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle, IMP::Float value)
6538 set_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
6540 return _IMP_kernel.Model_set_attribute(self, *args)
6542 def get_attribute(self, *args):
6544 get_attribute(Model self, FloatKey attribute_key, ParticleIndex particle) -> IMP::Float
6545 get_attribute(Model self, IntKey attribute_key, ParticleIndex particle) -> IMP::Int
6546 get_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle) -> IMP::Floats
6547 get_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle) -> Vector3D
6548 get_attribute(Model self, Vector4DKey attribute_key, ParticleIndex particle) -> Vector4D
6549 get_attribute(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle) -> Vector3D
6550 get_attribute(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle) -> Vector4D
6551 get_attribute(Model self, IntsKey attribute_key, ParticleIndex particle) -> IMP::Ints
6552 get_attribute(Model self, StringKey attribute_key, ParticleIndex particle) -> IMP::String
6553 get_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle) -> IMP::ParticleIndexes
6554 get_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle) -> ParticleIndex
6555 get_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle) -> Object
6556 get_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle) -> Object
6557 get_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle) -> IMP::String
6558 get_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle) -> IMP::Int
6559 get_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle) -> IMP::Float
6560 get_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle) -> ParticleIndex
6562 return _IMP_kernel.Model_get_attribute(self, *args)
6564 def set_is_optimized(self, *args):
6566 set_is_optimized(Model self, Vector3DDerivKey arg2, ParticleIndex arg3, bool arg4)
6567 set_is_optimized(Model self, Vector4DDerivKey arg2, ParticleIndex arg3, bool arg4)
6568 set_is_optimized(Model self, FloatKey arg2, ParticleIndex arg3, bool arg4)
6570 return _IMP_kernel.Model_set_is_optimized(self, *args)
6572 def add_to_derivative(self, *args):
6574 add_to_derivative(Model self, Vector3DDerivKey attribute_key, ParticleIndex particle, Vector3D v, DerivativeAccumulator da)
6575 add_to_derivative(Model self, Vector4DDerivKey attribute_key, ParticleIndex particle, Vector4D v, DerivativeAccumulator da)
6576 add_to_derivative(Model self, FloatKey k, ParticleIndex particle, double v, DerivativeAccumulator da)
6578 return _IMP_kernel.Model_add_to_derivative(self, *args)
6580 def get_particle(self, p):
6581 r"""get_particle(Model self, ParticleIndex p) -> Particle"""
6582 return _IMP_kernel.Model_get_particle(self, p)
6584 def get_has_particle(self, p):
6585 r"""get_has_particle(Model self, ParticleIndex p) -> bool"""
6586 return _IMP_kernel.Model_get_has_particle(self, p)
6589 r"""get_particle_indexes(Model self) -> IMP::ParticleIndexes"""
6590 return _IMP_kernel.Model_get_particle_indexes(self)
6592 def get_model_objects(self):
6593 r"""get_model_objects(Model self) -> IMP::ModelObjectsTemp"""
6594 return _IMP_kernel.Model_get_model_objects(self)
6596 def remove_particle(self, pi):
6597 r"""remove_particle(Model self, ParticleIndex pi)"""
6598 return _IMP_kernel.Model_remove_particle(self, pi)
6600 def add_data(self, mk, o):
6601 r"""add_data(Model self, ModelKey mk, Object o)"""
6602 return _IMP_kernel.Model_add_data(self, mk, o)
6604 def get_data(self, mk):
6605 r"""get_data(Model self, ModelKey mk) -> Object"""
6606 return _IMP_kernel.Model_get_data(self, mk)
6608 def remove_data(self, mk):
6609 r"""remove_data(Model self, ModelKey mk)"""
6610 return _IMP_kernel.Model_remove_data(self, mk)
6612 def get_has_data(self, mk):
6613 r"""get_has_data(Model self, ModelKey mk) -> bool"""
6614 return _IMP_kernel.Model_get_has_data(self, mk)
6617 r"""get_age(Model self) -> unsigned int"""
6618 return _IMP_kernel.Model_get_age(self)
6620 def get_trigger_last_updated(self, tk):
6621 r"""get_trigger_last_updated(Model self, TriggerKey tk) -> unsigned int"""
6622 return _IMP_kernel.Model_get_trigger_last_updated(self, tk)
6624 def set_trigger_updated(self, tk):
6625 r"""set_trigger_updated(Model self, TriggerKey tk)"""
6626 return _IMP_kernel.Model_set_trigger_updated(self, tk)
6628 def get_dependencies_updated(self):
6629 r"""get_dependencies_updated(Model self) -> unsigned int"""
6630 return _IMP_kernel.Model_get_dependencies_updated(self)
6632 def get_removed_particles_attributes_age(self):
6633 r"""get_removed_particles_attributes_age(Model self) -> unsigned int"""
6634 return _IMP_kernel.Model_get_removed_particles_attributes_age(self)
6636 def save_dependencies(self):
6637 r"""save_dependencies(Model self)"""
6638 return _IMP_kernel.Model_save_dependencies(self)
6640 def restore_dependencies(self):
6641 r"""restore_dependencies(Model self)"""
6642 return _IMP_kernel.Model_restore_dependencies(self)
6644 def get_particles_size(self):
6645 r"""get_particles_size(Model self) -> unsigned int"""
6646 return _IMP_kernel.Model_get_particles_size(self)
6648 def get_unique_id(self):
6649 r"""get_unique_id(Model self) -> uint32_t"""
6650 return _IMP_kernel.Model_get_unique_id(self)
6653 def get_by_unique_id(id):
6654 r"""get_by_unique_id(uint32_t id) -> Model"""
6655 return _IMP_kernel.Model_get_by_unique_id(id)
6658 r"""get_version_info(Model self) -> VersionInfo"""
6659 return _IMP_kernel.Model_get_version_info(self)
6660 __swig_destroy__ = _IMP_kernel.delete_Model
6662 r"""__del__(Model self)"""
6664 _director_objects.cleanup()
6671 r"""do_destroy(Model self)"""
6672 return _IMP_kernel.Model_do_destroy(self)
6675 r"""__str__(Model self) -> std::string"""
6676 return _IMP_kernel.Model___str__(self)
6679 r"""__repr__(Model self) -> std::string"""
6680 return _IMP_kernel.Model___repr__(self)
6684 return _object_cast_to_Model(o)
6687 def _get_as_binary(self):
6688 r"""_get_as_binary(Model self) -> PyObject *"""
6689 return _IMP_kernel.Model__get_as_binary(self)
6691 def _set_from_binary(self, p):
6692 r"""_set_from_binary(Model self, PyObject * p)"""
6693 return _IMP_kernel.Model__set_from_binary(self, p)
6695 def __getstate__(self):
6696 p = self._get_as_binary()
6697 if len(self.__dict__) > 1:
6698 d = self.__dict__.copy()
6703 def __setstate__(self, p):
6704 if not hasattr(self,
'this'):
6706 if isinstance(p, tuple):
6708 self.__dict__.update(d)
6709 return self._set_from_binary(p)
6713 """Get the model's attribute array for IntKey k as a NumPy array.
6714 The array is indexed by ParticleIndex; particles that don't have
6715 this attribute will either be off the end of the array or will have
6717 This is a NumPy view that shares memory with the Model. Thus,
6718 any changes to values in this list will be reflected in the Model.
6719 Also, if the Model attribute array moves in memory (e.g. if particles
6720 or attributes are added) this array will be invalidated, so it is
6721 unsafe to keep it around long term.
6722 If read_only is set True, values in the array cannot be changed.
6724 return _get_ints_numpy(self, k, self, read_only)
6727 """Get the model's attribute array for any type of Key
6728 k as a NumPy array. See Model::get_ints_numpy() for more details."""
6729 _numpy_meth_map = {IntKey: _get_ints_numpy,
6730 FloatKey: _get_floats_numpy,
6731 Vector3DKey: _get_vector3ds_numpy,
6732 Vector3DDerivKey: _get_vector3dderiv_numpy,
6733 Vector4DKey: _get_vector4ds_numpy,
6734 Vector4DDerivKey: _get_vector4dderiv_numpy}
6735 return _numpy_meth_map[type(k)](self, k, self, read_only)
6738 """Get the model's attribute array for FloatKey k as a NumPy array.
6739 See Model::get_ints_numpy() for more details."""
6740 return _get_floats_numpy(self, k, self, read_only)
6743 """Get the model's attribute derivatives array for key k
6744 as a NumPy array. See Model::get_ints_numpy() for more details."""
6746 FloatKey: _get_derivatives_numpy,
6747 Vector3DDerivKey: _get_vector3dderiv_derivatives_numpy,
6748 Vector4DDerivKey: _get_vector4dderiv_derivatives_numpy}
6749 return _numpy_meth_map[type(k)](self, k, self, read_only)
6752 """Get the model's attribute array for Vector3DKey k as a NumPy array.
6753 See Model::get_ints_numpy() for more details."""
6754 return _get_vector3ds_numpy(self, k, self, read_only)
6757 """Get the model's XYZR attribute arrays as NumPy arrays.
6758 The attribute arrays for Cartesian coordinates and radii are
6759 stored separately from those for other FloatKeys. This function
6760 returns a tuple of two NumPy arrays, the first of coordinates and
6761 the second of radii. See Model::get_ints_numpy() for more details."""
6762 return _get_spheres_numpy(self, self, read_only)
6765 """Get the model's XYZR attribute derivatives arrays as NumPy arrays.
6766 See Model::get_ints_numpy() for more details."""
6767 return _get_sphere_derivatives_numpy(self, self, read_only)
6770 """Get the model's internal coordinate array as a NumPy array.
6771 The attribute arrays for rigid body internal coordinates are
6772 stored separately from those for other FloatKeys.
6773 See Model::get_ints_numpy() for more details."""
6774 return _get_internal_coordinates_numpy(self, self, read_only)
6777 """Get the model's internal coordinate derivative array as a
6779 See Model::get_ints_numpy() for more details."""
6780 return _get_internal_coordinate_derivatives_numpy(
6781 self, self, read_only)
6785 _IMP_kernel.Model_swigregister(Model)
6787 r"""Proxy of C++ IMP::Decorator class."""
6789 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6790 __repr__ = _swig_repr
6792 def __init__(self, p):
6793 r"""__init__(Decorator self, _ParticleAdaptor p) -> Decorator"""
6794 _IMP_kernel.Decorator_swiginit(self, _IMP_kernel.new_Decorator(p))
6796 def __ne__(self, o):
6797 r"""__ne__(Decorator self, Object o) -> bool"""
6798 return _IMP_kernel.Decorator___ne__(self, o)
6800 def __lt__(self, o):
6801 r"""__lt__(Decorator self, Object o) -> bool"""
6802 return _IMP_kernel.Decorator___lt__(self, o)
6804 def __gt__(self, o):
6805 r"""__gt__(Decorator self, Object o) -> bool"""
6806 return _IMP_kernel.Decorator___gt__(self, o)
6808 def __ge__(self, o):
6809 r"""__ge__(Decorator self, Object o) -> bool"""
6810 return _IMP_kernel.Decorator___ge__(self, o)
6812 def __le__(self, o):
6813 r"""__le__(Decorator self, Object o) -> bool"""
6814 return _IMP_kernel.Decorator___le__(self, o)
6817 r"""get_particle(Decorator self) -> Particle"""
6818 return _IMP_kernel.Decorator_get_particle(self)
6820 def get_particle_index(self):
6821 r"""get_particle_index(Decorator self) -> ParticleIndex"""
6822 return _IMP_kernel.Decorator_get_particle_index(self)
6824 def get_model(self):
6825 m = _IMP_kernel.Decorator_get_model(self)
6826 if m
in _models_set:
6827 m = _models_set_get(m)
6832 def get_is_valid(self):
6833 r"""get_is_valid(Decorator self) -> bool"""
6834 return _IMP_kernel.Decorator_get_is_valid(self)
6837 r"""__hash__(Decorator self) -> std::size_t"""
6838 return _IMP_kernel.Decorator___hash__(self)
6840 def __eq__(self, *args):
6842 __eq__(Decorator self, Object o) -> bool
6843 __eq__(Decorator self, Decorator o) -> bool
6844 __eq__(Decorator self, Particle o) -> bool
6846 return _IMP_kernel.Decorator___eq__(self, *args)
6849 r"""__bool__(Decorator self) -> bool"""
6850 return _IMP_kernel.Decorator___bool__(self)
6851 __swig_destroy__ = _IMP_kernel.delete_Decorator
6854 _IMP_kernel.Decorator_swigregister(Decorator)
6856 def check_particle(m, pi):
6857 r"""check_particle(Model m, ParticleIndex pi)"""
6858 return _IMP_kernel.check_particle(m, pi)
6860 r"""Proxy of C++ IMP::UnaryFunction class."""
6862 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6864 def __init__(self, *args):
6865 r"""__init__(UnaryFunction self, std::string name="UnaryFunction%1%") -> UnaryFunction"""
6866 if self.__class__ == UnaryFunction:
6870 _IMP_kernel.UnaryFunction_swiginit(self, _IMP_kernel.new_UnaryFunction(_self, *args))
6872 if self.__class__ != UnaryFunction:
6873 _director_objects.register(self)
6878 def evaluate(self, feature):
6879 r"""evaluate(UnaryFunction self, double feature) -> double"""
6880 return _IMP_kernel.UnaryFunction_evaluate(self, feature)
6882 def evaluate_with_derivative(self, feature):
6883 r"""evaluate_with_derivative(UnaryFunction self, double feature) -> IMP::DerivativePair"""
6884 return _IMP_kernel.UnaryFunction_evaluate_with_derivative(self, feature)
6885 __swig_destroy__ = _IMP_kernel.delete_UnaryFunction
6888 r"""__str__(UnaryFunction self) -> std::string"""
6889 return _IMP_kernel.UnaryFunction___str__(self)
6892 r"""__repr__(UnaryFunction self) -> std::string"""
6893 return _IMP_kernel.UnaryFunction___repr__(self)
6897 return _object_cast_to_UnaryFunction(o)
6900 def do_show(self, out):
6905 return _object_cast_to_UnaryFunction(o)
6909 """Return a JAX implementation of this UnaryFunction.
6910 Implement this method in a UnaryFunction subclass to provide
6911 an equivalent function using [JAX](https://docs.jax.dev/)
6912 that scores the provided feature value.
6914 raise NotImplementedError(
6915 f
"No JAX implementation for {self} ({type(self)})")
6917 def __disown__(self):
6919 _IMP_kernel.disown_UnaryFunction(self)
6920 return weakref.proxy(self)
6923 r"""do_destroy(UnaryFunction self)"""
6924 return _IMP_kernel.UnaryFunction_do_destroy(self)
6927 _IMP_kernel.UnaryFunction_swigregister(UnaryFunction)
6929 r"""Proxy of C++ IMP::OptimizerState class."""
6931 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6933 def __init__(self, *args):
6935 __init__(OptimizerState self, Model m, std::string name) -> OptimizerState
6936 __init__(OptimizerState self) -> OptimizerState
6938 if self.__class__ == OptimizerState:
6942 _IMP_kernel.OptimizerState_swiginit(self, _IMP_kernel.new_OptimizerState(_self, *args))
6944 if self.__class__ != OptimizerState:
6945 _director_objects.register(self)
6951 r"""update(OptimizerState self)"""
6952 return _IMP_kernel.OptimizerState_update(self)
6954 def set_is_optimizing(self, arg0):
6955 r"""set_is_optimizing(OptimizerState self, bool arg0)"""
6956 return _IMP_kernel.OptimizerState_set_is_optimizing(self, arg0)
6958 def get_optimizer(self):
6959 r"""get_optimizer(OptimizerState self) -> Optimizer"""
6960 return _IMP_kernel.OptimizerState_get_optimizer(self)
6962 def set_period(self, p):
6963 r"""set_period(OptimizerState self, unsigned int p)"""
6964 return _IMP_kernel.OptimizerState_set_period(self, p)
6966 def get_period(self):
6967 r"""get_period(OptimizerState self) -> unsigned int"""
6968 return _IMP_kernel.OptimizerState_get_period(self)
6971 r"""reset(OptimizerState self)"""
6972 return _IMP_kernel.OptimizerState_reset(self)
6974 def update_always(self):
6975 r"""update_always(OptimizerState self)"""
6976 return _IMP_kernel.OptimizerState_update_always(self)
6978 def get_number_of_updates(self):
6979 r"""get_number_of_updates(OptimizerState self) -> unsigned int"""
6980 return _IMP_kernel.OptimizerState_get_number_of_updates(self)
6982 def set_number_of_updates(self, n):
6983 r"""set_number_of_updates(OptimizerState self, unsigned int n)"""
6984 return _IMP_kernel.OptimizerState_set_number_of_updates(self, n)
6985 __swig_destroy__ = _IMP_kernel.delete_OptimizerState
6987 def do_update(self, arg0):
6988 r"""do_update(OptimizerState self, unsigned int arg0)"""
6989 return _IMP_kernel.OptimizerState_do_update(self, arg0)
6991 def do_set_is_optimizing(self, arg0):
6992 r"""do_set_is_optimizing(OptimizerState self, bool arg0)"""
6993 return _IMP_kernel.OptimizerState_do_set_is_optimizing(self, arg0)
6995 def do_get_inputs(self):
6996 r"""do_get_inputs(OptimizerState self) -> IMP::ModelObjectsTemp"""
6997 return _IMP_kernel.OptimizerState_do_get_inputs(self)
6999 def do_get_outputs(self):
7000 r"""do_get_outputs(OptimizerState self) -> IMP::ModelObjectsTemp"""
7001 return _IMP_kernel.OptimizerState_do_get_outputs(self)
7004 r"""__str__(OptimizerState self) -> std::string"""
7005 return _IMP_kernel.OptimizerState___str__(self)
7008 r"""__repr__(OptimizerState self) -> std::string"""
7009 return _IMP_kernel.OptimizerState___repr__(self)
7013 return _object_cast_to_OptimizerState(o)
7016 def do_show(self, out):
7021 return _object_cast_to_OptimizerState(o)
7024 def _get_jax(self, state_index):
7025 """Add JAX support for this OptimizerState.
7027 Each OptimizerState must explicitly support how it is going to
7028 be called when the Optimizer is run via JAX.
7030 OptimizerStates can run as traditional IMP CPU code
7031 on the IMP Model object, in which case None should be returned here.
7032 The Optimizer will sync any necessary information from JAX back
7033 with the IMP Model before calling the OptimizerState. However,
7034 the OptimizerState is not permitted to modify the Model; any
7035 changes will not be propagated back to the Optimizer.
7036 (For example, a thermostat which tries to change particle
7037 velocities will not function correctly.)
7039 Alternatively, a pure JAX implementation can be provided.
7040 See _wrap_jax for more information.
7042 raise NotImplementedError(
7043 f
"No JAX implementation for {self} ({type(self)})")
7045 def _wrap_jax(self, init_func, apply_func):
7046 """Create the return value for _get_jax.
7047 Use this method in _get_jax() to wrap the JAX function
7048 with other OptimizerState-specific information.
7050 @param init_func a JAX function which, given a JAX Optimizer,
7051 does any necessary setup and returns a (possibly modified)
7052 JAX Optimizer. If any OptimizerState-specific
7053 persistent state is needed, it can be stored in
7054 `opt.optimizer_states[state_index]` and later retrieved or
7055 modified in apply_func.
7056 @param apply_func a JAX function which, given a JAX Optimizer,
7057 does the JAX equivalent of do_update() and returns a new
7060 from IMP._jax_util
import JAXOptimizerStateInfo
7061 return JAXOptimizerStateInfo(self, init_func, apply_func)
7063 def __disown__(self):
7065 _IMP_kernel.disown_OptimizerState(self)
7066 return weakref.proxy(self)
7069 r"""do_destroy(OptimizerState self)"""
7070 return _IMP_kernel.OptimizerState_do_destroy(self)
7072 def handle_set_has_required_score_states(self, arg0):
7073 r"""handle_set_has_required_score_states(OptimizerState self, bool arg0)"""
7074 return _IMP_kernel.OptimizerState_handle_set_has_required_score_states(self, arg0)
7076 def do_get_interactions(self):
7077 r"""do_get_interactions(OptimizerState self) -> IMP::ModelObjectsTemps"""
7078 return _IMP_kernel.OptimizerState_do_get_interactions(self)
7081 _IMP_kernel.OptimizerState_swigregister(OptimizerState)
7083 r"""Proxy of C++ IMP::Refiner class."""
7085 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7087 def __init__(self, *args):
7088 r"""__init__(Refiner self, std::string name="Refiner %1%", bool is_by_ref=False) -> Refiner"""
7089 if self.__class__ == Refiner:
7093 _IMP_kernel.Refiner_swiginit(self, _IMP_kernel.new_Refiner(_self, *args))
7095 if self.__class__ != Refiner:
7096 _director_objects.register(self)
7101 def get_can_refine(self, arg0):
7102 r"""get_can_refine(Refiner self, Particle arg0) -> bool"""
7103 return _IMP_kernel.Refiner_get_can_refine(self, arg0)
7105 def get_refined_indexes(self, m, pi):
7106 r"""get_refined_indexes(Refiner self, Model m, ParticleIndex pi) -> IMP::ParticleIndexes"""
7107 return _IMP_kernel.Refiner_get_refined_indexes(self, m, pi)
7109 def get_refined_indexes_by_ref(self, m, pi):
7110 r"""get_refined_indexes_by_ref(Refiner self, Model m, ParticleIndex pi) -> IMP::ParticleIndexes const &"""
7111 return _IMP_kernel.Refiner_get_refined_indexes_by_ref(self, m, pi)
7113 def get_is_by_ref_supported(self):
7114 r"""get_is_by_ref_supported(Refiner self) -> bool"""
7115 return _IMP_kernel.Refiner_get_is_by_ref_supported(self)
7117 def get_refined(self, *args):
7119 get_refined(Refiner self, Particle a) -> IMP::ParticlesTemp const
7120 get_refined(Refiner self, Particle a, unsigned int i) -> Particle
7122 return _IMP_kernel.Refiner_get_refined(self, *args)
7124 def get_number_of_refined(self, a):
7125 r"""get_number_of_refined(Refiner self, Particle a) -> unsigned int"""
7126 return _IMP_kernel.Refiner_get_number_of_refined(self, a)
7129 r"""__str__(Refiner self) -> std::string"""
7130 return _IMP_kernel.Refiner___str__(self)
7133 r"""__repr__(Refiner self) -> std::string"""
7134 return _IMP_kernel.Refiner___repr__(self)
7138 return _object_cast_to_Refiner(o)
7141 def do_show(self, out):
7146 return _object_cast_to_Refiner(o)
7148 __swig_destroy__ = _IMP_kernel.delete_Refiner
7149 def __disown__(self):
7151 _IMP_kernel.disown_Refiner(self)
7152 return weakref.proxy(self)
7154 def do_get_inputs(self, m, pis):
7155 r"""do_get_inputs(Refiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7156 return _IMP_kernel.Refiner_do_get_inputs(self, m, pis)
7159 r"""do_destroy(Refiner self)"""
7160 return _IMP_kernel.Refiner_do_destroy(self)
7163 _IMP_kernel.Refiner_swigregister(Refiner)
7165 r"""Proxy of C++ IMP::Optimizer class."""
