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 _InputAdaptor(object):
336 r"""Proxy of C++ IMP::InputAdaptor 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
344 def __getstate__(self):
345 raise NotImplementedError(str(self.__class__)
346 +
" does not support serialization")
348 __swig_destroy__ = _IMP_kernel.delete__InputAdaptor
351 _IMP_kernel._InputAdaptor_swigregister(_InputAdaptor)
352 class _NonCopyable(object):
353 r"""Proxy of C++ IMP::NonCopyable class."""
355 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
357 def __init__(self, *args, **kwargs):
358 raise AttributeError(
"No constructor defined")
359 __repr__ = _swig_repr
360 __swig_destroy__ = _IMP_kernel.delete__NonCopyable
363 _IMP_kernel._NonCopyable_swigregister(_NonCopyable)
364 class _RAII(_NonCopyable):
365 r"""Proxy of C++ IMP::RAII class."""
367 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
369 def __init__(self, *args, **kwargs):
370 raise AttributeError(
"No constructor defined")
371 __repr__ = _swig_repr
372 __swig_destroy__ = _IMP_kernel.delete__RAII
375 _IMP_kernel._RAII_swigregister(_RAII)
376 class _Value(object):
377 r"""Proxy of C++ IMP::Value class."""
379 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
381 def __init__(self, *args, **kwargs):
382 raise AttributeError(
"No constructor defined")
383 __repr__ = _swig_repr
385 def __getstate__(self):
386 raise NotImplementedError(str(self.__class__)
387 +
" does not support serialization")
389 __swig_destroy__ = _IMP_kernel.delete__Value
392 _IMP_kernel._Value_swigregister(_Value)
395 r"""get_executable_name() -> std::string"""
396 return _IMP_kernel.get_executable_name()
400 setup_from_argv(IMP::Strings const & argv, std::string description)
401 setup_from_argv(IMP::Strings const & argv, std::string description, std::string positional_description, int num_positional) -> IMP::Strings
403 return _IMP_kernel.setup_from_argv(*args)
406 r"""add_string_flag(std::string name, std::string default_value, std::string description)"""
407 return _IMP_kernel.add_string_flag(name, default_value, description)
410 r"""get_string_flag(std::string name) -> std::string"""
411 return _IMP_kernel.get_string_flag(name)
414 r"""add_int_flag(std::string name, size_t default_value, std::string description)"""
415 return _IMP_kernel.add_int_flag(name, default_value, description)
418 r"""get_int_flag(std::string name) -> size_t"""
419 return _IMP_kernel.get_int_flag(name)
422 r"""add_bool_flag(std::string name, std::string description)"""
423 return _IMP_kernel.add_bool_flag(name, description)
426 r"""get_bool_flag(std::string name) -> bool"""
427 return _IMP_kernel.get_bool_flag(name)
430 r"""add_float_flag(std::string name, double default_value, std::string description)"""
431 return _IMP_kernel.add_float_flag(name, default_value, description)
434 r"""get_float_flag(std::string name) -> double"""
435 return _IMP_kernel.get_float_flag(name)
438 r"""write_help(_ostream out=std::cerr)"""
439 return _IMP_kernel.write_help(*args)
442 r"""get_is_quick_test() -> bool"""
443 return _IMP_kernel.get_is_quick_test()
444 DEFAULT = _IMP_kernel.DEFAULT
446 SILENT = _IMP_kernel.SILENT
448 WARNING = _IMP_kernel.WARNING
450 PROGRESS = _IMP_kernel.PROGRESS
452 TERSE = _IMP_kernel.TERSE
454 VERBOSE = _IMP_kernel.VERBOSE
456 MEMORY = _IMP_kernel.MEMORY
458 ALL_LOG = _IMP_kernel.ALL_LOG
460 class VersionInfo(_Value):
461 r"""Proxy of C++ IMP::VersionInfo class."""
463 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
465 def __init__(self, *args):
467 __init__(VersionInfo self, std::string module, std::string version) -> VersionInfo
468 __init__(VersionInfo self) -> VersionInfo
470 _IMP_kernel.VersionInfo_swiginit(self, _IMP_kernel.new_VersionInfo(*args))
472 def get_module(self):
473 r"""get_module(VersionInfo self) -> std::string"""
474 return _IMP_kernel.VersionInfo_get_module(self)
476 def get_version(self):
477 r"""get_version(VersionInfo self) -> std::string"""
478 return _IMP_kernel.VersionInfo_get_version(self)
480 def show(self, *args):
481 r"""show(VersionInfo self, _ostream out=std::cout)"""
482 return _IMP_kernel.VersionInfo_show(self, *args)
484 def __cmp__(self, o):
485 r"""__cmp__(VersionInfo self, VersionInfo o) -> int"""
486 return _IMP_kernel.VersionInfo___cmp__(self, o)
489 r"""__eq__(VersionInfo self, VersionInfo o) -> bool"""
490 return _IMP_kernel.VersionInfo___eq__(self, o)
493 r"""__ne__(VersionInfo self, VersionInfo o) -> bool"""
494 return _IMP_kernel.VersionInfo___ne__(self, o)
497 r"""__lt__(VersionInfo self, VersionInfo o) -> bool"""
498 return _IMP_kernel.VersionInfo___lt__(self, o)
501 r"""__gt__(VersionInfo self, VersionInfo o) -> bool"""
502 return _IMP_kernel.VersionInfo___gt__(self, o)
505 r"""__ge__(VersionInfo self, VersionInfo o) -> bool"""
506 return _IMP_kernel.VersionInfo___ge__(self, o)
509 r"""__le__(VersionInfo self, VersionInfo o) -> bool"""
510 return _IMP_kernel.VersionInfo___le__(self, o)
513 r"""__str__(VersionInfo self) -> std::string"""
514 return _IMP_kernel.VersionInfo___str__(self)
517 r"""__repr__(VersionInfo self) -> std::string"""
518 return _IMP_kernel.VersionInfo___repr__(self)
520 def _get_as_binary(self):
521 r"""_get_as_binary(VersionInfo self) -> PyObject *"""
522 return _IMP_kernel.VersionInfo__get_as_binary(self)
524 def _set_from_binary(self, p):
525 r"""_set_from_binary(VersionInfo self, PyObject * p)"""
526 return _IMP_kernel.VersionInfo__set_from_binary(self, p)
528 def __getstate__(self):
529 p = self._get_as_binary()
530 if len(self.__dict__) > 1:
531 d = self.__dict__.copy()
536 def __setstate__(self, p):
537 if not hasattr(self,
'this'):
539 if isinstance(p, tuple):
541 self.__dict__.update(d)
542 return self._set_from_binary(p)
544 __swig_destroy__ = _IMP_kernel.delete_VersionInfo
547 _IMP_kernel.VersionInfo_swigregister(VersionInfo)
548 class TextOutput(_InputAdaptor):
549 r"""Proxy of C++ IMP::TextOutput class."""
551 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
552 __repr__ = _swig_repr
554 def __init__(self, *args):
556 __init__(TextOutput self, int arg2) -> TextOutput
557 __init__(TextOutput self, double arg2) -> TextOutput
558 __init__(TextOutput self, char const * c, bool append=False) -> TextOutput
559 __init__(TextOutput self, IMP::TextProxy< std::ostream > p) -> TextOutput
560 __init__(TextOutput self) -> TextOutput
561 __init__(TextOutput self, std::string file_name, bool append=False) -> TextOutput
563 _IMP_kernel.TextOutput_swiginit(self, _IMP_kernel.new_TextOutput(*args))
565 def show(self, *args):
566 r"""show(TextOutput self, _ostream out=std::cout)"""
567 return _IMP_kernel.TextOutput_show(self, *args)
570 r"""get_name(TextOutput self) -> std::string"""
571 return _IMP_kernel.TextOutput_get_name(self)
572 __swig_destroy__ = _IMP_kernel.delete_TextOutput
575 _IMP_kernel.TextOutput_swigregister(TextOutput)
576 class TextInput(_InputAdaptor):
577 r"""Proxy of C++ IMP::TextInput class."""
579 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
580 __repr__ = _swig_repr
582 def __init__(self, *args):
584 __init__(TextInput self, int arg2) -> TextInput
585 __init__(TextInput self, double arg2) -> TextInput
586 __init__(TextInput self, char const * c) -> TextInput
587 __init__(TextInput self, IMP::TextProxy< std::istream > p) -> TextInput
588 __init__(TextInput self) -> TextInput
589 __init__(TextInput self, std::string file_name) -> TextInput
591 _IMP_kernel.TextInput_swiginit(self, _IMP_kernel.new_TextInput(*args))
593 def show(self, *args):
594 r"""show(TextInput self, _ostream out=std::cout)"""
595 return _IMP_kernel.TextInput_show(self, *args)
598 r"""get_name(TextInput self) -> std::string"""
599 return _IMP_kernel.TextInput_get_name(self)
601 def set_binary_open_mode(self, binary):
602 r"""set_binary_open_mode(TextInput self, bool binary)"""
603 return _IMP_kernel.TextInput_set_binary_open_mode(self, binary)
604 __swig_destroy__ = _IMP_kernel.delete_TextInput
607 _IMP_kernel.TextInput_swigregister(TextInput)
608 class SetLogTarget(_RAII):
609 r"""Proxy of C++ IMP::SetLogTarget class."""
611 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
613 def __init__(self, *args):
615 __init__(SetLogTarget self) -> SetLogTarget
616 __init__(SetLogTarget self, TextOutput to) -> SetLogTarget
618 _IMP_kernel.SetLogTarget_swiginit(self, _IMP_kernel.new_SetLogTarget(*args))
621 r"""set(SetLogTarget self, TextOutput to)"""
622 return _IMP_kernel.SetLogTarget_set(self, to)
625 r"""reset(SetLogTarget self)"""
626 return _IMP_kernel.SetLogTarget_reset(self)
627 __swig_destroy__ = _IMP_kernel.delete_SetLogTarget
629 def show(self, *args):
630 r"""show(SetLogTarget self, _ostream out=std::cout)"""
631 return _IMP_kernel.SetLogTarget_show(self, *args)
635 def __exit__(self, exc_type, exc_val, exc_tb):
641 r"""__str__(SetLogTarget self) -> std::string"""
642 return _IMP_kernel.SetLogTarget___str__(self)
645 r"""__repr__(SetLogTarget self) -> std::string"""
646 return _IMP_kernel.SetLogTarget___repr__(self)
649 _IMP_kernel.SetLogTarget_swigregister(SetLogTarget)
652 r"""create_temporary_file(std::string prefix="imp_temp", std::string suffix="") -> TextOutput"""
653 return _IMP_kernel.create_temporary_file(*args)
656 r"""create_temporary_file_name(std::string prefix="imp_temp", std::string suffix="") -> std::string"""
657 return _IMP_kernel.create_temporary_file_name(*args)
660 r"""get_relative_path(std::string base, std::string relative) -> std::string"""
661 return _IMP_kernel.get_relative_path(base, relative)
664 r"""get_absolute_path(std::string file) -> std::string"""
665 return _IMP_kernel.get_absolute_path(file)
667 def push_log_context(functionname, object):
668 r"""push_log_context(char const * functionname, void const * object)"""
669 return _IMP_kernel.push_log_context(functionname, object)
671 def pop_log_context():
672 r"""pop_log_context()"""
673 return _IMP_kernel.pop_log_context()
677 add_to_log(std::string to_write)
678 add_to_log(IMP::LogLevel level, std::string to_write)
680 return _IMP_kernel.add_to_log(*args)
683 r"""set_log_level(IMP::LogLevel l)"""
684 return _IMP_kernel.set_log_level(l)
687 r"""set_log_timer(bool tb)"""
688 return _IMP_kernel.set_log_timer(tb)
691 r"""reset_log_timer()"""
692 return _IMP_kernel.reset_log_timer()
695 r"""get_log_level() -> IMP::LogLevel"""
696 return _IMP_kernel.get_log_level()
699 r"""set_progress_display(std::string description, unsigned int steps)"""
700 return _IMP_kernel.set_progress_display(description, steps)
703 r"""add_to_progress_display(unsigned int step=1)"""
704 return _IMP_kernel.add_to_progress_display(step)
705 class Object(_NonCopyable):
706 r"""Proxy of C++ IMP::Object class."""
708 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
710 def __init__(self, name):
711 r"""__init__(Object self, std::string name) -> Object"""
712 if self.__class__ == Object:
716 _IMP_kernel.Object_swiginit(self, _IMP_kernel.new_Object(_self, name))
718 if self.__class__ != Object:
719 _director_objects.register(self)
723 __swig_destroy__ = _IMP_kernel.delete_Object
726 r"""__hash__(Object self) -> std::size_t"""
727 return _IMP_kernel.Object___hash__(self)
730 r"""set_log_level(Object self, IMP::LogLevel l)"""
731 return _IMP_kernel.Object_set_log_level(self, l)
734 r"""set_check_level(Object self, IMP::CheckLevel l)"""
735 return _IMP_kernel.Object_set_check_level(self, l)
738 r"""get_log_level(Object self) -> IMP::LogLevel"""
739 return _IMP_kernel.Object_get_log_level(self)
742 r"""get_check_level(Object self) -> IMP::CheckLevel"""
743 return _IMP_kernel.Object_get_check_level(self)
745 def get_version_info(self):
746 r"""get_version_info(Object self) -> VersionInfo"""
747 val = _IMP_kernel.Object_get_version_info(self)
748 if val.get_module() ==
'none':
755 r"""get_name(Object self) -> std::string const &"""
756 return _IMP_kernel.Object_get_name(self)
758 def set_name(self, name):
759 r"""set_name(Object self, std::string name)"""
760 return _IMP_kernel.Object_set_name(self, name)
762 def get_type_name(self):
763 r"""get_type_name(Object self) -> std::string"""
764 val = _IMP_kernel.Object_get_type_name(self)
765 if val ==
'unknown object type':
766 val = self.__class__.__name__
769 def set_was_used(self, tf):
770 r"""set_was_used(Object self, bool tf)"""
771 return _IMP_kernel.Object_set_was_used(self, tf)
773 def show(self, *args):
774 r"""show(Object self, _ostream out=std::cout)"""
775 return _IMP_kernel.Object_show(self, *args)
777 def get_string(self):
778 r"""get_string(Object self) -> std::string"""
779 return _IMP_kernel.Object_get_string(self)
781 def _on_destruction(self):
782 r"""_on_destruction(Object self)"""
783 return _IMP_kernel.Object__on_destruction(self)
785 def get_is_valid(self):
786 r"""get_is_valid(Object self) -> bool"""
787 return _IMP_kernel.Object_get_is_valid(self)
789 def get_ref_count(self):
790 r"""get_ref_count(Object self) -> unsigned int"""
791 return _IMP_kernel.Object_get_ref_count(self)
794 def get_number_of_live_objects():
795 r"""get_number_of_live_objects() -> unsigned int"""
796 return _IMP_kernel.Object_get_number_of_live_objects()
798 def get_is_shared(self):
799 r"""get_is_shared(Object self) -> bool"""
800 return _IMP_kernel.Object_get_is_shared(self)
802 def clear_caches(self):
803 r"""clear_caches(Object self)"""
804 return _IMP_kernel.Object_clear_caches(self)
806 def do_destroy(self):
807 r"""do_destroy(Object self)"""
808 return _IMP_kernel.Object_do_destroy(self)
810 def __getstate__(self):
811 raise NotImplementedError(str(self.__class__)
812 +
" does not support serialization")
816 r"""__eq__(Object self, Object o) -> bool"""
817 return _IMP_kernel.Object___eq__(self, o)
820 r"""__ne__(Object self, Object o) -> bool"""
821 return _IMP_kernel.Object___ne__(self, o)
824 r"""__le__(Object self, Object o) -> bool"""
825 return _IMP_kernel.Object___le__(self, o)
828 r"""__lt__(Object self, Object o) -> bool"""
829 return _IMP_kernel.Object___lt__(self, o)
832 r"""__ge__(Object self, Object o) -> bool"""
833 return _IMP_kernel.Object___ge__(self, o)
836 r"""__gt__(Object self, Object o) -> bool"""
837 return _IMP_kernel.Object___gt__(self, o)
839 def _get_director_object(self):
840 r"""_get_director_object(Object self) -> PyObject *"""
841 return _IMP_kernel.Object__get_director_object(self)
844 """Return this object cast to the most derived subclass."""