7167 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7169 def set_is_optimizing_states(self, tf):
7170 r"""set_is_optimizing_states(Optimizer self, bool tf)"""
7171 return _IMP_kernel.Optimizer_set_is_optimizing_states(self, tf)
7173 def get_optimizer_state_inputs(self):
7174 r"""get_optimizer_state_inputs(Optimizer self) -> IMP::ModelObjectsTemp"""
7175 return _IMP_kernel.Optimizer_get_optimizer_state_inputs(self)
7177 def do_get_inputs(self):
7178 r"""do_get_inputs(Optimizer self) -> IMP::ModelObjectsTemp"""
7179 return _IMP_kernel.Optimizer_do_get_inputs(self)
7181 def do_get_outputs(self):
7182 r"""do_get_outputs(Optimizer self) -> IMP::ModelObjectsTemp"""
7183 return _IMP_kernel.Optimizer_do_get_outputs(self)
7185 def __init__(self, *args):
7187 __init__(Optimizer self, Model m, std::string name="Optimizer %1%") -> Optimizer
7188 __init__(Optimizer self) -> Optimizer
7190 if self.__class__ == Optimizer:
7194 _IMP_kernel.Optimizer_swiginit(self, _IMP_kernel.new_Optimizer(_self, *args))
7196 if self.__class__ != Optimizer:
7197 _director_objects.register(self)
7202 def optimize(self, max_steps):
7203 r"""optimize(Optimizer self, unsigned int max_steps) -> double"""
7204 return _IMP_kernel.Optimizer_optimize(self, max_steps)
7206 def set_stop_on_good_score(self, tf):
7207 r"""set_stop_on_good_score(Optimizer self, bool tf)"""
7208 return _IMP_kernel.Optimizer_set_stop_on_good_score(self, tf)
7210 def get_stop_on_good_score(self):
7211 r"""get_stop_on_good_score(Optimizer self) -> bool"""
7212 return _IMP_kernel.Optimizer_get_stop_on_good_score(self)
7214 def get_last_score(self):
7215 r"""get_last_score(Optimizer self) -> double"""
7216 return _IMP_kernel.Optimizer_get_last_score(self)
7218 def get_scoring_function(self):
7219 r"""get_scoring_function(Optimizer self) -> ScoringFunction"""
7220 return _IMP_kernel.Optimizer_get_scoring_function(self)
7221 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)
7222 def __set_optimizer_states(self, obj): _list_util.set_varlist(self.optimizer_states, obj)
7223 def __del_optimizer_states(self): _list_util.del_varlist(self.optimizer_states)
7224 optimizer_states = property(__get_optimizer_states, __set_optimizer_states, __del_optimizer_states, doc=
"List of ##ucnames")
7226 def remove_optimizer_state(self, d):
7227 r"""remove_optimizer_state(Optimizer self, OptimizerState d)"""
7228 return _IMP_kernel.Optimizer_remove_optimizer_state(self, d)
7230 def _python_index_optimizer_state(self, d, start, stop):
7231 r"""_python_index_optimizer_state(Optimizer self, OptimizerState d, unsigned int start, unsigned int stop) -> unsigned int"""
7232 return _IMP_kernel.Optimizer__python_index_optimizer_state(self, d, start, stop)
7234 def remove_optimizer_states(self, d):
7235 r"""remove_optimizer_states(Optimizer self, IMP::OptimizerStates const & d)"""
7236 return _IMP_kernel.Optimizer_remove_optimizer_states(self, d)
7238 def set_optimizer_states(self, ps):
7239 r"""set_optimizer_states(Optimizer self, IMP::OptimizerStates const & ps)"""
7240 return _IMP_kernel.Optimizer_set_optimizer_states(self, ps)
7242 def set_optimizer_states_order(self, objs):
7243 r"""set_optimizer_states_order(Optimizer self, IMP::OptimizerStates const & objs)"""
7244 return _IMP_kernel.Optimizer_set_optimizer_states_order(self, objs)
7246 def add_optimizer_state(self, obj):
7247 r"""add_optimizer_state(Optimizer self, OptimizerState obj) -> unsigned int"""
7248 return _IMP_kernel.Optimizer_add_optimizer_state(self, obj)
7250 def add_optimizer_states(self, objs):
7251 r"""add_optimizer_states(Optimizer self, IMP::OptimizerStates const & objs)"""
7252 return _IMP_kernel.Optimizer_add_optimizer_states(self, objs)
7254 def clear_optimizer_states(self):
7255 r"""clear_optimizer_states(Optimizer self)"""
7256 return _IMP_kernel.Optimizer_clear_optimizer_states(self)
7258 def get_number_of_optimizer_states(self):
7259 r"""get_number_of_optimizer_states(Optimizer self) -> unsigned int"""
7260 return _IMP_kernel.Optimizer_get_number_of_optimizer_states(self)
7262 def get_has_optimizer_states(self):
7263 r"""get_has_optimizer_states(Optimizer self) -> bool"""
7264 return _IMP_kernel.Optimizer_get_has_optimizer_states(self)
7266 def get_optimizer_state(self, i):
7267 r"""get_optimizer_state(Optimizer self, unsigned int i) -> OptimizerState"""
7268 return _IMP_kernel.Optimizer_get_optimizer_state(self, i)
7270 def get_optimizer_states(self):
7271 r"""get_optimizer_states(Optimizer self) -> IMP::OptimizerStates"""
7272 return _IMP_kernel.Optimizer_get_optimizer_states(self)
7274 def erase_optimizer_state(self, i):
7275 r"""erase_optimizer_state(Optimizer self, unsigned int i)"""
7276 return _IMP_kernel.Optimizer_erase_optimizer_state(self, i)
7278 def reserve_optimizer_states(self, sz):
7279 r"""reserve_optimizer_states(Optimizer self, unsigned int sz)"""
7280 return _IMP_kernel.Optimizer_reserve_optimizer_states(self, sz)
7282 def set_scoring_function(self, sf):
7283 r"""set_scoring_function(Optimizer self, _ScoringFunctionAdaptor sf)"""
7284 return _IMP_kernel.Optimizer_set_scoring_function(self, sf)
7285 __swig_destroy__ = _IMP_kernel.delete_Optimizer
7287 r"""__del__(Optimizer self)"""
7289 _director_objects.cleanup()
7295 def do_optimize(self, ns):
7296 r"""do_optimize(Optimizer self, unsigned int ns) -> double"""
7297 return _IMP_kernel.Optimizer_do_optimize(self, ns)
7299 def update_states(self):
7300 r"""update_states(Optimizer self)"""
7301 return _IMP_kernel.Optimizer_update_states(self)
7304 r"""__str__(Optimizer self) -> std::string"""
7305 return _IMP_kernel.Optimizer___str__(self)
7308 r"""__repr__(Optimizer self) -> std::string"""
7309 return _IMP_kernel.Optimizer___repr__(self)
7313 return _object_cast_to_Optimizer(o)
7316 def do_show(self, out):
7321 return _object_cast_to_Optimizer(o)
7323 def __disown__(self):
7325 _IMP_kernel.disown_Optimizer(self)
7326 return weakref.proxy(self)
7329 r"""do_destroy(Optimizer self)"""
7330 return _IMP_kernel.Optimizer_do_destroy(self)
7332 def handle_set_has_required_score_states(self, arg0):
7333 r"""handle_set_has_required_score_states(Optimizer self, bool arg0)"""
7334 return _IMP_kernel.Optimizer_handle_set_has_required_score_states(self, arg0)
7336 def do_get_interactions(self):
7337 r"""do_get_interactions(Optimizer self) -> IMP::ModelObjectsTemps"""
7338 return _IMP_kernel.Optimizer_do_get_interactions(self)
7341 _IMP_kernel.Optimizer_swigregister(Optimizer)
7343 r"""Proxy of C++ IMP::AttributeOptimizer class."""
7345 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7347 def __init__(self, *args):
7349 __init__(AttributeOptimizer self, Model m, std::string name="Optimizer %1%") -> AttributeOptimizer
7350 __init__(AttributeOptimizer self) -> AttributeOptimizer
7352 if self.__class__ == AttributeOptimizer:
7356 _IMP_kernel.AttributeOptimizer_swiginit(self, _IMP_kernel.new_AttributeOptimizer(_self, *args))
7358 if self.__class__ != AttributeOptimizer:
7359 _director_objects.register(self)
7364 def get_optimized_attributes(self):
7365 r"""get_optimized_attributes(AttributeOptimizer self) -> IMP::FloatIndexes"""
7366 return _IMP_kernel.AttributeOptimizer_get_optimized_attributes(self)
7368 def set_value(self, fi, v):
7369 r"""set_value(AttributeOptimizer self, FloatIndex fi, double v)"""
7370 return _IMP_kernel.AttributeOptimizer_set_value(self, fi, v)
7372 def get_value(self, fi):
7373 r"""get_value(AttributeOptimizer self, FloatIndex fi) -> IMP::Float"""
7374 return _IMP_kernel.AttributeOptimizer_get_value(self, fi)
7376 def get_derivative(self, fi):
7377 r"""get_derivative(AttributeOptimizer self, FloatIndex fi) -> IMP::Float"""
7378 return _IMP_kernel.AttributeOptimizer_get_derivative(self, fi)
7380 def get_width(self, k):
7381 r"""get_width(AttributeOptimizer self, FloatKey k) -> double"""
7382 return _IMP_kernel.AttributeOptimizer_get_width(self, k)
7384 def set_scaled_value(self, fi, v):
7385 r"""set_scaled_value(AttributeOptimizer self, FloatIndex fi, IMP::Float v)"""
7386 return _IMP_kernel.AttributeOptimizer_set_scaled_value(self, fi, v)
7388 def get_scaled_value(self, fi):
7389 r"""get_scaled_value(AttributeOptimizer self, FloatIndex fi) -> double"""
7390 return _IMP_kernel.AttributeOptimizer_get_scaled_value(self, fi)
7392 def get_scaled_derivative(self, fi):
7393 r"""get_scaled_derivative(AttributeOptimizer self, FloatIndex fi) -> double"""
7394 return _IMP_kernel.AttributeOptimizer_get_scaled_derivative(self, fi)
7396 def clear_range_cache(self):
7397 r"""clear_range_cache(AttributeOptimizer self)"""
7398 return _IMP_kernel.AttributeOptimizer_clear_range_cache(self)
7401 r"""__str__(AttributeOptimizer self) -> std::string"""
7402 return _IMP_kernel.AttributeOptimizer___str__(self)
7405 r"""__repr__(AttributeOptimizer self) -> std::string"""
7406 return _IMP_kernel.AttributeOptimizer___repr__(self)
7410 return _object_cast_to_AttributeOptimizer(o)
7413 def do_show(self, out):
7418 return _object_cast_to_AttributeOptimizer(o)
7420 __swig_destroy__ = _IMP_kernel.delete_AttributeOptimizer
7421 def __disown__(self):
7423 _IMP_kernel.disown_AttributeOptimizer(self)
7424 return weakref.proxy(self)
7427 r"""do_destroy(AttributeOptimizer self)"""
7428 return _IMP_kernel.AttributeOptimizer_do_destroy(self)
7430 def handle_set_has_required_score_states(self, arg0):
7431 r"""handle_set_has_required_score_states(AttributeOptimizer self, bool arg0)"""
7432 return _IMP_kernel.AttributeOptimizer_handle_set_has_required_score_states(self, arg0)
7434 def do_get_inputs(self):
7435 r"""do_get_inputs(AttributeOptimizer self) -> IMP::ModelObjectsTemp"""
7436 return _IMP_kernel.AttributeOptimizer_do_get_inputs(self)
7438 def do_get_outputs(self):
7439 r"""do_get_outputs(AttributeOptimizer self) -> IMP::ModelObjectsTemp"""
7440 return _IMP_kernel.AttributeOptimizer_do_get_outputs(self)
7442 def do_get_interactions(self):
7443 r"""do_get_interactions(AttributeOptimizer self) -> IMP::ModelObjectsTemps"""
7444 return _IMP_kernel.AttributeOptimizer_do_get_interactions(self)
7446 def do_optimize(self, ns):
7447 r"""do_optimize(AttributeOptimizer self, unsigned int ns) -> double"""
7448 return _IMP_kernel.AttributeOptimizer_do_optimize(self, ns)
7451 _IMP_kernel.AttributeOptimizer_swigregister(AttributeOptimizer)
7453 r"""Proxy of C++ IMP::ConfigurationSet class."""
7455 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7457 def __init__(self, *args):
7458 r"""__init__(ConfigurationSet self, Model m, std::string name="ConfigurationSet %1%") -> ConfigurationSet"""
7459 _IMP_kernel.ConfigurationSet_swiginit(self, _IMP_kernel.new_ConfigurationSet(*args))
7461 def save_configuration(self):
7462 r"""save_configuration(ConfigurationSet self)"""
7463 return _IMP_kernel.ConfigurationSet_save_configuration(self)
7465 def get_number_of_configurations(self):
7466 r"""get_number_of_configurations(ConfigurationSet self) -> unsigned int"""
7467 return _IMP_kernel.ConfigurationSet_get_number_of_configurations(self)
7469 def load_configuration(self, i):
7470 r"""load_configuration(ConfigurationSet self, int i)"""
7471 return _IMP_kernel.ConfigurationSet_load_configuration(self, i)
7473 def remove_configuration(self, i):
7474 r"""remove_configuration(ConfigurationSet self, unsigned int i)"""
7475 return _IMP_kernel.ConfigurationSet_remove_configuration(self, i)
7477 def get_model(self):
7478 r"""get_model(ConfigurationSet self) -> Model"""
7479 return _IMP_kernel.ConfigurationSet_get_model(self)
7482 r"""get_version_info(ConfigurationSet self) -> VersionInfo"""
7483 return _IMP_kernel.ConfigurationSet_get_version_info(self)
7484 __swig_destroy__ = _IMP_kernel.delete_ConfigurationSet
7487 r"""__str__(ConfigurationSet self) -> std::string"""
7488 return _IMP_kernel.ConfigurationSet___str__(self)
7491 r"""__repr__(ConfigurationSet self) -> std::string"""
7492 return _IMP_kernel.ConfigurationSet___repr__(self)
7496 return _object_cast_to_ConfigurationSet(o)
7500 _IMP_kernel.ConfigurationSet_swigregister(ConfigurationSet)
7502 r"""Proxy of C++ IMP::SaveToConfigurationSetOptimizerState class."""
7504 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7506 def __init__(self, cs):
7507 r"""__init__(SaveToConfigurationSetOptimizerState self, ConfigurationSet cs) -> SaveToConfigurationSetOptimizerState"""
7508 _IMP_kernel.SaveToConfigurationSetOptimizerState_swiginit(self, _IMP_kernel.new_SaveToConfigurationSetOptimizerState(cs))
7511 r"""get_version_info(SaveToConfigurationSetOptimizerState self) -> VersionInfo"""
7512 return _IMP_kernel.SaveToConfigurationSetOptimizerState_get_version_info(self)
7513 __swig_destroy__ = _IMP_kernel.delete_SaveToConfigurationSetOptimizerState
7516 r"""__str__(SaveToConfigurationSetOptimizerState self) -> std::string"""
7517 return _IMP_kernel.SaveToConfigurationSetOptimizerState___str__(self)
7520 r"""__repr__(SaveToConfigurationSetOptimizerState self) -> std::string"""
7521 return _IMP_kernel.SaveToConfigurationSetOptimizerState___repr__(self)
7525 return _object_cast_to_SaveToConfigurationSetOptimizerState(o)
7529 _IMP_kernel.SaveToConfigurationSetOptimizerState_swigregister(SaveToConfigurationSetOptimizerState)
7531 r"""Proxy of C++ IMP::Configuration class."""
7533 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7535 def __init__(self, *args):
7537 __init__(Configuration self, Model m, std::string name="Configuration %1%") -> Configuration
7538 __init__(Configuration self, Model m, Configuration base, std::string name="Configuration %1%") -> Configuration
7540 _IMP_kernel.Configuration_swiginit(self, _IMP_kernel.new_Configuration(*args))
7542 def load_configuration(self):
7543 r"""load_configuration(Configuration self)"""
7544 return _IMP_kernel.Configuration_load_configuration(self)
7546 def swap_configuration(self):
7547 r"""swap_configuration(Configuration self)"""
7548 return _IMP_kernel.Configuration_swap_configuration(self)
7551 r"""get_version_info(Configuration self) -> VersionInfo"""
7552 return _IMP_kernel.Configuration_get_version_info(self)
7553 __swig_destroy__ = _IMP_kernel.delete_Configuration
7556 r"""__str__(Configuration self) -> std::string"""
7557 return _IMP_kernel.Configuration___str__(self)
7560 r"""__repr__(Configuration self) -> std::string"""
7561 return _IMP_kernel.Configuration___repr__(self)
7565 return _object_cast_to_Configuration(o)
7569 _IMP_kernel.Configuration_swigregister(Configuration)
7571 r"""Proxy of C++ IMP::Sampler class."""
7573 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7575 def __init__(self, *args):
7576 r"""__init__(Sampler self, Model m, std::string name="Sampler %1%") -> Sampler"""
7577 if self.__class__ == Sampler:
7581 _IMP_kernel.Sampler_swiginit(self, _IMP_kernel.new_Sampler(_self, *args))
7583 if self.__class__ != Sampler:
7584 _director_objects.register(self)
7589 def create_sample(self):
7590 r"""create_sample(Sampler self) -> ConfigurationSet"""
7591 return _IMP_kernel.Sampler_create_sample(self)
7593 def get_scoring_function(self):
7594 r"""get_scoring_function(Sampler self) -> ScoringFunction"""
7595 return _IMP_kernel.Sampler_get_scoring_function(self)
7597 def set_scoring_function(self, sf):
7598 r"""set_scoring_function(Sampler self, _ScoringFunctionAdaptor sf)"""
7599 return _IMP_kernel.Sampler_set_scoring_function(self, sf)
7601 def get_model(self):
7602 r"""get_model(Sampler self) -> Model"""
7603 return _IMP_kernel.Sampler_get_model(self)
7605 def do_sample(self):
7606 r"""do_sample(Sampler self) -> ConfigurationSet"""
7607 return _IMP_kernel.Sampler_do_sample(self)
7608 __swig_destroy__ = _IMP_kernel.delete_Sampler
7611 r"""__str__(Sampler self) -> std::string"""
7612 return _IMP_kernel.Sampler___str__(self)
7615 r"""__repr__(Sampler self) -> std::string"""
7616 return _IMP_kernel.Sampler___repr__(self)
7620 return _object_cast_to_Sampler(o)
7623 def do_show(self, out):
7628 return _object_cast_to_Sampler(o)
7630 def __disown__(self):
7632 _IMP_kernel.disown_Sampler(self)
7633 return weakref.proxy(self)
7636 r"""do_destroy(Sampler self)"""
7637 return _IMP_kernel.Sampler_do_destroy(self)
7640 _IMP_kernel.Sampler_swigregister(Sampler)
7642 r"""Proxy of C++ IMP::PairModifier class."""
7644 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7646 def __init__(self, *args):
7647 r"""__init__(PairModifier self, std::string name="PairModifier %1%") -> PairModifier"""
7648 if self.__class__ == PairModifier:
7652 _IMP_kernel.PairModifier_swiginit(self, _IMP_kernel.new_PairModifier(_self, *args))
7654 if self.__class__ != PairModifier:
7655 _director_objects.register(self)
7660 def apply_index(self, m, v):
7661 r"""apply_index(PairModifier self, Model m, IMP::ParticleIndexPair const & v)"""
7662 return _IMP_kernel.PairModifier_apply_index(self, m, v)
7664 def apply_indexes(self, m, o, lower_bound, upper_bound):
7665 r"""apply_indexes(PairModifier self, Model m, IMP::ParticleIndexPairs const & o, unsigned int lower_bound, unsigned int upper_bound)"""
7666 return _IMP_kernel.PairModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
7668 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
7669 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)"""
7670 return _IMP_kernel.PairModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
7673 r"""__str__(PairModifier self) -> std::string"""
7674 return _IMP_kernel.PairModifier___str__(self)
7677 r"""__repr__(PairModifier self) -> std::string"""
7678 return _IMP_kernel.PairModifier___repr__(self)
7682 return _object_cast_to_PairModifier(o)
7685 def do_show(self, out):
7690 return _object_cast_to_PairModifier(o)
7692 __swig_destroy__ = _IMP_kernel.delete_PairModifier
7693 def __disown__(self):
7695 _IMP_kernel.disown_PairModifier(self)
7696 return weakref.proxy(self)
7698 def do_get_inputs(self, m, pis):
7699 r"""do_get_inputs(PairModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7700 return _IMP_kernel.PairModifier_do_get_inputs(self, m, pis)
7702 def do_get_outputs(self, m, pis):
7703 r"""do_get_outputs(PairModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7704 return _IMP_kernel.PairModifier_do_get_outputs(self, m, pis)
7707 r"""do_destroy(PairModifier self)"""
7708 return _IMP_kernel.PairModifier_do_destroy(self)
7711 _IMP_kernel.PairModifier_swigregister(PairModifier)
7713 r"""Proxy of C++ IMP::PairScore class."""
7715 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7717 def __init__(self, *args):
7718 r"""__init__(PairScore self, std::string name="PairScore %1%") -> PairScore"""
7719 if self.__class__ == PairScore:
7723 _IMP_kernel.PairScore_swiginit(self, _IMP_kernel.new_PairScore(_self, *args))
7725 if self.__class__ != PairScore:
7726 _director_objects.register(self)
7731 def evaluate_index(self, m, vt, da):
7732 r"""evaluate_index(PairScore self, Model m, IMP::ParticleIndexPair const & vt, DerivativeAccumulator da) -> double"""
7733 return _IMP_kernel.PairScore_evaluate_index(self, m, vt, da)
7735 def check_indexes(self, m, pis):
7736 r"""check_indexes(PairScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
7737 return _IMP_kernel.PairScore_check_indexes(self, m, pis)
7739 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
7740 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"""
7741 return _IMP_kernel.PairScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
7743 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7744 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"""
7745 return _IMP_kernel.PairScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
7747 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
7748 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"""
7749 return _IMP_kernel.PairScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
7751 def evaluate_if_good_index(self, m, vt, da, max):
7752 r"""evaluate_if_good_index(PairScore self, Model m, IMP::ParticleIndexPair const & vt, DerivativeAccumulator da, double max) -> double"""
7753 return _IMP_kernel.PairScore_evaluate_if_good_index(self, m, vt, da, max)
7755 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7756 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"""
7757 return _IMP_kernel.PairScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
7759 def create_current_decomposition(self, m, vt):
7760 r"""create_current_decomposition(PairScore self, Model m, IMP::ParticleIndexPair const & vt) -> IMP::Restraints"""
7761 return _IMP_kernel.PairScore_create_current_decomposition(self, m, vt)
7763 def do_create_current_decomposition(self, m, vt):
7764 r"""do_create_current_decomposition(PairScore self, Model m, IMP::ParticleIndexPair const & vt) -> IMP::Restraints"""
7765 return _IMP_kernel.PairScore_do_create_current_decomposition(self, m, vt)
7766 __swig_destroy__ = _IMP_kernel.delete_PairScore
7769 r"""__str__(PairScore self) -> std::string"""
7770 return _IMP_kernel.PairScore___str__(self)
7773 r"""__repr__(PairScore self) -> std::string"""
7774 return _IMP_kernel.PairScore___repr__(self)
7778 return _object_cast_to_PairScore(o)
7781 def do_show(self, out):
7786 return _object_cast_to_PairScore(o)
7789 def _wrap_jax(self, m, score_func, keys=None):
7790 """Create the return value for _get_jax.
7791 Use this method in _get_jax() to wrap the JAX scoring function
7792 with other score-specific information.
7794 @param m The IMP.Model that the score will act on.
7795 @param score_func A function implemented using JAX that takes
7796 one argument (the current JAX Model) and returns the total
7798 @param keys Model attributes used by the PairScore.
7799 See IMP::Restraint::_wrap_jax.
7801 from IMP._jax_util
import JAXScoreInfo
7802 return JAXScoreInfo(m, score_func=score_func, keys=keys)
7804 def _get_jax(self, m, indexes):
7805 """Return a JAX implementation of this PairScore.
7806 Implement this method in a PairScore subclass to provide
7807 an equivalent function using [JAX](https://docs.jax.dev/)
7808 that scores the current JAX Model with a given set of
7809 ParticlePairIndexes. See also _wrap_jax.
7811 @param m The IMP.Model that the score will act on.
7812 @param indexes The ParticlePairIndexes that the score will act on.
7814 raise NotImplementedError(
7815 f
"No JAX implementation for {self} ({type(self)})")
7817 def __disown__(self):
7819 _IMP_kernel.disown_PairScore(self)
7820 return weakref.proxy(self)
7822 def do_get_inputs(self, m, pis):
7823 r"""do_get_inputs(PairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7824 return _IMP_kernel.PairScore_do_get_inputs(self, m, pis)
7827 r"""do_destroy(PairScore self)"""
7828 return _IMP_kernel.PairScore_do_destroy(self)
7831 _IMP_kernel.PairScore_swigregister(PairScore)
7833 r"""Proxy of C++ IMP::PairPredicate class."""
7835 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7837 def __init__(self, *args):
7838 r"""__init__(PairPredicate self, std::string name="PairPredicate %1%") -> PairPredicate"""
7839 if self.__class__ == PairPredicate:
7843 _IMP_kernel.PairPredicate_swiginit(self, _IMP_kernel.new_PairPredicate(_self, *args))
7845 if self.__class__ != PairPredicate:
7846 _director_objects.register(self)
7851 def setup_for_get_value_index_in_batch(self, arg0):
7852 r"""setup_for_get_value_index_in_batch(PairPredicate self, Model arg0)"""
7853 return _IMP_kernel.PairPredicate_setup_for_get_value_index_in_batch(self, arg0)
7855 def get_value_index_in_batch(self, m, vt):
7856 r"""get_value_index_in_batch(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int"""
7857 return _IMP_kernel.PairPredicate_get_value_index_in_batch(self, m, vt)
7859 def __call__(self, m, vt):
7860 r"""__call__(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int"""
7861 return _IMP_kernel.PairPredicate___call__(self, m, vt)
7863 def get_value_index(self, *args):
7865 get_value_index(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int
7866 get_value_index(PairPredicate self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
7868 return _IMP_kernel.PairPredicate_get_value_index(self, *args)
7869 __swig_destroy__ = _IMP_kernel.delete_PairPredicate
7872 r"""__str__(PairPredicate self) -> std::string"""
7873 return _IMP_kernel.PairPredicate___str__(self)
7876 r"""__repr__(PairPredicate self) -> std::string"""
7877 return _IMP_kernel.PairPredicate___repr__(self)
7881 return _object_cast_to_PairPredicate(o)
7884 def do_show(self, out):
7889 return _object_cast_to_PairPredicate(o)
7891 def __disown__(self):
7893 _IMP_kernel.disown_PairPredicate(self)
7894 return weakref.proxy(self)
7896 def do_get_inputs(self, m, pis):
7897 r"""do_get_inputs(PairPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7898 return _IMP_kernel.PairPredicate_do_get_inputs(self, m, pis)
7901 r"""do_destroy(PairPredicate self)"""
7902 return _IMP_kernel.PairPredicate_do_destroy(self)
7905 _IMP_kernel.PairPredicate_swigregister(PairPredicate)
7907 r"""Proxy of C++ IMP::PairContainer class."""
7909 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7911 def apply_generic(self, m):
7912 r"""apply_generic(PairContainer self, PairModifier m)"""
7913 return _IMP_kernel.PairContainer_apply_generic(self, m)
7915 def apply_generic_moved(self, m, moved_pis, reset_pis):
7916 r"""apply_generic_moved(PairContainer self, PairModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7917 return _IMP_kernel.PairContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
7919 def apply(self, sm):
7920 r"""apply(PairContainer self, PairModifier sm)"""
7921 return _IMP_kernel.PairContainer_apply(self, sm)
7923 def apply_moved(self, sm, moved_pis, reset_pis):
7924 r"""apply_moved(PairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7925 return _IMP_kernel.PairContainer_apply_moved(self, sm, moved_pis, reset_pis)
7927 def get_range_indexes(self):
7928 r"""get_range_indexes(PairContainer self) -> IMP::ParticleIndexPairs"""
7929 return _IMP_kernel.PairContainer_get_range_indexes(self)
7931 def get_contents(self):
7932 r"""get_contents(PairContainer self) -> IMP::ParticleIndexPairs const &"""
7933 return _IMP_kernel.PairContainer_get_contents(self)
7936 r"""get_indexes(PairContainer self) -> IMP::ParticleIndexPairs"""
7937 return _IMP_kernel.PairContainer_get_indexes(self)
7939 def get(self, *args):
7941 get(PairContainer self) -> IMP::ParticlePairsTemp
7942 get(PairContainer self, unsigned int i) -> IMP::ParticlePair
7944 return _IMP_kernel.PairContainer_get(self, *args)
7946 def get_number(self):
7947 r"""get_number(PairContainer self) -> unsigned int"""
7948 return _IMP_kernel.PairContainer_get_number(self)
7950 def __init__(self, *args):
7952 __init__(PairContainer self, Model m, std::string name="PairContainer %1%") -> PairContainer
7953 __init__(PairContainer self) -> PairContainer
7955 if self.__class__ == PairContainer:
7959 _IMP_kernel.PairContainer_swiginit(self, _IMP_kernel.new_PairContainer(_self, *args))
7961 if self.__class__ != PairContainer:
7962 _director_objects.register(self)
7967 def do_apply(self, sm):
7968 r"""do_apply(PairContainer self, PairModifier sm)"""
7969 return _IMP_kernel.PairContainer_do_apply(self, sm)
7971 def do_apply_moved(self, sm, moved_pis, reset_pis):
7972 r"""do_apply_moved(PairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7973 return _IMP_kernel.PairContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
7975 def do_get_provides_access(self):
7976 r"""do_get_provides_access(PairContainer self) -> bool"""
7977 return _IMP_kernel.PairContainer_do_get_provides_access(self)
7978 __swig_destroy__ = _IMP_kernel.delete_PairContainer
7981 r"""__str__(PairContainer self) -> std::string"""
7982 return _IMP_kernel.PairContainer___str__(self)
7985 r"""__repr__(PairContainer self) -> std::string"""
7986 return _IMP_kernel.PairContainer___repr__(self)
7990 return _object_cast_to_PairContainer(o)
7993 def do_show(self, out):
7998 return _object_cast_to_PairContainer(o)
8000 def __disown__(self):
8002 _IMP_kernel.disown_PairContainer(self)
8003 return weakref.proxy(self)
8006 r"""do_destroy(PairContainer self)"""
8007 return _IMP_kernel.PairContainer_do_destroy(self)
8009 def handle_set_has_required_score_states(self, arg0):
8010 r"""handle_set_has_required_score_states(PairContainer self, bool arg0)"""
8011 return _IMP_kernel.PairContainer_handle_set_has_required_score_states(self, arg0)
8013 def do_get_inputs(self):
8014 r"""do_get_inputs(PairContainer self) -> IMP::ModelObjectsTemp"""
8015 return _IMP_kernel.PairContainer_do_get_inputs(self)
8017 def do_get_interactions(self):
8018 r"""do_get_interactions(PairContainer self) -> IMP::ModelObjectsTemps"""
8019 return _IMP_kernel.PairContainer_do_get_interactions(self)
8021 def do_get_contents_hash(self):
8022 r"""do_get_contents_hash(PairContainer self) -> std::size_t"""
8023 return _IMP_kernel.PairContainer_do_get_contents_hash(self)
8026 _IMP_kernel.PairContainer_swigregister(PairContainer)
8027 class _PairContainerAdaptor(_InputAdaptor):
8028 r"""Proxy of C++ IMP::PairContainerAdaptor class."""
8030 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8031 __repr__ = _swig_repr
8033 def __init__(self, *args):
8035 __init__(_PairContainerAdaptor self) -> _PairContainerAdaptor
8036 __init__(_PairContainerAdaptor self, PairContainer c) -> _PairContainerAdaptor
8037 __init__(_PairContainerAdaptor self, IMP::ParticlePairsTemp const & t) -> _PairContainerAdaptor
8039 _IMP_kernel._PairContainerAdaptor_swiginit(self, _IMP_kernel.new__PairContainerAdaptor(*args))
8041 def set_name_if_default(self, name):
8042 r"""set_name_if_default(_PairContainerAdaptor self, std::string name)"""
8043 return _IMP_kernel._PairContainerAdaptor_set_name_if_default(self, name)
8044 __swig_destroy__ = _IMP_kernel.delete__PairContainerAdaptor
8047 _IMP_kernel._PairContainerAdaptor_swigregister(_PairContainerAdaptor)
8049 r"""Proxy of C++ IMP::QuadModifier class."""
8051 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8053 def __init__(self, *args):
8054 r"""__init__(QuadModifier self, std::string name="QuadModifier %1%") -> QuadModifier"""
8055 if self.__class__ == QuadModifier:
8059 _IMP_kernel.QuadModifier_swiginit(self, _IMP_kernel.new_QuadModifier(_self, *args))
8061 if self.__class__ != QuadModifier:
8062 _director_objects.register(self)
8067 def apply_index(self, m, v):
8068 r"""apply_index(QuadModifier self, Model m, IMP::ParticleIndexQuad const & v)"""
8069 return _IMP_kernel.QuadModifier_apply_index(self, m, v)
8071 def apply_indexes(self, m, o, lower_bound, upper_bound):
8072 r"""apply_indexes(QuadModifier self, Model m, IMP::ParticleIndexQuads const & o, unsigned int lower_bound, unsigned int upper_bound)"""
8073 return _IMP_kernel.QuadModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
8075 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
8076 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)"""
8077 return _IMP_kernel.QuadModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
8080 r"""__str__(QuadModifier self) -> std::string"""
8081 return _IMP_kernel.QuadModifier___str__(self)
8084 r"""__repr__(QuadModifier self) -> std::string"""
8085 return _IMP_kernel.QuadModifier___repr__(self)
8089 return _object_cast_to_QuadModifier(o)
8092 def do_show(self, out):
8097 return _object_cast_to_QuadModifier(o)
8099 __swig_destroy__ = _IMP_kernel.delete_QuadModifier
8100 def __disown__(self):
8102 _IMP_kernel.disown_QuadModifier(self)
8103 return weakref.proxy(self)
8105 def do_get_inputs(self, m, pis):
8106 r"""do_get_inputs(QuadModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8107 return _IMP_kernel.QuadModifier_do_get_inputs(self, m, pis)
8109 def do_get_outputs(self, m, pis):
8110 r"""do_get_outputs(QuadModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8111 return _IMP_kernel.QuadModifier_do_get_outputs(self, m, pis)
8114 r"""do_destroy(QuadModifier self)"""
8115 return _IMP_kernel.QuadModifier_do_destroy(self)
8118 _IMP_kernel.QuadModifier_swigregister(QuadModifier)
8120 r"""Proxy of C++ IMP::QuadScore class."""
8122 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8124 def __init__(self, *args):
8125 r"""__init__(QuadScore self, std::string name="QuadScore %1%") -> QuadScore"""
8126 if self.__class__ == QuadScore:
8130 _IMP_kernel.QuadScore_swiginit(self, _IMP_kernel.new_QuadScore(_self, *args))
8132 if self.__class__ != QuadScore:
8133 _director_objects.register(self)
8138 def evaluate_index(self, m, vt, da):
8139 r"""evaluate_index(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt, DerivativeAccumulator da) -> double"""
8140 return _IMP_kernel.QuadScore_evaluate_index(self, m, vt, da)
8142 def check_indexes(self, m, pis):
8143 r"""check_indexes(QuadScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
8144 return _IMP_kernel.QuadScore_check_indexes(self, m, pis)
8146 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
8147 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"""
8148 return _IMP_kernel.QuadScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
8150 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
8151 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"""
8152 return _IMP_kernel.QuadScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
8154 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
8155 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"""
8156 return _IMP_kernel.QuadScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
8158 def evaluate_if_good_index(self, m, vt, da, max):
8159 r"""evaluate_if_good_index(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt, DerivativeAccumulator da, double max) -> double"""
8160 return _IMP_kernel.QuadScore_evaluate_if_good_index(self, m, vt, da, max)
8162 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
8163 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"""
8164 return _IMP_kernel.QuadScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
8166 def create_current_decomposition(self, m, vt):
8167 r"""create_current_decomposition(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt) -> IMP::Restraints"""
8168 return _IMP_kernel.QuadScore_create_current_decomposition(self, m, vt)
8170 def do_create_current_decomposition(self, m, vt):
8171 r"""do_create_current_decomposition(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt) -> IMP::Restraints"""
8172 return _IMP_kernel.QuadScore_do_create_current_decomposition(self, m, vt)
8173 __swig_destroy__ = _IMP_kernel.delete_QuadScore
8176 r"""__str__(QuadScore self) -> std::string"""
8177 return _IMP_kernel.QuadScore___str__(self)
8180 r"""__repr__(QuadScore self) -> std::string"""
8181 return _IMP_kernel.QuadScore___repr__(self)
8185 return _object_cast_to_QuadScore(o)
8188 def do_show(self, out):
8193 return _object_cast_to_QuadScore(o)
8195 def __disown__(self):
8197 _IMP_kernel.disown_QuadScore(self)
8198 return weakref.proxy(self)
8200 def do_get_inputs(self, m, pis):
8201 r"""do_get_inputs(QuadScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8202 return _IMP_kernel.QuadScore_do_get_inputs(self, m, pis)
8205 r"""do_destroy(QuadScore self)"""
8206 return _IMP_kernel.QuadScore_do_destroy(self)
8209 _IMP_kernel.QuadScore_swigregister(QuadScore)
8211 r"""Proxy of C++ IMP::QuadPredicate class."""
8213 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8215 def __init__(self, *args):
8216 r"""__init__(QuadPredicate self, std::string name="QuadPredicate %1%") -> QuadPredicate"""
8217 if self.__class__ == QuadPredicate:
8221 _IMP_kernel.QuadPredicate_swiginit(self, _IMP_kernel.new_QuadPredicate(_self, *args))
8223 if self.__class__ != QuadPredicate:
8224 _director_objects.register(self)
8229 def setup_for_get_value_index_in_batch(self, arg0):
8230 r"""setup_for_get_value_index_in_batch(QuadPredicate self, Model arg0)"""
8231 return _IMP_kernel.QuadPredicate_setup_for_get_value_index_in_batch(self, arg0)
8233 def get_value_index_in_batch(self, m, vt):
8234 r"""get_value_index_in_batch(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int"""
8235 return _IMP_kernel.QuadPredicate_get_value_index_in_batch(self, m, vt)
8237 def __call__(self, m, vt):
8238 r"""__call__(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int"""
8239 return _IMP_kernel.QuadPredicate___call__(self, m, vt)
8241 def get_value_index(self, *args):
8243 get_value_index(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int
8244 get_value_index(QuadPredicate self, Model m, IMP::ParticleIndexQuads const & o) -> IMP::Ints
8246 return _IMP_kernel.QuadPredicate_get_value_index(self, *args)
8247 __swig_destroy__ = _IMP_kernel.delete_QuadPredicate
8250 r"""__str__(QuadPredicate self) -> std::string"""
8251 return _IMP_kernel.QuadPredicate___str__(self)
8254 r"""__repr__(QuadPredicate self) -> std::string"""
8255 return _IMP_kernel.QuadPredicate___repr__(self)
8259 return _object_cast_to_QuadPredicate(o)
8262 def do_show(self, out):
8267 return _object_cast_to_QuadPredicate(o)
8269 def __disown__(self):
8271 _IMP_kernel.disown_QuadPredicate(self)
8272 return weakref.proxy(self)
8274 def do_get_inputs(self, m, pis):
8275 r"""do_get_inputs(QuadPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8276 return _IMP_kernel.QuadPredicate_do_get_inputs(self, m, pis)
8279 r"""do_destroy(QuadPredicate self)"""
8280 return _IMP_kernel.QuadPredicate_do_destroy(self)
8283 _IMP_kernel.QuadPredicate_swigregister(QuadPredicate)
8285 r"""Proxy of C++ IMP::QuadContainer class."""
8287 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8289 def apply_generic(self, m):
8290 r"""apply_generic(QuadContainer self, QuadModifier m)"""
8291 return _IMP_kernel.QuadContainer_apply_generic(self, m)
8293 def apply_generic_moved(self, m, moved_pis, reset_pis):
8294 r"""apply_generic_moved(QuadContainer self, QuadModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8295 return _IMP_kernel.QuadContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
8297 def apply(self, sm):
8298 r"""apply(QuadContainer self, QuadModifier sm)"""
8299 return _IMP_kernel.QuadContainer_apply(self, sm)
8301 def apply_moved(self, sm, moved_pis, reset_pis):
8302 r"""apply_moved(QuadContainer self, QuadModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8303 return _IMP_kernel.QuadContainer_apply_moved(self, sm, moved_pis, reset_pis)
8305 def get_range_indexes(self):
8306 r"""get_range_indexes(QuadContainer self) -> IMP::ParticleIndexQuads"""
8307 return _IMP_kernel.QuadContainer_get_range_indexes(self)
8309 def get_contents(self):
8310 r"""get_contents(QuadContainer self) -> IMP::ParticleIndexQuads const &"""
8311 return _IMP_kernel.QuadContainer_get_contents(self)
8314 r"""get_indexes(QuadContainer self) -> IMP::ParticleIndexQuads"""
8315 return _IMP_kernel.QuadContainer_get_indexes(self)
8317 def get(self, *args):
8319 get(QuadContainer self) -> IMP::ParticleQuadsTemp
8320 get(QuadContainer self, unsigned int i) -> IMP::ParticleQuad
8322 return _IMP_kernel.QuadContainer_get(self, *args)
8324 def get_number(self):
8325 r"""get_number(QuadContainer self) -> unsigned int"""
8326 return _IMP_kernel.QuadContainer_get_number(self)
8328 def __init__(self, *args):
8330 __init__(QuadContainer self, Model m, std::string name="QuadContainer %1%") -> QuadContainer
8331 __init__(QuadContainer self) -> QuadContainer
8333 if self.__class__ == QuadContainer:
8337 _IMP_kernel.QuadContainer_swiginit(self, _IMP_kernel.new_QuadContainer(_self, *args))
8339 if self.__class__ != QuadContainer:
8340 _director_objects.register(self)
8345 def do_apply(self, sm):
8346 r"""do_apply(QuadContainer self, QuadModifier sm)"""
8347 return _IMP_kernel.QuadContainer_do_apply(self, sm)
8349 def do_apply_moved(self, sm, moved_pis, reset_pis):
8350 r"""do_apply_moved(QuadContainer self, QuadModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8351 return _IMP_kernel.QuadContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
8353 def do_get_provides_access(self):
8354 r"""do_get_provides_access(QuadContainer self) -> bool"""
8355 return _IMP_kernel.QuadContainer_do_get_provides_access(self)
8356 __swig_destroy__ = _IMP_kernel.delete_QuadContainer
8359 r"""__str__(QuadContainer self) -> std::string"""
8360 return _IMP_kernel.QuadContainer___str__(self)
8363 r"""__repr__(QuadContainer self) -> std::string"""
8364 return _IMP_kernel.QuadContainer___repr__(self)
8368 return _object_cast_to_QuadContainer(o)
8371 def do_show(self, out):
8376 return _object_cast_to_QuadContainer(o)
8378 def __disown__(self):
8380 _IMP_kernel.disown_QuadContainer(self)
8381 return weakref.proxy(self)
8384 r"""do_destroy(QuadContainer self)"""
8385 return _IMP_kernel.QuadContainer_do_destroy(self)
8387 def handle_set_has_required_score_states(self, arg0):
8388 r"""handle_set_has_required_score_states(QuadContainer self, bool arg0)"""
8389 return _IMP_kernel.QuadContainer_handle_set_has_required_score_states(self, arg0)
8391 def do_get_inputs(self):
8392 r"""do_get_inputs(QuadContainer self) -> IMP::ModelObjectsTemp"""
8393 return _IMP_kernel.QuadContainer_do_get_inputs(self)
8395 def do_get_interactions(self):
8396 r"""do_get_interactions(QuadContainer self) -> IMP::ModelObjectsTemps"""
8397 return _IMP_kernel.QuadContainer_do_get_interactions(self)
8399 def do_get_contents_hash(self):
8400 r"""do_get_contents_hash(QuadContainer self) -> std::size_t"""
8401 return _IMP_kernel.QuadContainer_do_get_contents_hash(self)
8404 _IMP_kernel.QuadContainer_swigregister(QuadContainer)
8405 class _QuadContainerAdaptor(_InputAdaptor):
8406 r"""Proxy of C++ IMP::QuadContainerAdaptor class."""
8408 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8409 __repr__ = _swig_repr
8411 def __init__(self, *args):
8413 __init__(_QuadContainerAdaptor self) -> _QuadContainerAdaptor
8414 __init__(_QuadContainerAdaptor self, QuadContainer c) -> _QuadContainerAdaptor
8415 __init__(_QuadContainerAdaptor self, IMP::ParticleQuadsTemp const & t) -> _QuadContainerAdaptor
8417 _IMP_kernel._QuadContainerAdaptor_swiginit(self, _IMP_kernel.new__QuadContainerAdaptor(*args))
8419 def set_name_if_default(self, name):
8420 r"""set_name_if_default(_QuadContainerAdaptor self, std::string name)"""
8421 return _IMP_kernel._QuadContainerAdaptor_set_name_if_default(self, name)
8422 __swig_destroy__ = _IMP_kernel.delete__QuadContainerAdaptor
8425 _IMP_kernel._QuadContainerAdaptor_swigregister(_QuadContainerAdaptor)
8427 r"""Proxy of C++ IMP::SingletonModifier class."""
8429 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8431 def __init__(self, *args):
8432 r"""__init__(SingletonModifier self, std::string name="SingletonModifier %1%") -> SingletonModifier"""
8433 if self.__class__ == SingletonModifier:
8437 _IMP_kernel.SingletonModifier_swiginit(self, _IMP_kernel.new_SingletonModifier(_self, *args))
8439 if self.__class__ != SingletonModifier:
8440 _director_objects.register(self)
8445 def apply_index(self, m, v):
8446 r"""apply_index(SingletonModifier self, Model m, ParticleIndex v)"""
8447 return _IMP_kernel.SingletonModifier_apply_index(self, m, v)
8449 def apply_indexes(self, m, o, lower_bound, upper_bound):
8450 r"""apply_indexes(SingletonModifier self, Model m, IMP::ParticleIndexes const & o, unsigned int lower_bound, unsigned int upper_bound)"""
8451 return _IMP_kernel.SingletonModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
8453 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
8454 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)"""
8455 return _IMP_kernel.SingletonModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
8458 r"""__str__(SingletonModifier self) -> std::string"""
8459 return _IMP_kernel.SingletonModifier___str__(self)
8462 r"""__repr__(SingletonModifier self) -> std::string"""
8463 return _IMP_kernel.SingletonModifier___repr__(self)
8467 return _object_cast_to_SingletonModifier(o)
8470 def do_show(self, out):
8475 return _object_cast_to_SingletonModifier(o)
8478 def _wrap_jax(self, apply_func, keys=None):
8479 """Create the return value for _get_jax.
8480 Use this method in _get_jax() to wrap the JAX function
8481 with other modifier-specific information.
8483 @param apply_func A function implemented using JAX that takes
8484 one argument (the current JAX Model) and returns a new
8486 @param keys Model attributes used by the SingletonModifier.
8487 See IMP::Restraint::_wrap_jax.
8489 from IMP._jax_util
import JAXModifierInfo
8490 return JAXModifierInfo(apply_func=apply_func, keys=keys)
8492 def _get_jax(self, m, indexes):
8493 """Return a JAX implementation of this SingletonModifier.
8494 Implement this method in a SingletonModifier subclass to provide
8495 an equivalent function using [JAX](https://docs.jax.dev/)
8496 that modifies the current JAX Model. See also _wrap_jax.
8498 @param m The IMP.Model that the modifier will act on.
8499 @param indexes The ParticleIndexes that the modifier will act on.
8501 raise NotImplementedError(
8502 f
"No JAX implementation for {self} ({type(self)})")
8504 __swig_destroy__ = _IMP_kernel.delete_SingletonModifier
8505 def __disown__(self):
8507 _IMP_kernel.disown_SingletonModifier(self)
8508 return weakref.proxy(self)
8510 def do_get_inputs(self, m, pis):
8511 r"""do_get_inputs(SingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8512 return _IMP_kernel.SingletonModifier_do_get_inputs(self, m, pis)
8514 def do_get_outputs(self, m, pis):
8515 r"""do_get_outputs(SingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8516 return _IMP_kernel.SingletonModifier_do_get_outputs(self, m, pis)
8519 r"""do_destroy(SingletonModifier self)"""
8520 return _IMP_kernel.SingletonModifier_do_destroy(self)
8523 _IMP_kernel.SingletonModifier_swigregister(SingletonModifier)
8525 r"""Proxy of C++ IMP::SingletonScore class."""
8527 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8529 def __init__(self, *args):
8530 r"""__init__(SingletonScore self, std::string name="SingletonScore %1%") -> SingletonScore"""
8531 if self.__class__ == SingletonScore:
8535 _IMP_kernel.SingletonScore_swiginit(self, _IMP_kernel.new_SingletonScore(_self, *args))
8537 if self.__class__ != SingletonScore:
8538 _director_objects.register(self)
8543 def evaluate_index(self, m, vt, da):
8544 r"""evaluate_index(SingletonScore self, Model m, ParticleIndex vt, DerivativeAccumulator da) -> double"""
8545 return _IMP_kernel.SingletonScore_evaluate_index(self, m, vt, da)
8547 def check_indexes(self, m, pis):
8548 r"""check_indexes(SingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
8549 return _IMP_kernel.SingletonScore_check_indexes(self, m, pis)
8551 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
8552 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"""
8553 return _IMP_kernel.SingletonScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
8555 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
8556 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"""
8557 return _IMP_kernel.SingletonScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
8559 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
8560 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"""
8561 return _IMP_kernel.SingletonScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
8563 def evaluate_if_good_index(self, m, vt, da, max):
8564 r"""evaluate_if_good_index(SingletonScore self, Model m, ParticleIndex vt, DerivativeAccumulator da, double max) -> double"""
8565 return _IMP_kernel.SingletonScore_evaluate_if_good_index(self, m, vt, da, max)
8567 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
8568 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"""
8569 return _IMP_kernel.SingletonScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
8571 def create_current_decomposition(self, m, vt):
8572 r"""create_current_decomposition(SingletonScore self, Model m, ParticleIndex vt) -> IMP::Restraints"""
8573 return _IMP_kernel.SingletonScore_create_current_decomposition(self, m, vt)
8575 def do_create_current_decomposition(self, m, vt):
8576 r"""do_create_current_decomposition(SingletonScore self, Model m, ParticleIndex vt) -> IMP::Restraints"""
8577 return _IMP_kernel.SingletonScore_do_create_current_decomposition(self, m, vt)
8578 __swig_destroy__ = _IMP_kernel.delete_SingletonScore
8581 r"""__str__(SingletonScore self) -> std::string"""
8582 return _IMP_kernel.SingletonScore___str__(self)
8585 r"""__repr__(SingletonScore self) -> std::string"""
8586 return _IMP_kernel.SingletonScore___repr__(self)
8590 return _object_cast_to_SingletonScore(o)
8593 def do_show(self, out):
8598 return _object_cast_to_SingletonScore(o)
8601 def _wrap_jax(self, m, score_func, keys=None):
8602 """See IMP::PairScore::_wrap_jax"""
8603 from IMP._jax_util
import JAXScoreInfo
8604 return JAXScoreInfo(m, score_func=score_func, keys=keys)
8606 def _get_jax(self, m, indexes):
8607 """See IMP::PairScore::_get_jax"""
8608 raise NotImplementedError(
8609 f
"No JAX implementation for {self} ({type(self)})")
8611 def __disown__(self):
8613 _IMP_kernel.disown_SingletonScore(self)
8614 return weakref.proxy(self)
8616 def do_get_inputs(self, m, pis):
8617 r"""do_get_inputs(SingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8618 return _IMP_kernel.SingletonScore_do_get_inputs(self, m, pis)
8621 r"""do_destroy(SingletonScore self)"""
8622 return _IMP_kernel.SingletonScore_do_destroy(self)
8625 _IMP_kernel.SingletonScore_swigregister(SingletonScore)
8627 r"""Proxy of C++ IMP::SingletonPredicate class."""
8629 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8631 def __init__(self, *args):
8632 r"""__init__(SingletonPredicate self, std::string name="SingletonPredicate %1%") -> SingletonPredicate"""
8633 if self.__class__ == SingletonPredicate:
8637 _IMP_kernel.SingletonPredicate_swiginit(self, _IMP_kernel.new_SingletonPredicate(_self, *args))
8639 if self.__class__ != SingletonPredicate:
8640 _director_objects.register(self)
8645 def setup_for_get_value_index_in_batch(self, arg0):
8646 r"""setup_for_get_value_index_in_batch(SingletonPredicate self, Model arg0)"""
8647 return _IMP_kernel.SingletonPredicate_setup_for_get_value_index_in_batch(self, arg0)
8649 def get_value_index_in_batch(self, m, vt):
8650 r"""get_value_index_in_batch(SingletonPredicate self, Model m, ParticleIndex vt) -> int"""
8651 return _IMP_kernel.SingletonPredicate_get_value_index_in_batch(self, m, vt)
8653 def __call__(self, m, vt):
8654 r"""__call__(SingletonPredicate self, Model m, ParticleIndex vt) -> int"""
8655 return _IMP_kernel.SingletonPredicate___call__(self, m, vt)
8657 def get_value_index(self, *args):
8659 get_value_index(SingletonPredicate self, Model m, ParticleIndex vt) -> int
8660 get_value_index(SingletonPredicate self, Model m, IMP::ParticleIndexes const & o) -> IMP::Ints
8662 return _IMP_kernel.SingletonPredicate_get_value_index(self, *args)
8663 __swig_destroy__ = _IMP_kernel.delete_SingletonPredicate
8666 r"""__str__(SingletonPredicate self) -> std::string"""
8667 return _IMP_kernel.SingletonPredicate___str__(self)
8670 r"""__repr__(SingletonPredicate self) -> std::string"""
8671 return _IMP_kernel.SingletonPredicate___repr__(self)
8675 return _object_cast_to_SingletonPredicate(o)
8678 def do_show(self, out):
8683 return _object_cast_to_SingletonPredicate(o)
8685 def __disown__(self):
8687 _IMP_kernel.disown_SingletonPredicate(self)
8688 return weakref.proxy(self)
8690 def do_get_inputs(self, m, pis):
8691 r"""do_get_inputs(SingletonPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8692 return _IMP_kernel.SingletonPredicate_do_get_inputs(self, m, pis)
8695 r"""do_destroy(SingletonPredicate self)"""
8696 return _IMP_kernel.SingletonPredicate_do_destroy(self)
8699 _IMP_kernel.SingletonPredicate_swigregister(SingletonPredicate)
8701 r"""Proxy of C++ IMP::SingletonContainer class."""