846 pyobj = self._get_director_object()
847 if pyobj
is not None:
851 modname = self.get_version_info().get_module().replace(
'::',
'.')
852 type_name = self.get_type_name()
855 if modname ==
'IMP' and type_name ==
'GenericRestraintsScoringFunction':
857 type_name =
'RestraintsScoringFunction'
858 modobj = sys.modules[modname]
859 clsobj = getattr(modobj, type_name)
860 return clsobj.get_from(self)
864 r"""__str__(Object self) -> std::string"""
865 return _IMP_kernel.Object___str__(self)
868 r"""__repr__(Object self) -> std::string"""
869 return _IMP_kernel.Object___repr__(self)
873 return _object_cast_to_Object(o)
875 def __disown__(self):
877 _IMP_kernel.disown_Object(self)
878 return weakref.proxy(self)
881 _IMP_kernel.Object_swigregister(Object)
882 class SetLogState(_RAII):
883 r"""Proxy of C++ IMP::SetLogState class."""
885 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
888 r"""reset(SetLogState self)"""
889 return _IMP_kernel.SetLogState_reset(self)
890 __swig_destroy__ = _IMP_kernel.delete_SetLogState
892 def show(self, *args):
893 r"""show(SetLogState self, _ostream out=std::cout)"""
894 return _IMP_kernel.SetLogState_show(self, *args)
896 def __init__(self, *args):
898 __init__(SetLogState self) -> SetLogState
899 __init__(SetLogState self, Object o, IMP::LogLevel l) -> SetLogState
900 __init__(SetLogState self, IMP::LogLevel l) -> SetLogState
902 _IMP_kernel.SetLogState_swiginit(self, _IMP_kernel.new_SetLogState(*args))
904 def set(self, *args):
906 set(SetLogState self, Object o, IMP::LogLevel l)
907 set(SetLogState self, IMP::LogLevel l)
909 return _IMP_kernel.SetLogState_set(self, *args)
913 def __exit__(self, exc_type, exc_val, exc_tb):
919 r"""__str__(SetLogState self) -> std::string"""
920 return _IMP_kernel.SetLogState___str__(self)
923 r"""__repr__(SetLogState self) -> std::string"""
924 return _IMP_kernel.SetLogState___repr__(self)
927 _IMP_kernel.SetLogState_swigregister(SetLogState)
928 class WarningContext(object):
929 r"""Proxy of C++ IMP::WarningContext class."""
931 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
932 data_ = property(_IMP_kernel.WarningContext_data__get, _IMP_kernel.WarningContext_data__set, doc=
r"""data_ : boost::unordered_set<(std::string)>""")
934 def add_warning(self, key, warning):
935 r"""add_warning(WarningContext self, std::string key, std::string warning)"""
936 return _IMP_kernel.WarningContext_add_warning(self, key, warning)
938 def clear_warnings(self):
939 r"""clear_warnings(WarningContext self)"""
940 return _IMP_kernel.WarningContext_clear_warnings(self)
942 def dump_warnings(self):
943 r"""dump_warnings(WarningContext self)"""
944 return _IMP_kernel.WarningContext_dump_warnings(self)
945 __swig_destroy__ = _IMP_kernel.delete_WarningContext
947 def show(self, *args):
948 r"""show(WarningContext self, _ostream out=std::cout)"""
949 return _IMP_kernel.WarningContext_show(self, *args)
953 def __exit__(self, exc_type, exc_val, exc_tb):
959 r"""__str__(WarningContext self) -> std::string"""
960 return _IMP_kernel.WarningContext___str__(self)
963 r"""__repr__(WarningContext self) -> std::string"""
964 return _IMP_kernel.WarningContext___repr__(self)
967 r"""__init__(WarningContext self) -> WarningContext"""
968 _IMP_kernel.WarningContext_swiginit(self, _IMP_kernel.new_WarningContext())
971 _IMP_kernel.WarningContext_swigregister(WarningContext)
972 class CreateLogContext(_RAII):
973 r"""Proxy of C++ IMP::CreateLogContext class."""
975 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
977 def __init__(self, *args):
979 __init__(CreateLogContext self, std::string fname, Object object=None) -> CreateLogContext
980 __init__(CreateLogContext self) -> CreateLogContext
981 __init__(CreateLogContext self, char const * fname, Object object=None) -> CreateLogContext
983 _IMP_kernel.CreateLogContext_swiginit(self, _IMP_kernel.new_CreateLogContext(*args))
985 def set(self, fname, object=None):
986 r"""set(CreateLogContext self, char const * fname, Object object=None)"""
987 return _IMP_kernel.CreateLogContext_set(self, fname, object)
990 r"""reset(CreateLogContext self)"""
991 return _IMP_kernel.CreateLogContext_reset(self)
992 __swig_destroy__ = _IMP_kernel.delete_CreateLogContext
994 def show(self, *args):
995 r"""show(CreateLogContext self, _ostream out=std::cout)"""
996 return _IMP_kernel.CreateLogContext_show(self, *args)
1000 def __exit__(self, exc_type, exc_val, exc_tb):
1006 r"""__str__(CreateLogContext self) -> std::string"""
1007 return _IMP_kernel.CreateLogContext___str__(self)
1010 r"""__repr__(CreateLogContext self) -> std::string"""
1011 return _IMP_kernel.CreateLogContext___repr__(self)
1014 _IMP_kernel.CreateLogContext_swigregister(CreateLogContext)
1015 class SetCheckState(_RAII):
1016 r"""Proxy of C++ IMP::SetCheckState class."""
1018 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1021 r"""reset(SetCheckState self)"""
1022 return _IMP_kernel.SetCheckState_reset(self)
1023 __swig_destroy__ = _IMP_kernel.delete_SetCheckState
1025 def show(self, *args):
1026 r"""show(SetCheckState self, _ostream out=std::cout)"""
1027 return _IMP_kernel.SetCheckState_show(self, *args)
1029 def __init__(self, *args):
1031 __init__(SetCheckState self) -> SetCheckState
1032 __init__(SetCheckState self, Object o, IMP::CheckLevel l) -> SetCheckState
1033 __init__(SetCheckState self, IMP::CheckLevel l) -> SetCheckState
1035 _IMP_kernel.SetCheckState_swiginit(self, _IMP_kernel.new_SetCheckState(*args))
1037 def set(self, *args):
1039 set(SetCheckState self, Object o, IMP::CheckLevel l)
1040 set(SetCheckState self, IMP::CheckLevel l)
1042 return _IMP_kernel.SetCheckState_set(self, *args)
1044 def __enter__(self):
1046 def __exit__(self, exc_type, exc_val, exc_tb):
1052 r"""__str__(SetCheckState self) -> std::string"""
1053 return _IMP_kernel.SetCheckState___str__(self)
1056 r"""__repr__(SetCheckState self) -> std::string"""
1057 return _IMP_kernel.SetCheckState___repr__(self)
1060 _IMP_kernel.SetCheckState_swigregister(SetCheckState)
1063 r"""get_unique_name(std::string templ) -> std::string"""
1064 return _IMP_kernel.get_unique_name(templ)
1067 r"""get_copyright() -> std::string"""
1068 return _IMP_kernel.get_copyright()
1069 class _Protection(object):
1070 r"""Proxy of C++ IMP::internal::_Protection class."""
1072 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1074 def __init__(self, *args, **kwargs):
1075 raise AttributeError(
"No constructor defined")
1077 def show(self, *args):
1078 r"""show(_Protection self, _ostream out=std::cout)"""
1079 return _IMP_kernel._Protection_show(self, *args)
1082 r"""__str__(_Protection self) -> std::string"""
1083 return _IMP_kernel._Protection___str__(self)
1086 r"""__repr__(_Protection self) -> std::string"""
1087 return _IMP_kernel._Protection___repr__(self)
1088 __swig_destroy__ = _IMP_kernel.delete__Protection
1091 _IMP_kernel._Protection_swigregister(_Protection)
1095 return _IMP_kernel._test_log()
1097 def _test_intranges(ips):
1098 r"""_test_intranges(IMP::IntRanges const & ips) -> int"""
1099 return _IMP_kernel._test_intranges(ips)
1101 def _test_intrange(*args):
1103 _test_intrange(IMP::IntRange const & ips) -> IMP::IntRange
1104 _test_intrange() -> IMP::IntRange
1106 return _IMP_kernel._test_intrange(*args)
1109 r"""_test_ifile(TextInput a) -> std::string"""
1110 return _IMP_kernel._test_ifile(a)
1113 r"""_test_ofile(TextOutput a) -> std::string"""
1114 return _IMP_kernel._test_ofile(a)
1116 def _test_ifile_overloaded(*args):
1118 _test_ifile_overloaded(TextInput a, int i) -> std::string
1119 _test_ifile_overloaded(TextInput a, std::string st) -> std::string
1121 return _IMP_kernel._test_ifile_overloaded(*args)
1123 def _test_ofile_overloaded(*args):
1125 _test_ofile_overloaded(TextOutput a, int i) -> std::string
1126 _test_ofile_overloaded(TextOutput a, std::string st) -> std::string
1128 return _IMP_kernel._test_ofile_overloaded(*args)
1129 class _TestValue(object):
1130 r"""Proxy of C++ IMP::internal::_TestValue class."""
1132 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1134 def __init__(self, i):
1135 r"""__init__(_TestValue self, int i) -> _TestValue"""
1136 _IMP_kernel._TestValue_swiginit(self, _IMP_kernel.new__TestValue(i))
1138 def show(self, *args):
1139 r"""show(_TestValue self, _ostream out=std::cout)"""
1140 return _IMP_kernel._TestValue_show(self, *args)
1142 def __cmp__(self, o):
1143 r"""__cmp__(_TestValue self, _TestValue o) -> int"""
1144 return _IMP_kernel._TestValue___cmp__(self, o)
1146 def __eq__(self, o):
1147 r"""__eq__(_TestValue self, _TestValue o) -> bool"""
1148 return _IMP_kernel._TestValue___eq__(self, o)
1150 def __ne__(self, o):
1151 r"""__ne__(_TestValue self, _TestValue o) -> bool"""
1152 return _IMP_kernel._TestValue___ne__(self, o)
1154 def __lt__(self, o):
1155 r"""__lt__(_TestValue self, _TestValue o) -> bool"""
1156 return _IMP_kernel._TestValue___lt__(self, o)
1158 def __gt__(self, o):
1159 r"""__gt__(_TestValue self, _TestValue o) -> bool"""
1160 return _IMP_kernel._TestValue___gt__(self, o)
1162 def __ge__(self, o):
1163 r"""__ge__(_TestValue self, _TestValue o) -> bool"""
1164 return _IMP_kernel._TestValue___ge__(self, o)
1166 def __le__(self, o):
1167 r"""__le__(_TestValue self, _TestValue o) -> bool"""
1168 return _IMP_kernel._TestValue___le__(self, o)
1171 r"""get(_TestValue self) -> int"""
1172 return _IMP_kernel._TestValue_get(self)
1174 def get_float(self):
1175 r"""get_float(_TestValue self) -> float const &"""
1176 return _IMP_kernel._TestValue_get_float(self)
1178 def get_double(self):
1179 r"""get_double(_TestValue self) -> double const &"""
1180 return _IMP_kernel._TestValue_get_double(self)
1182 def get_Float(self):
1183 r"""get_Float(_TestValue self) -> IMP::Float const &"""
1184 return _IMP_kernel._TestValue_get_Float(self)
1187 r"""get_int(_TestValue self) -> int const &"""
1188 return _IMP_kernel._TestValue_get_int(self)
1191 r"""get_Int(_TestValue self) -> IMP::Int const &"""
1192 return _IMP_kernel._TestValue_get_Int(self)
1194 def get_string(self):
1195 r"""get_string(_TestValue self) -> std::string const &"""
1196 return _IMP_kernel._TestValue_get_string(self)
1198 def get_String(self):
1199 r"""get_String(_TestValue self) -> IMP::String const &"""
1200 return _IMP_kernel._TestValue_get_String(self)
1203 r"""__str__(_TestValue self) -> std::string"""
1204 return _IMP_kernel._TestValue___str__(self)
1207 r"""__repr__(_TestValue self) -> std::string"""
1208 return _IMP_kernel._TestValue___repr__(self)
1209 __swig_destroy__ = _IMP_kernel.delete__TestValue
1212 _IMP_kernel._TestValue_swigregister(_TestValue)
1214 def _pass_plain_pair(p):
1215 r"""_pass_plain_pair(IMP::FloatPair p) -> IMP::FloatPair"""
1216 return _IMP_kernel._pass_plain_pair(p)
1218 def _pass_overloaded_strings(*args):
1220 _pass_overloaded_strings(IMP::Strings const & a, int arg2) -> IMP::Strings
1221 _pass_overloaded_strings(IMP::Strings const & a) -> IMP::Strings
1223 return _IMP_kernel._pass_overloaded_strings(*args)
1226 r"""_pass_pair(IMP::DerivativePair const & p) -> IMP::DerivativePair"""
1227 return _IMP_kernel._pass_pair(p)
1229 def _pass_floats(input):
1230 r"""_pass_floats(IMP::Floats const & input) -> IMP::Floats"""
1231 return _IMP_kernel._pass_floats(input)
1233 def _pass_ints(input):
1234 r"""_pass_ints(IMP::Ints input) -> IMP::Ints"""
1235 return _IMP_kernel._pass_ints(input)
1237 def _pass_ints_list(input):
1238 r"""_pass_ints_list(IMP::IntsList const & input) -> IMP::IntsList"""
1239 return _IMP_kernel._pass_ints_list(input)
1241 def _pass_ints_lists(input):
1242 r"""_pass_ints_lists(IMP::IntsLists const & input) -> IMP::IntsLists"""
1243 return _IMP_kernel._pass_ints_lists(input)
1245 def _pass_strings(input):
1246 r"""_pass_strings(IMP::Strings const & input) -> IMP::Strings const &"""
1247 return _IMP_kernel._pass_strings(input)
1248 class _TestObject(
Object):
1249 r"""Proxy of C++ IMP::internal::_TestObject class."""
1251 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1254 r"""__init__(_TestObject self) -> _TestObject"""
1255 _IMP_kernel._TestObject_swiginit(self, _IMP_kernel.new__TestObject())
1258 r"""get_version_info(_TestObject self) -> VersionInfo"""
1259 return _IMP_kernel._TestObject_get_version_info(self)
1260 __swig_destroy__ = _IMP_kernel.delete__TestObject
1263 r"""__str__(_TestObject self) -> std::string"""
1264 return _IMP_kernel._TestObject___str__(self)
1267 r"""__repr__(_TestObject self) -> std::string"""
1268 return _IMP_kernel._TestObject___repr__(self)
1272 return _object_cast_to__TestObject(o)
1276 _IMP_kernel._TestObject_swigregister(_TestObject)
1279 r"""get_live_object_names() -> IMP::Strings"""
1280 return _IMP_kernel.get_live_object_names()
1283 r"""get_live_objects() -> IMP::Objects"""
1284 return _IMP_kernel.get_live_objects()
1287 r"""set_show_leaked_objects(bool tf)"""
1288 return _IMP_kernel.set_show_leaked_objects(tf)
1291 r"""set_deprecation_warnings(bool tf)"""
1292 return _IMP_kernel.set_deprecation_warnings(tf)
1295 r"""set_deprecation_exceptions(bool tf)"""
1296 return _IMP_kernel.set_deprecation_exceptions(tf)
1299 r"""get_deprecation_exceptions() -> bool"""
1300 return _IMP_kernel.get_deprecation_exceptions()
1303 r"""handle_use_deprecated(std::string message)"""
1304 return _IMP_kernel.handle_use_deprecated(message)
1307 r"""get_number_of_threads() -> unsigned int"""
1308 return _IMP_kernel.get_number_of_threads()
1311 r"""set_number_of_threads(unsigned int n)"""
1312 return _IMP_kernel.set_number_of_threads(n)
1313 class SetNumberOfThreads(_RAII):
1314 r"""Proxy of C++ IMP::SetNumberOfThreads class."""
1316 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1318 def __init__(self, *args):
1320 __init__(SetNumberOfThreads self) -> SetNumberOfThreads
1321 __init__(SetNumberOfThreads self, unsigned int n) -> SetNumberOfThreads
1323 _IMP_kernel.SetNumberOfThreads_swiginit(self, _IMP_kernel.new_SetNumberOfThreads(*args))
1326 r"""set(SetNumberOfThreads self, unsigned int n)"""
1327 return _IMP_kernel.SetNumberOfThreads_set(self, n)
1330 r"""reset(SetNumberOfThreads self)"""
1331 return _IMP_kernel.SetNumberOfThreads_reset(self)
1332 __swig_destroy__ = _IMP_kernel.delete_SetNumberOfThreads
1334 def show(self, *args):
1335 r"""show(SetNumberOfThreads self, _ostream out=std::cout)"""
1336 return _IMP_kernel.SetNumberOfThreads_show(self, *args)
1338 def __enter__(self):
1340 def __exit__(self, exc_type, exc_val, exc_tb):
1346 r"""__str__(SetNumberOfThreads self) -> std::string"""
1347 return _IMP_kernel.SetNumberOfThreads___str__(self)
1350 r"""__repr__(SetNumberOfThreads self) -> std::string"""
1351 return _IMP_kernel.SetNumberOfThreads___repr__(self)
1354 _IMP_kernel.SetNumberOfThreads_swigregister(SetNumberOfThreads)
1357 i_m_p=
"IMP_MODULE_PATH"
1358 if i_m_p
in os.environ.keys():
1359 __path__.insert(0, os.environ[i_m_p])
1361 def _forward_add_attribute(self, name, value, opt=None):
1363 self.get_particle().add_attribute(name, value, opt)
1365 self.get_particle().add_attribute(name, value)
1366 def _forward_get_value(self, name):
1367 self.get_particle().get_value(name)
1368 def _forward_set_value(self, name, value):
1369 self.get_particle().set_value(name, value)
1375 _object_types.append(
"Constraint")
1378 def _object_cast_to_Constraint(o):
1379 r"""_object_cast_to_Constraint(Object o) -> Constraint"""
1380 return _IMP_kernel._object_cast_to_Constraint(o)
1382 _object_types.append(
"Undecorator")
1385 def _object_cast_to_Undecorator(o):
1386 r"""_object_cast_to_Undecorator(Object o) -> Undecorator"""
1387 return _IMP_kernel._object_cast_to_Undecorator(o)
1389 _object_types.append(
"Container")
1392 def _object_cast_to_Container(o):
1393 r"""_object_cast_to_Container(Object o) -> Container"""
1394 return _IMP_kernel._object_cast_to_Container(o)
1396 _object_types.append(
"Optimizer")
1399 def _object_cast_to_Optimizer(o):
1400 r"""_object_cast_to_Optimizer(Object o) -> Optimizer"""
1401 return _IMP_kernel._object_cast_to_Optimizer(o)
1403 _object_types.append(
"AttributeOptimizer")
1406 def _object_cast_to_AttributeOptimizer(o):
1407 r"""_object_cast_to_AttributeOptimizer(Object o) -> AttributeOptimizer"""
1408 return _IMP_kernel._object_cast_to_AttributeOptimizer(o)
1410 _object_types.append(
"OptimizerState")
1413 def _object_cast_to_OptimizerState(o):
1414 r"""_object_cast_to_OptimizerState(Object o) -> OptimizerState"""
1415 return _IMP_kernel._object_cast_to_OptimizerState(o)
1417 _object_types.append(
"PairContainer")
1420 def _object_cast_to_PairContainer(o):
1421 r"""_object_cast_to_PairContainer(Object o) -> PairContainer"""
1422 return _IMP_kernel._object_cast_to_PairContainer(o)
1424 _object_types.append(
"PairModifier")
1427 def _object_cast_to_PairModifier(o):
1428 r"""_object_cast_to_PairModifier(Object o) -> PairModifier"""
1429 return _IMP_kernel._object_cast_to_PairModifier(o)
1431 _object_types.append(
"PairScore")
1434 def _object_cast_to_PairScore(o):
1435 r"""_object_cast_to_PairScore(Object o) -> PairScore"""
1436 return _IMP_kernel._object_cast_to_PairScore(o)
1438 _object_types.append(
"QuadContainer")
1441 def _object_cast_to_QuadContainer(o):
1442 r"""_object_cast_to_QuadContainer(Object o) -> QuadContainer"""
1443 return _IMP_kernel._object_cast_to_QuadContainer(o)
1445 _object_types.append(
"QuadModifier")
1448 def _object_cast_to_QuadModifier(o):
1449 r"""_object_cast_to_QuadModifier(Object o) -> QuadModifier"""
1450 return _IMP_kernel._object_cast_to_QuadModifier(o)
1452 _object_types.append(
"QuadScore")
1455 def _object_cast_to_QuadScore(o):
1456 r"""_object_cast_to_QuadScore(Object o) -> QuadScore"""
1457 return _IMP_kernel._object_cast_to_QuadScore(o)
1459 _object_types.append(
"Refiner")
1462 def _object_cast_to_Refiner(o):
1463 r"""_object_cast_to_Refiner(Object o) -> Refiner"""
1464 return _IMP_kernel._object_cast_to_Refiner(o)
1466 _object_types.append(
"Restraint")
1469 def _object_cast_to_Restraint(o):
1470 r"""_object_cast_to_Restraint(Object o) -> Restraint"""
1471 return _IMP_kernel._object_cast_to_Restraint(o)
1473 _object_types.append(
"Sampler")
1476 def _object_cast_to_Sampler(o):
1477 r"""_object_cast_to_Sampler(Object o) -> Sampler"""
1478 return _IMP_kernel._object_cast_to_Sampler(o)
1480 _object_types.append(
"ScoreState")
1483 def _object_cast_to_ScoreState(o):
1484 r"""_object_cast_to_ScoreState(Object o) -> ScoreState"""
1485 return _IMP_kernel._object_cast_to_ScoreState(o)
1487 _object_types.append(
"SingletonContainer")
1490 def _object_cast_to_SingletonContainer(o):
1491 r"""_object_cast_to_SingletonContainer(Object o) -> SingletonContainer"""
1492 return _IMP_kernel._object_cast_to_SingletonContainer(o)
1494 _object_types.append(
"SingletonModifier")
1497 def _object_cast_to_SingletonModifier(o):
1498 r"""_object_cast_to_SingletonModifier(Object o) -> SingletonModifier"""
1499 return _IMP_kernel._object_cast_to_SingletonModifier(o)
1501 _object_types.append(
"SingletonScore")
1504 def _object_cast_to_SingletonScore(o):
1505 r"""_object_cast_to_SingletonScore(Object o) -> SingletonScore"""
1506 return _IMP_kernel._object_cast_to_SingletonScore(o)
1508 _object_types.append(
"TripletContainer")
1511 def _object_cast_to_TripletContainer(o):
1512 r"""_object_cast_to_TripletContainer(Object o) -> TripletContainer"""
1513 return _IMP_kernel._object_cast_to_TripletContainer(o)
1515 _object_types.append(
"TripletModifier")
1518 def _object_cast_to_TripletModifier(o):
1519 r"""_object_cast_to_TripletModifier(Object o) -> TripletModifier"""
1520 return _IMP_kernel._object_cast_to_TripletModifier(o)
1522 _object_types.append(
"TripletScore")
1525 def _object_cast_to_TripletScore(o):
1526 r"""_object_cast_to_TripletScore(Object o) -> TripletScore"""
1527 return _IMP_kernel._object_cast_to_TripletScore(o)
1529 _object_types.append(
"UnaryFunction")
1532 def _object_cast_to_UnaryFunction(o):
1533 r"""_object_cast_to_UnaryFunction(Object o) -> UnaryFunction"""
1534 return _IMP_kernel._object_cast_to_UnaryFunction(o)
1536 _object_types.append(
"RestraintInfo")
1539 def _object_cast_to_RestraintInfo(o):
1540 r"""_object_cast_to_RestraintInfo(Object o) -> RestraintInfo"""
1541 return _IMP_kernel._object_cast_to_RestraintInfo(o)
1543 _object_types.append(
"ConfigurationSet")
1546 def _object_cast_to_ConfigurationSet(o):
1547 r"""_object_cast_to_ConfigurationSet(Object o) -> ConfigurationSet"""
1548 return _IMP_kernel._object_cast_to_ConfigurationSet(o)
1550 _object_types.append(
"Configuration")
1553 def _object_cast_to_Configuration(o):
1554 r"""_object_cast_to_Configuration(Object o) -> Configuration"""
1555 return _IMP_kernel._object_cast_to_Configuration(o)
1557 _object_types.append(
"Model")
1560 def _object_cast_to_Model(o):
1561 r"""_object_cast_to_Model(Object o) -> Model"""
1562 return _IMP_kernel._object_cast_to_Model(o)
1564 _object_types.append(
"Particle")
1567 def _object_cast_to_Particle(o):
1568 r"""_object_cast_to_Particle(Object o) -> Particle"""
1569 return _IMP_kernel._object_cast_to_Particle(o)
1571 _object_types.append(
"RestraintSet")
1574 def _object_cast_to_RestraintSet(o):
1575 r"""_object_cast_to_RestraintSet(Object o) -> RestraintSet"""
1576 return _IMP_kernel._object_cast_to_RestraintSet(o)
1578 ParticlePairsTemp=list
1579 _plural_types.append(
"ParticlePairsTemp")
1580 _value_types.append(
"ParticlePair")
1583 ParticleTripletsTemp=list
1584 _plural_types.append(
"ParticleTripletsTemp")
1585 _value_types.append(
"ParticleTriplet")
1588 ParticleQuadsTemp=list
1589 _plural_types.append(
"ParticleQuadsTemp")
1590 _value_types.append(
"ParticleQuad")
1593 ParticleIndexPairs=list
1594 _plural_types.append(
"ParticleIndexPairs")
1595 _value_types.append(
"ParticleIndexPair")
1598 ParticleIndexTriplets=list
1599 _plural_types.append(
"ParticleIndexTriplets")
1600 _value_types.append(
"ParticleIndexTriplet")
1603 ParticleIndexQuads=list
1604 _plural_types.append(
"ParticleIndexQuads")
1605 _value_types.append(
"ParticleIndexQuad")
1608 _object_types.append(
"SingletonPredicate")
1611 def _object_cast_to_SingletonPredicate(o):
1612 r"""_object_cast_to_SingletonPredicate(Object o) -> SingletonPredicate"""
1613 return _IMP_kernel._object_cast_to_SingletonPredicate(o)
1615 _object_types.append(
"PairPredicate")
1618 def _object_cast_to_PairPredicate(o):
1619 r"""_object_cast_to_PairPredicate(Object o) -> PairPredicate"""
1620 return _IMP_kernel._object_cast_to_PairPredicate(o)
1622 _object_types.append(
"TripletPredicate")
1625 def _object_cast_to_TripletPredicate(o):
1626 r"""_object_cast_to_TripletPredicate(Object o) -> TripletPredicate"""
1627 return _IMP_kernel._object_cast_to_TripletPredicate(o)
1629 _object_types.append(
"QuadPredicate")
1632 def _object_cast_to_QuadPredicate(o):
1633 r"""_object_cast_to_QuadPredicate(Object o) -> QuadPredicate"""
1634 return _IMP_kernel._object_cast_to_QuadPredicate(o)
1636 _object_types.append(
"SaveToConfigurationSetOptimizerState")
1639 def _object_cast_to_SaveToConfigurationSetOptimizerState(o):
1640 r"""_object_cast_to_SaveToConfigurationSetOptimizerState(Object o) -> SaveToConfigurationSetOptimizerState"""
1641 return _IMP_kernel._object_cast_to_SaveToConfigurationSetOptimizerState(o)
1643 EvaluationStates=list
1644 _plural_types.append(
"EvaluationStates")
1645 _value_types.append(
"EvaluationState")
1648 ScoreAccumulators=list
1649 _plural_types.append(
"ScoreAccumulators")
1650 _value_types.append(
"ScoreAccumulator")
1653 ParticleIndexes=list
1654 _plural_types.append(
"ParticleIndexes")
1655 _value_types.append(
"ParticleIndex")
1659 _plural_types.append(
"FloatIndexes")
1660 _value_types.append(
"FloatIndex")
1664 _plural_types.append(
"FloatKeys")
1665 _value_types.append(
"FloatKey")
1669 _plural_types.append(
"FloatsKeys")
1670 _value_types.append(
"FloatsKey")
1674 _plural_types.append(
"IntKeys")
1675 _value_types.append(
"IntKey")
1679 _plural_types.append(
"IntsKeys")
1680 _value_types.append(
"IntsKey")
1684 _plural_types.append(
"StringKeys")
1685 _value_types.append(
"StringKey")
1688 ParticleIndexKeys=list
1689 _plural_types.append(
"ParticleIndexKeys")
1690 _value_types.append(
"ParticleIndexKey")
1693 ParticleIndexesKeys=list
1694 _plural_types.append(
"ParticleIndexesKeys")
1695 _value_types.append(
"ParticleIndexesKey")
1699 _plural_types.append(
"ObjectKeys")
1700 _value_types.append(
"ObjectKey")
1704 _plural_types.append(
"ModelKeys")
1705 _value_types.append(
"ModelKey")
1709 _plural_types.append(
"TriggerKeys")
1710 _value_types.append(
"TriggerKey")
1713 SparseFloatKeys=list
1714 _plural_types.append(
"SparseFloatKeys")
1715 _value_types.append(
"SparseFloatKey")
1719 _plural_types.append(
"SparseIntKeys")
1720 _value_types.append(
"SparseIntKey")
1723 SparseStringKeys=list
1724 _plural_types.append(
"SparseStringKeys")
1725 _value_types.append(
"SparseStringKey")
1728 SparseParticleIndexKeys=list
1729 _plural_types.append(
"SparseParticleIndexKeys")
1730 _value_types.append(
"SparseParticleIndexKey")
1734 _plural_types.append(
"Vector3DKeys")
1735 _value_types.append(
"Vector3DKey")
1738 _raii_types.append(
"ScopedSetFloatAttribute")
1741 _object_types.append(
"ScoringFunction")
1744 def _object_cast_to_ScoringFunction(o):
1745 r"""_object_cast_to_ScoringFunction(Object o) -> ScoringFunction"""
1746 return _IMP_kernel._object_cast_to_ScoringFunction(o)
1748 _object_types.append(
"ModelObject")
1751 def _object_cast_to_ModelObject(o):
1752 r"""_object_cast_to_ModelObject(Object o) -> ModelObject"""
1753 return _IMP_kernel._object_cast_to_ModelObject(o)
1755 def _TrivialDecorators(l=[]):
1756 return [_TrivialDecorator(x)
for x
in l]
1757 _plural_types.append(
"_TrivialDecorators")
1760 _value_types.append(
"_TrivialDecorator")
1763 def _TrivialDerivedDecorators(l=[]):
1764 return [_TrivialDerivedDecorator(x)
for x
in l]
1765 _plural_types.append(
"_TrivialDerivedDecorators")
1768 _value_types.append(
"_TrivialDerivedDecorator")
1771 def _TrivialTraitsDecorators(l=[]):
1772 return [_TrivialTraitsDecorator(x)
for x
in l]
1773 _plural_types.append(
"_TrivialTraitsDecorators")
1776 _value_types.append(
"_TrivialTraitsDecorator")
1779 _object_types.append(
"_ConstRestraint")
1782 def _object_cast_to__ConstRestraint(o):
1783 r"""_object_cast_to__ConstRestraint(Object o) -> _ConstRestraint"""
1784 return _IMP_kernel._object_cast_to__ConstRestraint(o)
1786 _object_types.append(
"_ConstOptimizer")
1789 def _object_cast_to__ConstOptimizer(o):
1790 r"""_object_cast_to__ConstOptimizer(Object o) -> _ConstOptimizer"""
1791 return _IMP_kernel._object_cast_to__ConstOptimizer(o)
1793 _object_types.append(
"_ConstSingletonScore")
1796 def _object_cast_to__ConstSingletonScore(o):
1797 r"""_object_cast_to__ConstSingletonScore(Object o) -> _ConstSingletonScore"""
1798 return _IMP_kernel._object_cast_to__ConstSingletonScore(o)
1800 _object_types.append(
"_ConstPairScore")
1803 def _object_cast_to__ConstPairScore(o):
1804 r"""_object_cast_to__ConstPairScore(Object o) -> _ConstPairScore"""
1805 return _IMP_kernel._object_cast_to__ConstPairScore(o)
1807 r"""Proxy of C++ IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex > class."""