8703 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8705 def apply_generic(self, m):
8706 r"""apply_generic(SingletonContainer self, SingletonModifier m)"""
8707 return _IMP_kernel.SingletonContainer_apply_generic(self, m)
8709 def apply_generic_moved(self, m, moved_pis, reset_pis):
8710 r"""apply_generic_moved(SingletonContainer self, SingletonModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8711 return _IMP_kernel.SingletonContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
8713 def apply(self, sm):
8714 r"""apply(SingletonContainer self, SingletonModifier sm)"""
8715 return _IMP_kernel.SingletonContainer_apply(self, sm)
8717 def apply_moved(self, sm, moved_pis, reset_pis):
8718 r"""apply_moved(SingletonContainer self, SingletonModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8719 return _IMP_kernel.SingletonContainer_apply_moved(self, sm, moved_pis, reset_pis)
8721 def get_range_indexes(self):
8722 r"""get_range_indexes(SingletonContainer self) -> IMP::ParticleIndexes"""
8723 return _IMP_kernel.SingletonContainer_get_range_indexes(self)
8725 def get_contents(self):
8726 r"""get_contents(SingletonContainer self) -> IMP::ParticleIndexes const &"""
8727 return _IMP_kernel.SingletonContainer_get_contents(self)
8730 r"""get_indexes(SingletonContainer self) -> IMP::ParticleIndexes"""
8731 return _IMP_kernel.SingletonContainer_get_indexes(self)
8733 def get(self, *args):
8735 get(SingletonContainer self) -> IMP::ParticlesTemp
8736 get(SingletonContainer self, unsigned int i) -> Particle
8738 return _IMP_kernel.SingletonContainer_get(self, *args)
8740 def get_number(self):
8741 r"""get_number(SingletonContainer self) -> unsigned int"""
8742 return _IMP_kernel.SingletonContainer_get_number(self)
8744 def __init__(self, *args):
8746 __init__(SingletonContainer self, Model m, std::string name="SingletonContainer %1%") -> SingletonContainer
8747 __init__(SingletonContainer self) -> SingletonContainer
8749 if self.__class__ == SingletonContainer:
8753 _IMP_kernel.SingletonContainer_swiginit(self, _IMP_kernel.new_SingletonContainer(_self, *args))
8755 if self.__class__ != SingletonContainer:
8756 _director_objects.register(self)
8761 def do_apply(self, sm):
8762 r"""do_apply(SingletonContainer self, SingletonModifier sm)"""
8763 return _IMP_kernel.SingletonContainer_do_apply(self, sm)
8765 def do_apply_moved(self, sm, moved_pis, reset_pis):
8766 r"""do_apply_moved(SingletonContainer self, SingletonModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8767 return _IMP_kernel.SingletonContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
8769 def do_get_provides_access(self):
8770 r"""do_get_provides_access(SingletonContainer self) -> bool"""
8771 return _IMP_kernel.SingletonContainer_do_get_provides_access(self)
8772 __swig_destroy__ = _IMP_kernel.delete_SingletonContainer
8775 r"""__str__(SingletonContainer self) -> std::string"""
8776 return _IMP_kernel.SingletonContainer___str__(self)
8779 r"""__repr__(SingletonContainer self) -> std::string"""
8780 return _IMP_kernel.SingletonContainer___repr__(self)
8784 return _object_cast_to_SingletonContainer(o)
8787 def do_show(self, out):
8792 return _object_cast_to_SingletonContainer(o)
8794 def __disown__(self):
8796 _IMP_kernel.disown_SingletonContainer(self)
8797 return weakref.proxy(self)
8800 r"""do_destroy(SingletonContainer self)"""
8801 return _IMP_kernel.SingletonContainer_do_destroy(self)
8803 def handle_set_has_required_score_states(self, arg0):
8804 r"""handle_set_has_required_score_states(SingletonContainer self, bool arg0)"""
8805 return _IMP_kernel.SingletonContainer_handle_set_has_required_score_states(self, arg0)
8807 def do_get_inputs(self):
8808 r"""do_get_inputs(SingletonContainer self) -> IMP::ModelObjectsTemp"""
8809 return _IMP_kernel.SingletonContainer_do_get_inputs(self)
8811 def do_get_interactions(self):
8812 r"""do_get_interactions(SingletonContainer self) -> IMP::ModelObjectsTemps"""
8813 return _IMP_kernel.SingletonContainer_do_get_interactions(self)
8815 def do_get_contents_hash(self):
8816 r"""do_get_contents_hash(SingletonContainer self) -> std::size_t"""
8817 return _IMP_kernel.SingletonContainer_do_get_contents_hash(self)
8820 _IMP_kernel.SingletonContainer_swigregister(SingletonContainer)
8821 class _SingletonContainerAdaptor(_InputAdaptor):
8822 r"""Proxy of C++ IMP::SingletonContainerAdaptor class."""
8824 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8825 __repr__ = _swig_repr
8827 def __init__(self, *args):
8829 __init__(_SingletonContainerAdaptor self) -> _SingletonContainerAdaptor
8830 __init__(_SingletonContainerAdaptor self, SingletonContainer c) -> _SingletonContainerAdaptor
8831 __init__(_SingletonContainerAdaptor self, IMP::ParticlesTemp const & t) -> _SingletonContainerAdaptor
8833 _IMP_kernel._SingletonContainerAdaptor_swiginit(self, _IMP_kernel.new__SingletonContainerAdaptor(*args))
8835 def set_name_if_default(self, name):
8836 r"""set_name_if_default(_SingletonContainerAdaptor self, std::string name)"""
8837 return _IMP_kernel._SingletonContainerAdaptor_set_name_if_default(self, name)
8838 __swig_destroy__ = _IMP_kernel.delete__SingletonContainerAdaptor
8841 _IMP_kernel._SingletonContainerAdaptor_swigregister(_SingletonContainerAdaptor)
8843 r"""Proxy of C++ IMP::TripletModifier class."""
8845 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8847 def __init__(self, *args):
8848 r"""__init__(TripletModifier self, std::string name="TripletModifier %1%") -> TripletModifier"""
8849 if self.__class__ == TripletModifier:
8853 _IMP_kernel.TripletModifier_swiginit(self, _IMP_kernel.new_TripletModifier(_self, *args))
8855 if self.__class__ != TripletModifier:
8856 _director_objects.register(self)
8861 def apply_index(self, m, v):
8862 r"""apply_index(TripletModifier self, Model m, IMP::ParticleIndexTriplet const & v)"""
8863 return _IMP_kernel.TripletModifier_apply_index(self, m, v)
8865 def apply_indexes(self, m, o, lower_bound, upper_bound):
8866 r"""apply_indexes(TripletModifier self, Model m, IMP::ParticleIndexTriplets const & o, unsigned int lower_bound, unsigned int upper_bound)"""
8867 return _IMP_kernel.TripletModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
8869 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
8870 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)"""
8871 return _IMP_kernel.TripletModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
8874 r"""__str__(TripletModifier self) -> std::string"""
8875 return _IMP_kernel.TripletModifier___str__(self)
8878 r"""__repr__(TripletModifier self) -> std::string"""
8879 return _IMP_kernel.TripletModifier___repr__(self)
8883 return _object_cast_to_TripletModifier(o)
8886 def do_show(self, out):
8891 return _object_cast_to_TripletModifier(o)
8893 __swig_destroy__ = _IMP_kernel.delete_TripletModifier
8894 def __disown__(self):
8896 _IMP_kernel.disown_TripletModifier(self)
8897 return weakref.proxy(self)
8899 def do_get_inputs(self, m, pis):
8900 r"""do_get_inputs(TripletModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8901 return _IMP_kernel.TripletModifier_do_get_inputs(self, m, pis)
8903 def do_get_outputs(self, m, pis):
8904 r"""do_get_outputs(TripletModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8905 return _IMP_kernel.TripletModifier_do_get_outputs(self, m, pis)
8908 r"""do_destroy(TripletModifier self)"""
8909 return _IMP_kernel.TripletModifier_do_destroy(self)
8912 _IMP_kernel.TripletModifier_swigregister(TripletModifier)
8914 r"""Proxy of C++ IMP::TripletScore class."""
8916 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8918 def __init__(self, *args):
8919 r"""__init__(TripletScore self, std::string name="TripletScore %1%") -> TripletScore"""
8920 if self.__class__ == TripletScore:
8924 _IMP_kernel.TripletScore_swiginit(self, _IMP_kernel.new_TripletScore(_self, *args))
8926 if self.__class__ != TripletScore:
8927 _director_objects.register(self)
8932 def evaluate_index(self, m, vt, da):
8933 r"""evaluate_index(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt, DerivativeAccumulator da) -> double"""
8934 return _IMP_kernel.TripletScore_evaluate_index(self, m, vt, da)
8936 def check_indexes(self, m, pis):
8937 r"""check_indexes(TripletScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
8938 return _IMP_kernel.TripletScore_check_indexes(self, m, pis)
8940 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
8941 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"""
8942 return _IMP_kernel.TripletScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
8944 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
8945 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"""
8946 return _IMP_kernel.TripletScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
8948 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
8949 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"""
8950 return _IMP_kernel.TripletScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
8952 def evaluate_if_good_index(self, m, vt, da, max):
8953 r"""evaluate_if_good_index(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt, DerivativeAccumulator da, double max) -> double"""
8954 return _IMP_kernel.TripletScore_evaluate_if_good_index(self, m, vt, da, max)
8956 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
8957 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"""
8958 return _IMP_kernel.TripletScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
8960 def create_current_decomposition(self, m, vt):
8961 r"""create_current_decomposition(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt) -> IMP::Restraints"""
8962 return _IMP_kernel.TripletScore_create_current_decomposition(self, m, vt)
8964 def do_create_current_decomposition(self, m, vt):
8965 r"""do_create_current_decomposition(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt) -> IMP::Restraints"""
8966 return _IMP_kernel.TripletScore_do_create_current_decomposition(self, m, vt)
8967 __swig_destroy__ = _IMP_kernel.delete_TripletScore
8970 r"""__str__(TripletScore self) -> std::string"""
8971 return _IMP_kernel.TripletScore___str__(self)
8974 r"""__repr__(TripletScore self) -> std::string"""
8975 return _IMP_kernel.TripletScore___repr__(self)
8979 return _object_cast_to_TripletScore(o)
8982 def do_show(self, out):
8987 return _object_cast_to_TripletScore(o)
8989 def __disown__(self):
8991 _IMP_kernel.disown_TripletScore(self)
8992 return weakref.proxy(self)
8994 def do_get_inputs(self, m, pis):
8995 r"""do_get_inputs(TripletScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
8996 return _IMP_kernel.TripletScore_do_get_inputs(self, m, pis)
8999 r"""do_destroy(TripletScore self)"""
9000 return _IMP_kernel.TripletScore_do_destroy(self)
9003 _IMP_kernel.TripletScore_swigregister(TripletScore)
9005 r"""Proxy of C++ IMP::TripletPredicate class."""
9007 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9009 def __init__(self, *args):
9010 r"""__init__(TripletPredicate self, std::string name="TripletPredicate %1%") -> TripletPredicate"""
9011 if self.__class__ == TripletPredicate:
9015 _IMP_kernel.TripletPredicate_swiginit(self, _IMP_kernel.new_TripletPredicate(_self, *args))
9017 if self.__class__ != TripletPredicate:
9018 _director_objects.register(self)
9023 def setup_for_get_value_index_in_batch(self, arg0):
9024 r"""setup_for_get_value_index_in_batch(TripletPredicate self, Model arg0)"""
9025 return _IMP_kernel.TripletPredicate_setup_for_get_value_index_in_batch(self, arg0)
9027 def get_value_index_in_batch(self, m, vt):
9028 r"""get_value_index_in_batch(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int"""
9029 return _IMP_kernel.TripletPredicate_get_value_index_in_batch(self, m, vt)
9031 def __call__(self, m, vt):
9032 r"""__call__(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int"""
9033 return _IMP_kernel.TripletPredicate___call__(self, m, vt)
9035 def get_value_index(self, *args):
9037 get_value_index(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int
9038 get_value_index(TripletPredicate self, Model m, IMP::ParticleIndexTriplets const & o) -> IMP::Ints
9040 return _IMP_kernel.TripletPredicate_get_value_index(self, *args)
9041 __swig_destroy__ = _IMP_kernel.delete_TripletPredicate
9044 r"""__str__(TripletPredicate self) -> std::string"""
9045 return _IMP_kernel.TripletPredicate___str__(self)
9048 r"""__repr__(TripletPredicate self) -> std::string"""
9049 return _IMP_kernel.TripletPredicate___repr__(self)
9053 return _object_cast_to_TripletPredicate(o)
9056 def do_show(self, out):
9061 return _object_cast_to_TripletPredicate(o)
9063 def __disown__(self):
9065 _IMP_kernel.disown_TripletPredicate(self)
9066 return weakref.proxy(self)
9068 def do_get_inputs(self, m, pis):
9069 r"""do_get_inputs(TripletPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
9070 return _IMP_kernel.TripletPredicate_do_get_inputs(self, m, pis)
9073 r"""do_destroy(TripletPredicate self)"""
9074 return _IMP_kernel.TripletPredicate_do_destroy(self)
9077 _IMP_kernel.TripletPredicate_swigregister(TripletPredicate)
9079 r"""Proxy of C++ IMP::TripletContainer class."""
9081 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9083 def apply_generic(self, m):
9084 r"""apply_generic(TripletContainer self, TripletModifier m)"""
9085 return _IMP_kernel.TripletContainer_apply_generic(self, m)
9087 def apply_generic_moved(self, m, moved_pis, reset_pis):
9088 r"""apply_generic_moved(TripletContainer self, TripletModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
9089 return _IMP_kernel.TripletContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
9091 def apply(self, sm):
9092 r"""apply(TripletContainer self, TripletModifier sm)"""
9093 return _IMP_kernel.TripletContainer_apply(self, sm)
9095 def apply_moved(self, sm, moved_pis, reset_pis):
9096 r"""apply_moved(TripletContainer self, TripletModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
9097 return _IMP_kernel.TripletContainer_apply_moved(self, sm, moved_pis, reset_pis)
9099 def get_range_indexes(self):
9100 r"""get_range_indexes(TripletContainer self) -> IMP::ParticleIndexTriplets"""
9101 return _IMP_kernel.TripletContainer_get_range_indexes(self)
9103 def get_contents(self):
9104 r"""get_contents(TripletContainer self) -> IMP::ParticleIndexTriplets const &"""
9105 return _IMP_kernel.TripletContainer_get_contents(self)
9108 r"""get_indexes(TripletContainer self) -> IMP::ParticleIndexTriplets"""
9109 return _IMP_kernel.TripletContainer_get_indexes(self)
9111 def get(self, *args):
9113 get(TripletContainer self) -> IMP::ParticleTripletsTemp
9114 get(TripletContainer self, unsigned int i) -> IMP::ParticleTriplet
9116 return _IMP_kernel.TripletContainer_get(self, *args)
9118 def get_number(self):
9119 r"""get_number(TripletContainer self) -> unsigned int"""
9120 return _IMP_kernel.TripletContainer_get_number(self)
9122 def __init__(self, *args):
9124 __init__(TripletContainer self, Model m, std::string name="TripletContainer %1%") -> TripletContainer
9125 __init__(TripletContainer self) -> TripletContainer
9127 if self.__class__ == TripletContainer:
9131 _IMP_kernel.TripletContainer_swiginit(self, _IMP_kernel.new_TripletContainer(_self, *args))
9133 if self.__class__ != TripletContainer:
9134 _director_objects.register(self)
9139 def do_apply(self, sm):
9140 r"""do_apply(TripletContainer self, TripletModifier sm)"""
9141 return _IMP_kernel.TripletContainer_do_apply(self, sm)
9143 def do_apply_moved(self, sm, moved_pis, reset_pis):
9144 r"""do_apply_moved(TripletContainer self, TripletModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
9145 return _IMP_kernel.TripletContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
9147 def do_get_provides_access(self):
9148 r"""do_get_provides_access(TripletContainer self) -> bool"""
9149 return _IMP_kernel.TripletContainer_do_get_provides_access(self)
9150 __swig_destroy__ = _IMP_kernel.delete_TripletContainer
9153 r"""__str__(TripletContainer self) -> std::string"""
9154 return _IMP_kernel.TripletContainer___str__(self)
9157 r"""__repr__(TripletContainer self) -> std::string"""
9158 return _IMP_kernel.TripletContainer___repr__(self)
9162 return _object_cast_to_TripletContainer(o)
9165 def do_show(self, out):
9170 return _object_cast_to_TripletContainer(o)
9172 def __disown__(self):
9174 _IMP_kernel.disown_TripletContainer(self)
9175 return weakref.proxy(self)
9178 r"""do_destroy(TripletContainer self)"""
9179 return _IMP_kernel.TripletContainer_do_destroy(self)
9181 def handle_set_has_required_score_states(self, arg0):
9182 r"""handle_set_has_required_score_states(TripletContainer self, bool arg0)"""
9183 return _IMP_kernel.TripletContainer_handle_set_has_required_score_states(self, arg0)
9185 def do_get_inputs(self):
9186 r"""do_get_inputs(TripletContainer self) -> IMP::ModelObjectsTemp"""
9187 return _IMP_kernel.TripletContainer_do_get_inputs(self)
9189 def do_get_interactions(self):
9190 r"""do_get_interactions(TripletContainer self) -> IMP::ModelObjectsTemps"""
9191 return _IMP_kernel.TripletContainer_do_get_interactions(self)
9193 def do_get_contents_hash(self):
9194 r"""do_get_contents_hash(TripletContainer self) -> std::size_t"""
9195 return _IMP_kernel.TripletContainer_do_get_contents_hash(self)
9198 _IMP_kernel.TripletContainer_swigregister(TripletContainer)
9199 class _TripletContainerAdaptor(_InputAdaptor):
9200 r"""Proxy of C++ IMP::TripletContainerAdaptor class."""
9202 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9203 __repr__ = _swig_repr
9205 def __init__(self, *args):
9207 __init__(_TripletContainerAdaptor self) -> _TripletContainerAdaptor
9208 __init__(_TripletContainerAdaptor self, TripletContainer c) -> _TripletContainerAdaptor
9209 __init__(_TripletContainerAdaptor self, IMP::ParticleTripletsTemp const & t) -> _TripletContainerAdaptor
9211 _IMP_kernel._TripletContainerAdaptor_swiginit(self, _IMP_kernel.new__TripletContainerAdaptor(*args))
9213 def set_name_if_default(self, name):
9214 r"""set_name_if_default(_TripletContainerAdaptor self, std::string name)"""
9215 return _IMP_kernel._TripletContainerAdaptor_set_name_if_default(self, name)
9216 __swig_destroy__ = _IMP_kernel.delete__TripletContainerAdaptor
9219 _IMP_kernel._TripletContainerAdaptor_swigregister(_TripletContainerAdaptor)
9222 r"""write_particles_to_buffer(IMP::ParticlesTemp const & particles, IMP::FloatKeys const & keys) -> IMP::Vector< char,std::allocator< char > >"""
9223 return _IMP_kernel.write_particles_to_buffer(particles, keys)
9226 r"""read_particles_from_buffer(IMP::Vector< char,std::allocator< char > > const & buffer, IMP::ParticlesTemp const & particles, IMP::FloatKeys const & keys)"""
9227 return _IMP_kernel.read_particles_from_buffer(buffer, particles, keys)
9230 r"""get_particles(Model m, IMP::ParticleIndexes const & ps) -> IMP::ParticlesTemp"""
9231 return _IMP_kernel.get_particles(m, ps)
9235 get_indexes(IMP::ParticlesTemp const & ps) -> IMP::ParticleIndexes
9236 get_indexes(IMP::ParticlePairsTemp const & ps) -> IMP::ParticleIndexPairs
9238 return _IMP_kernel.get_indexes(*args)
9239 class _ParticleIndexAdaptor(object):
9240 r"""Proxy of C++ IMP::ParticleIndexAdaptor class."""
9242 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9243 __repr__ = _swig_repr
9245 def __init__(self, *args):
9247 __init__(_ParticleIndexAdaptor self, Particle p) -> _ParticleIndexAdaptor
9248 __init__(_ParticleIndexAdaptor self, ParticleIndex pi) -> _ParticleIndexAdaptor
9249 __init__(_ParticleIndexAdaptor self, Decorator d) -> _ParticleIndexAdaptor
9251 _IMP_kernel._ParticleIndexAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexAdaptor(*args))
9252 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexAdaptor
9255 _IMP_kernel._ParticleIndexAdaptor_swigregister(_ParticleIndexAdaptor)
9256 class _ParticleIndexesAdaptor(_InputAdaptor):
9257 r"""Proxy of C++ IMP::ParticleIndexesAdaptor class."""
9259 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9260 __repr__ = _swig_repr
9262 def __init__(self, *args):
9264 __init__(_ParticleIndexesAdaptor self, IMP::ParticlesTemp const & ps) -> _ParticleIndexesAdaptor
9265 __init__(_ParticleIndexesAdaptor self, IMP::ParticleIndexes const & pi) -> _ParticleIndexesAdaptor
9266 __init__(_ParticleIndexesAdaptor self) -> _ParticleIndexesAdaptor
9268 _IMP_kernel._ParticleIndexesAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexesAdaptor(*args))
9269 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexesAdaptor
9272 _IMP_kernel._ParticleIndexesAdaptor_swigregister(_ParticleIndexesAdaptor)
9273 class _ParticleIndexPairsAdaptor(object):
9274 r"""Proxy of C++ IMP::ParticleIndexPairsAdaptor class."""
9276 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9277 __repr__ = _swig_repr
9279 def __init__(self, *args):
9281 __init__(_ParticleIndexPairsAdaptor self, IMP::ParticlePairsTemp const & ps) -> _ParticleIndexPairsAdaptor
9282 __init__(_ParticleIndexPairsAdaptor self, IMP::ParticleIndexPairs const & pi) -> _ParticleIndexPairsAdaptor
9283 __init__(_ParticleIndexPairsAdaptor self) -> _ParticleIndexPairsAdaptor
9285 _IMP_kernel._ParticleIndexPairsAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexPairsAdaptor(*args))
9286 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexPairsAdaptor
9289 _IMP_kernel._ParticleIndexPairsAdaptor_swigregister(_ParticleIndexPairsAdaptor)
9291 r"""Proxy of C++ IMP::internal::_ConstRestraint class."""
9293 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9295 def __init__(self, *args):
9297 __init__(_ConstRestraint self, Model m, IMP::ParticleIndexes const & pis, double v) -> _ConstRestraint
9298 __init__(_ConstRestraint self) -> _ConstRestraint
9300 _IMP_kernel._ConstRestraint_swiginit(self, _IMP_kernel.new__ConstRestraint(*args))
9302 def get_value(self):
9303 r"""get_value(_ConstRestraint self) -> double"""
9304 return _IMP_kernel._ConstRestraint_get_value(self)
9306 def do_create_decomposition(self):
9307 r"""do_create_decomposition(_ConstRestraint self) -> IMP::Restraints"""
9308 return _IMP_kernel._ConstRestraint_do_create_decomposition(self)
9310 def do_get_inputs(self):
9311 r"""do_get_inputs(_ConstRestraint self) -> IMP::ModelObjectsTemp"""
9312 return _IMP_kernel._ConstRestraint_do_get_inputs(self)
9315 r"""get_version_info(_ConstRestraint self) -> VersionInfo"""
9316 return _IMP_kernel._ConstRestraint_get_version_info(self)
9317 __swig_destroy__ = _IMP_kernel.delete__ConstRestraint
9320 r"""__str__(_ConstRestraint self) -> std::string"""
9321 return _IMP_kernel._ConstRestraint___str__(self)
9324 r"""__repr__(_ConstRestraint self) -> std::string"""
9325 return _IMP_kernel._ConstRestraint___repr__(self)
9329 return _object_cast_to__ConstRestraint(o)
9332 def _get_as_binary(self):
9333 r"""_get_as_binary(_ConstRestraint self) -> PyObject *"""
9334 return _IMP_kernel._ConstRestraint__get_as_binary(self)
9336 def _set_from_binary(self, p):
9337 r"""_set_from_binary(_ConstRestraint self, PyObject * p)"""
9338 return _IMP_kernel._ConstRestraint__set_from_binary(self, p)
9340 def __getstate__(self):
9341 p = self._get_as_binary()
9342 if len(self.__dict__) > 1:
9343 d = self.__dict__.copy()
9348 def __setstate__(self, p):
9349 if not hasattr(self,
'this'):
9351 if isinstance(p, tuple):
9353 self.__dict__.update(d)
9354 return self._set_from_binary(p)
9358 value = self.get_value()
9360 return self._wrap_jax(
lambda jm: value)
9364 _IMP_kernel._ConstRestraint_swigregister(_ConstRestraint)
9366 r"""Proxy of C++ IMP::internal::_ConstSingletonScore class."""
9368 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9370 def __init__(self, *args):
9372 __init__(_ConstSingletonScore self, double v) -> _ConstSingletonScore
9373 __init__(_ConstSingletonScore self) -> _ConstSingletonScore
9375 _IMP_kernel._ConstSingletonScore_swiginit(self, _IMP_kernel.new__ConstSingletonScore(*args))
9377 def get_value(self):
9378 r"""get_value(_ConstSingletonScore self) -> double"""
9379 return _IMP_kernel._ConstSingletonScore_get_value(self)
9381 def do_get_inputs(self, arg2, arg3):
9382 r"""do_get_inputs(_ConstSingletonScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
9383 return _IMP_kernel._ConstSingletonScore_do_get_inputs(self, arg2, arg3)
9385 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
9386 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"""
9387 return _IMP_kernel._ConstSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
9389 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
9390 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"""
9391 return _IMP_kernel._ConstSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
9393 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
9394 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"""
9395 return _IMP_kernel._ConstSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
9397 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
9398 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"""
9399 return _IMP_kernel._ConstSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
9402 r"""get_version_info(_ConstSingletonScore self) -> VersionInfo"""
9403 return _IMP_kernel._ConstSingletonScore_get_version_info(self)
9404 __swig_destroy__ = _IMP_kernel.delete__ConstSingletonScore
9407 r"""__str__(_ConstSingletonScore self) -> std::string"""
9408 return _IMP_kernel._ConstSingletonScore___str__(self)
9411 r"""__repr__(_ConstSingletonScore self) -> std::string"""
9412 return _IMP_kernel._ConstSingletonScore___repr__(self)
9416 return _object_cast_to__ConstSingletonScore(o)
9419 def _get_as_binary(self):
9420 r"""_get_as_binary(_ConstSingletonScore self) -> PyObject *"""
9421 return _IMP_kernel._ConstSingletonScore__get_as_binary(self)
9423 def _set_from_binary(self, p):
9424 r"""_set_from_binary(_ConstSingletonScore self, PyObject * p)"""
9425 return _IMP_kernel._ConstSingletonScore__set_from_binary(self, p)
9427 def __getstate__(self):
9428 p = self._get_as_binary()
9429 if len(self.__dict__) > 1:
9430 d = self.__dict__.copy()
9435 def __setstate__(self, p):
9436 if not hasattr(self,
'this'):
9438 if isinstance(p, tuple):
9440 self.__dict__.update(d)
9441 return self._set_from_binary(p)
9444 def _get_jax(self, m, indexes):
9445 value = self.get_value()
9447 return self._wrap_jax(m,
lambda jm: value)
9451 _IMP_kernel._ConstSingletonScore_swigregister(_ConstSingletonScore)
9453 r"""Proxy of C++ IMP::internal::_ConstPairScore class."""
9455 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9457 def __init__(self, *args):
9459 __init__(_ConstPairScore self, double v) -> _ConstPairScore
9460 __init__(_ConstPairScore self) -> _ConstPairScore
9462 _IMP_kernel._ConstPairScore_swiginit(self, _IMP_kernel.new__ConstPairScore(*args))
9464 def get_value(self):
9465 r"""get_value(_ConstPairScore self) -> double"""
9466 return _IMP_kernel._ConstPairScore_get_value(self)
9468 def do_get_inputs(self, arg2, arg3):
9469 r"""do_get_inputs(_ConstPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
9470 return _IMP_kernel._ConstPairScore_do_get_inputs(self, arg2, arg3)
9472 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
9473 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"""
9474 return _IMP_kernel._ConstPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
9476 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
9477 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"""
9478 return _IMP_kernel._ConstPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
9480 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
9481 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"""
9482 return _IMP_kernel._ConstPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
9484 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
9485 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"""
9486 return _IMP_kernel._ConstPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
9489 r"""get_version_info(_ConstPairScore self) -> VersionInfo"""
9490 return _IMP_kernel._ConstPairScore_get_version_info(self)
9491 __swig_destroy__ = _IMP_kernel.delete__ConstPairScore
9494 r"""__str__(_ConstPairScore self) -> std::string"""
9495 return _IMP_kernel._ConstPairScore___str__(self)
9498 r"""__repr__(_ConstPairScore self) -> std::string"""
9499 return _IMP_kernel._ConstPairScore___repr__(self)
9503 return _object_cast_to__ConstPairScore(o)
9506 def _get_as_binary(self):
9507 r"""_get_as_binary(_ConstPairScore self) -> PyObject *"""
9508 return _IMP_kernel._ConstPairScore__get_as_binary(self)
9510 def _set_from_binary(self, p):
9511 r"""_set_from_binary(_ConstPairScore self, PyObject * p)"""
9512 return _IMP_kernel._ConstPairScore__set_from_binary(self, p)
9514 def __getstate__(self):
9515 p = self._get_as_binary()
9516 if len(self.__dict__) > 1:
9517 d = self.__dict__.copy()
9522 def __setstate__(self, p):
9523 if not hasattr(self,
'this'):
9525 if isinstance(p, tuple):
9527 self.__dict__.update(d)
9528 return self._set_from_binary(p)
9531 def _get_jax(self, m, indexes):
9532 value = self.get_value()
9534 return self._wrap_jax(m,
lambda jm: value)
9538 _IMP_kernel._ConstPairScore_swigregister(_ConstPairScore)
9540 r"""Proxy of C++ IMP::internal::_TrivialDecorator class."""
9542 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9544 def __init__(self, *args):
9546 __init__(_TrivialDecorator self) -> _TrivialDecorator
9547 __init__(_TrivialDecorator self, Model m, ParticleIndex id) -> _TrivialDecorator
9548 __init__(_TrivialDecorator self, _ParticleAdaptor d) -> _TrivialDecorator
9550 _IMP_kernel._TrivialDecorator_swiginit(self, _IMP_kernel.new__TrivialDecorator(*args))
9552 def show(self, *args):
9553 r"""show(_TrivialDecorator self, _ostream out=std::cout)"""
9554 return _IMP_kernel._TrivialDecorator_show(self, *args)
9557 def setup_particle(*args):
9559 setup_particle(Model m, ParticleIndex pi) -> _TrivialDecorator
9560 setup_particle(_ParticleAdaptor pa) -> _TrivialDecorator
9562 return _IMP_kernel._TrivialDecorator_setup_particle(*args)
9565 def get_is_setup(*args):
9567 get_is_setup(_ParticleAdaptor p) -> bool
9568 get_is_setup(Model m, ParticleIndex pi) -> bool
9570 return _IMP_kernel._TrivialDecorator_get_is_setup(*args)
9574 add_attribute(_TrivialDecorator self, FloatKey k, IMP::Float v, bool opt)
9575 add_attribute(_TrivialDecorator self, FloatKey a0, IMP::Float a1)
9576 add_attribute(_TrivialDecorator self, IntKey a0, IMP::Int a1)
9577 add_attribute(_TrivialDecorator self, FloatsKey a0, IMP::Floats a1)
9578 add_attribute(_TrivialDecorator self, IntsKey a0, IMP::Ints a1)
9579 add_attribute(_TrivialDecorator self, StringKey a0, IMP::String a1)
9580 add_attribute(_TrivialDecorator self, ParticleIndexKey a0, Particle a1)
9581 add_attribute(_TrivialDecorator self, ObjectKey a0, Object a1)
9582 add_attribute(_TrivialDecorator self, SparseFloatKey a0, IMP::Float a1)
9583 add_attribute(_TrivialDecorator self, SparseIntKey a0, IMP::Int a1)
9584 add_attribute(_TrivialDecorator self, SparseStringKey a0, IMP::String a1)
9585 add_attribute(_TrivialDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
9587 return _IMP_kernel._TrivialDecorator_add_attribute(self, *args)
9589 def get_value(self, *args):
9591 get_value(_TrivialDecorator self, FloatKey a0) -> IMP::Float
9592 get_value(_TrivialDecorator self, IntKey a0) -> IMP::Int
9593 get_value(_TrivialDecorator self, FloatsKey a0) -> IMP::Floats
9594 get_value(_TrivialDecorator self, IntsKey a0) -> IMP::Ints
9595 get_value(_TrivialDecorator self, StringKey a0) -> IMP::String
9596 get_value(_TrivialDecorator self, ParticleIndexKey a0) -> Particle
9597 get_value(_TrivialDecorator self, ObjectKey a0) -> Object
9598 get_value(_TrivialDecorator self, SparseFloatKey a0) -> IMP::Float
9599 get_value(_TrivialDecorator self, SparseIntKey a0) -> IMP::Int
9600 get_value(_TrivialDecorator self, SparseStringKey a0) -> IMP::String
9601 get_value(_TrivialDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
9603 return _IMP_kernel._TrivialDecorator_get_value(self, *args)
9605 def set_value(self, *args):
9607 set_value(_TrivialDecorator self, FloatKey a0, IMP::Float a1)
9608 set_value(_TrivialDecorator self, IntKey a0, IMP::Int a1)
9609 set_value(_TrivialDecorator self, FloatsKey a0, IMP::Floats a1)
9610 set_value(_TrivialDecorator self, IntsKey a0, IMP::Ints a1)
9611 set_value(_TrivialDecorator self, StringKey a0, IMP::String a1)
9612 set_value(_TrivialDecorator self, ParticleIndexKey a0, Particle a1)
9613 set_value(_TrivialDecorator self, ObjectKey a0, Object a1)
9614 set_value(_TrivialDecorator self, SparseFloatKey a0, IMP::Float a1)
9615 set_value(_TrivialDecorator self, SparseIntKey a0, IMP::Int a1)
9616 set_value(_TrivialDecorator self, SparseStringKey a0, IMP::String a1)
9617 set_value(_TrivialDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
9619 return _IMP_kernel._TrivialDecorator_set_value(self, *args)
9623 remove_attribute(_TrivialDecorator self, FloatKey a0)
9624 remove_attribute(_TrivialDecorator self, IntKey a0)
9625 remove_attribute(_TrivialDecorator self, FloatsKey a0)
9626 remove_attribute(_TrivialDecorator self, IntsKey a0)
9627 remove_attribute(_TrivialDecorator self, StringKey a0)
9628 remove_attribute(_TrivialDecorator self, ParticleIndexKey a0)
9629 remove_attribute(_TrivialDecorator self, ObjectKey a0)
9630 remove_attribute(_TrivialDecorator self, SparseFloatKey a0)
9631 remove_attribute(_TrivialDecorator self, SparseIntKey a0)
9632 remove_attribute(_TrivialDecorator self, SparseStringKey a0)
9633 remove_attribute(_TrivialDecorator self, SparseParticleIndexKey a0)
9635 return _IMP_kernel._TrivialDecorator_remove_attribute(self, *args)
9637 def has_attribute(self, *args):
9639 has_attribute(_TrivialDecorator self, FloatKey a0) -> bool
9640 has_attribute(_TrivialDecorator self, IntKey a0) -> bool
9641 has_attribute(_TrivialDecorator self, FloatsKey a0) -> bool
9642 has_attribute(_TrivialDecorator self, IntsKey a0) -> bool
9643 has_attribute(_TrivialDecorator self, StringKey a0) -> bool
9644 has_attribute(_TrivialDecorator self, ParticleIndexKey a0) -> bool
9645 has_attribute(_TrivialDecorator self, ObjectKey a0) -> bool
9646 has_attribute(_TrivialDecorator self, SparseFloatKey a0) -> bool
9647 has_attribute(_TrivialDecorator self, SparseIntKey a0) -> bool
9648 has_attribute(_TrivialDecorator self, SparseStringKey a0) -> bool
9649 has_attribute(_TrivialDecorator self, SparseParticleIndexKey a0) -> bool
9651 return _IMP_kernel._TrivialDecorator_has_attribute(self, *args)
9653 def get_derivative(self, a0):
9654 r"""get_derivative(_TrivialDecorator self, FloatKey a0) -> double"""
9655 return _IMP_kernel._TrivialDecorator_get_derivative(self, a0)
9658 r"""get_name(_TrivialDecorator self) -> std::string"""
9659 return _IMP_kernel._TrivialDecorator_get_name(self)
9662 r"""clear_caches(_TrivialDecorator self)"""
9663 return _IMP_kernel._TrivialDecorator_clear_caches(self)
9665 def set_name(self, a0):
9666 r"""set_name(_TrivialDecorator self, std::string a0)"""
9667 return _IMP_kernel._TrivialDecorator_set_name(self, a0)
9670 r"""set_check_level(_TrivialDecorator self, IMP::CheckLevel a0)"""
9671 return _IMP_kernel._TrivialDecorator_set_check_level(self, a0)
9673 def add_to_derivative(self, a0, a1, a2):
9674 r"""add_to_derivative(_TrivialDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9675 return _IMP_kernel._TrivialDecorator_add_to_derivative(self, a0, a1, a2)
9678 r"""set_is_optimized(_TrivialDecorator self, FloatKey a0, bool a1)"""
9679 return _IMP_kernel._TrivialDecorator_set_is_optimized(self, a0, a1)
9681 def get_is_optimized(self, a0):
9682 r"""get_is_optimized(_TrivialDecorator self, FloatKey a0) -> bool"""
9683 return _IMP_kernel._TrivialDecorator_get_is_optimized(self, a0)
9685 def get_check_level(self):
9686 r"""get_check_level(_TrivialDecorator self) -> IMP::CheckLevel"""
9687 return _IMP_kernel._TrivialDecorator_get_check_level(self)
9689 def __eq__(self, *args):
9691 __eq__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9692 __eq__(_TrivialDecorator self, Particle d) -> bool
9694 return _IMP_kernel._TrivialDecorator___eq__(self, *args)
9696 def __ne__(self, *args):
9698 __ne__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9699 __ne__(_TrivialDecorator self, Particle d) -> bool
9701 return _IMP_kernel._TrivialDecorator___ne__(self, *args)
9703 def __le__(self, *args):
9705 __le__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9706 __le__(_TrivialDecorator self, Particle d) -> bool
9708 return _IMP_kernel._TrivialDecorator___le__(self, *args)
9710 def __lt__(self, *args):
9712 __lt__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9713 __lt__(_TrivialDecorator self, Particle d) -> bool
9715 return _IMP_kernel._TrivialDecorator___lt__(self, *args)
9717 def __ge__(self, *args):
9719 __ge__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9720 __ge__(_TrivialDecorator self, Particle d) -> bool
9722 return _IMP_kernel._TrivialDecorator___ge__(self, *args)
9724 def __gt__(self, *args):
9726 __gt__(_TrivialDecorator self, _TrivialDecorator o) -> bool
9727 __gt__(_TrivialDecorator self, Particle d) -> bool
9729 return _IMP_kernel._TrivialDecorator___gt__(self, *args)
9732 r"""__hash__(_TrivialDecorator self) -> std::size_t"""
9733 return _IMP_kernel._TrivialDecorator___hash__(self)
9736 r"""__str__(_TrivialDecorator self) -> std::string"""
9737 return _IMP_kernel._TrivialDecorator___str__(self)
9740 r"""__repr__(_TrivialDecorator self) -> std::string"""
9741 return _IMP_kernel._TrivialDecorator___repr__(self)
9743 def _get_as_binary(self):
9744 r"""_get_as_binary(_TrivialDecorator self) -> PyObject *"""
9745 return _IMP_kernel._TrivialDecorator__get_as_binary(self)
9747 def _set_from_binary(self, p):
9748 r"""_set_from_binary(_TrivialDecorator self, PyObject * p)"""
9749 return _IMP_kernel._TrivialDecorator__set_from_binary(self, p)
9751 def __getstate__(self):
9752 p = self._get_as_binary()
9753 if len(self.__dict__) > 1:
9754 d = self.__dict__.copy()
9759 def __setstate__(self, p):
9760 if not hasattr(self,
'this'):
9762 if isinstance(p, tuple):
9764 self.__dict__.update(d)
9765 return self._set_from_binary(p)
9767 __swig_destroy__ = _IMP_kernel.delete__TrivialDecorator
9770 _IMP_kernel._TrivialDecorator_swigregister(_TrivialDecorator)
9771 class _TrivialDerivedDecorator(_TrivialDecorator):
9772 r"""Proxy of C++ IMP::internal::_TrivialDerivedDecorator class."""
9774 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9776 def __init__(self, *args):
9778 __init__(_TrivialDerivedDecorator self) -> _TrivialDerivedDecorator
9779 __init__(_TrivialDerivedDecorator self, Model m, ParticleIndex id) -> _TrivialDerivedDecorator
9780 __init__(_TrivialDerivedDecorator self, _ParticleAdaptor d) -> _TrivialDerivedDecorator
9782 _IMP_kernel._TrivialDerivedDecorator_swiginit(self, _IMP_kernel.new__TrivialDerivedDecorator(*args))
9784 def show(self, *args):
9785 r"""show(_TrivialDerivedDecorator self, _ostream out=std::cout)"""
9786 return _IMP_kernel._TrivialDerivedDecorator_show(self, *args)
9789 def setup_particle(*args):
9791 setup_particle(Model m, ParticleIndex pi) -> _TrivialDerivedDecorator
9792 setup_particle(_ParticleAdaptor pa) -> _TrivialDerivedDecorator
9794 return _IMP_kernel._TrivialDerivedDecorator_setup_particle(*args)
9797 def get_is_setup(*args):
9799 get_is_setup(_ParticleAdaptor p) -> bool
9800 get_is_setup(Model m, ParticleIndex pi) -> bool
9802 return _IMP_kernel._TrivialDerivedDecorator_get_is_setup(*args)
9806 add_attribute(_TrivialDerivedDecorator self, FloatKey k, IMP::Float v, bool opt)
9807 add_attribute(_TrivialDerivedDecorator self, FloatKey a0, IMP::Float a1)
9808 add_attribute(_TrivialDerivedDecorator self, IntKey a0, IMP::Int a1)
9809 add_attribute(_TrivialDerivedDecorator self, FloatsKey a0, IMP::Floats a1)
9810 add_attribute(_TrivialDerivedDecorator self, IntsKey a0, IMP::Ints a1)
9811 add_attribute(_TrivialDerivedDecorator self, StringKey a0, IMP::String a1)
9812 add_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0, Particle a1)
9813 add_attribute(_TrivialDerivedDecorator self, ObjectKey a0, Object a1)
9814 add_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0, IMP::Float a1)
9815 add_attribute(_TrivialDerivedDecorator self, SparseIntKey a0, IMP::Int a1)
9816 add_attribute(_TrivialDerivedDecorator self, SparseStringKey a0, IMP::String a1)
9817 add_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
9819 return _IMP_kernel._TrivialDerivedDecorator_add_attribute(self, *args)
9821 def get_value(self, *args):
9823 get_value(_TrivialDerivedDecorator self, FloatKey a0) -> IMP::Float
9824 get_value(_TrivialDerivedDecorator self, IntKey a0) -> IMP::Int
9825 get_value(_TrivialDerivedDecorator self, FloatsKey a0) -> IMP::Floats
9826 get_value(_TrivialDerivedDecorator self, IntsKey a0) -> IMP::Ints
9827 get_value(_TrivialDerivedDecorator self, StringKey a0) -> IMP::String
9828 get_value(_TrivialDerivedDecorator self, ParticleIndexKey a0) -> Particle
9829 get_value(_TrivialDerivedDecorator self, ObjectKey a0) -> Object
9830 get_value(_TrivialDerivedDecorator self, SparseFloatKey a0) -> IMP::Float
9831 get_value(_TrivialDerivedDecorator self, SparseIntKey a0) -> IMP::Int
9832 get_value(_TrivialDerivedDecorator self, SparseStringKey a0) -> IMP::String
9833 get_value(_TrivialDerivedDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
9835 return _IMP_kernel._TrivialDerivedDecorator_get_value(self, *args)
9837 def set_value(self, *args):
9839 set_value(_TrivialDerivedDecorator self, FloatKey a0, IMP::Float a1)
9840 set_value(_TrivialDerivedDecorator self, IntKey a0, IMP::Int a1)
9841 set_value(_TrivialDerivedDecorator self, FloatsKey a0, IMP::Floats a1)
9842 set_value(_TrivialDerivedDecorator self, IntsKey a0, IMP::Ints a1)
9843 set_value(_TrivialDerivedDecorator self, StringKey a0, IMP::String a1)
9844 set_value(_TrivialDerivedDecorator self, ParticleIndexKey a0, Particle a1)
9845 set_value(_TrivialDerivedDecorator self, ObjectKey a0, Object a1)
9846 set_value(_TrivialDerivedDecorator self, SparseFloatKey a0, IMP::Float a1)
9847 set_value(_TrivialDerivedDecorator self, SparseIntKey a0, IMP::Int a1)
9848 set_value(_TrivialDerivedDecorator self, SparseStringKey a0, IMP::String a1)
9849 set_value(_TrivialDerivedDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
9851 return _IMP_kernel._TrivialDerivedDecorator_set_value(self, *args)
9855 remove_attribute(_TrivialDerivedDecorator self, FloatKey a0)
9856 remove_attribute(_TrivialDerivedDecorator self, IntKey a0)
9857 remove_attribute(_TrivialDerivedDecorator self, FloatsKey a0)
9858 remove_attribute(_TrivialDerivedDecorator self, IntsKey a0)
9859 remove_attribute(_TrivialDerivedDecorator self, StringKey a0)
9860 remove_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0)
9861 remove_attribute(_TrivialDerivedDecorator self, ObjectKey a0)
9862 remove_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0)
9863 remove_attribute(_TrivialDerivedDecorator self, SparseIntKey a0)
9864 remove_attribute(_TrivialDerivedDecorator self, SparseStringKey a0)
9865 remove_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0)
9867 return _IMP_kernel._TrivialDerivedDecorator_remove_attribute(self, *args)
9869 def has_attribute(self, *args):
9871 has_attribute(_TrivialDerivedDecorator self, FloatKey a0) -> bool
9872 has_attribute(_TrivialDerivedDecorator self, IntKey a0) -> bool
9873 has_attribute(_TrivialDerivedDecorator self, FloatsKey a0) -> bool
9874 has_attribute(_TrivialDerivedDecorator self, IntsKey a0) -> bool
9875 has_attribute(_TrivialDerivedDecorator self, StringKey a0) -> bool
9876 has_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0) -> bool
9877 has_attribute(_TrivialDerivedDecorator self, ObjectKey a0) -> bool
9878 has_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0) -> bool
9879 has_attribute(_TrivialDerivedDecorator self, SparseIntKey a0) -> bool
9880 has_attribute(_TrivialDerivedDecorator self, SparseStringKey a0) -> bool
9881 has_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0) -> bool
9883 return _IMP_kernel._TrivialDerivedDecorator_has_attribute(self, *args)
9885 def get_derivative(self, a0):
9886 r"""get_derivative(_TrivialDerivedDecorator self, FloatKey a0) -> double"""
9887 return _IMP_kernel._TrivialDerivedDecorator_get_derivative(self, a0)
9890 r"""get_name(_TrivialDerivedDecorator self) -> std::string"""
9891 return _IMP_kernel._TrivialDerivedDecorator_get_name(self)
9894 r"""clear_caches(_TrivialDerivedDecorator self)"""
9895 return _IMP_kernel._TrivialDerivedDecorator_clear_caches(self)
9897 def set_name(self, a0):
9898 r"""set_name(_TrivialDerivedDecorator self, std::string a0)"""
9899 return _IMP_kernel._TrivialDerivedDecorator_set_name(self, a0)
9902 r"""set_check_level(_TrivialDerivedDecorator self, IMP::CheckLevel a0)"""
9903 return _IMP_kernel._TrivialDerivedDecorator_set_check_level(self, a0)
9905 def add_to_derivative(self, a0, a1, a2):
9906 r"""add_to_derivative(_TrivialDerivedDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
9907 return _IMP_kernel._TrivialDerivedDecorator_add_to_derivative(self, a0, a1, a2)
9910 r"""set_is_optimized(_TrivialDerivedDecorator self, FloatKey a0, bool a1)"""
9911 return _IMP_kernel._TrivialDerivedDecorator_set_is_optimized(self, a0, a1)
9913 def get_is_optimized(self, a0):
9914 r"""get_is_optimized(_TrivialDerivedDecorator self, FloatKey a0) -> bool"""
9915 return _IMP_kernel._TrivialDerivedDecorator_get_is_optimized(self, a0)
9917 def get_check_level(self):
9918 r"""get_check_level(_TrivialDerivedDecorator self) -> IMP::CheckLevel"""
9919 return _IMP_kernel._TrivialDerivedDecorator_get_check_level(self)
9921 def __eq__(self, *args):
9923 __eq__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
9924 __eq__(_TrivialDerivedDecorator self, Particle d) -> bool
9926 return _IMP_kernel._TrivialDerivedDecorator___eq__(self, *args)
9928 def __ne__(self, *args):
9930 __ne__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
9931 __ne__(_TrivialDerivedDecorator self, Particle d) -> bool
9933 return _IMP_kernel._TrivialDerivedDecorator___ne__(self, *args)
9935 def __le__(self, *args):
9937 __le__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
9938 __le__(_TrivialDerivedDecorator self, Particle d) -> bool
9940 return _IMP_kernel._TrivialDerivedDecorator___le__(self, *args)
9942 def __lt__(self, *args):
9944 __lt__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
9945 __lt__(_TrivialDerivedDecorator self, Particle d) -> bool
9947 return _IMP_kernel._TrivialDerivedDecorator___lt__(self, *args)
9949 def __ge__(self, *args):
9951 __ge__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
9952 __ge__(_TrivialDerivedDecorator self, Particle d) -> bool
9954 return _IMP_kernel._TrivialDerivedDecorator___ge__(self, *args)
9956 def __gt__(self, *args):
9958 __gt__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
9959 __gt__(_TrivialDerivedDecorator self, Particle d) -> bool
9961 return _IMP_kernel._TrivialDerivedDecorator___gt__(self, *args)
9964 r"""__hash__(_TrivialDerivedDecorator self) -> std::size_t"""
9965 return _IMP_kernel._TrivialDerivedDecorator___hash__(self)
9968 r"""__str__(_TrivialDerivedDecorator self) -> std::string"""
9969 return _IMP_kernel._TrivialDerivedDecorator___str__(self)
9972 r"""__repr__(_TrivialDerivedDecorator self) -> std::string"""
9973 return _IMP_kernel._TrivialDerivedDecorator___repr__(self)
9975 def _get_as_binary(self):
9976 r"""_get_as_binary(_TrivialDerivedDecorator self) -> PyObject *"""
9977 return _IMP_kernel._TrivialDerivedDecorator__get_as_binary(self)
9979 def _set_from_binary(self, p):
9980 r"""_set_from_binary(_TrivialDerivedDecorator self, PyObject * p)"""
9981 return _IMP_kernel._TrivialDerivedDecorator__set_from_binary(self, p)
9983 def __getstate__(self):
9984 p = self._get_as_binary()
9985 if len(self.__dict__) > 1:
9986 d = self.__dict__.copy()
9991 def __setstate__(self, p):
9992 if not hasattr(self,
'this'):
9994 if isinstance(p, tuple):
9996 self.__dict__.update(d)
9997 return self._set_from_binary(p)
9999 __swig_destroy__ = _IMP_kernel.delete__TrivialDerivedDecorator
10002 _IMP_kernel._TrivialDerivedDecorator_swigregister(_TrivialDerivedDecorator)
10003 class _TrivialTraitsDecorator(
Decorator):
10004 r"""Proxy of C++ IMP::internal::_TrivialTraitsDecorator class."""