1809 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1810 __repr__ = _swig_repr
1813 r"""__init__(DependencyGraph self) -> DependencyGraph"""
1814 _IMP_kernel.DependencyGraph_swiginit(self, _IMP_kernel.new_DependencyGraph())
1816 def get_graph(self):
1817 r"""get_graph(DependencyGraph self) -> IMP::DependencyGraph const &"""
1818 return _IMP_kernel.DependencyGraph_get_graph(self)
1821 r"""get_vertices(DependencyGraph self) -> IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptors"""
1822 return _IMP_kernel.DependencyGraph_get_vertices(self)
1824 def get_vertex_name(self, i):
1825 r"""get_vertex_name(DependencyGraph self, IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor i) -> ModelObject"""
1826 return _IMP_kernel.DependencyGraph_get_vertex_name(self, i)
1828 def get_in_neighbors(self, v):
1829 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"""
1830 return _IMP_kernel.DependencyGraph_get_in_neighbors(self, v)
1832 def get_out_neighbors(self, v):
1833 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"""
1834 return _IMP_kernel.DependencyGraph_get_out_neighbors(self, v)
1837 r"""show_graphviz(DependencyGraph self, _ostream out=std::cout)"""
1838 return _IMP_kernel.DependencyGraph_show_graphviz(self, *args)
1840 def get_graphviz_string(self):
1841 r"""get_graphviz_string(DependencyGraph self) -> std::string"""
1842 return _IMP_kernel.DependencyGraph_get_graphviz_string(self)
1844 def add_edge(self, v0, v1):
1845 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)"""
1846 return _IMP_kernel.DependencyGraph_add_edge(self, v0, v1)
1848 def add_vertex(self, l):
1849 r"""add_vertex(DependencyGraph self, ModelObject l) -> IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor"""
1850 return _IMP_kernel.DependencyGraph_add_vertex(self, l)
1852 def remove_vertex(self, l):
1853 r"""remove_vertex(DependencyGraph self, IMP::internal::BoostDigraph< IMP::DependencyGraph,IMP::ModelObject *,IMP::ShowDependencyGraphVertex >::VertexDescriptor l)"""
1854 return _IMP_kernel.DependencyGraph_remove_vertex(self, l)
1855 __swig_destroy__ = _IMP_kernel.delete_DependencyGraph
1858 _IMP_kernel.DependencyGraph_swigregister(DependencyGraph)
1860 _value_types.append(
"DependencyGraph")
1863 r"""Proxy of C++ IMP::Key< 0 > class."""
1865 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1867 def __init__(self, *args):
1869 __init__(FloatKey self) -> FloatKey
1870 __init__(FloatKey self, std::string const & c, bool is_implicit_add_permitted=True) -> FloatKey
1871 __init__(FloatKey self, unsigned int i) -> FloatKey
1873 _IMP_kernel.FloatKey_swiginit(self, _IMP_kernel.new_FloatKey(*args))
1877 r"""add_key(std::string sc) -> unsigned int"""
1878 return _IMP_kernel.FloatKey_add_key(sc)
1881 def get_key_exists(sc):
1882 r"""get_key_exists(std::string sc) -> bool"""
1883 return _IMP_kernel.FloatKey_get_key_exists(sc)
1885 def get_string(self):
1886 r"""get_string(FloatKey self) -> std::string const"""
1887 return _IMP_kernel.FloatKey_get_string(self)
1889 def __cmp__(self, o):
1890 r"""__cmp__(FloatKey self, FloatKey o) -> int"""
1891 return _IMP_kernel.FloatKey___cmp__(self, o)
1893 def __eq__(self, o):
1894 r"""__eq__(FloatKey self, FloatKey o) -> bool"""
1895 return _IMP_kernel.FloatKey___eq__(self, o)
1897 def __ne__(self, o):
1898 r"""__ne__(FloatKey self, FloatKey o) -> bool"""
1899 return _IMP_kernel.FloatKey___ne__(self, o)
1901 def __lt__(self, o):
1902 r"""__lt__(FloatKey self, FloatKey o) -> bool"""
1903 return _IMP_kernel.FloatKey___lt__(self, o)
1905 def __gt__(self, o):
1906 r"""__gt__(FloatKey self, FloatKey o) -> bool"""
1907 return _IMP_kernel.FloatKey___gt__(self, o)
1909 def __ge__(self, o):
1910 r"""__ge__(FloatKey self, FloatKey o) -> bool"""
1911 return _IMP_kernel.FloatKey___ge__(self, o)
1913 def __le__(self, o):
1914 r"""__le__(FloatKey self, FloatKey o) -> bool"""
1915 return _IMP_kernel.FloatKey___le__(self, o)
1918 r"""__hash__(FloatKey self) -> std::size_t"""
1919 return _IMP_kernel.FloatKey___hash__(self)
1921 def show(self, *args):
1922 r"""show(FloatKey self, _ostream out=std::cout)"""
1923 return _IMP_kernel.FloatKey_show(self, *args)
1926 def add_alias(old_key, new_name):
1927 r"""add_alias(FloatKey old_key, std::string new_name) -> FloatKey"""
1928 return _IMP_kernel.FloatKey_add_alias(old_key, new_name)
1931 def get_number_of_keys():
1932 r"""get_number_of_keys() -> unsigned int"""
1933 return _IMP_kernel.FloatKey_get_number_of_keys()
1936 r"""get_index(FloatKey self) -> unsigned int"""
1937 return _IMP_kernel.FloatKey_get_index(self)
1941 r"""show_all(_ostream out)"""
1942 return _IMP_kernel.FloatKey_show_all(out)
1945 def get_all_strings():
1946 r"""get_all_strings() -> IMP::Vector< std::string >"""
1947 return _IMP_kernel.FloatKey_get_all_strings()
1950 def get_number_unique():
1951 r"""get_number_unique() -> unsigned int"""
1952 return _IMP_kernel.FloatKey_get_number_unique()
1955 r"""__str__(FloatKey self) -> std::string"""
1956 return _IMP_kernel.FloatKey___str__(self)
1959 r"""__repr__(FloatKey self) -> std::string"""
1960 return _IMP_kernel.FloatKey___repr__(self)
1961 __swig_destroy__ = _IMP_kernel.delete_FloatKey
1964 _IMP_kernel.FloatKey_swigregister(FloatKey)
1966 r"""Proxy of C++ IMP::Key< 1 > class."""
1968 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
1970 def __init__(self, *args):
1972 __init__(IntKey self) -> IntKey
1973 __init__(IntKey self, std::string const & c, bool is_implicit_add_permitted=True) -> IntKey
1974 __init__(IntKey self, unsigned int i) -> IntKey
1976 _IMP_kernel.IntKey_swiginit(self, _IMP_kernel.new_IntKey(*args))
1980 r"""add_key(std::string sc) -> unsigned int"""
1981 return _IMP_kernel.IntKey_add_key(sc)
1984 def get_key_exists(sc):
1985 r"""get_key_exists(std::string sc) -> bool"""
1986 return _IMP_kernel.IntKey_get_key_exists(sc)
1988 def get_string(self):
1989 r"""get_string(IntKey self) -> std::string const"""
1990 return _IMP_kernel.IntKey_get_string(self)
1992 def __cmp__(self, o):
1993 r"""__cmp__(IntKey self, IntKey o) -> int"""
1994 return _IMP_kernel.IntKey___cmp__(self, o)
1996 def __eq__(self, o):
1997 r"""__eq__(IntKey self, IntKey o) -> bool"""
1998 return _IMP_kernel.IntKey___eq__(self, o)
2000 def __ne__(self, o):
2001 r"""__ne__(IntKey self, IntKey o) -> bool"""
2002 return _IMP_kernel.IntKey___ne__(self, o)
2004 def __lt__(self, o):
2005 r"""__lt__(IntKey self, IntKey o) -> bool"""
2006 return _IMP_kernel.IntKey___lt__(self, o)
2008 def __gt__(self, o):
2009 r"""__gt__(IntKey self, IntKey o) -> bool"""
2010 return _IMP_kernel.IntKey___gt__(self, o)
2012 def __ge__(self, o):
2013 r"""__ge__(IntKey self, IntKey o) -> bool"""
2014 return _IMP_kernel.IntKey___ge__(self, o)
2016 def __le__(self, o):
2017 r"""__le__(IntKey self, IntKey o) -> bool"""
2018 return _IMP_kernel.IntKey___le__(self, o)
2021 r"""__hash__(IntKey self) -> std::size_t"""
2022 return _IMP_kernel.IntKey___hash__(self)
2024 def show(self, *args):
2025 r"""show(IntKey self, _ostream out=std::cout)"""
2026 return _IMP_kernel.IntKey_show(self, *args)
2029 def add_alias(old_key, new_name):
2030 r"""add_alias(IntKey old_key, std::string new_name) -> IntKey"""
2031 return _IMP_kernel.IntKey_add_alias(old_key, new_name)
2034 def get_number_of_keys():
2035 r"""get_number_of_keys() -> unsigned int"""
2036 return _IMP_kernel.IntKey_get_number_of_keys()
2039 r"""get_index(IntKey self) -> unsigned int"""
2040 return _IMP_kernel.IntKey_get_index(self)
2044 r"""show_all(_ostream out)"""
2045 return _IMP_kernel.IntKey_show_all(out)
2048 def get_all_strings():
2049 r"""get_all_strings() -> IMP::Vector< std::string >"""
2050 return _IMP_kernel.IntKey_get_all_strings()
2053 def get_number_unique():
2054 r"""get_number_unique() -> unsigned int"""
2055 return _IMP_kernel.IntKey_get_number_unique()
2058 r"""__str__(IntKey self) -> std::string"""
2059 return _IMP_kernel.IntKey___str__(self)
2062 r"""__repr__(IntKey self) -> std::string"""
2063 return _IMP_kernel.IntKey___repr__(self)
2064 __swig_destroy__ = _IMP_kernel.delete_IntKey
2067 _IMP_kernel.IntKey_swigregister(IntKey)
2069 r"""Proxy of C++ IMP::Key< 2 > class."""
2071 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2073 def __init__(self, *args):
2075 __init__(StringKey self) -> StringKey
2076 __init__(StringKey self, std::string const & c, bool is_implicit_add_permitted=True) -> StringKey
2077 __init__(StringKey self, unsigned int i) -> StringKey
2079 _IMP_kernel.StringKey_swiginit(self, _IMP_kernel.new_StringKey(*args))
2083 r"""add_key(std::string sc) -> unsigned int"""
2084 return _IMP_kernel.StringKey_add_key(sc)
2087 def get_key_exists(sc):
2088 r"""get_key_exists(std::string sc) -> bool"""
2089 return _IMP_kernel.StringKey_get_key_exists(sc)
2091 def get_string(self):
2092 r"""get_string(StringKey self) -> std::string const"""
2093 return _IMP_kernel.StringKey_get_string(self)
2095 def __cmp__(self, o):
2096 r"""__cmp__(StringKey self, StringKey o) -> int"""
2097 return _IMP_kernel.StringKey___cmp__(self, o)
2099 def __eq__(self, o):
2100 r"""__eq__(StringKey self, StringKey o) -> bool"""
2101 return _IMP_kernel.StringKey___eq__(self, o)
2103 def __ne__(self, o):
2104 r"""__ne__(StringKey self, StringKey o) -> bool"""
2105 return _IMP_kernel.StringKey___ne__(self, o)
2107 def __lt__(self, o):
2108 r"""__lt__(StringKey self, StringKey o) -> bool"""
2109 return _IMP_kernel.StringKey___lt__(self, o)
2111 def __gt__(self, o):
2112 r"""__gt__(StringKey self, StringKey o) -> bool"""
2113 return _IMP_kernel.StringKey___gt__(self, o)
2115 def __ge__(self, o):
2116 r"""__ge__(StringKey self, StringKey o) -> bool"""
2117 return _IMP_kernel.StringKey___ge__(self, o)
2119 def __le__(self, o):
2120 r"""__le__(StringKey self, StringKey o) -> bool"""
2121 return _IMP_kernel.StringKey___le__(self, o)
2124 r"""__hash__(StringKey self) -> std::size_t"""
2125 return _IMP_kernel.StringKey___hash__(self)
2127 def show(self, *args):
2128 r"""show(StringKey self, _ostream out=std::cout)"""
2129 return _IMP_kernel.StringKey_show(self, *args)
2132 def add_alias(old_key, new_name):
2133 r"""add_alias(StringKey old_key, std::string new_name) -> StringKey"""
2134 return _IMP_kernel.StringKey_add_alias(old_key, new_name)
2137 def get_number_of_keys():
2138 r"""get_number_of_keys() -> unsigned int"""
2139 return _IMP_kernel.StringKey_get_number_of_keys()
2142 r"""get_index(StringKey self) -> unsigned int"""
2143 return _IMP_kernel.StringKey_get_index(self)
2147 r"""show_all(_ostream out)"""
2148 return _IMP_kernel.StringKey_show_all(out)
2151 def get_all_strings():
2152 r"""get_all_strings() -> IMP::Vector< std::string >"""
2153 return _IMP_kernel.StringKey_get_all_strings()
2156 def get_number_unique():
2157 r"""get_number_unique() -> unsigned int"""
2158 return _IMP_kernel.StringKey_get_number_unique()
2161 r"""__str__(StringKey self) -> std::string"""
2162 return _IMP_kernel.StringKey___str__(self)
2165 r"""__repr__(StringKey self) -> std::string"""
2166 return _IMP_kernel.StringKey___repr__(self)
2167 __swig_destroy__ = _IMP_kernel.delete_StringKey
2170 _IMP_kernel.StringKey_swigregister(StringKey)
2172 r"""Proxy of C++ IMP::Key< 3 > class."""
2174 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2176 def __init__(self, *args):
2178 __init__(ParticleIndexKey self) -> ParticleIndexKey
2179 __init__(ParticleIndexKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ParticleIndexKey
2180 __init__(ParticleIndexKey self, unsigned int i) -> ParticleIndexKey
2182 _IMP_kernel.ParticleIndexKey_swiginit(self, _IMP_kernel.new_ParticleIndexKey(*args))
2186 r"""add_key(std::string sc) -> unsigned int"""
2187 return _IMP_kernel.ParticleIndexKey_add_key(sc)
2190 def get_key_exists(sc):
2191 r"""get_key_exists(std::string sc) -> bool"""
2192 return _IMP_kernel.ParticleIndexKey_get_key_exists(sc)
2194 def get_string(self):
2195 r"""get_string(ParticleIndexKey self) -> std::string const"""
2196 return _IMP_kernel.ParticleIndexKey_get_string(self)
2198 def __cmp__(self, o):
2199 r"""__cmp__(ParticleIndexKey self, ParticleIndexKey o) -> int"""
2200 return _IMP_kernel.ParticleIndexKey___cmp__(self, o)
2202 def __eq__(self, o):
2203 r"""__eq__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2204 return _IMP_kernel.ParticleIndexKey___eq__(self, o)
2206 def __ne__(self, o):
2207 r"""__ne__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2208 return _IMP_kernel.ParticleIndexKey___ne__(self, o)
2210 def __lt__(self, o):
2211 r"""__lt__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2212 return _IMP_kernel.ParticleIndexKey___lt__(self, o)
2214 def __gt__(self, o):
2215 r"""__gt__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2216 return _IMP_kernel.ParticleIndexKey___gt__(self, o)
2218 def __ge__(self, o):
2219 r"""__ge__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2220 return _IMP_kernel.ParticleIndexKey___ge__(self, o)
2222 def __le__(self, o):
2223 r"""__le__(ParticleIndexKey self, ParticleIndexKey o) -> bool"""
2224 return _IMP_kernel.ParticleIndexKey___le__(self, o)
2227 r"""__hash__(ParticleIndexKey self) -> std::size_t"""
2228 return _IMP_kernel.ParticleIndexKey___hash__(self)
2230 def show(self, *args):
2231 r"""show(ParticleIndexKey self, _ostream out=std::cout)"""
2232 return _IMP_kernel.ParticleIndexKey_show(self, *args)
2235 def add_alias(old_key, new_name):
2236 r"""add_alias(ParticleIndexKey old_key, std::string new_name) -> ParticleIndexKey"""
2237 return _IMP_kernel.ParticleIndexKey_add_alias(old_key, new_name)
2240 def get_number_of_keys():
2241 r"""get_number_of_keys() -> unsigned int"""
2242 return _IMP_kernel.ParticleIndexKey_get_number_of_keys()
2245 r"""get_index(ParticleIndexKey self) -> unsigned int"""
2246 return _IMP_kernel.ParticleIndexKey_get_index(self)
2250 r"""show_all(_ostream out)"""
2251 return _IMP_kernel.ParticleIndexKey_show_all(out)
2254 def get_all_strings():
2255 r"""get_all_strings() -> IMP::Vector< std::string >"""
2256 return _IMP_kernel.ParticleIndexKey_get_all_strings()
2259 def get_number_unique():
2260 r"""get_number_unique() -> unsigned int"""
2261 return _IMP_kernel.ParticleIndexKey_get_number_unique()
2264 r"""__str__(ParticleIndexKey self) -> std::string"""
2265 return _IMP_kernel.ParticleIndexKey___str__(self)
2268 r"""__repr__(ParticleIndexKey self) -> std::string"""
2269 return _IMP_kernel.ParticleIndexKey___repr__(self)
2270 __swig_destroy__ = _IMP_kernel.delete_ParticleIndexKey
2273 _IMP_kernel.ParticleIndexKey_swigregister(ParticleIndexKey)
2275 r"""Proxy of C++ IMP::Key< 4 > class."""
2277 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2279 def __init__(self, *args):
2281 __init__(ObjectKey self) -> ObjectKey
2282 __init__(ObjectKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ObjectKey
2283 __init__(ObjectKey self, unsigned int i) -> ObjectKey
2285 _IMP_kernel.ObjectKey_swiginit(self, _IMP_kernel.new_ObjectKey(*args))
2289 r"""add_key(std::string sc) -> unsigned int"""
2290 return _IMP_kernel.ObjectKey_add_key(sc)
2293 def get_key_exists(sc):
2294 r"""get_key_exists(std::string sc) -> bool"""
2295 return _IMP_kernel.ObjectKey_get_key_exists(sc)
2297 def get_string(self):
2298 r"""get_string(ObjectKey self) -> std::string const"""
2299 return _IMP_kernel.ObjectKey_get_string(self)
2301 def __cmp__(self, o):
2302 r"""__cmp__(ObjectKey self, ObjectKey o) -> int"""
2303 return _IMP_kernel.ObjectKey___cmp__(self, o)
2305 def __eq__(self, o):
2306 r"""__eq__(ObjectKey self, ObjectKey o) -> bool"""
2307 return _IMP_kernel.ObjectKey___eq__(self, o)
2309 def __ne__(self, o):
2310 r"""__ne__(ObjectKey self, ObjectKey o) -> bool"""
2311 return _IMP_kernel.ObjectKey___ne__(self, o)
2313 def __lt__(self, o):
2314 r"""__lt__(ObjectKey self, ObjectKey o) -> bool"""
2315 return _IMP_kernel.ObjectKey___lt__(self, o)
2317 def __gt__(self, o):
2318 r"""__gt__(ObjectKey self, ObjectKey o) -> bool"""
2319 return _IMP_kernel.ObjectKey___gt__(self, o)
2321 def __ge__(self, o):
2322 r"""__ge__(ObjectKey self, ObjectKey o) -> bool"""
2323 return _IMP_kernel.ObjectKey___ge__(self, o)
2325 def __le__(self, o):
2326 r"""__le__(ObjectKey self, ObjectKey o) -> bool"""
2327 return _IMP_kernel.ObjectKey___le__(self, o)
2330 r"""__hash__(ObjectKey self) -> std::size_t"""
2331 return _IMP_kernel.ObjectKey___hash__(self)
2333 def show(self, *args):
2334 r"""show(ObjectKey self, _ostream out=std::cout)"""
2335 return _IMP_kernel.ObjectKey_show(self, *args)
2338 def add_alias(old_key, new_name):
2339 r"""add_alias(ObjectKey old_key, std::string new_name) -> ObjectKey"""
2340 return _IMP_kernel.ObjectKey_add_alias(old_key, new_name)
2343 def get_number_of_keys():
2344 r"""get_number_of_keys() -> unsigned int"""
2345 return _IMP_kernel.ObjectKey_get_number_of_keys()
2348 r"""get_index(ObjectKey self) -> unsigned int"""
2349 return _IMP_kernel.ObjectKey_get_index(self)
2353 r"""show_all(_ostream out)"""
2354 return _IMP_kernel.ObjectKey_show_all(out)
2357 def get_all_strings():
2358 r"""get_all_strings() -> IMP::Vector< std::string >"""
2359 return _IMP_kernel.ObjectKey_get_all_strings()
2362 def get_number_unique():
2363 r"""get_number_unique() -> unsigned int"""
2364 return _IMP_kernel.ObjectKey_get_number_unique()
2367 r"""__str__(ObjectKey self) -> std::string"""
2368 return _IMP_kernel.ObjectKey___str__(self)
2371 r"""__repr__(ObjectKey self) -> std::string"""
2372 return _IMP_kernel.ObjectKey___repr__(self)
2373 __swig_destroy__ = _IMP_kernel.delete_ObjectKey
2376 _IMP_kernel.ObjectKey_swigregister(ObjectKey)
2378 r"""Proxy of C++ IMP::Key< 5 > class."""
2380 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2382 def __init__(self, *args):
2384 __init__(IntsKey self) -> IntsKey
2385 __init__(IntsKey self, std::string const & c, bool is_implicit_add_permitted=True) -> IntsKey
2386 __init__(IntsKey self, unsigned int i) -> IntsKey
2388 _IMP_kernel.IntsKey_swiginit(self, _IMP_kernel.new_IntsKey(*args))
2392 r"""add_key(std::string sc) -> unsigned int"""
2393 return _IMP_kernel.IntsKey_add_key(sc)
2396 def get_key_exists(sc):
2397 r"""get_key_exists(std::string sc) -> bool"""
2398 return _IMP_kernel.IntsKey_get_key_exists(sc)
2400 def get_string(self):
2401 r"""get_string(IntsKey self) -> std::string const"""
2402 return _IMP_kernel.IntsKey_get_string(self)
2404 def __cmp__(self, o):
2405 r"""__cmp__(IntsKey self, IntsKey o) -> int"""
2406 return _IMP_kernel.IntsKey___cmp__(self, o)
2408 def __eq__(self, o):
2409 r"""__eq__(IntsKey self, IntsKey o) -> bool"""
2410 return _IMP_kernel.IntsKey___eq__(self, o)
2412 def __ne__(self, o):
2413 r"""__ne__(IntsKey self, IntsKey o) -> bool"""
2414 return _IMP_kernel.IntsKey___ne__(self, o)
2416 def __lt__(self, o):
2417 r"""__lt__(IntsKey self, IntsKey o) -> bool"""
2418 return _IMP_kernel.IntsKey___lt__(self, o)
2420 def __gt__(self, o):
2421 r"""__gt__(IntsKey self, IntsKey o) -> bool"""
2422 return _IMP_kernel.IntsKey___gt__(self, o)
2424 def __ge__(self, o):
2425 r"""__ge__(IntsKey self, IntsKey o) -> bool"""
2426 return _IMP_kernel.IntsKey___ge__(self, o)
2428 def __le__(self, o):
2429 r"""__le__(IntsKey self, IntsKey o) -> bool"""
2430 return _IMP_kernel.IntsKey___le__(self, o)
2433 r"""__hash__(IntsKey self) -> std::size_t"""
2434 return _IMP_kernel.IntsKey___hash__(self)
2436 def show(self, *args):
2437 r"""show(IntsKey self, _ostream out=std::cout)"""
2438 return _IMP_kernel.IntsKey_show(self, *args)
2441 def add_alias(old_key, new_name):
2442 r"""add_alias(IntsKey old_key, std::string new_name) -> IntsKey"""
2443 return _IMP_kernel.IntsKey_add_alias(old_key, new_name)
2446 def get_number_of_keys():
2447 r"""get_number_of_keys() -> unsigned int"""
2448 return _IMP_kernel.IntsKey_get_number_of_keys()
2451 r"""get_index(IntsKey self) -> unsigned int"""
2452 return _IMP_kernel.IntsKey_get_index(self)
2456 r"""show_all(_ostream out)"""
2457 return _IMP_kernel.IntsKey_show_all(out)
2460 def get_all_strings():
2461 r"""get_all_strings() -> IMP::Vector< std::string >"""
2462 return _IMP_kernel.IntsKey_get_all_strings()
2465 def get_number_unique():
2466 r"""get_number_unique() -> unsigned int"""
2467 return _IMP_kernel.IntsKey_get_number_unique()
2470 r"""__str__(IntsKey self) -> std::string"""
2471 return _IMP_kernel.IntsKey___str__(self)
2474 r"""__repr__(IntsKey self) -> std::string"""
2475 return _IMP_kernel.IntsKey___repr__(self)
2476 __swig_destroy__ = _IMP_kernel.delete_IntsKey
2479 _IMP_kernel.IntsKey_swigregister(IntsKey)
2481 r"""Proxy of C++ IMP::Key< 6 > class."""
2483 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2485 def __init__(self, *args):
2487 __init__(ParticleIndexesKey self) -> ParticleIndexesKey
2488 __init__(ParticleIndexesKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ParticleIndexesKey
2489 __init__(ParticleIndexesKey self, unsigned int i) -> ParticleIndexesKey
2491 _IMP_kernel.ParticleIndexesKey_swiginit(self, _IMP_kernel.new_ParticleIndexesKey(*args))
2495 r"""add_key(std::string sc) -> unsigned int"""
2496 return _IMP_kernel.ParticleIndexesKey_add_key(sc)
2499 def get_key_exists(sc):
2500 r"""get_key_exists(std::string sc) -> bool"""
2501 return _IMP_kernel.ParticleIndexesKey_get_key_exists(sc)
2503 def get_string(self):
2504 r"""get_string(ParticleIndexesKey self) -> std::string const"""
2505 return _IMP_kernel.ParticleIndexesKey_get_string(self)
2507 def __cmp__(self, o):
2508 r"""__cmp__(ParticleIndexesKey self, ParticleIndexesKey o) -> int"""
2509 return _IMP_kernel.ParticleIndexesKey___cmp__(self, o)
2511 def __eq__(self, o):
2512 r"""__eq__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
2513 return _IMP_kernel.ParticleIndexesKey___eq__(self, o)
2515 def __ne__(self, o):
2516 r"""__ne__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
2517 return _IMP_kernel.ParticleIndexesKey___ne__(self, o)
2519 def __lt__(self, o):
2520 r"""__lt__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
2521 return _IMP_kernel.ParticleIndexesKey___lt__(self, o)
2523 def __gt__(self, o):
2524 r"""__gt__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
2525 return _IMP_kernel.ParticleIndexesKey___gt__(self, o)
2527 def __ge__(self, o):
2528 r"""__ge__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
2529 return _IMP_kernel.ParticleIndexesKey___ge__(self, o)
2531 def __le__(self, o):
2532 r"""__le__(ParticleIndexesKey self, ParticleIndexesKey o) -> bool"""
2533 return _IMP_kernel.ParticleIndexesKey___le__(self, o)
2536 r"""__hash__(ParticleIndexesKey self) -> std::size_t"""
2537 return _IMP_kernel.ParticleIndexesKey___hash__(self)
2539 def show(self, *args):
2540 r"""show(ParticleIndexesKey self, _ostream out=std::cout)"""
2541 return _IMP_kernel.ParticleIndexesKey_show(self, *args)
2544 def add_alias(old_key, new_name):
2545 r"""add_alias(ParticleIndexesKey old_key, std::string new_name) -> ParticleIndexesKey"""
2546 return _IMP_kernel.ParticleIndexesKey_add_alias(old_key, new_name)
2549 def get_number_of_keys():
2550 r"""get_number_of_keys() -> unsigned int"""
2551 return _IMP_kernel.ParticleIndexesKey_get_number_of_keys()
2554 r"""get_index(ParticleIndexesKey self) -> unsigned int"""
2555 return _IMP_kernel.ParticleIndexesKey_get_index(self)
2559 r"""show_all(_ostream out)"""
2560 return _IMP_kernel.ParticleIndexesKey_show_all(out)
2563 def get_all_strings():
2564 r"""get_all_strings() -> IMP::Vector< std::string >"""
2565 return _IMP_kernel.ParticleIndexesKey_get_all_strings()
2568 def get_number_unique():
2569 r"""get_number_unique() -> unsigned int"""
2570 return _IMP_kernel.ParticleIndexesKey_get_number_unique()
2573 r"""__str__(ParticleIndexesKey self) -> std::string"""
2574 return _IMP_kernel.ParticleIndexesKey___str__(self)
2577 r"""__repr__(ParticleIndexesKey self) -> std::string"""
2578 return _IMP_kernel.ParticleIndexesKey___repr__(self)
2579 __swig_destroy__ = _IMP_kernel.delete_ParticleIndexesKey
2582 _IMP_kernel.ParticleIndexesKey_swigregister(ParticleIndexesKey)
2584 r"""Proxy of C++ IMP::Key< 8 > class."""
2586 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2588 def __init__(self, *args):
2590 __init__(ModelKey self) -> ModelKey
2591 __init__(ModelKey self, std::string const & c, bool is_implicit_add_permitted=True) -> ModelKey
2592 __init__(ModelKey self, unsigned int i) -> ModelKey
2594 _IMP_kernel.ModelKey_swiginit(self, _IMP_kernel.new_ModelKey(*args))
2598 r"""add_key(std::string sc) -> unsigned int"""
2599 return _IMP_kernel.ModelKey_add_key(sc)
2602 def get_key_exists(sc):
2603 r"""get_key_exists(std::string sc) -> bool"""
2604 return _IMP_kernel.ModelKey_get_key_exists(sc)
2606 def get_string(self):
2607 r"""get_string(ModelKey self) -> std::string const"""
2608 return _IMP_kernel.ModelKey_get_string(self)
2610 def __cmp__(self, o):
2611 r"""__cmp__(ModelKey self, ModelKey o) -> int"""
2612 return _IMP_kernel.ModelKey___cmp__(self, o)
2614 def __eq__(self, o):
2615 r"""__eq__(ModelKey self, ModelKey o) -> bool"""
2616 return _IMP_kernel.ModelKey___eq__(self, o)
2618 def __ne__(self, o):
2619 r"""__ne__(ModelKey self, ModelKey o) -> bool"""
2620 return _IMP_kernel.ModelKey___ne__(self, o)
2622 def __lt__(self, o):
2623 r"""__lt__(ModelKey self, ModelKey o) -> bool"""
2624 return _IMP_kernel.ModelKey___lt__(self, o)
2626 def __gt__(self, o):
2627 r"""__gt__(ModelKey self, ModelKey o) -> bool"""
2628 return _IMP_kernel.ModelKey___gt__(self, o)
2630 def __ge__(self, o):
2631 r"""__ge__(ModelKey self, ModelKey o) -> bool"""
2632 return _IMP_kernel.ModelKey___ge__(self, o)
2634 def __le__(self, o):
2635 r"""__le__(ModelKey self, ModelKey o) -> bool"""
2636 return _IMP_kernel.ModelKey___le__(self, o)
2639 r"""__hash__(ModelKey self) -> std::size_t"""
2640 return _IMP_kernel.ModelKey___hash__(self)
2642 def show(self, *args):
2643 r"""show(ModelKey self, _ostream out=std::cout)"""
2644 return _IMP_kernel.ModelKey_show(self, *args)
2647 def add_alias(old_key, new_name):
2648 r"""add_alias(ModelKey old_key, std::string new_name) -> ModelKey"""
2649 return _IMP_kernel.ModelKey_add_alias(old_key, new_name)
2652 def get_number_of_keys():
2653 r"""get_number_of_keys() -> unsigned int"""
2654 return _IMP_kernel.ModelKey_get_number_of_keys()
2657 r"""get_index(ModelKey self) -> unsigned int"""
2658 return _IMP_kernel.ModelKey_get_index(self)
2662 r"""show_all(_ostream out)"""
2663 return _IMP_kernel.ModelKey_show_all(out)
2666 def get_all_strings():
2667 r"""get_all_strings() -> IMP::Vector< std::string >"""
2668 return _IMP_kernel.ModelKey_get_all_strings()
2671 def get_number_unique():
2672 r"""get_number_unique() -> unsigned int"""
2673 return _IMP_kernel.ModelKey_get_number_unique()
2676 r"""__str__(ModelKey self) -> std::string"""
2677 return _IMP_kernel.ModelKey___str__(self)
2680 r"""__repr__(ModelKey self) -> std::string"""
2681 return _IMP_kernel.ModelKey___repr__(self)
2682 __swig_destroy__ = _IMP_kernel.delete_ModelKey
2685 _IMP_kernel.ModelKey_swigregister(ModelKey)
2687 r"""Proxy of C++ IMP::Key< 11 > class."""