10006 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10008 def get_decorator_traits(self):
10009 r"""get_decorator_traits(_TrivialTraitsDecorator self) -> StringKey"""
10010 return _IMP_kernel._TrivialTraitsDecorator_get_decorator_traits(self)
10013 def get_default_decorator_traits():
10014 r"""get_default_decorator_traits() -> StringKey"""
10015 return _IMP_kernel._TrivialTraitsDecorator_get_default_decorator_traits()
10017 def __init__(self, *args):
10019 __init__(_TrivialTraitsDecorator self) -> _TrivialTraitsDecorator
10020 __init__(_TrivialTraitsDecorator self, Model m, ParticleIndex id, StringKey tr=get_default_key()) -> _TrivialTraitsDecorator
10021 __init__(_TrivialTraitsDecorator self, _ParticleAdaptor d, StringKey tr=get_default_key()) -> _TrivialTraitsDecorator
10023 _IMP_kernel._TrivialTraitsDecorator_swiginit(self, _IMP_kernel.new__TrivialTraitsDecorator(*args))
10025 def show(self, *args):
10026 r"""show(_TrivialTraitsDecorator self, _ostream out=std::cout)"""
10027 return _IMP_kernel._TrivialTraitsDecorator_show(self, *args)
10030 def setup_particle(*args):
10032 setup_particle(Model m, ParticleIndex pi, StringKey tr=IMP::internal::_TrivialTraitsDecorator::get_default_decorator_traits()) -> _TrivialTraitsDecorator
10033 setup_particle(_ParticleAdaptor d, StringKey tr=IMP::internal::_TrivialTraitsDecorator::get_default_decorator_traits()) -> _TrivialTraitsDecorator
10035 return _IMP_kernel._TrivialTraitsDecorator_setup_particle(*args)
10038 def get_is_setup(*args):
10040 get_is_setup(_ParticleAdaptor p, StringKey tr=get_default_key()) -> bool
10041 get_is_setup(Model m, ParticleIndex pi, StringKey k=get_default_key()) -> bool
10043 return _IMP_kernel._TrivialTraitsDecorator_get_is_setup(*args)
10046 def get_default_key():
10047 r"""get_default_key() -> StringKey"""
10048 return _IMP_kernel._TrivialTraitsDecorator_get_default_key()
10052 add_attribute(_TrivialTraitsDecorator self, FloatKey k, IMP::Float v, bool opt)
10053 add_attribute(_TrivialTraitsDecorator self, FloatKey a0, IMP::Float a1)
10054 add_attribute(_TrivialTraitsDecorator self, IntKey a0, IMP::Int a1)
10055 add_attribute(_TrivialTraitsDecorator self, FloatsKey a0, IMP::Floats a1)
10056 add_attribute(_TrivialTraitsDecorator self, IntsKey a0, IMP::Ints a1)
10057 add_attribute(_TrivialTraitsDecorator self, StringKey a0, IMP::String a1)
10058 add_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0, Particle a1)
10059 add_attribute(_TrivialTraitsDecorator self, ObjectKey a0, Object a1)
10060 add_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0, IMP::Float a1)
10061 add_attribute(_TrivialTraitsDecorator self, SparseIntKey a0, IMP::Int a1)
10062 add_attribute(_TrivialTraitsDecorator self, SparseStringKey a0, IMP::String a1)
10063 add_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
10065 return _IMP_kernel._TrivialTraitsDecorator_add_attribute(self, *args)
10067 def get_value(self, *args):
10069 get_value(_TrivialTraitsDecorator self, FloatKey a0) -> IMP::Float
10070 get_value(_TrivialTraitsDecorator self, IntKey a0) -> IMP::Int
10071 get_value(_TrivialTraitsDecorator self, FloatsKey a0) -> IMP::Floats
10072 get_value(_TrivialTraitsDecorator self, IntsKey a0) -> IMP::Ints
10073 get_value(_TrivialTraitsDecorator self, StringKey a0) -> IMP::String
10074 get_value(_TrivialTraitsDecorator self, ParticleIndexKey a0) -> Particle
10075 get_value(_TrivialTraitsDecorator self, ObjectKey a0) -> Object
10076 get_value(_TrivialTraitsDecorator self, SparseFloatKey a0) -> IMP::Float
10077 get_value(_TrivialTraitsDecorator self, SparseIntKey a0) -> IMP::Int
10078 get_value(_TrivialTraitsDecorator self, SparseStringKey a0) -> IMP::String
10079 get_value(_TrivialTraitsDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
10081 return _IMP_kernel._TrivialTraitsDecorator_get_value(self, *args)
10083 def set_value(self, *args):
10085 set_value(_TrivialTraitsDecorator self, FloatKey a0, IMP::Float a1)
10086 set_value(_TrivialTraitsDecorator self, IntKey a0, IMP::Int a1)
10087 set_value(_TrivialTraitsDecorator self, FloatsKey a0, IMP::Floats a1)
10088 set_value(_TrivialTraitsDecorator self, IntsKey a0, IMP::Ints a1)
10089 set_value(_TrivialTraitsDecorator self, StringKey a0, IMP::String a1)
10090 set_value(_TrivialTraitsDecorator self, ParticleIndexKey a0, Particle a1)
10091 set_value(_TrivialTraitsDecorator self, ObjectKey a0, Object a1)
10092 set_value(_TrivialTraitsDecorator self, SparseFloatKey a0, IMP::Float a1)
10093 set_value(_TrivialTraitsDecorator self, SparseIntKey a0, IMP::Int a1)
10094 set_value(_TrivialTraitsDecorator self, SparseStringKey a0, IMP::String a1)
10095 set_value(_TrivialTraitsDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
10097 return _IMP_kernel._TrivialTraitsDecorator_set_value(self, *args)
10101 remove_attribute(_TrivialTraitsDecorator self, FloatKey a0)
10102 remove_attribute(_TrivialTraitsDecorator self, IntKey a0)
10103 remove_attribute(_TrivialTraitsDecorator self, FloatsKey a0)
10104 remove_attribute(_TrivialTraitsDecorator self, IntsKey a0)
10105 remove_attribute(_TrivialTraitsDecorator self, StringKey a0)
10106 remove_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0)
10107 remove_attribute(_TrivialTraitsDecorator self, ObjectKey a0)
10108 remove_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0)
10109 remove_attribute(_TrivialTraitsDecorator self, SparseIntKey a0)
10110 remove_attribute(_TrivialTraitsDecorator self, SparseStringKey a0)
10111 remove_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0)
10113 return _IMP_kernel._TrivialTraitsDecorator_remove_attribute(self, *args)
10115 def has_attribute(self, *args):
10117 has_attribute(_TrivialTraitsDecorator self, FloatKey a0) -> bool
10118 has_attribute(_TrivialTraitsDecorator self, IntKey a0) -> bool
10119 has_attribute(_TrivialTraitsDecorator self, FloatsKey a0) -> bool
10120 has_attribute(_TrivialTraitsDecorator self, IntsKey a0) -> bool
10121 has_attribute(_TrivialTraitsDecorator self, StringKey a0) -> bool
10122 has_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0) -> bool
10123 has_attribute(_TrivialTraitsDecorator self, ObjectKey a0) -> bool
10124 has_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0) -> bool
10125 has_attribute(_TrivialTraitsDecorator self, SparseIntKey a0) -> bool
10126 has_attribute(_TrivialTraitsDecorator self, SparseStringKey a0) -> bool
10127 has_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0) -> bool
10129 return _IMP_kernel._TrivialTraitsDecorator_has_attribute(self, *args)
10131 def get_derivative(self, a0):
10132 r"""get_derivative(_TrivialTraitsDecorator self, FloatKey a0) -> double"""
10133 return _IMP_kernel._TrivialTraitsDecorator_get_derivative(self, a0)
10135 def get_name(self):
10136 r"""get_name(_TrivialTraitsDecorator self) -> std::string"""
10137 return _IMP_kernel._TrivialTraitsDecorator_get_name(self)
10140 r"""clear_caches(_TrivialTraitsDecorator self)"""
10141 return _IMP_kernel._TrivialTraitsDecorator_clear_caches(self)
10143 def set_name(self, a0):
10144 r"""set_name(_TrivialTraitsDecorator self, std::string a0)"""
10145 return _IMP_kernel._TrivialTraitsDecorator_set_name(self, a0)
10148 r"""set_check_level(_TrivialTraitsDecorator self, IMP::CheckLevel a0)"""
10149 return _IMP_kernel._TrivialTraitsDecorator_set_check_level(self, a0)
10151 def add_to_derivative(self, a0, a1, a2):
10152 r"""add_to_derivative(_TrivialTraitsDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
10153 return _IMP_kernel._TrivialTraitsDecorator_add_to_derivative(self, a0, a1, a2)
10156 r"""set_is_optimized(_TrivialTraitsDecorator self, FloatKey a0, bool a1)"""
10157 return _IMP_kernel._TrivialTraitsDecorator_set_is_optimized(self, a0, a1)
10159 def get_is_optimized(self, a0):
10160 r"""get_is_optimized(_TrivialTraitsDecorator self, FloatKey a0) -> bool"""
10161 return _IMP_kernel._TrivialTraitsDecorator_get_is_optimized(self, a0)
10163 def get_check_level(self):
10164 r"""get_check_level(_TrivialTraitsDecorator self) -> IMP::CheckLevel"""
10165 return _IMP_kernel._TrivialTraitsDecorator_get_check_level(self)
10167 def __eq__(self, *args):
10169 __eq__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10170 __eq__(_TrivialTraitsDecorator self, Particle d) -> bool
10172 return _IMP_kernel._TrivialTraitsDecorator___eq__(self, *args)
10174 def __ne__(self, *args):
10176 __ne__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10177 __ne__(_TrivialTraitsDecorator self, Particle d) -> bool
10179 return _IMP_kernel._TrivialTraitsDecorator___ne__(self, *args)
10181 def __le__(self, *args):
10183 __le__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10184 __le__(_TrivialTraitsDecorator self, Particle d) -> bool
10186 return _IMP_kernel._TrivialTraitsDecorator___le__(self, *args)
10188 def __lt__(self, *args):
10190 __lt__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10191 __lt__(_TrivialTraitsDecorator self, Particle d) -> bool
10193 return _IMP_kernel._TrivialTraitsDecorator___lt__(self, *args)
10195 def __ge__(self, *args):
10197 __ge__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10198 __ge__(_TrivialTraitsDecorator self, Particle d) -> bool
10200 return _IMP_kernel._TrivialTraitsDecorator___ge__(self, *args)
10202 def __gt__(self, *args):
10204 __gt__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
10205 __gt__(_TrivialTraitsDecorator self, Particle d) -> bool
10207 return _IMP_kernel._TrivialTraitsDecorator___gt__(self, *args)
10209 def __hash__(self):
10210 r"""__hash__(_TrivialTraitsDecorator self) -> std::size_t"""
10211 return _IMP_kernel._TrivialTraitsDecorator___hash__(self)
10214 r"""__str__(_TrivialTraitsDecorator self) -> std::string"""
10215 return _IMP_kernel._TrivialTraitsDecorator___str__(self)
10217 def __repr__(self):
10218 r"""__repr__(_TrivialTraitsDecorator self) -> std::string"""
10219 return _IMP_kernel._TrivialTraitsDecorator___repr__(self)
10220 __swig_destroy__ = _IMP_kernel.delete__TrivialTraitsDecorator
10223 _IMP_kernel._TrivialTraitsDecorator_swigregister(_TrivialTraitsDecorator)
10225 def __lshift__(*args):
10227 __lshift__(_ostream out, _TrivialDecorator n) -> _ostream
10228 __lshift__(_ostream out, _TrivialDerivedDecorator n) -> _ostream
10229 __lshift__(_ostream out, _TrivialTraitsDecorator n) -> _ostream
10231 return _IMP_kernel.__lshift__(*args)
10233 r"""Proxy of C++ IMP::internal::_ConstOptimizer class."""
10235 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10237 def __init__(self, *args):
10239 __init__(_ConstOptimizer self, Model m) -> _ConstOptimizer
10240 __init__(_ConstOptimizer self) -> _ConstOptimizer
10242 _IMP_kernel._ConstOptimizer_swiginit(self, _IMP_kernel.new__ConstOptimizer(*args))
10244 def do_optimize(self, max_steps):
10245 r"""do_optimize(_ConstOptimizer self, unsigned int max_steps) -> IMP::Float"""
10246 return _IMP_kernel._ConstOptimizer_do_optimize(self, max_steps)
10249 r"""get_version_info(_ConstOptimizer self) -> VersionInfo"""
10250 return _IMP_kernel._ConstOptimizer_get_version_info(self)
10251 __swig_destroy__ = _IMP_kernel.delete__ConstOptimizer
10254 r"""__str__(_ConstOptimizer self) -> std::string"""
10255 return _IMP_kernel._ConstOptimizer___str__(self)
10257 def __repr__(self):
10258 r"""__repr__(_ConstOptimizer self) -> std::string"""
10259 return _IMP_kernel._ConstOptimizer___repr__(self)
10263 return _object_cast_to__ConstOptimizer(o)
10266 def _get_as_binary(self):
10267 r"""_get_as_binary(_ConstOptimizer self) -> PyObject *"""
10268 return _IMP_kernel._ConstOptimizer__get_as_binary(self)
10270 def _set_from_binary(self, p):
10271 r"""_set_from_binary(_ConstOptimizer self, PyObject * p)"""
10272 return _IMP_kernel._ConstOptimizer__set_from_binary(self, p)
10274 def __getstate__(self):
10275 p = self._get_as_binary()
10276 if len(self.__dict__) > 1:
10277 d = self.__dict__.copy()
10282 def __setstate__(self, p):
10283 if not hasattr(self,
'this'):
10285 if isinstance(p, tuple):
10287 self.__dict__.update(d)
10288 return self._set_from_binary(p)
10292 _IMP_kernel._ConstOptimizer_swigregister(_ConstOptimizer)
10295 r"""get_particle(Particle p) -> Particle"""
10296 return _IMP_kernel.get_particle(p)
10298 def _decorator_test(p):
10299 r"""_decorator_test(Particle p)"""
10300 return _IMP_kernel._decorator_test(p)
10302 def _overloaded_decorator(*args):
10304 _overloaded_decorator(_TrivialDecorator a) -> int
10305 _overloaded_decorator(_TrivialDerivedDecorator a) -> int
10307 return _IMP_kernel._overloaded_decorator(*args)
10309 def _take_particles(*args):
10311 _take_particles(IMP::Particles const & ps) -> unsigned int
10312 _take_particles(Model m, IMP::Particles const & ps) -> unsigned int
10313 _take_particles(Model m, IMP::Particles const & ps, TextOutput out) -> unsigned int
10315 return _IMP_kernel._take_particles(*args)
10317 def _give_particles(m):
10318 r"""_give_particles(Model m) -> IMP::Particles const &"""
10319 return _IMP_kernel._give_particles(m)
10321 def _pass_particles(ps):
10322 r"""_pass_particles(IMP::Particles const & ps) -> IMP::Particles const &"""
10323 return _IMP_kernel._pass_particles(ps)
10325 def _pass_particle(ps):
10326 r"""_pass_particle(Particle ps) -> Particle"""
10327 return _IMP_kernel._pass_particle(ps)
10329 def _pass_particle_pair(pp):
10330 r"""_pass_particle_pair(IMP::ParticlePair const & pp) -> IMP::ParticlePair const &"""
10331 return _IMP_kernel._pass_particle_pair(pp)
10333 def _give_particles_copy(m):
10334 r"""_give_particles_copy(Model m) -> IMP::Particles"""
10335 return _IMP_kernel._give_particles_copy(m)
10337 def _pass_float_keys(input):
10338 r"""_pass_float_keys(IMP::FloatKeys const & input) -> IMP::FloatKeys"""
10339 return _IMP_kernel._pass_float_keys(input)
10343 _pass(IMP::Particles const & p) -> IMP::Particles const
10344 _pass(IMP::Restraints const & p) -> IMP::Restraints const &
10346 return _IMP_kernel._pass(*args)
10348 def _pass_decorators(p):
10349 r"""_pass_decorators(IMP::internal::_TrivialDecorators const & p) -> IMP::internal::_TrivialDecorators const &"""
10350 return _IMP_kernel._pass_decorators(p)
10352 def _pass_decorator_traits(p):
10353 r"""_pass_decorator_traits(IMP::internal::_TrivialTraitsDecorators const & p) -> IMP::internal::_TrivialTraitsDecorators const &"""
10354 return _IMP_kernel._pass_decorator_traits(p)
10356 def _pass_particle_pairs(p):
10357 r"""_pass_particle_pairs(IMP::ParticlePairsTemp const & p) -> IMP::ParticlePairsTemp"""
10358 return _IMP_kernel._pass_particle_pairs(p)
10360 def _pass_particle_index_pairs(p):
10361 r"""_pass_particle_index_pairs(IMP::ParticleIndexPairs const & p) -> IMP::ParticleIndexPairs"""
10362 return _IMP_kernel._pass_particle_index_pairs(p)
10364 def _pass_model_objects(p):
10365 r"""_pass_model_objects(IMP::ModelObjectsTemp const & p) -> IMP::ModelObjectsTemp"""
10366 return _IMP_kernel._pass_model_objects(p)
10368 def _pass_particles_temps(ps):
10369 r"""_pass_particles_temps(IMP::ParticlesTemps const & ps) -> IMP::ParticlesTemps"""
10370 return _IMP_kernel._pass_particles_temps(ps)
10372 def _test_overload(*args):
10374 _test_overload(IMP::Particles const & ps) -> int
10375 _test_overload(IMP::Restraints const & ps) -> int
10377 return _IMP_kernel._test_overload(*args)
10379 def _get_range(m, k):
10380 r"""_get_range(Model m, FloatKey k) -> IMP::FloatRange"""
10381 return _IMP_kernel._get_range(m, k)
10383 def _create_particles_from_pdb(name, m):
10384 r"""_create_particles_from_pdb(std::string name, Model m) -> IMP::ParticleIndexes"""
10385 return _IMP_kernel._create_particles_from_pdb(name, m)
10387 r"""Proxy of C++ IMP::internal::_LogPairScore class."""
10389 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10390 __repr__ = _swig_repr
10392 def __init__(self):
10393 r"""__init__(_LogPairScore self) -> _LogPairScore"""
10394 _IMP_kernel._LogPairScore_swiginit(self, _IMP_kernel.new__LogPairScore())
10396 def do_get_inputs(self, arg2, arg3):
10397 r"""do_get_inputs(_LogPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
10398 return _IMP_kernel._LogPairScore_do_get_inputs(self, arg2, arg3)
10400 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
10401 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"""
10402 return _IMP_kernel._LogPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
10404 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
10405 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"""
10406 return _IMP_kernel._LogPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
10408 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
10409 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"""
10410 return _IMP_kernel._LogPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
10412 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
10413 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"""
10414 return _IMP_kernel._LogPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
10417 r"""get_version_info(_LogPairScore self) -> VersionInfo"""
10418 return _IMP_kernel._LogPairScore_get_version_info(self)
10419 __swig_destroy__ = _IMP_kernel.delete__LogPairScore
10421 def get_particle_pairs(self):
10422 r"""get_particle_pairs(_LogPairScore self) -> IMP::ParticlePairsTemp"""
10423 return _IMP_kernel._LogPairScore_get_particle_pairs(self)
10426 r"""clear(_LogPairScore self)"""
10427 return _IMP_kernel._LogPairScore_clear(self)
10429 def get_contains(self, pp):
10430 r"""get_contains(_LogPairScore self, IMP::ParticlePair const & pp) -> bool"""
10431 return _IMP_kernel._LogPairScore_get_contains(self, pp)
10434 _IMP_kernel._LogPairScore_swigregister(_LogPairScore)
10436 def _overloaded_particles(*args):
10438 _overloaded_particles(Particle arg1)
10439 _overloaded_particles(IMP::Particles const & arg1)
10440 _overloaded_particles(IMP::ParticlesTemp const & arg1)
10441 _overloaded_particles(Model arg1, IMP::ParticleIndexes const & arg2)
10442 _overloaded_particles(IMP::internal::_TrivialDecorators const & arg1)
10443 _overloaded_particles(_TrivialDecorator arg1)
10445 return _IMP_kernel._overloaded_particles(*args)
10446 class _ImplicitParticles(object):
10447 r"""Proxy of C++ IMP::internal::_ImplicitParticles class."""
10449 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10450 __repr__ = _swig_repr
10452 def __init__(self, *args):
10454 __init__(_ImplicitParticles self, Particle arg2) -> _ImplicitParticles
10455 __init__(_ImplicitParticles self, IMP::Particles const & arg2) -> _ImplicitParticles
10456 __init__(_ImplicitParticles self, IMP::ParticlesTemp const & arg2) -> _ImplicitParticles
10457 __init__(_ImplicitParticles self, Model arg2, IMP::ParticleIndexes const & arg3) -> _ImplicitParticles
10458 __init__(_ImplicitParticles self, IMP::internal::_TrivialDecorators const & arg2) -> _ImplicitParticles
10459 __init__(_ImplicitParticles self, _TrivialDecorator arg2) -> _ImplicitParticles
10461 _IMP_kernel._ImplicitParticles_swiginit(self, _IMP_kernel.new__ImplicitParticles(*args))
10462 __swig_destroy__ = _IMP_kernel.delete__ImplicitParticles
10465 _IMP_kernel._ImplicitParticles_swigregister(_ImplicitParticles)
10467 def _implicit_particles(arg1):
10468 r"""_implicit_particles(_ImplicitParticles arg1)"""
10469 return _IMP_kernel._implicit_particles(arg1)
10471 def _take_particle_adaptor(pa):
10472 r"""_take_particle_adaptor(_ParticleAdaptor pa) -> ParticleIndex"""
10473 return _IMP_kernel._take_particle_adaptor(pa)
10475 def _take_particle_indexes_adaptor(pa):
10476 r"""_take_particle_indexes_adaptor(_ParticleIndexesAdaptor pa) -> IMP::ParticleIndexes"""
10477 return _IMP_kernel._take_particle_indexes_adaptor(pa)
10478 class Vector1D(_VectorBase1D):
10479 r"""Proxy of C++ IMP::VectorD< 1 > class."""
10481 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10483 def get_unit_vector(self):
10484 r"""get_unit_vector(Vector1D self) -> Vector1D"""
10485 return _IMP_kernel.Vector1D_get_unit_vector(self)
10487 def __truediv__(self, *args):
10488 return _IMP_kernel.Vector1D___truediv__(self, *args)
10489 __div__ = __truediv__
10494 r"""__neg__(Vector1D self) -> Vector1D"""
10495 return _IMP_kernel.Vector1D___neg__(self)
10497 def __sub__(self, o):
10498 r"""__sub__(Vector1D self, Vector1D o) -> Vector1D"""
10499 return _IMP_kernel.Vector1D___sub__(self, o)
10501 def __add__(self, ret):
10502 r"""__add__(Vector1D self, Vector1D ret) -> Vector1D"""
10503 return _IMP_kernel.Vector1D___add__(self, ret)
10505 def __mul__(self, *args):
10507 __mul__(Vector1D self, double s) -> Vector1D
10508 __mul__(Vector1D self, Vector1D o) -> double
10510 return _IMP_kernel.Vector1D___mul__(self, *args)
10512 def __init__(self, *args):
10514 __init__(Vector1D self, IMP::Floats const & f) -> Vector1D
10515 __init__(Vector1D self) -> Vector1D
10516 __init__(Vector1D self, double x) -> Vector1D
10518 _IMP_kernel.Vector1D_swiginit(self, _IMP_kernel.new_Vector1D(*args))
10520 def __iadd__(self, *args):
10521 _IMP_kernel.Vector1D___iadd__(self, *args)
10526 def __imul__(self, *args):
10527 _IMP_kernel.Vector1D___imul__(self, *args)
10532 def __idiv__(self, *args):
10533 _IMP_kernel.Vector1D___idiv__(self, *args)
10538 def __isub__(self, *args):
10539 _IMP_kernel.Vector1D___isub__(self, *args)
10545 r"""__len__(Vector1D self) -> unsigned int"""
10546 return _IMP_kernel.Vector1D___len__(self)
10548 def __rmul__(self, f):
10549 r"""__rmul__(Vector1D self, double f) -> Vector1D"""
10550 return _IMP_kernel.Vector1D___rmul__(self, f)
10553 r"""__str__(Vector1D self) -> std::string"""
10554 return _IMP_kernel.Vector1D___str__(self)
10556 def __repr__(self):
10557 r"""__repr__(Vector1D self) -> std::string"""
10558 return _IMP_kernel.Vector1D___repr__(self)
10560 def __cmp__(self, arg2):
10561 r"""__cmp__(Vector1D self, Vector1D arg2) -> int"""
10562 return _IMP_kernel.Vector1D___cmp__(self, arg2)
10564 def __eq__(self, arg2):
10565 r"""__eq__(Vector1D self, Vector1D arg2) -> bool"""
10566 return _IMP_kernel.Vector1D___eq__(self, arg2)
10568 __truediv__ = __div__
10569 __itruediv__ = __idiv__
10572 def _get_as_binary(self):
10573 r"""_get_as_binary(Vector1D self) -> PyObject *"""
10574 return _IMP_kernel.Vector1D__get_as_binary(self)
10576 def _set_from_binary(self, p):
10577 r"""_set_from_binary(Vector1D self, PyObject * p)"""
10578 return _IMP_kernel.Vector1D__set_from_binary(self, p)
10580 def __getstate__(self):
10581 p = self._get_as_binary()
10582 if len(self.__dict__) > 1:
10583 d = self.__dict__.copy()
10588 def __setstate__(self, p):
10589 if not hasattr(self,
'this'):
10591 if isinstance(p, tuple):
10593 self.__dict__.update(d)
10594 return self._set_from_binary(p)
10597 def __getitem__(self, index):
10598 if isinstance(index, slice):
10599 return [self[i]
for i
in range(*index.indices(len(self)))]
10601 return _IMP_kernel.Vector1D___getitem__(self, index)
10605 def __setitem__(self, index, val):
10606 if isinstance(index, slice):
10607 if not hasattr(val,
'__iter__'):
10608 raise TypeError(
"must assign iterable to extended slice")
10609 inds = range(*index.indices(len(self)))
10610 if len(inds) != len(val):
10612 "attempt to assign sequence of size %d "
10613 "to extended slice of size %d" % (len(val), len(inds)))
10614 for ind, v
in zip(inds, val):
10617 return _IMP_kernel.Vector1D___setitem__(self, index, val)
10620 __swig_destroy__ = _IMP_kernel.delete_Vector1D
10623 _IMP_kernel.Vector1D_swigregister(Vector1D)
10624 class Vector2D(_VectorBase2D):
10625 r"""Proxy of C++ IMP::VectorD< 2 > class."""