2689 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2691 def __init__(self, *args):
2693 __init__(TriggerKey self) -> TriggerKey
2694 __init__(TriggerKey self, std::string const & c, bool is_implicit_add_permitted=True) -> TriggerKey
2695 __init__(TriggerKey self, unsigned int i) -> TriggerKey
2697 _IMP_kernel.TriggerKey_swiginit(self, _IMP_kernel.new_TriggerKey(*args))
2701 r"""add_key(std::string sc) -> unsigned int"""
2702 return _IMP_kernel.TriggerKey_add_key(sc)
2705 def get_key_exists(sc):
2706 r"""get_key_exists(std::string sc) -> bool"""
2707 return _IMP_kernel.TriggerKey_get_key_exists(sc)
2709 def get_string(self):
2710 r"""get_string(TriggerKey self) -> std::string const"""
2711 return _IMP_kernel.TriggerKey_get_string(self)
2713 def __cmp__(self, o):
2714 r"""__cmp__(TriggerKey self, TriggerKey o) -> int"""
2715 return _IMP_kernel.TriggerKey___cmp__(self, o)
2717 def __eq__(self, o):
2718 r"""__eq__(TriggerKey self, TriggerKey o) -> bool"""
2719 return _IMP_kernel.TriggerKey___eq__(self, o)
2721 def __ne__(self, o):
2722 r"""__ne__(TriggerKey self, TriggerKey o) -> bool"""
2723 return _IMP_kernel.TriggerKey___ne__(self, o)
2725 def __lt__(self, o):
2726 r"""__lt__(TriggerKey self, TriggerKey o) -> bool"""
2727 return _IMP_kernel.TriggerKey___lt__(self, o)
2729 def __gt__(self, o):
2730 r"""__gt__(TriggerKey self, TriggerKey o) -> bool"""
2731 return _IMP_kernel.TriggerKey___gt__(self, o)
2733 def __ge__(self, o):
2734 r"""__ge__(TriggerKey self, TriggerKey o) -> bool"""
2735 return _IMP_kernel.TriggerKey___ge__(self, o)
2737 def __le__(self, o):
2738 r"""__le__(TriggerKey self, TriggerKey o) -> bool"""
2739 return _IMP_kernel.TriggerKey___le__(self, o)
2742 r"""__hash__(TriggerKey self) -> std::size_t"""
2743 return _IMP_kernel.TriggerKey___hash__(self)
2745 def show(self, *args):
2746 r"""show(TriggerKey self, _ostream out=std::cout)"""
2747 return _IMP_kernel.TriggerKey_show(self, *args)
2750 def add_alias(old_key, new_name):
2751 r"""add_alias(TriggerKey old_key, std::string new_name) -> TriggerKey"""
2752 return _IMP_kernel.TriggerKey_add_alias(old_key, new_name)
2755 def get_number_of_keys():
2756 r"""get_number_of_keys() -> unsigned int"""
2757 return _IMP_kernel.TriggerKey_get_number_of_keys()
2760 r"""get_index(TriggerKey self) -> unsigned int"""
2761 return _IMP_kernel.TriggerKey_get_index(self)
2765 r"""show_all(_ostream out)"""
2766 return _IMP_kernel.TriggerKey_show_all(out)
2769 def get_all_strings():
2770 r"""get_all_strings() -> IMP::Vector< std::string >"""
2771 return _IMP_kernel.TriggerKey_get_all_strings()
2774 def get_number_unique():
2775 r"""get_number_unique() -> unsigned int"""
2776 return _IMP_kernel.TriggerKey_get_number_unique()
2779 r"""__str__(TriggerKey self) -> std::string"""
2780 return _IMP_kernel.TriggerKey___str__(self)
2783 r"""__repr__(TriggerKey self) -> std::string"""
2784 return _IMP_kernel.TriggerKey___repr__(self)
2785 __swig_destroy__ = _IMP_kernel.delete_TriggerKey
2788 _IMP_kernel.TriggerKey_swigregister(TriggerKey)
2790 r"""Proxy of C++ IMP::Index< IMP::ParticleIndexTag > class."""
2792 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2794 def __init__(self, *args):
2796 __init__(ParticleIndex self, int i) -> ParticleIndex
2797 __init__(ParticleIndex self) -> ParticleIndex
2799 _IMP_kernel.ParticleIndex_swiginit(self, _IMP_kernel.new_ParticleIndex(*args))
2802 r"""get_index(ParticleIndex self) -> int"""
2803 return _IMP_kernel.ParticleIndex_get_index(self)
2805 def __cmp__(self, o):
2806 r"""__cmp__(ParticleIndex self, ParticleIndex o) -> int"""
2807 return _IMP_kernel.ParticleIndex___cmp__(self, o)
2809 def __eq__(self, o):
2810 r"""__eq__(ParticleIndex self, ParticleIndex o) -> bool"""
2811 return _IMP_kernel.ParticleIndex___eq__(self, o)
2813 def __ne__(self, o):
2814 r"""__ne__(ParticleIndex self, ParticleIndex o) -> bool"""
2815 return _IMP_kernel.ParticleIndex___ne__(self, o)
2817 def __lt__(self, o):
2818 r"""__lt__(ParticleIndex self, ParticleIndex o) -> bool"""
2819 return _IMP_kernel.ParticleIndex___lt__(self, o)
2821 def __gt__(self, o):
2822 r"""__gt__(ParticleIndex self, ParticleIndex o) -> bool"""
2823 return _IMP_kernel.ParticleIndex___gt__(self, o)
2825 def __ge__(self, o):
2826 r"""__ge__(ParticleIndex self, ParticleIndex o) -> bool"""
2827 return _IMP_kernel.ParticleIndex___ge__(self, o)
2829 def __le__(self, o):
2830 r"""__le__(ParticleIndex self, ParticleIndex o) -> bool"""
2831 return _IMP_kernel.ParticleIndex___le__(self, o)
2833 def show(self, *args):
2834 r"""show(ParticleIndex self, _ostream out=std::cout)"""
2835 return _IMP_kernel.ParticleIndex_show(self, *args)
2838 r"""__hash__(ParticleIndex self) -> std::size_t"""
2839 return _IMP_kernel.ParticleIndex___hash__(self)
2842 r"""__str__(ParticleIndex self) -> std::string"""
2843 return _IMP_kernel.ParticleIndex___str__(self)
2846 r"""__repr__(ParticleIndex self) -> std::string"""
2847 return _IMP_kernel.ParticleIndex___repr__(self)
2848 __swig_destroy__ = _IMP_kernel.delete_ParticleIndex
2851 _IMP_kernel.ParticleIndex_swigregister(ParticleIndex)
2853 r"""Proxy of C++ IMP::Key< 10 > class."""
2855 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2857 def __init__(self, *args):
2859 __init__(FloatsKey self) -> FloatsKey
2860 __init__(FloatsKey self, std::string const & c, bool is_implicit_add_permitted=True) -> FloatsKey
2861 __init__(FloatsKey self, unsigned int i) -> FloatsKey
2863 _IMP_kernel.FloatsKey_swiginit(self, _IMP_kernel.new_FloatsKey(*args))
2867 r"""add_key(std::string sc) -> unsigned int"""
2868 return _IMP_kernel.FloatsKey_add_key(sc)
2871 def get_key_exists(sc):
2872 r"""get_key_exists(std::string sc) -> bool"""
2873 return _IMP_kernel.FloatsKey_get_key_exists(sc)
2875 def get_string(self):
2876 r"""get_string(FloatsKey self) -> std::string const"""
2877 return _IMP_kernel.FloatsKey_get_string(self)
2879 def __cmp__(self, o):
2880 r"""__cmp__(FloatsKey self, FloatsKey o) -> int"""
2881 return _IMP_kernel.FloatsKey___cmp__(self, o)
2883 def __eq__(self, o):
2884 r"""__eq__(FloatsKey self, FloatsKey o) -> bool"""
2885 return _IMP_kernel.FloatsKey___eq__(self, o)
2887 def __ne__(self, o):
2888 r"""__ne__(FloatsKey self, FloatsKey o) -> bool"""
2889 return _IMP_kernel.FloatsKey___ne__(self, o)
2891 def __lt__(self, o):
2892 r"""__lt__(FloatsKey self, FloatsKey o) -> bool"""
2893 return _IMP_kernel.FloatsKey___lt__(self, o)
2895 def __gt__(self, o):
2896 r"""__gt__(FloatsKey self, FloatsKey o) -> bool"""
2897 return _IMP_kernel.FloatsKey___gt__(self, o)
2899 def __ge__(self, o):
2900 r"""__ge__(FloatsKey self, FloatsKey o) -> bool"""
2901 return _IMP_kernel.FloatsKey___ge__(self, o)
2903 def __le__(self, o):
2904 r"""__le__(FloatsKey self, FloatsKey o) -> bool"""
2905 return _IMP_kernel.FloatsKey___le__(self, o)
2908 r"""__hash__(FloatsKey self) -> std::size_t"""
2909 return _IMP_kernel.FloatsKey___hash__(self)
2911 def show(self, *args):
2912 r"""show(FloatsKey self, _ostream out=std::cout)"""
2913 return _IMP_kernel.FloatsKey_show(self, *args)
2916 def add_alias(old_key, new_name):
2917 r"""add_alias(FloatsKey old_key, std::string new_name) -> FloatsKey"""
2918 return _IMP_kernel.FloatsKey_add_alias(old_key, new_name)
2921 def get_number_of_keys():
2922 r"""get_number_of_keys() -> unsigned int"""
2923 return _IMP_kernel.FloatsKey_get_number_of_keys()
2926 r"""get_index(FloatsKey self) -> unsigned int"""
2927 return _IMP_kernel.FloatsKey_get_index(self)
2931 r"""show_all(_ostream out)"""
2932 return _IMP_kernel.FloatsKey_show_all(out)
2935 def get_all_strings():
2936 r"""get_all_strings() -> IMP::Vector< std::string >"""
2937 return _IMP_kernel.FloatsKey_get_all_strings()
2940 def get_number_unique():
2941 r"""get_number_unique() -> unsigned int"""
2942 return _IMP_kernel.FloatsKey_get_number_unique()
2945 r"""__str__(FloatsKey self) -> std::string"""
2946 return _IMP_kernel.FloatsKey___str__(self)
2949 r"""__repr__(FloatsKey self) -> std::string"""
2950 return _IMP_kernel.FloatsKey___repr__(self)
2951 __swig_destroy__ = _IMP_kernel.delete_FloatsKey
2954 _IMP_kernel.FloatsKey_swigregister(FloatsKey)
2956 r"""Proxy of C++ IMP::Key< 12 > class."""
2958 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
2960 def __init__(self, *args):
2962 __init__(SparseStringKey self) -> SparseStringKey
2963 __init__(SparseStringKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseStringKey
2964 __init__(SparseStringKey self, unsigned int i) -> SparseStringKey
2966 _IMP_kernel.SparseStringKey_swiginit(self, _IMP_kernel.new_SparseStringKey(*args))
2970 r"""add_key(std::string sc) -> unsigned int"""
2971 return _IMP_kernel.SparseStringKey_add_key(sc)
2974 def get_key_exists(sc):
2975 r"""get_key_exists(std::string sc) -> bool"""
2976 return _IMP_kernel.SparseStringKey_get_key_exists(sc)
2978 def get_string(self):
2979 r"""get_string(SparseStringKey self) -> std::string const"""
2980 return _IMP_kernel.SparseStringKey_get_string(self)
2982 def __cmp__(self, o):
2983 r"""__cmp__(SparseStringKey self, SparseStringKey o) -> int"""
2984 return _IMP_kernel.SparseStringKey___cmp__(self, o)
2986 def __eq__(self, o):
2987 r"""__eq__(SparseStringKey self, SparseStringKey o) -> bool"""
2988 return _IMP_kernel.SparseStringKey___eq__(self, o)
2990 def __ne__(self, o):
2991 r"""__ne__(SparseStringKey self, SparseStringKey o) -> bool"""
2992 return _IMP_kernel.SparseStringKey___ne__(self, o)
2994 def __lt__(self, o):
2995 r"""__lt__(SparseStringKey self, SparseStringKey o) -> bool"""
2996 return _IMP_kernel.SparseStringKey___lt__(self, o)
2998 def __gt__(self, o):
2999 r"""__gt__(SparseStringKey self, SparseStringKey o) -> bool"""
3000 return _IMP_kernel.SparseStringKey___gt__(self, o)
3002 def __ge__(self, o):
3003 r"""__ge__(SparseStringKey self, SparseStringKey o) -> bool"""
3004 return _IMP_kernel.SparseStringKey___ge__(self, o)
3006 def __le__(self, o):
3007 r"""__le__(SparseStringKey self, SparseStringKey o) -> bool"""
3008 return _IMP_kernel.SparseStringKey___le__(self, o)
3011 r"""__hash__(SparseStringKey self) -> std::size_t"""
3012 return _IMP_kernel.SparseStringKey___hash__(self)
3014 def show(self, *args):
3015 r"""show(SparseStringKey self, _ostream out=std::cout)"""
3016 return _IMP_kernel.SparseStringKey_show(self, *args)
3019 def add_alias(old_key, new_name):
3020 r"""add_alias(SparseStringKey old_key, std::string new_name) -> SparseStringKey"""
3021 return _IMP_kernel.SparseStringKey_add_alias(old_key, new_name)
3024 def get_number_of_keys():
3025 r"""get_number_of_keys() -> unsigned int"""
3026 return _IMP_kernel.SparseStringKey_get_number_of_keys()
3029 r"""get_index(SparseStringKey self) -> unsigned int"""
3030 return _IMP_kernel.SparseStringKey_get_index(self)
3034 r"""show_all(_ostream out)"""
3035 return _IMP_kernel.SparseStringKey_show_all(out)
3038 def get_all_strings():
3039 r"""get_all_strings() -> IMP::Vector< std::string >"""
3040 return _IMP_kernel.SparseStringKey_get_all_strings()
3043 def get_number_unique():
3044 r"""get_number_unique() -> unsigned int"""
3045 return _IMP_kernel.SparseStringKey_get_number_unique()
3048 r"""__str__(SparseStringKey self) -> std::string"""
3049 return _IMP_kernel.SparseStringKey___str__(self)
3052 r"""__repr__(SparseStringKey self) -> std::string"""
3053 return _IMP_kernel.SparseStringKey___repr__(self)
3054 __swig_destroy__ = _IMP_kernel.delete_SparseStringKey
3057 _IMP_kernel.SparseStringKey_swigregister(SparseStringKey)
3059 r"""Proxy of C++ IMP::Key< 13 > class."""
3061 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3063 def __init__(self, *args):
3065 __init__(SparseIntKey self) -> SparseIntKey
3066 __init__(SparseIntKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseIntKey
3067 __init__(SparseIntKey self, unsigned int i) -> SparseIntKey
3069 _IMP_kernel.SparseIntKey_swiginit(self, _IMP_kernel.new_SparseIntKey(*args))
3073 r"""add_key(std::string sc) -> unsigned int"""
3074 return _IMP_kernel.SparseIntKey_add_key(sc)
3077 def get_key_exists(sc):
3078 r"""get_key_exists(std::string sc) -> bool"""
3079 return _IMP_kernel.SparseIntKey_get_key_exists(sc)
3081 def get_string(self):
3082 r"""get_string(SparseIntKey self) -> std::string const"""
3083 return _IMP_kernel.SparseIntKey_get_string(self)
3085 def __cmp__(self, o):
3086 r"""__cmp__(SparseIntKey self, SparseIntKey o) -> int"""
3087 return _IMP_kernel.SparseIntKey___cmp__(self, o)
3089 def __eq__(self, o):
3090 r"""__eq__(SparseIntKey self, SparseIntKey o) -> bool"""
3091 return _IMP_kernel.SparseIntKey___eq__(self, o)
3093 def __ne__(self, o):
3094 r"""__ne__(SparseIntKey self, SparseIntKey o) -> bool"""
3095 return _IMP_kernel.SparseIntKey___ne__(self, o)
3097 def __lt__(self, o):
3098 r"""__lt__(SparseIntKey self, SparseIntKey o) -> bool"""
3099 return _IMP_kernel.SparseIntKey___lt__(self, o)
3101 def __gt__(self, o):
3102 r"""__gt__(SparseIntKey self, SparseIntKey o) -> bool"""
3103 return _IMP_kernel.SparseIntKey___gt__(self, o)
3105 def __ge__(self, o):
3106 r"""__ge__(SparseIntKey self, SparseIntKey o) -> bool"""
3107 return _IMP_kernel.SparseIntKey___ge__(self, o)
3109 def __le__(self, o):
3110 r"""__le__(SparseIntKey self, SparseIntKey o) -> bool"""
3111 return _IMP_kernel.SparseIntKey___le__(self, o)
3114 r"""__hash__(SparseIntKey self) -> std::size_t"""
3115 return _IMP_kernel.SparseIntKey___hash__(self)
3117 def show(self, *args):
3118 r"""show(SparseIntKey self, _ostream out=std::cout)"""
3119 return _IMP_kernel.SparseIntKey_show(self, *args)
3122 def add_alias(old_key, new_name):
3123 r"""add_alias(SparseIntKey old_key, std::string new_name) -> SparseIntKey"""
3124 return _IMP_kernel.SparseIntKey_add_alias(old_key, new_name)
3127 def get_number_of_keys():
3128 r"""get_number_of_keys() -> unsigned int"""
3129 return _IMP_kernel.SparseIntKey_get_number_of_keys()
3132 r"""get_index(SparseIntKey self) -> unsigned int"""
3133 return _IMP_kernel.SparseIntKey_get_index(self)
3137 r"""show_all(_ostream out)"""
3138 return _IMP_kernel.SparseIntKey_show_all(out)
3141 def get_all_strings():
3142 r"""get_all_strings() -> IMP::Vector< std::string >"""
3143 return _IMP_kernel.SparseIntKey_get_all_strings()
3146 def get_number_unique():
3147 r"""get_number_unique() -> unsigned int"""
3148 return _IMP_kernel.SparseIntKey_get_number_unique()
3151 r"""__str__(SparseIntKey self) -> std::string"""
3152 return _IMP_kernel.SparseIntKey___str__(self)
3155 r"""__repr__(SparseIntKey self) -> std::string"""
3156 return _IMP_kernel.SparseIntKey___repr__(self)
3157 __swig_destroy__ = _IMP_kernel.delete_SparseIntKey
3160 _IMP_kernel.SparseIntKey_swigregister(SparseIntKey)
3162 r"""Proxy of C++ IMP::Key< 14 > class."""
3164 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3166 def __init__(self, *args):
3168 __init__(SparseFloatKey self) -> SparseFloatKey
3169 __init__(SparseFloatKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseFloatKey
3170 __init__(SparseFloatKey self, unsigned int i) -> SparseFloatKey
3172 _IMP_kernel.SparseFloatKey_swiginit(self, _IMP_kernel.new_SparseFloatKey(*args))
3176 r"""add_key(std::string sc) -> unsigned int"""
3177 return _IMP_kernel.SparseFloatKey_add_key(sc)
3180 def get_key_exists(sc):
3181 r"""get_key_exists(std::string sc) -> bool"""
3182 return _IMP_kernel.SparseFloatKey_get_key_exists(sc)
3184 def get_string(self):
3185 r"""get_string(SparseFloatKey self) -> std::string const"""
3186 return _IMP_kernel.SparseFloatKey_get_string(self)
3188 def __cmp__(self, o):
3189 r"""__cmp__(SparseFloatKey self, SparseFloatKey o) -> int"""
3190 return _IMP_kernel.SparseFloatKey___cmp__(self, o)
3192 def __eq__(self, o):
3193 r"""__eq__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3194 return _IMP_kernel.SparseFloatKey___eq__(self, o)
3196 def __ne__(self, o):
3197 r"""__ne__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3198 return _IMP_kernel.SparseFloatKey___ne__(self, o)
3200 def __lt__(self, o):
3201 r"""__lt__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3202 return _IMP_kernel.SparseFloatKey___lt__(self, o)
3204 def __gt__(self, o):
3205 r"""__gt__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3206 return _IMP_kernel.SparseFloatKey___gt__(self, o)
3208 def __ge__(self, o):
3209 r"""__ge__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3210 return _IMP_kernel.SparseFloatKey___ge__(self, o)
3212 def __le__(self, o):
3213 r"""__le__(SparseFloatKey self, SparseFloatKey o) -> bool"""
3214 return _IMP_kernel.SparseFloatKey___le__(self, o)
3217 r"""__hash__(SparseFloatKey self) -> std::size_t"""
3218 return _IMP_kernel.SparseFloatKey___hash__(self)
3220 def show(self, *args):
3221 r"""show(SparseFloatKey self, _ostream out=std::cout)"""
3222 return _IMP_kernel.SparseFloatKey_show(self, *args)
3225 def add_alias(old_key, new_name):
3226 r"""add_alias(SparseFloatKey old_key, std::string new_name) -> SparseFloatKey"""
3227 return _IMP_kernel.SparseFloatKey_add_alias(old_key, new_name)
3230 def get_number_of_keys():
3231 r"""get_number_of_keys() -> unsigned int"""
3232 return _IMP_kernel.SparseFloatKey_get_number_of_keys()
3235 r"""get_index(SparseFloatKey self) -> unsigned int"""
3236 return _IMP_kernel.SparseFloatKey_get_index(self)
3240 r"""show_all(_ostream out)"""
3241 return _IMP_kernel.SparseFloatKey_show_all(out)
3244 def get_all_strings():
3245 r"""get_all_strings() -> IMP::Vector< std::string >"""
3246 return _IMP_kernel.SparseFloatKey_get_all_strings()
3249 def get_number_unique():
3250 r"""get_number_unique() -> unsigned int"""
3251 return _IMP_kernel.SparseFloatKey_get_number_unique()
3254 r"""__str__(SparseFloatKey self) -> std::string"""
3255 return _IMP_kernel.SparseFloatKey___str__(self)
3258 r"""__repr__(SparseFloatKey self) -> std::string"""
3259 return _IMP_kernel.SparseFloatKey___repr__(self)
3260 __swig_destroy__ = _IMP_kernel.delete_SparseFloatKey
3263 _IMP_kernel.SparseFloatKey_swigregister(SparseFloatKey)
3265 r"""Proxy of C++ IMP::Key< 15 > class."""
3267 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3269 def __init__(self, *args):
3271 __init__(SparseParticleIndexKey self) -> SparseParticleIndexKey
3272 __init__(SparseParticleIndexKey self, std::string const & c, bool is_implicit_add_permitted=True) -> SparseParticleIndexKey
3273 __init__(SparseParticleIndexKey self, unsigned int i) -> SparseParticleIndexKey
3275 _IMP_kernel.SparseParticleIndexKey_swiginit(self, _IMP_kernel.new_SparseParticleIndexKey(*args))
3279 r"""add_key(std::string sc) -> unsigned int"""
3280 return _IMP_kernel.SparseParticleIndexKey_add_key(sc)
3283 def get_key_exists(sc):
3284 r"""get_key_exists(std::string sc) -> bool"""
3285 return _IMP_kernel.SparseParticleIndexKey_get_key_exists(sc)
3287 def get_string(self):
3288 r"""get_string(SparseParticleIndexKey self) -> std::string const"""
3289 return _IMP_kernel.SparseParticleIndexKey_get_string(self)
3291 def __cmp__(self, o):
3292 r"""__cmp__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> int"""
3293 return _IMP_kernel.SparseParticleIndexKey___cmp__(self, o)
3295 def __eq__(self, o):
3296 r"""__eq__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3297 return _IMP_kernel.SparseParticleIndexKey___eq__(self, o)
3299 def __ne__(self, o):
3300 r"""__ne__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3301 return _IMP_kernel.SparseParticleIndexKey___ne__(self, o)
3303 def __lt__(self, o):
3304 r"""__lt__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3305 return _IMP_kernel.SparseParticleIndexKey___lt__(self, o)
3307 def __gt__(self, o):
3308 r"""__gt__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3309 return _IMP_kernel.SparseParticleIndexKey___gt__(self, o)
3311 def __ge__(self, o):
3312 r"""__ge__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3313 return _IMP_kernel.SparseParticleIndexKey___ge__(self, o)
3315 def __le__(self, o):
3316 r"""__le__(SparseParticleIndexKey self, SparseParticleIndexKey o) -> bool"""
3317 return _IMP_kernel.SparseParticleIndexKey___le__(self, o)
3320 r"""__hash__(SparseParticleIndexKey self) -> std::size_t"""
3321 return _IMP_kernel.SparseParticleIndexKey___hash__(self)
3323 def show(self, *args):
3324 r"""show(SparseParticleIndexKey self, _ostream out=std::cout)"""
3325 return _IMP_kernel.SparseParticleIndexKey_show(self, *args)
3328 def add_alias(old_key, new_name):
3329 r"""add_alias(SparseParticleIndexKey old_key, std::string new_name) -> SparseParticleIndexKey"""
3330 return _IMP_kernel.SparseParticleIndexKey_add_alias(old_key, new_name)
3333 def get_number_of_keys():
3334 r"""get_number_of_keys() -> unsigned int"""
3335 return _IMP_kernel.SparseParticleIndexKey_get_number_of_keys()
3338 r"""get_index(SparseParticleIndexKey self) -> unsigned int"""
3339 return _IMP_kernel.SparseParticleIndexKey_get_index(self)
3343 r"""show_all(_ostream out)"""
3344 return _IMP_kernel.SparseParticleIndexKey_show_all(out)
3347 def get_all_strings():
3348 r"""get_all_strings() -> IMP::Vector< std::string >"""
3349 return _IMP_kernel.SparseParticleIndexKey_get_all_strings()
3352 def get_number_unique():
3353 r"""get_number_unique() -> unsigned int"""
3354 return _IMP_kernel.SparseParticleIndexKey_get_number_unique()
3357 r"""__str__(SparseParticleIndexKey self) -> std::string"""
3358 return _IMP_kernel.SparseParticleIndexKey___str__(self)
3361 r"""__repr__(SparseParticleIndexKey self) -> std::string"""
3362 return _IMP_kernel.SparseParticleIndexKey___repr__(self)
3363 __swig_destroy__ = _IMP_kernel.delete_SparseParticleIndexKey
3366 _IMP_kernel.SparseParticleIndexKey_swigregister(SparseParticleIndexKey)
3368 r"""Proxy of C++ IMP::Key< 16 > class."""
3370 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3372 def __init__(self, *args):
3374 __init__(Vector3DKey self) -> Vector3DKey
3375 __init__(Vector3DKey self, std::string const & c, bool is_implicit_add_permitted=True) -> Vector3DKey
3376 __init__(Vector3DKey self, unsigned int i) -> Vector3DKey
3378 _IMP_kernel.Vector3DKey_swiginit(self, _IMP_kernel.new_Vector3DKey(*args))
3382 r"""add_key(std::string sc) -> unsigned int"""
3383 return _IMP_kernel.Vector3DKey_add_key(sc)
3386 def get_key_exists(sc):
3387 r"""get_key_exists(std::string sc) -> bool"""
3388 return _IMP_kernel.Vector3DKey_get_key_exists(sc)
3390 def get_string(self):
3391 r"""get_string(Vector3DKey self) -> std::string const"""
3392 return _IMP_kernel.Vector3DKey_get_string(self)
3394 def __cmp__(self, o):
3395 r"""__cmp__(Vector3DKey self, Vector3DKey o) -> int"""
3396 return _IMP_kernel.Vector3DKey___cmp__(self, o)
3398 def __eq__(self, o):
3399 r"""__eq__(Vector3DKey self, Vector3DKey o) -> bool"""
3400 return _IMP_kernel.Vector3DKey___eq__(self, o)
3402 def __ne__(self, o):
3403 r"""__ne__(Vector3DKey self, Vector3DKey o) -> bool"""
3404 return _IMP_kernel.Vector3DKey___ne__(self, o)
3406 def __lt__(self, o):
3407 r"""__lt__(Vector3DKey self, Vector3DKey o) -> bool"""
3408 return _IMP_kernel.Vector3DKey___lt__(self, o)
3410 def __gt__(self, o):
3411 r"""__gt__(Vector3DKey self, Vector3DKey o) -> bool"""
3412 return _IMP_kernel.Vector3DKey___gt__(self, o)
3414 def __ge__(self, o):
3415 r"""__ge__(Vector3DKey self, Vector3DKey o) -> bool"""
3416 return _IMP_kernel.Vector3DKey___ge__(self, o)
3418 def __le__(self, o):
3419 r"""__le__(Vector3DKey self, Vector3DKey o) -> bool"""
3420 return _IMP_kernel.Vector3DKey___le__(self, o)
3423 r"""__hash__(Vector3DKey self) -> std::size_t"""
3424 return _IMP_kernel.Vector3DKey___hash__(self)
3426 def show(self, *args):
3427 r"""show(Vector3DKey self, _ostream out=std::cout)"""
3428 return _IMP_kernel.Vector3DKey_show(self, *args)
3431 def add_alias(old_key, new_name):
3432 r"""add_alias(Vector3DKey old_key, std::string new_name) -> Vector3DKey"""
3433 return _IMP_kernel.Vector3DKey_add_alias(old_key, new_name)
3436 def get_number_of_keys():
3437 r"""get_number_of_keys() -> unsigned int"""
3438 return _IMP_kernel.Vector3DKey_get_number_of_keys()
3441 r"""get_index(Vector3DKey self) -> unsigned int"""
3442 return _IMP_kernel.Vector3DKey_get_index(self)
3446 r"""show_all(_ostream out)"""
3447 return _IMP_kernel.Vector3DKey_show_all(out)
3450 def get_all_strings():
3451 r"""get_all_strings() -> IMP::Vector< std::string >"""
3452 return _IMP_kernel.Vector3DKey_get_all_strings()
3455 def get_number_unique():
3456 r"""get_number_unique() -> unsigned int"""
3457 return _IMP_kernel.Vector3DKey_get_number_unique()
3460 r"""__str__(Vector3DKey self) -> std::string"""
3461 return _IMP_kernel.Vector3DKey___str__(self)
3464 r"""__repr__(Vector3DKey self) -> std::string"""
3465 return _IMP_kernel.Vector3DKey___repr__(self)
3466 __swig_destroy__ = _IMP_kernel.delete_Vector3DKey
3469 _IMP_kernel.Vector3DKey_swigregister(Vector3DKey)
3478 class FloatIndex(_Value):
3479 r"""Proxy of C++ IMP::FloatIndex class."""