10627 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10629 def get_unit_vector(self):
10630 r"""get_unit_vector(Vector2D self) -> Vector2D"""
10631 return _IMP_kernel.Vector2D_get_unit_vector(self)
10633 def __truediv__(self, *args):
10634 return _IMP_kernel.Vector2D___truediv__(self, *args)
10635 __div__ = __truediv__
10640 r"""__neg__(Vector2D self) -> Vector2D"""
10641 return _IMP_kernel.Vector2D___neg__(self)
10643 def __sub__(self, o):
10644 r"""__sub__(Vector2D self, Vector2D o) -> Vector2D"""
10645 return _IMP_kernel.Vector2D___sub__(self, o)
10647 def __add__(self, ret):
10648 r"""__add__(Vector2D self, Vector2D ret) -> Vector2D"""
10649 return _IMP_kernel.Vector2D___add__(self, ret)
10651 def __mul__(self, *args):
10653 __mul__(Vector2D self, double s) -> Vector2D
10654 __mul__(Vector2D self, Vector2D o) -> double
10656 return _IMP_kernel.Vector2D___mul__(self, *args)
10658 def __init__(self, *args):
10660 __init__(Vector2D self, IMP::Floats const & f) -> Vector2D
10661 __init__(Vector2D self) -> Vector2D
10662 __init__(Vector2D self, double x, double y) -> Vector2D
10664 _IMP_kernel.Vector2D_swiginit(self, _IMP_kernel.new_Vector2D(*args))
10666 def __iadd__(self, *args):
10667 _IMP_kernel.Vector2D___iadd__(self, *args)
10672 def __imul__(self, *args):
10673 _IMP_kernel.Vector2D___imul__(self, *args)
10678 def __idiv__(self, *args):
10679 _IMP_kernel.Vector2D___idiv__(self, *args)
10684 def __isub__(self, *args):
10685 _IMP_kernel.Vector2D___isub__(self, *args)
10691 r"""__len__(Vector2D self) -> unsigned int"""
10692 return _IMP_kernel.Vector2D___len__(self)
10694 def __rmul__(self, f):
10695 r"""__rmul__(Vector2D self, double f) -> Vector2D"""
10696 return _IMP_kernel.Vector2D___rmul__(self, f)
10699 r"""__str__(Vector2D self) -> std::string"""
10700 return _IMP_kernel.Vector2D___str__(self)
10702 def __repr__(self):
10703 r"""__repr__(Vector2D self) -> std::string"""
10704 return _IMP_kernel.Vector2D___repr__(self)
10706 def __cmp__(self, arg2):
10707 r"""__cmp__(Vector2D self, Vector2D arg2) -> int"""
10708 return _IMP_kernel.Vector2D___cmp__(self, arg2)
10710 def __eq__(self, arg2):
10711 r"""__eq__(Vector2D self, Vector2D arg2) -> bool"""
10712 return _IMP_kernel.Vector2D___eq__(self, arg2)
10714 __truediv__ = __div__
10715 __itruediv__ = __idiv__
10718 def _get_as_binary(self):
10719 r"""_get_as_binary(Vector2D self) -> PyObject *"""
10720 return _IMP_kernel.Vector2D__get_as_binary(self)
10722 def _set_from_binary(self, p):
10723 r"""_set_from_binary(Vector2D self, PyObject * p)"""
10724 return _IMP_kernel.Vector2D__set_from_binary(self, p)
10726 def __getstate__(self):
10727 p = self._get_as_binary()
10728 if len(self.__dict__) > 1:
10729 d = self.__dict__.copy()
10734 def __setstate__(self, p):
10735 if not hasattr(self,
'this'):
10737 if isinstance(p, tuple):
10739 self.__dict__.update(d)
10740 return self._set_from_binary(p)
10743 def __getitem__(self, index):
10744 if isinstance(index, slice):
10745 return [self[i]
for i
in range(*index.indices(len(self)))]
10747 return _IMP_kernel.Vector2D___getitem__(self, index)
10751 def __setitem__(self, index, val):
10752 if isinstance(index, slice):
10753 if not hasattr(val,
'__iter__'):
10754 raise TypeError(
"must assign iterable to extended slice")
10755 inds = range(*index.indices(len(self)))
10756 if len(inds) != len(val):
10758 "attempt to assign sequence of size %d "
10759 "to extended slice of size %d" % (len(val), len(inds)))
10760 for ind, v
in zip(inds, val):
10763 return _IMP_kernel.Vector2D___setitem__(self, index, val)
10766 __swig_destroy__ = _IMP_kernel.delete_Vector2D
10769 _IMP_kernel.Vector2D_swigregister(Vector2D)
10770 class Vector3D(_VectorBase3D):
10771 r"""Proxy of C++ IMP::VectorD< 3 > class."""
10773 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10775 def get_unit_vector(self):
10776 r"""get_unit_vector(Vector3D self) -> Vector3D"""
10777 return _IMP_kernel.Vector3D_get_unit_vector(self)
10779 def __truediv__(self, *args):
10780 return _IMP_kernel.Vector3D___truediv__(self, *args)
10781 __div__ = __truediv__
10786 r"""__neg__(Vector3D self) -> Vector3D"""
10787 return _IMP_kernel.Vector3D___neg__(self)
10789 def __sub__(self, o):
10790 r"""__sub__(Vector3D self, Vector3D o) -> Vector3D"""
10791 return _IMP_kernel.Vector3D___sub__(self, o)
10793 def __add__(self, ret):
10794 r"""__add__(Vector3D self, Vector3D ret) -> Vector3D"""
10795 return _IMP_kernel.Vector3D___add__(self, ret)
10797 def __mul__(self, *args):
10799 __mul__(Vector3D self, double s) -> Vector3D
10800 __mul__(Vector3D self, Vector3D o) -> double
10802 return _IMP_kernel.Vector3D___mul__(self, *args)
10804 def __init__(self, *args):
10806 __init__(Vector3D self, IMP::Floats const & f) -> Vector3D
10807 __init__(Vector3D self) -> Vector3D
10808 __init__(Vector3D self, double x, double y, double z) -> Vector3D
10810 _IMP_kernel.Vector3D_swiginit(self, _IMP_kernel.new_Vector3D(*args))
10812 def __iadd__(self, *args):
10813 _IMP_kernel.Vector3D___iadd__(self, *args)
10818 def __imul__(self, *args):
10819 _IMP_kernel.Vector3D___imul__(self, *args)
10824 def __idiv__(self, *args):
10825 _IMP_kernel.Vector3D___idiv__(self, *args)
10830 def __isub__(self, *args):
10831 _IMP_kernel.Vector3D___isub__(self, *args)
10837 r"""__len__(Vector3D self) -> unsigned int"""
10838 return _IMP_kernel.Vector3D___len__(self)
10840 def __rmul__(self, f):
10841 r"""__rmul__(Vector3D self, double f) -> Vector3D"""
10842 return _IMP_kernel.Vector3D___rmul__(self, f)
10845 r"""__str__(Vector3D self) -> std::string"""
10846 return _IMP_kernel.Vector3D___str__(self)
10848 def __repr__(self):
10849 r"""__repr__(Vector3D self) -> std::string"""
10850 return _IMP_kernel.Vector3D___repr__(self)
10852 def __cmp__(self, arg2):
10853 r"""__cmp__(Vector3D self, Vector3D arg2) -> int"""
10854 return _IMP_kernel.Vector3D___cmp__(self, arg2)
10856 def __eq__(self, arg2):
10857 r"""__eq__(Vector3D self, Vector3D arg2) -> bool"""
10858 return _IMP_kernel.Vector3D___eq__(self, arg2)
10860 __truediv__ = __div__
10861 __itruediv__ = __idiv__
10864 def _get_as_binary(self):
10865 r"""_get_as_binary(Vector3D self) -> PyObject *"""
10866 return _IMP_kernel.Vector3D__get_as_binary(self)
10868 def _set_from_binary(self, p):
10869 r"""_set_from_binary(Vector3D self, PyObject * p)"""
10870 return _IMP_kernel.Vector3D__set_from_binary(self, p)
10872 def __getstate__(self):
10873 p = self._get_as_binary()
10874 if len(self.__dict__) > 1:
10875 d = self.__dict__.copy()
10880 def __setstate__(self, p):
10881 if not hasattr(self,
'this'):
10883 if isinstance(p, tuple):
10885 self.__dict__.update(d)
10886 return self._set_from_binary(p)
10889 def __getitem__(self, index):
10890 if isinstance(index, slice):
10891 return [self[i]
for i
in range(*index.indices(len(self)))]
10893 return _IMP_kernel.Vector3D___getitem__(self, index)
10897 def __setitem__(self, index, val):
10898 if isinstance(index, slice):
10899 if not hasattr(val,
'__iter__'):
10900 raise TypeError(
"must assign iterable to extended slice")
10901 inds = range(*index.indices(len(self)))
10902 if len(inds) != len(val):
10904 "attempt to assign sequence of size %d "
10905 "to extended slice of size %d" % (len(val), len(inds)))
10906 for ind, v
in zip(inds, val):
10909 return _IMP_kernel.Vector3D___setitem__(self, index, val)
10912 __swig_destroy__ = _IMP_kernel.delete_Vector3D
10915 _IMP_kernel.Vector3D_swigregister(Vector3D)
10916 class Vector4D(_VectorBase4D):
10917 r"""Proxy of C++ IMP::VectorD< 4 > class."""
10919 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
10921 def get_unit_vector(self):
10922 r"""get_unit_vector(Vector4D self) -> Vector4D"""
10923 return _IMP_kernel.Vector4D_get_unit_vector(self)
10925 def __truediv__(self, *args):
10926 return _IMP_kernel.Vector4D___truediv__(self, *args)
10927 __div__ = __truediv__
10932 r"""__neg__(Vector4D self) -> Vector4D"""
10933 return _IMP_kernel.Vector4D___neg__(self)
10935 def __sub__(self, o):
10936 r"""__sub__(Vector4D self, Vector4D o) -> Vector4D"""
10937 return _IMP_kernel.Vector4D___sub__(self, o)
10939 def __add__(self, ret):
10940 r"""__add__(Vector4D self, Vector4D ret) -> Vector4D"""
10941 return _IMP_kernel.Vector4D___add__(self, ret)
10943 def __mul__(self, *args):
10945 __mul__(Vector4D self, double s) -> Vector4D
10946 __mul__(Vector4D self, Vector4D o) -> double
10948 return _IMP_kernel.Vector4D___mul__(self, *args)
10950 def __init__(self, *args):
10952 __init__(Vector4D self, IMP::Floats const & f) -> Vector4D
10953 __init__(Vector4D self) -> Vector4D
10954 __init__(Vector4D self, double x0, double x1, double x2, double x3) -> Vector4D
10956 _IMP_kernel.Vector4D_swiginit(self, _IMP_kernel.new_Vector4D(*args))
10958 def __iadd__(self, *args):
10959 _IMP_kernel.Vector4D___iadd__(self, *args)
10964 def __imul__(self, *args):
10965 _IMP_kernel.Vector4D___imul__(self, *args)
10970 def __idiv__(self, *args):
10971 _IMP_kernel.Vector4D___idiv__(self, *args)
10976 def __isub__(self, *args):
10977 _IMP_kernel.Vector4D___isub__(self, *args)
10983 r"""__len__(Vector4D self) -> unsigned int"""
10984 return _IMP_kernel.Vector4D___len__(self)
10986 def __rmul__(self, f):
10987 r"""__rmul__(Vector4D self, double f) -> Vector4D"""
10988 return _IMP_kernel.Vector4D___rmul__(self, f)
10991 r"""__str__(Vector4D self) -> std::string"""
10992 return _IMP_kernel.Vector4D___str__(self)
10994 def __repr__(self):
10995 r"""__repr__(Vector4D self) -> std::string"""
10996 return _IMP_kernel.Vector4D___repr__(self)
10998 def __cmp__(self, arg2):
10999 r"""__cmp__(Vector4D self, Vector4D arg2) -> int"""
11000 return _IMP_kernel.Vector4D___cmp__(self, arg2)
11002 def __eq__(self, arg2):
11003 r"""__eq__(Vector4D self, Vector4D arg2) -> bool"""
11004 return _IMP_kernel.Vector4D___eq__(self, arg2)
11006 __truediv__ = __div__
11007 __itruediv__ = __idiv__
11010 def _get_as_binary(self):
11011 r"""_get_as_binary(Vector4D self) -> PyObject *"""
11012 return _IMP_kernel.Vector4D__get_as_binary(self)
11014 def _set_from_binary(self, p):
11015 r"""_set_from_binary(Vector4D self, PyObject * p)"""
11016 return _IMP_kernel.Vector4D__set_from_binary(self, p)
11018 def __getstate__(self):
11019 p = self._get_as_binary()
11020 if len(self.__dict__) > 1:
11021 d = self.__dict__.copy()
11026 def __setstate__(self, p):
11027 if not hasattr(self,
'this'):
11029 if isinstance(p, tuple):
11031 self.__dict__.update(d)
11032 return self._set_from_binary(p)
11035 def __getitem__(self, index):
11036 if isinstance(index, slice):
11037 return [self[i]
for i
in range(*index.indices(len(self)))]
11039 return _IMP_kernel.Vector4D___getitem__(self, index)
11043 def __setitem__(self, index, val):
11044 if isinstance(index, slice):
11045 if not hasattr(val,
'__iter__'):
11046 raise TypeError(
"must assign iterable to extended slice")
11047 inds = range(*index.indices(len(self)))
11048 if len(inds) != len(val):
11050 "attempt to assign sequence of size %d "
11051 "to extended slice of size %d" % (len(val), len(inds)))
11052 for ind, v
in zip(inds, val):
11055 return _IMP_kernel.Vector4D___setitem__(self, index, val)
11058 __swig_destroy__ = _IMP_kernel.delete_Vector4D
11061 _IMP_kernel.Vector4D_swigregister(Vector4D)
11062 class Vector5D(_VectorBase5D):
11063 r"""Proxy of C++ IMP::VectorD< 5 > class."""
11065 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11067 def get_unit_vector(self):
11068 r"""get_unit_vector(Vector5D self) -> Vector5D"""
11069 return _IMP_kernel.Vector5D_get_unit_vector(self)
11071 def __truediv__(self, *args):
11072 return _IMP_kernel.Vector5D___truediv__(self, *args)
11073 __div__ = __truediv__
11078 r"""__neg__(Vector5D self) -> Vector5D"""
11079 return _IMP_kernel.Vector5D___neg__(self)
11081 def __sub__(self, o):
11082 r"""__sub__(Vector5D self, Vector5D o) -> Vector5D"""
11083 return _IMP_kernel.Vector5D___sub__(self, o)
11085 def __add__(self, ret):
11086 r"""__add__(Vector5D self, Vector5D ret) -> Vector5D"""
11087 return _IMP_kernel.Vector5D___add__(self, ret)
11089 def __mul__(self, *args):
11091 __mul__(Vector5D self, double s) -> Vector5D
11092 __mul__(Vector5D self, Vector5D o) -> double
11094 return _IMP_kernel.Vector5D___mul__(self, *args)
11096 def __init__(self, *args):
11098 __init__(Vector5D self, IMP::Floats const & f) -> Vector5D
11099 __init__(Vector5D self) -> Vector5D
11100 __init__(Vector5D self, double x0, double x1, double x2, double x3, double x4) -> Vector5D
11102 _IMP_kernel.Vector5D_swiginit(self, _IMP_kernel.new_Vector5D(*args))
11104 def __iadd__(self, *args):
11105 _IMP_kernel.Vector5D___iadd__(self, *args)
11110 def __imul__(self, *args):
11111 _IMP_kernel.Vector5D___imul__(self, *args)
11116 def __idiv__(self, *args):
11117 _IMP_kernel.Vector5D___idiv__(self, *args)
11122 def __isub__(self, *args):
11123 _IMP_kernel.Vector5D___isub__(self, *args)
11129 r"""__len__(Vector5D self) -> unsigned int"""
11130 return _IMP_kernel.Vector5D___len__(self)
11132 def __rmul__(self, f):
11133 r"""__rmul__(Vector5D self, double f) -> Vector5D"""
11134 return _IMP_kernel.Vector5D___rmul__(self, f)
11137 r"""__str__(Vector5D self) -> std::string"""
11138 return _IMP_kernel.Vector5D___str__(self)
11140 def __repr__(self):
11141 r"""__repr__(Vector5D self) -> std::string"""
11142 return _IMP_kernel.Vector5D___repr__(self)
11144 def __cmp__(self, arg2):
11145 r"""__cmp__(Vector5D self, Vector5D arg2) -> int"""
11146 return _IMP_kernel.Vector5D___cmp__(self, arg2)
11148 def __eq__(self, arg2):
11149 r"""__eq__(Vector5D self, Vector5D arg2) -> bool"""
11150 return _IMP_kernel.Vector5D___eq__(self, arg2)
11152 __truediv__ = __div__
11153 __itruediv__ = __idiv__
11156 def _get_as_binary(self):
11157 r"""_get_as_binary(Vector5D self) -> PyObject *"""
11158 return _IMP_kernel.Vector5D__get_as_binary(self)
11160 def _set_from_binary(self, p):
11161 r"""_set_from_binary(Vector5D self, PyObject * p)"""
11162 return _IMP_kernel.Vector5D__set_from_binary(self, p)
11164 def __getstate__(self):
11165 p = self._get_as_binary()
11166 if len(self.__dict__) > 1:
11167 d = self.__dict__.copy()
11172 def __setstate__(self, p):
11173 if not hasattr(self,
'this'):
11175 if isinstance(p, tuple):
11177 self.__dict__.update(d)
11178 return self._set_from_binary(p)
11181 def __getitem__(self, index):
11182 if isinstance(index, slice):
11183 return [self[i]
for i
in range(*index.indices(len(self)))]
11185 return _IMP_kernel.Vector5D___getitem__(self, index)
11189 def __setitem__(self, index, val):
11190 if isinstance(index, slice):
11191 if not hasattr(val,
'__iter__'):
11192 raise TypeError(
"must assign iterable to extended slice")
11193 inds = range(*index.indices(len(self)))
11194 if len(inds) != len(val):
11196 "attempt to assign sequence of size %d "
11197 "to extended slice of size %d" % (len(val), len(inds)))
11198 for ind, v
in zip(inds, val):
11201 return _IMP_kernel.Vector5D___setitem__(self, index, val)
11204 __swig_destroy__ = _IMP_kernel.delete_Vector5D
11207 _IMP_kernel.Vector5D_swigregister(Vector5D)
11208 class Vector6D(_VectorBase6D):
11209 r"""Proxy of C++ IMP::VectorD< 6 > class."""
11211 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11213 def get_unit_vector(self):
11214 r"""get_unit_vector(Vector6D self) -> Vector6D"""
11215 return _IMP_kernel.Vector6D_get_unit_vector(self)
11217 def __truediv__(self, *args):
11218 return _IMP_kernel.Vector6D___truediv__(self, *args)
11219 __div__ = __truediv__
11224 r"""__neg__(Vector6D self) -> Vector6D"""
11225 return _IMP_kernel.Vector6D___neg__(self)
11227 def __sub__(self, o):
11228 r"""__sub__(Vector6D self, Vector6D o) -> Vector6D"""
11229 return _IMP_kernel.Vector6D___sub__(self, o)
11231 def __add__(self, ret):
11232 r"""__add__(Vector6D self, Vector6D ret) -> Vector6D"""
11233 return _IMP_kernel.Vector6D___add__(self, ret)
11235 def __mul__(self, *args):
11237 __mul__(Vector6D self, double s) -> Vector6D
11238 __mul__(Vector6D self, Vector6D o) -> double
11240 return _IMP_kernel.Vector6D___mul__(self, *args)
11242 def __init__(self, *args):
11244 __init__(Vector6D self, IMP::Floats const & f) -> Vector6D
11245 __init__(Vector6D self) -> Vector6D
11246 __init__(Vector6D self, double x0, double x1, double x2, double x3, double x4, double x5) -> Vector6D
11248 _IMP_kernel.Vector6D_swiginit(self, _IMP_kernel.new_Vector6D(*args))
11250 def __iadd__(self, *args):
11251 _IMP_kernel.Vector6D___iadd__(self, *args)
11256 def __imul__(self, *args):
11257 _IMP_kernel.Vector6D___imul__(self, *args)
11262 def __idiv__(self, *args):
11263 _IMP_kernel.Vector6D___idiv__(self, *args)
11268 def __isub__(self, *args):
11269 _IMP_kernel.Vector6D___isub__(self, *args)
11275 r"""__len__(Vector6D self) -> unsigned int"""
11276 return _IMP_kernel.Vector6D___len__(self)
11278 def __rmul__(self, f):
11279 r"""__rmul__(Vector6D self, double f) -> Vector6D"""
11280 return _IMP_kernel.Vector6D___rmul__(self, f)
11283 r"""__str__(Vector6D self) -> std::string"""
11284 return _IMP_kernel.Vector6D___str__(self)
11286 def __repr__(self):
11287 r"""__repr__(Vector6D self) -> std::string"""
11288 return _IMP_kernel.Vector6D___repr__(self)
11290 def __cmp__(self, arg2):
11291 r"""__cmp__(Vector6D self, Vector6D arg2) -> int"""
11292 return _IMP_kernel.Vector6D___cmp__(self, arg2)
11294 def __eq__(self, arg2):
11295 r"""__eq__(Vector6D self, Vector6D arg2) -> bool"""
11296 return _IMP_kernel.Vector6D___eq__(self, arg2)
11298 __truediv__ = __div__
11299 __itruediv__ = __idiv__
11302 def _get_as_binary(self):
11303 r"""_get_as_binary(Vector6D self) -> PyObject *"""
11304 return _IMP_kernel.Vector6D__get_as_binary(self)
11306 def _set_from_binary(self, p):
11307 r"""_set_from_binary(Vector6D self, PyObject * p)"""
11308 return _IMP_kernel.Vector6D__set_from_binary(self, p)
11310 def __getstate__(self):
11311 p = self._get_as_binary()
11312 if len(self.__dict__) > 1:
11313 d = self.__dict__.copy()
11318 def __setstate__(self, p):
11319 if not hasattr(self,
'this'):
11321 if isinstance(p, tuple):
11323 self.__dict__.update(d)
11324 return self._set_from_binary(p)
11327 def __getitem__(self, index):
11328 if isinstance(index, slice):
11329 return [self[i]
for i
in range(*index.indices(len(self)))]
11331 return _IMP_kernel.Vector6D___getitem__(self, index)
11335 def __setitem__(self, index, val):
11336 if isinstance(index, slice):
11337 if not hasattr(val,
'__iter__'):
11338 raise TypeError(
"must assign iterable to extended slice")
11339 inds = range(*index.indices(len(self)))
11340 if len(inds) != len(val):
11342 "attempt to assign sequence of size %d "
11343 "to extended slice of size %d" % (len(val), len(inds)))
11344 for ind, v
in zip(inds, val):
11347 return _IMP_kernel.Vector6D___setitem__(self, index, val)
11350 __swig_destroy__ = _IMP_kernel.delete_Vector6D
11353 _IMP_kernel.Vector6D_swigregister(Vector6D)
11354 class VectorKD(_VectorBaseKD):
11355 r"""Proxy of C++ IMP::VectorD< -1 > class."""
11357 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11359 def get_unit_vector(self):
11360 r"""get_unit_vector(VectorKD self) -> VectorKD"""
11361 return _IMP_kernel.VectorKD_get_unit_vector(self)
11363 def __truediv__(self, *args):
11364 return _IMP_kernel.VectorKD___truediv__(self, *args)
11365 __div__ = __truediv__
11370 r"""__neg__(VectorKD self) -> VectorKD"""
11371 return _IMP_kernel.VectorKD___neg__(self)
11373 def __sub__(self, o):
11374 r"""__sub__(VectorKD self, VectorKD o) -> VectorKD"""
11375 return _IMP_kernel.VectorKD___sub__(self, o)
11377 def __add__(self, ret):
11378 r"""__add__(VectorKD self, VectorKD ret) -> VectorKD"""
11379 return _IMP_kernel.VectorKD___add__(self, ret)
11381 def __mul__(self, *args):
11383 __mul__(VectorKD self, double s) -> VectorKD
11384 __mul__(VectorKD self, VectorKD o) -> double
11386 return _IMP_kernel.VectorKD___mul__(self, *args)
11388 def __init__(self, *args):
11390 __init__(VectorKD self, IMP::Floats const & f) -> VectorKD
11391 __init__(VectorKD self) -> VectorKD
11392 __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
11394 _IMP_kernel.VectorKD_swiginit(self, _IMP_kernel.new_VectorKD(*args))
11396 def __iadd__(self, *args):
11397 _IMP_kernel.VectorKD___iadd__(self, *args)
11402 def __imul__(self, *args):
11403 _IMP_kernel.VectorKD___imul__(self, *args)
11408 def __idiv__(self, *args):
11409 _IMP_kernel.VectorKD___idiv__(self, *args)
11414 def __isub__(self, *args):
11415 _IMP_kernel.VectorKD___isub__(self, *args)
11421 r"""__len__(VectorKD self) -> unsigned int"""
11422 return _IMP_kernel.VectorKD___len__(self)
11424 def __rmul__(self, f):
11425 r"""__rmul__(VectorKD self, double f) -> VectorKD"""
11426 return _IMP_kernel.VectorKD___rmul__(self, f)
11429 r"""__str__(VectorKD self) -> std::string"""
11430 return _IMP_kernel.VectorKD___str__(self)
11432 def __repr__(self):
11433 r"""__repr__(VectorKD self) -> std::string"""
11434 return _IMP_kernel.VectorKD___repr__(self)
11436 def __cmp__(self, arg2):
11437 r"""__cmp__(VectorKD self, VectorKD arg2) -> int"""
11438 return _IMP_kernel.VectorKD___cmp__(self, arg2)
11440 def __eq__(self, arg2):
11441 r"""__eq__(VectorKD self, VectorKD arg2) -> bool"""
11442 return _IMP_kernel.VectorKD___eq__(self, arg2)
11444 __truediv__ = __div__
11445 __itruediv__ = __idiv__
11448 def _get_as_binary(self):
11449 r"""_get_as_binary(VectorKD self) -> PyObject *"""
11450 return _IMP_kernel.VectorKD__get_as_binary(self)
11452 def _set_from_binary(self, p):
11453 r"""_set_from_binary(VectorKD self, PyObject * p)"""
11454 return _IMP_kernel.VectorKD__set_from_binary(self, p)
11456 def __getstate__(self):
11457 p = self._get_as_binary()
11458 if len(self.__dict__) > 1:
11459 d = self.__dict__.copy()
11464 def __setstate__(self, p):
11465 if not hasattr(self,
'this'):
11467 if isinstance(p, tuple):
11469 self.__dict__.update(d)
11470 return self._set_from_binary(p)
11473 def __getitem__(self, index):
11474 if isinstance(index, slice):
11475 return [self[i]
for i
in range(*index.indices(len(self)))]
11477 return _IMP_kernel.VectorKD___getitem__(self, index)
11481 def __setitem__(self, index, val):
11482 if isinstance(index, slice):
11483 if not hasattr(val,
'__iter__'):
11484 raise TypeError(
"must assign iterable to extended slice")
11485 inds = range(*index.indices(len(self)))
11486 if len(inds) != len(val):
11488 "attempt to assign sequence of size %d "
11489 "to extended slice of size %d" % (len(val), len(inds)))
11490 for ind, v
in zip(inds, val):
11493 return _IMP_kernel.VectorKD___setitem__(self, index, val)
11496 __swig_destroy__ = _IMP_kernel.delete_VectorKD
11499 _IMP_kernel.VectorKD_swigregister(VectorKD)
11501 def get_basis_vector_1d(coordinate):
11502 r"""get_basis_vector_1d(unsigned int coordinate) -> Vector1D"""
11503 return _IMP_kernel.get_basis_vector_1d(coordinate)
11505 def get_basis_vector_2d(coordinate):
11506 r"""get_basis_vector_2d(unsigned int coordinate) -> Vector2D"""
11507 return _IMP_kernel.get_basis_vector_2d(coordinate)
11509 def get_basis_vector_3d(coordinate):
11510 r"""get_basis_vector_3d(unsigned int coordinate) -> Vector3D"""
11511 return _IMP_kernel.get_basis_vector_3d(coordinate)
11513 def get_basis_vector_4d(coordinate):
11514 r"""get_basis_vector_4d(unsigned int coordinate) -> Vector4D"""
11515 return _IMP_kernel.get_basis_vector_4d(coordinate)
11517 def get_basis_vector_5d(coordinate):
11518 r"""get_basis_vector_5d(unsigned int coordinate) -> Vector5D"""
11519 return _IMP_kernel.get_basis_vector_5d(coordinate)
11521 def get_basis_vector_6d(coordinate):
11522 r"""get_basis_vector_6d(unsigned int coordinate) -> Vector6D"""
11523 return _IMP_kernel.get_basis_vector_6d(coordinate)
11525 def get_zero_vector_1d():
11526 r"""get_zero_vector_1d() -> Vector1D"""
11527 return _IMP_kernel.get_zero_vector_1d()
11529 def get_zero_vector_2d():
11530 r"""get_zero_vector_2d() -> Vector2D"""
11531 return _IMP_kernel.get_zero_vector_2d()
11533 def get_zero_vector_3d():
11534 r"""get_zero_vector_3d() -> Vector3D"""
11535 return _IMP_kernel.get_zero_vector_3d()
11537 def get_zero_vector_4d():
11538 r"""get_zero_vector_4d() -> Vector4D"""
11539 return _IMP_kernel.get_zero_vector_4d()
11541 def get_zero_vector_5d():
11542 r"""get_zero_vector_5d() -> Vector5D"""
11543 return _IMP_kernel.get_zero_vector_5d()
11545 def get_zero_vector_6d():
11546 r"""get_zero_vector_6d() -> Vector6D"""
11547 return _IMP_kernel.get_zero_vector_6d()
11549 def get_ones_vector_1d(v=1):
11550 r"""get_ones_vector_1d(double v=1) -> Vector1D"""
11551 return _IMP_kernel.get_ones_vector_1d(v)
11553 def get_ones_vector_2d(v=1):
11554 r"""get_ones_vector_2d(double v=1) -> Vector2D"""
11555 return _IMP_kernel.get_ones_vector_2d(v)
11557 def get_ones_vector_3d(v=1):
11558 r"""get_ones_vector_3d(double v=1) -> Vector3D"""
11559 return _IMP_kernel.get_ones_vector_3d(v)
11561 def get_ones_vector_4d(v=1):
11562 r"""get_ones_vector_4d(double v=1) -> Vector4D"""
11563 return _IMP_kernel.get_ones_vector_4d(v)
11565 def get_ones_vector_5d(v=1):
11566 r"""get_ones_vector_5d(double v=1) -> Vector5D"""
11567 return _IMP_kernel.get_ones_vector_5d(v)
11569 def get_ones_vector_6d(v=1):
11570 r"""get_ones_vector_6d(double v=1) -> Vector6D"""
11571 return _IMP_kernel.get_ones_vector_6d(v)
11573 r"""Proxy of C++ IMP::internal::GenericRestraintsScoringFunction< ::IMP::Restraints > class."""
11575 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11576 __repr__ = _swig_repr
11578 def __init__(self, *args):
11580 __init__(_RestraintsScoringFunction self, IMP::RestraintsTemp const & rs, double weight=1.0, double max=NO_MAX, std::string name="RestraintsScoringFunction%1%") -> _RestraintsScoringFunction
11581 __init__(_RestraintsScoringFunction self) -> _RestraintsScoringFunction
11583 _IMP_kernel._RestraintsScoringFunction_swiginit(self, _IMP_kernel.new__RestraintsScoringFunction(*args))
11585 def do_add_score_and_derivatives(self, sa, ss):
11586 r"""do_add_score_and_derivatives(_RestraintsScoringFunction self, ScoreAccumulator sa, IMP::ScoreStatesTemp const & ss)"""
11587 return _IMP_kernel._RestraintsScoringFunction_do_add_score_and_derivatives(self, sa, ss)
11589 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss):
11590 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)"""
11591 return _IMP_kernel._RestraintsScoringFunction_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss)
11593 def do_get_inputs(self):
11594 r"""do_get_inputs(_RestraintsScoringFunction self) -> IMP::ModelObjectsTemp"""
11595 return _IMP_kernel._RestraintsScoringFunction_do_get_inputs(self)
11597 def get_restraints(self):
11598 r"""get_restraints(_RestraintsScoringFunction self) -> IMP::Vector< IMP::Pointer< IMP::Restraint >,std::allocator< IMP::Pointer< IMP::Restraint > > > const &"""
11599 return _IMP_kernel._RestraintsScoringFunction_get_restraints(self)
11601 def set_restraints(self, s):
11602 r"""set_restraints(_RestraintsScoringFunction self, IMP::RestraintsTemp const & s)"""
11603 return _IMP_kernel._RestraintsScoringFunction_set_restraints(self, s)
11605 def get_number_of_restraints(self):
11606 r"""get_number_of_restraints(_RestraintsScoringFunction self) -> unsigned int"""
11607 return _IMP_kernel._RestraintsScoringFunction_get_number_of_restraints(self)
11609 def clear_restraints(self):
11610 r"""clear_restraints(_RestraintsScoringFunction self)"""
11611 return _IMP_kernel._RestraintsScoringFunction_clear_restraints(self)
11613 def get_restraint(self, i):
11614 r"""get_restraint(_RestraintsScoringFunction self, unsigned int i) -> Restraint"""
11615 return _IMP_kernel._RestraintsScoringFunction_get_restraint(self, i)
11617 def erase_restraint(self, i):
11618 r"""erase_restraint(_RestraintsScoringFunction self, unsigned int i)"""
11619 return _IMP_kernel._RestraintsScoringFunction_erase_restraint(self, i)
11622 r"""add_restraint(_RestraintsScoringFunction self, Restraint r) -> unsigned int"""
11623 return _IMP_kernel._RestraintsScoringFunction_add_restraint(self, r)
11626 r"""add_restraints(_RestraintsScoringFunction self, IMP::Vector< IMP::Pointer< IMP::Restraint >,std::allocator< IMP::Pointer< IMP::Restraint > > > const & r)"""
11627 return _IMP_kernel._RestraintsScoringFunction_add_restraints(self, r)
11629 def _python_index_restraint(self, r, start, stop):
11630 r"""_python_index_restraint(_RestraintsScoringFunction self, Restraint r, unsigned int start, unsigned int stop) -> unsigned int"""
11631 return _IMP_kernel._RestraintsScoringFunction__python_index_restraint(self, r, start, stop)
11634 r"""get_version_info(_RestraintsScoringFunction self) -> VersionInfo"""
11635 return _IMP_kernel._RestraintsScoringFunction_get_version_info(self)
11636 __swig_destroy__ = _IMP_kernel.delete__RestraintsScoringFunction
11640 return _object_cast_to__RestraintsScoringFunction(o)
11643 def __get_restraints(self):
11644 return _list_util.VarList(
11645 getdimfunc=self.get_number_of_restraints,
11646 getfunc=self.get_restraint, erasefunc=self.erase_restraint,
11647 appendfunc=self.add_restraint, extendfunc=self.add_restraints,
11648 clearfunc=self.clear_restraints,
11649 indexfunc=self._python_index_restraint)
11651 def __set_restraints(self, obj):
11652 _list_util.set_varlist(self.restraints, obj)
11654 def __del_restraints(self):
11655 _list_util.del_varlist(self.restraints)
11657 restraints = property(__get_restraints, __set_restraints,
11658 __del_restraints, doc=
"List of Restraints")
11661 def _get_jax(self):
11662 import IMP._jax_util
11663 jis = [r.get_derived_object()._get_jax()
for r
in self.restraints]
11664 funcs = [j.score_func
for j
in jis]
11665 keys = frozenset(x
for j
in jis
for x
in j._keys)
11667 return sum(f(jm)
for f
in funcs)
11668 return IMP._jax_util.JAXRestraintInfo(
11669 m=self.get_model(), score_func=jax_sf, weight=1.0, keys=keys)
11673 _IMP_kernel._RestraintsScoringFunction_swigregister(_RestraintsScoringFunction)
11675 r"""Proxy of C++ IMP::ScopedSetAttribute< IMP::FloatKey,IMP::Float > class."""
11677 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
11679 def __init__(self, *args):
11681 __init__(ScopedSetFloatAttribute self) -> ScopedSetFloatAttribute
11682 __init__(ScopedSetFloatAttribute self, Particle p, FloatKey key, double const & value) -> ScopedSetFloatAttribute
11684 _IMP_kernel.ScopedSetFloatAttribute_swiginit(self, _IMP_kernel.new_ScopedSetFloatAttribute(*args))
11686 def set(self, p, key, value):
11687 r"""set(ScopedSetFloatAttribute self, Particle p, FloatKey key, double const & value)"""
11688 return _IMP_kernel.ScopedSetFloatAttribute_set(self, p, key, value)
11691 r"""reset(ScopedSetFloatAttribute self)"""
11692 return _IMP_kernel.ScopedSetFloatAttribute_reset(self)
11693 __swig_destroy__ = _IMP_kernel.delete_ScopedSetFloatAttribute
11695 def show(self, *args):
11696 r"""show(ScopedSetFloatAttribute self, _ostream out=std::cout)"""
11697 return _IMP_kernel.ScopedSetFloatAttribute_show(self, *args)
11700 r"""__str__(ScopedSetFloatAttribute self) -> std::string"""
11701 return _IMP_kernel.ScopedSetFloatAttribute___str__(self)
11703 def __repr__(self):
11704 r"""__repr__(ScopedSetFloatAttribute self) -> std::string"""
11705 return _IMP_kernel.ScopedSetFloatAttribute___repr__(self)
11708 _IMP_kernel.ScopedSetFloatAttribute_swigregister(ScopedSetFloatAttribute)
11710 def _get_module_data_path(module, file_name):
11711 r"""_get_module_data_path(std::string module, std::string file_name) -> std::string"""
11712 return _IMP_kernel._get_module_data_path(module, file_name)
11714 def _get_module_example_path(module, file_name):
11715 r"""_get_module_example_path(std::string module, std::string file_name) -> std::string"""
11716 return _IMP_kernel._get_module_example_path(module, file_name)
11725 if sys.platform ==
'win32' and 'IMP_LD_PATH' in os.environ:
11726 dirs = os.environ[
'IMP_LD_PATH'].split(
":")
11727 pathcomps = os.environ[
'PATH'].split(
";")
11729 if d
not in pathcomps:
11730 os.environ[
'PATH'] = d +
';' + os.environ[
'PATH']
11738 """Allow command line tools to easily implement multiple commands.
11739 Typically, an IMP command line tool will use an instance of this class
11740 to provide a consistent interface to multiple distinct commands
11741 from a single binary, rather than providing a potentially large
11742 number of binaries. This is similar to the way a number of common
11743 command line tools outside of IMP function (e.g. Git provides a single
11744 `git` tool which implements multiple commands - `git add`, `git commit`,
11745 `git push` and so on).
11747 Each command is implemented with a Python module of the same name
11748 that can be imported from the module (for example, if `module_name`
11749 is `IMP.foo`, the `bar` command is provided by the `IMP.foo.bar` Python
11750 module, which would usually be found as `modules/foo/pyext/src/bar.py`).
11751 Each such module should have a docstring and a `%main()` method
11752 that takes no arguments (the module should also call its `%main()` method
11753 if it is run directly, i.e. with something like
11754 `if __name__=="__main__": %main()`). The encompassing module
11755 (`IMP.foo` in the example) should define `_all_commands` as a Python
11756 list of all valid commands.
11758 See the `multifit` and `cnmultifit` command line tools for example
11764 @param short_help A few words that describe the command line tool.
11765 @param long_help Longer text, used in the `help` command.
11766 @param module_name Name of the module (e.g. `IMP.foo`) that
11767 implements the commands.
11769 self.short_help = short_help
11770 self.long_help = long_help
11771 self.module_name = module_name
11772 self._all_commands = self.import_module()._all_commands
11773 self._progname = os.path.basename(sys.argv[0])
11776 """Call this method to act upon the user-provided command line"""
11777 if len(sys.argv) <= 1:
11778 print(self.short_help +
" Use '%s help' for help." % self._progname)
11780 command = sys.argv[1]
11781 if command
in (
'help',
'--help',
'-h'):
11782 if len(sys.argv) == 3:
11783 self.show_command_help(sys.argv[2])
11786 elif command ==
'--version':
11787 self.show_version()
11788 elif command
in self._all_commands:
11789 self.do_command(command)
11791 self.unknown_command(command)
11793 def import_module(self, mod=None):
11794 modname = self.module_name
11795 if mod
is not None:
11796 modname +=
"." + mod
11797 return __import__(modname, {}, {}, [
''])
11799 def unknown_command(self, command):
11800 print(
"Unknown command: '%s'" % command)
11801 print(
"Use '%s help' for help." % self._progname)
11804 def _get_version(self):
11807 def show_version(self):
11808 print(self._progname +
' ' + self._get_version())
11810 def show_help(self):
11811 ver = self._get_version()
11812 print(
"%s, version %s." % (self._progname, ver))
11813 print(self.long_help +
"""
11815 This program is part of IMP, the Integrative Modeling Platform,
11817 For additional information about IMP, see <https://integrativemodeling.org>.
11819 Usage: %s <command> [options] [args]
11822 commands = self._all_commands[:] + [
'help']
11824 cmdlen = max([len(c)
for c
in commands])
11827 doc =
'Get help on using %s.' % self._progname
11829 doc = self.import_module(c).__doc__
or "<no help>"
11830 c +=
' ' * (cmdlen - len(c))
11831 print(
' ' + c +
' ' + doc)
11833 Use "%s help <command>" for detailed help on any command
11834 or "%s --version" to see the version number.""" % (self._progname,
11837 def do_command(self, command):
11838 mod = self.import_module(command)
11839 sys.argv[0] = self._progname +
' ' + command
11843 def show_command_help(self, command):
11844 if command ==
'help':
11846 elif command
in self._all_commands
or command ==
'help':
11847 mod = self.import_module(command)
11848 sys.argv = [self._progname +
' ' + command,
'--help']
11851 self.unknown_command(command)
11858 g = networkx.DiGraph()
11859 if len(ig.get_vertices()) == 0:
11868 return self.p.get_name()
11870 def __call__(self, name):
11871 return self.p.__call__(name)
11873 for vi
in ig.get_vertices():
11874 n = ig.get_vertex_name(vi)
11875 g.add_node(NodeWrapper(n))
11876 for vi
in ig.get_vertices():
11877 n = ig.get_vertex_name(vi)
11878 for ni
in ig.get_out_neighbors(vi):
11879 nn = ig.get_vertex_name(ni)
11880 g.add_edge(NodeWrapper(n), NodeWrapper(nn))
11887 n0 = name.get_name()
11890 n1 = str(n0).replace(
'"',
'')
11891 n2 = n1.replace(
"\n",
'')
11894 from altgraph
import Graph, Dot
11895 graph = Graph.Graph()
11896 for i, v
in enumerate(g.get_vertices()):
11898 for i, v
in enumerate(g.get_vertices()):
11899 for n
in g.get_out_neighbors(v):
11900 graph.add_edge(v, n)
11901 dot = Dot.Dot(graph)
11902 for i, v
in enumerate(g.get_vertices()):
11903 dot.node_style(i, label=clean(g.get_vertex_name(v)))
11911 st = g.get_graphviz_string()
11912 with open(tfn,
"w")
as fh:
11915 print(
"running dot")
11916 sp = subprocess.Popen([
"dot",
"-Tpdf", tfn,
"-o" + tfon])
11920 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")
11923 if platform.system() ==
"Darwin":
11926 cmd = [
"gv",
"acroread",
"xpdf"]
11929 print(
"launching viewer " + c)
11931 subprocess.check_call([c, tfon])
11937 print(
"Could not display file. It is saved at " + tfon)
11947 """Mark a Python module as deprecated.
11948 @note The `module` argument would normally be `__name__`.
11949 @see [deprecation support](@ref deprecation)."""
11951 "Module %s is deprecated. %s\n" % (module, help_message))
11954 """Python decorator to mark a class as deprecated.
11955 @see [deprecation support](@ref deprecation)."""
11957 orig_init = obj.__init__
11960 @functools.wraps(orig_init, (
'__name__',
'__doc__'))
11961 def __init__(obj, *args, **keys):
11963 % (type(obj), help_message))
11964 orig_init(obj, *args, **keys)
11965 obj.__init__ = __init__
11970 """Python decorator to mark a method as deprecated.
11971 @see [deprecation support](@ref deprecation)."""
11972 def out_wrapper(obj):
11973 @functools.wraps(obj)
11974 def wrapper(cls, *args, **keys):
11976 % (obj.__name__, type(cls), help_message))
11977 return obj(cls, *args, **keys)
11982 """Python decorator to mark a function as deprecated.
11983 @see [deprecation support](@ref deprecation)."""
11984 def out_wrapper(obj):
11985 @functools.wraps(obj)
11986 def wrapper(*args, **keys):
11988 % (obj.__name__, help_message))
11989 return obj(*args, **keys)
11993 @contextlib.contextmanager
11995 """Context manager to temporarily allow (or disallow) deprecated code.
11996 @see [deprecation support](@ref deprecation)."""
12003 def _get_all_flags(ntokens):
12004 r"""_get_all_flags(unsigned int ntokens) -> IMP::Strings"""
12005 return _IMP_kernel._get_all_flags(ntokens)
12007 def _print_internal_help(out, description):
12008 r"""_print_internal_help(_ostream out, std::string description)"""
12009 return _IMP_kernel._print_internal_help(out, description)
12015 class _PassThroughAction(argparse.Action):
12016 """Pass an argument through to the IMP Boost parser"""
12017 def __call__(self, parser, namespace, values, option_string=None):
12018 parser._boost_command_line.append(option_string)
12020 parser._boost_command_line.append(values)
12023 if option_string
in (
'-h',
'--help',
'--help_advanced',
'--version'):
12024 parser._handle_boost()
12028 """IMP-specific subclass of argparse.ArgumentParser.
12029 This adds options common to all IMP applications
12030 (see IMP::setup_from_argv()).
12033 def __init__(self, *args, **kwargs):
12035 kwargs[
'add_help'] =
False
12036 super().__init__(*args, **kwargs)
12037 for ntoken
in (0, 1):
12038 flags = _get_all_flags(ntoken)
12040 arg = [
'-h',
'--help']
if f ==
'help' else [
'--' + f]
12041 self.add_argument(*arg, help=argparse.SUPPRESS,
12042 nargs=
None if ntoken
else 0,
12043 action=_PassThroughAction,
12044 default=argparse.SUPPRESS)
12047 """Parse the command line and return optional and positional arguments.
12048 This functions in the same way as the method in the base class
12049 argparse.ArgumentParser, except that it also processes optional
12050 arguments common to all IMP applications (these are not returned
12051 in `args`, but can be obtained in the usual way, e.g. by calling
12052 IMP::get_string_flag()).
12055 self._boost_command_line = [sys.argv[0]]
12057 if len(self._boost_command_line) > 1:
12058 self._handle_boost()
12061 def _get_description(self):
12062 return self.format_help() +
"\nOptions common to all IMP applications:"
12064 def print_help(self, file=None):
12065 _print_internal_help(file
if file
else sys.stdout,
12066 self._get_description())
12068 def _handle_boost(self):
12070 self._get_description(),
12073 class RandomNumberGenerator(object):
12074 r"""Proxy of C++ IMP::RandomNumberGenerator class."""
12076 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
12077 __repr__ = _swig_repr
12080 r"""seed(RandomNumberGenerator self, int x)"""
12081 return _IMP_kernel.RandomNumberGenerator_seed(self, x)
12083 def __call__(self):
12084 r"""__call__(RandomNumberGenerator self) -> int"""
12085 return _IMP_kernel.RandomNumberGenerator___call__(self)
12087 def __init__(self):
12088 r"""__init__(RandomNumberGenerator self) -> RandomNumberGenerator"""
12089 _IMP_kernel.RandomNumberGenerator_swiginit(self, _IMP_kernel.new_RandomNumberGenerator())
12090 __swig_destroy__ = _IMP_kernel.delete_RandomNumberGenerator
12093 _IMP_kernel.RandomNumberGenerator_swigregister(RandomNumberGenerator)
12097 get_random_float_uniform() -> float
12098 get_random_float_uniform(float min, float max) -> float
12100 return _IMP_kernel.get_random_float_uniform(*args)
12104 get_random_double_uniform() -> double
12105 get_random_double_uniform(double min, double max) -> double
12107 return _IMP_kernel.get_random_double_uniform(*args)
12109 def get_random_floats_normal(n, mean=0.0, stddev=1.0):
12110 r"""get_random_floats_normal(unsigned int n, float mean=0.0, float stddev=1.0) -> IMP::Vector< float,std::allocator< float > >"""
12111 return _IMP_kernel.get_random_floats_normal(n, mean, stddev)
12113 def get_random_doubles_normal(n, mean=0.0, stddev=1.0):
12114 r"""get_random_doubles_normal(unsigned int n, double mean=0.0, double stddev=1.0) -> IMP::Vector< double,std::allocator< double > >"""
12115 return _IMP_kernel.get_random_doubles_normal(n, mean, stddev)
12117 def get_random_floats_uniform(n):
12118 r"""get_random_floats_uniform(unsigned int n) -> IMP::Vector< float,std::allocator< float > >"""
12119 return _IMP_kernel.get_random_floats_uniform(n)
12121 def get_random_doubles_uniform(n):
12122 r"""get_random_doubles_uniform(unsigned int n) -> IMP::Vector< double,std::allocator< double > >"""
12123 return _IMP_kernel.get_random_doubles_uniform(n)
12126 r"""get_random_seed() -> boost::uint64_t"""
12127 return _IMP_kernel.get_random_seed()
12129 def _get_derivatives_numpy(m, k, m_pyobj, read_only):
12130 r"""_get_derivatives_numpy(Model m, FloatKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12131 return _IMP_kernel._get_derivatives_numpy(m, k, m_pyobj, read_only)
12133 def _get_floats_numpy(m, k, m_pyobj, read_only):
12134 r"""_get_floats_numpy(Model m, FloatKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12135 return _IMP_kernel._get_floats_numpy(m, k, m_pyobj, read_only)
12137 def _get_ints_numpy(m, k, m_pyobj, read_only):
12138 r"""_get_ints_numpy(Model m, IntKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12139 return _IMP_kernel._get_ints_numpy(m, k, m_pyobj, read_only)
12141 def _get_vector3ds_numpy(m, k, m_pyobj, read_only):
12142 r"""_get_vector3ds_numpy(Model m, Vector3DKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12143 return _IMP_kernel._get_vector3ds_numpy(m, k, m_pyobj, read_only)
12145 def _get_vector3dderiv_numpy(m, k, m_pyobj, read_only):
12146 r"""_get_vector3dderiv_numpy(Model m, Vector3DDerivKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12147 return _IMP_kernel._get_vector3dderiv_numpy(m, k, m_pyobj, read_only)
12149 def _get_vector3dderiv_derivatives_numpy(m, k, m_pyobj, read_only):
12150 r"""_get_vector3dderiv_derivatives_numpy(Model m, Vector3DDerivKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12151 return _IMP_kernel._get_vector3dderiv_derivatives_numpy(m, k, m_pyobj, read_only)
12153 def _get_vector4ds_numpy(m, k, m_pyobj, read_only):
12154 r"""_get_vector4ds_numpy(Model m, Vector4DKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12155 return _IMP_kernel._get_vector4ds_numpy(m, k, m_pyobj, read_only)
12157 def _get_vector4dderiv_numpy(m, k, m_pyobj, read_only):
12158 r"""_get_vector4dderiv_numpy(Model m, Vector4DDerivKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12159 return _IMP_kernel._get_vector4dderiv_numpy(m, k, m_pyobj, read_only)
12161 def _get_vector4dderiv_derivatives_numpy(m, k, m_pyobj, read_only):
12162 r"""_get_vector4dderiv_derivatives_numpy(Model m, Vector4DDerivKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12163 return _IMP_kernel._get_vector4dderiv_derivatives_numpy(m, k, m_pyobj, read_only)
12165 def _get_spheres_numpy(m, m_pyobj, read_only):
12166 r"""_get_spheres_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12167 return _IMP_kernel._get_spheres_numpy(m, m_pyobj, read_only)
12169 def _get_sphere_derivatives_numpy(m, m_pyobj, read_only):
12170 r"""_get_sphere_derivatives_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12171 return _IMP_kernel._get_sphere_derivatives_numpy(m, m_pyobj, read_only)
12173 def _get_internal_coordinates_numpy(m, m_pyobj, read_only):
12174 r"""_get_internal_coordinates_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12175 return _IMP_kernel._get_internal_coordinates_numpy(m, m_pyobj, read_only)
12177 def _get_internal_coordinate_derivatives_numpy(m, m_pyobj, read_only):
12178 r"""_get_internal_coordinate_derivatives_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
12179 return _IMP_kernel._get_internal_coordinate_derivatives_numpy(m, m_pyobj, read_only)
12183 ParticleIndex = numpy.intc
12184 except ImportError:
12189 """Warning for incomplete JAX support or different behavior of JAX code"""
12193 def get_module_name():
12194 r"""get_module_name() -> std::string const"""
12195 return _IMP_kernel.get_module_name()
12198 r"""get_module_version() -> std::string const"""
12199 return _IMP_kernel.get_module_version()
12202 r"""get_example_path(std::string fname) -> std::string"""
12203 return _IMP_kernel.get_example_path(fname)
12206 r"""get_data_path(std::string fname) -> std::string"""
12207 return _IMP_kernel.get_data_path(fname)
12209 from .
import _version_check
12214 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.
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.
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.