3481 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3483 def __init__(self, *args):
3484 r"""__init__(FloatIndex self, ParticleIndex i0=ParticleIndex(), FloatKey i1=FloatKey()) -> FloatIndex"""
3485 _IMP_kernel.FloatIndex_swiginit(self, _IMP_kernel.new_FloatIndex(*args))
3488 r"""__hash__(FloatIndex self) -> std::size_t"""
3489 return _IMP_kernel.FloatIndex___hash__(self)
3491 def show(self, *args):
3492 r"""show(FloatIndex self, _ostream out=std::cout)"""
3493 return _IMP_kernel.FloatIndex_show(self, *args)
3495 def __cmp__(self, o):
3496 r"""__cmp__(FloatIndex self, FloatIndex o) -> int"""
3497 return _IMP_kernel.FloatIndex___cmp__(self, o)
3499 def __eq__(self, o):
3500 r"""__eq__(FloatIndex self, FloatIndex o) -> bool"""
3501 return _IMP_kernel.FloatIndex___eq__(self, o)
3503 def __ne__(self, o):
3504 r"""__ne__(FloatIndex self, FloatIndex o) -> bool"""
3505 return _IMP_kernel.FloatIndex___ne__(self, o)
3507 def __lt__(self, o):
3508 r"""__lt__(FloatIndex self, FloatIndex o) -> bool"""
3509 return _IMP_kernel.FloatIndex___lt__(self, o)
3511 def __gt__(self, o):
3512 r"""__gt__(FloatIndex self, FloatIndex o) -> bool"""
3513 return _IMP_kernel.FloatIndex___gt__(self, o)
3515 def __ge__(self, o):
3516 r"""__ge__(FloatIndex self, FloatIndex o) -> bool"""
3517 return _IMP_kernel.FloatIndex___ge__(self, o)
3519 def __le__(self, o):
3520 r"""__le__(FloatIndex self, FloatIndex o) -> bool"""
3521 return _IMP_kernel.FloatIndex___le__(self, o)
3523 def get_particle(self):
3524 r"""get_particle(FloatIndex self) -> ParticleIndex const &"""
3525 return _IMP_kernel.FloatIndex_get_particle(self)
3527 def set_particle(self, v):
3528 r"""set_particle(FloatIndex self, ParticleIndex const & v)"""
3529 return _IMP_kernel.FloatIndex_set_particle(self, v)
3532 r"""get_key(FloatIndex self) -> FloatKey const &"""
3533 return _IMP_kernel.FloatIndex_get_key(self)
3535 def set_key(self, v):
3536 r"""set_key(FloatIndex self, FloatKey const & v)"""
3537 return _IMP_kernel.FloatIndex_set_key(self, v)
3540 r"""__str__(FloatIndex self) -> std::string"""
3541 return _IMP_kernel.FloatIndex___str__(self)
3544 r"""__repr__(FloatIndex self) -> std::string"""
3545 return _IMP_kernel.FloatIndex___repr__(self)
3546 __swig_destroy__ = _IMP_kernel.delete_FloatIndex
3549 _IMP_kernel.FloatIndex_swigregister(FloatIndex)
3550 class _ParticleIndexTag(object):
3551 r"""Proxy of C++ IMP::ParticleIndexTag class."""
3553 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3554 __repr__ = _swig_repr
3557 r"""__init__(_ParticleIndexTag self) -> _ParticleIndexTag"""
3558 _IMP_kernel._ParticleIndexTag_swiginit(self, _IMP_kernel.new__ParticleIndexTag())
3559 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexTag
3562 _IMP_kernel._ParticleIndexTag_swigregister(_ParticleIndexTag)
3563 class ModelObject(
Object):
3564 r"""Proxy of C++ IMP::ModelObject class."""
3566 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3568 def __init__(self, *args):
3570 __init__(ModelObject self, Model m, std::string name) -> ModelObject
3571 __init__(ModelObject self) -> ModelObject
3573 if self.__class__ == ModelObject:
3577 _IMP_kernel.ModelObject_swiginit(self, _IMP_kernel.new_ModelObject(_self, *args))
3579 if self.__class__ != ModelObject:
3580 _director_objects.register(self)
3584 __swig_destroy__ = _IMP_kernel.delete_ModelObject
3586 def get_model(self):
3587 m = _IMP_kernel.ModelObject_get_model(self)
3588 if m
in _models_set:
3589 m = _models_set_get(m)
3594 def get_inputs(self):
3595 r"""get_inputs(ModelObject self) -> IMP::ModelObjectsTemp"""
3596 return _IMP_kernel.ModelObject_get_inputs(self)
3598 def get_outputs(self):
3599 r"""get_outputs(ModelObject self) -> IMP::ModelObjectsTemp"""
3600 return _IMP_kernel.ModelObject_get_outputs(self)
3602 def get_interactions(self):
3603 r"""get_interactions(ModelObject self) -> IMP::ModelObjectsTemps"""
3604 return _IMP_kernel.ModelObject_get_interactions(self)
3606 def get_has_dependencies(self):
3607 r"""get_has_dependencies(ModelObject self) -> bool"""
3608 return _IMP_kernel.ModelObject_get_has_dependencies(self)
3610 def set_has_dependencies(self, tf):
3611 r"""set_has_dependencies(ModelObject self, bool tf)"""
3612 return _IMP_kernel.ModelObject_set_has_dependencies(self, tf)
3614 def set_has_required_score_states(self, tf):
3615 r"""set_has_required_score_states(ModelObject self, bool tf)"""
3616 return _IMP_kernel.ModelObject_set_has_required_score_states(self, tf)
3618 def get_has_required_score_states(self):
3619 r"""get_has_required_score_states(ModelObject self) -> bool"""
3620 return _IMP_kernel.ModelObject_get_has_required_score_states(self)
3622 def get_required_score_states(self):
3623 r"""get_required_score_states(ModelObject self) -> IMP::ScoreStatesTemp const &"""
3624 return _IMP_kernel.ModelObject_get_required_score_states(self)
3626 def handle_set_has_required_score_states(self, arg0):
3627 r"""handle_set_has_required_score_states(ModelObject self, bool arg0)"""
3628 return _IMP_kernel.ModelObject_handle_set_has_required_score_states(self, arg0)
3630 def do_get_inputs(self):
3631 r"""do_get_inputs(ModelObject self) -> IMP::ModelObjectsTemp"""
3632 return _IMP_kernel.ModelObject_do_get_inputs(self)
3634 def do_get_outputs(self):
3635 r"""do_get_outputs(ModelObject self) -> IMP::ModelObjectsTemp"""
3636 return _IMP_kernel.ModelObject_do_get_outputs(self)
3638 def do_get_interactions(self):
3639 r"""do_get_interactions(ModelObject self) -> IMP::ModelObjectsTemps"""
3640 return _IMP_kernel.ModelObject_do_get_interactions(self)
3643 r"""__str__(ModelObject self) -> std::string"""
3644 return _IMP_kernel.ModelObject___str__(self)
3647 r"""__repr__(ModelObject self) -> std::string"""
3648 return _IMP_kernel.ModelObject___repr__(self)
3652 return _object_cast_to_ModelObject(o)
3655 def do_show(self, out):
3660 return _object_cast_to_ModelObject(o)
3662 def __disown__(self):
3664 _IMP_kernel.disown_ModelObject(self)
3665 return weakref.proxy(self)
3668 r"""do_destroy(ModelObject self)"""
3669 return _IMP_kernel.ModelObject_do_destroy(self)
3672 _IMP_kernel.ModelObject_swigregister(ModelObject)
3673 cvar = _IMP_kernel.cvar
3674 NO_MAX = cvar.NO_MAX
3675 BAD_SCORE = cvar.BAD_SCORE
3677 class _ParticleInputs(object):
3678 r"""Proxy of C++ IMP::ParticleInputs class."""
3680 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3682 def __init__(self, *args, **kwargs):
3683 raise AttributeError(
"No constructor defined - class is abstract")
3684 __repr__ = _swig_repr
3686 def get_inputs(self, m, pis):
3687 r"""get_inputs(_ParticleInputs self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3688 return _IMP_kernel._ParticleInputs_get_inputs(self, m, pis)
3691 _IMP_kernel._ParticleInputs_swigregister(_ParticleInputs)
3692 class _ParticleOutputs(object):
3693 r"""Proxy of C++ IMP::ParticleOutputs class."""
3695 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3697 def __init__(self, *args, **kwargs):
3698 raise AttributeError(
"No constructor defined - class is abstract")
3699 __repr__ = _swig_repr
3701 def get_outputs(self, m, pis):
3702 r"""get_outputs(_ParticleOutputs self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
3703 return _IMP_kernel._ParticleOutputs_get_outputs(self, m, pis)
3706 _IMP_kernel._ParticleOutputs_swigregister(_ParticleOutputs)
3709 r"""get_input_particles(IMP::ModelObjectsTemp const & mos) -> IMP::ParticlesTemp"""
3710 return _IMP_kernel.get_input_particles(mos)
3713 r"""get_input_containers(IMP::ModelObjectsTemp const & mos) -> IMP::ContainersTemp"""
3714 return _IMP_kernel.get_input_containers(mos)
3717 r"""get_output_particles(IMP::ModelObjectsTemp const & mos) -> IMP::ParticlesTemp"""
3718 return _IMP_kernel.get_output_particles(mos)
3721 r"""get_output_containers(IMP::ModelObjectsTemp const & mos) -> IMP::ContainersTemp"""
3722 return _IMP_kernel.get_output_containers(mos)
3723 class DerivativeAccumulator(object):
3724 r"""Proxy of C++ IMP::DerivativeAccumulator class."""
3726 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3727 __repr__ = _swig_repr
3729 def __init__(self, *args):
3731 __init__(DerivativeAccumulator self, DerivativeAccumulator arg2) -> DerivativeAccumulator
3732 __init__(DerivativeAccumulator self, double weight=1.0) -> DerivativeAccumulator
3733 __init__(DerivativeAccumulator self, DerivativeAccumulator copy, double weight) -> DerivativeAccumulator
3735 _IMP_kernel.DerivativeAccumulator_swiginit(self, _IMP_kernel.new_DerivativeAccumulator(*args))
3737 def __call__(self, value):
3738 r"""__call__(DerivativeAccumulator self, double const value) -> double"""
3739 return _IMP_kernel.DerivativeAccumulator___call__(self, value)
3741 def get_weight(self):
3742 r"""get_weight(DerivativeAccumulator self) -> double"""
3743 return _IMP_kernel.DerivativeAccumulator_get_weight(self)
3745 def show(self, *args):
3746 r"""show(DerivativeAccumulator self, _ostream out=std::cout)"""
3747 return _IMP_kernel.DerivativeAccumulator_show(self, *args)
3748 __swig_destroy__ = _IMP_kernel.delete_DerivativeAccumulator
3751 _IMP_kernel.DerivativeAccumulator_swigregister(DerivativeAccumulator)
3752 class EvaluationState(object):
3753 r"""Proxy of C++ IMP::EvaluationState class."""
3755 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3756 score = property(_IMP_kernel.EvaluationState_score_get, _IMP_kernel.EvaluationState_score_set, doc=
r"""score : double""")
3757 good = property(_IMP_kernel.EvaluationState_good_get, _IMP_kernel.EvaluationState_good_set, doc=
r"""good : bool""")
3759 def __init__(self, *args):
3761 __init__(EvaluationState self, double oscore, bool ogood) -> EvaluationState
3762 __init__(EvaluationState self) -> EvaluationState
3764 _IMP_kernel.EvaluationState_swiginit(self, _IMP_kernel.new_EvaluationState(*args))
3766 def show(self, *args):
3767 r"""show(EvaluationState self, _ostream out=std::cout)"""
3768 return _IMP_kernel.EvaluationState_show(self, *args)
3771 r"""__str__(EvaluationState self) -> std::string"""
3772 return _IMP_kernel.EvaluationState___str__(self)
3775 r"""__repr__(EvaluationState self) -> std::string"""
3776 return _IMP_kernel.EvaluationState___repr__(self)
3777 __swig_destroy__ = _IMP_kernel.delete_EvaluationState
3780 _IMP_kernel.EvaluationState_swigregister(EvaluationState)
3781 class ScoreAccumulator(_Value):
3782 r"""Proxy of C++ IMP::ScoreAccumulator class."""
3784 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3786 def __init__(self, *args):
3788 __init__(ScoreAccumulator self, ScoreAccumulator arg2) -> ScoreAccumulator
3789 __init__(ScoreAccumulator self) -> ScoreAccumulator
3790 __init__(ScoreAccumulator self, ScoreAccumulator o, Restraint r) -> ScoreAccumulator
3791 __init__(ScoreAccumulator self, ScoreAccumulator o, double weight, double local_max) -> ScoreAccumulator
3793 _IMP_kernel.ScoreAccumulator_swiginit(self, _IMP_kernel.new_ScoreAccumulator(*args))
3795 def add_score(self, score):
3796 r"""add_score(ScoreAccumulator self, double score)"""
3797 return _IMP_kernel.ScoreAccumulator_add_score(self, score)
3799 def get_abort_evaluation(self):
3800 r"""get_abort_evaluation(ScoreAccumulator self) -> bool"""
3801 return _IMP_kernel.ScoreAccumulator_get_abort_evaluation(self)
3803 def get_is_evaluate_if_below(self):
3804 r"""get_is_evaluate_if_below(ScoreAccumulator self) -> bool"""
3805 return _IMP_kernel.ScoreAccumulator_get_is_evaluate_if_below(self)
3807 def get_is_evaluate_if_good(self):
3808 r"""get_is_evaluate_if_good(ScoreAccumulator self) -> bool"""
3809 return _IMP_kernel.ScoreAccumulator_get_is_evaluate_if_good(self)
3811 def get_maximum(self):
3812 r"""get_maximum(ScoreAccumulator self) -> double"""
3813 return _IMP_kernel.ScoreAccumulator_get_maximum(self)
3815 def get_derivative_accumulator(self):
3816 r"""get_derivative_accumulator(ScoreAccumulator self) -> DerivativeAccumulator"""
3817 return _IMP_kernel.ScoreAccumulator_get_derivative_accumulator(self)
3819 def show(self, *args):
3820 r"""show(ScoreAccumulator self, _ostream out=std::cout)"""
3821 return _IMP_kernel.ScoreAccumulator_show(self, *args)
3824 r"""__str__(ScoreAccumulator self) -> std::string"""
3825 return _IMP_kernel.ScoreAccumulator___str__(self)
3828 r"""__repr__(ScoreAccumulator self) -> std::string"""
3829 return _IMP_kernel.ScoreAccumulator___repr__(self)
3830 __swig_destroy__ = _IMP_kernel.delete_ScoreAccumulator
3833 _IMP_kernel.ScoreAccumulator_swigregister(ScoreAccumulator)
3834 class ScoreState(ModelObject):
3835 r"""Proxy of C++ IMP::ScoreState class."""
3837 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3839 def set_can_skip(self, can_skip):
3840 r"""set_can_skip(ScoreState self, bool can_skip)"""
3841 return _IMP_kernel.ScoreState_set_can_skip(self, can_skip)
3843 def __init__(self, *args):
3845 __init__(ScoreState self, Model m, std::string name) -> ScoreState
3846 __init__(ScoreState self) -> ScoreState
3848 if self.__class__ == ScoreState:
3852 _IMP_kernel.ScoreState_swiginit(self, _IMP_kernel.new_ScoreState(_self, *args))
3854 if self.__class__ != ScoreState:
3855 _director_objects.register(self)
3860 def before_evaluate(self):
3861 r"""before_evaluate(ScoreState self)"""
3862 return _IMP_kernel.ScoreState_before_evaluate(self)
3864 def after_evaluate(self, accpt):
3865 r"""after_evaluate(ScoreState self, DerivativeAccumulator accpt)"""
3866 return _IMP_kernel.ScoreState_after_evaluate(self, accpt)
3868 def get_can_skip(self):
3869 r"""get_can_skip(ScoreState self) -> bool"""
3870 return _IMP_kernel.ScoreState_get_can_skip(self)
3872 def get_has_update_order(self):
3873 r"""get_has_update_order(ScoreState self) -> bool"""
3874 return _IMP_kernel.ScoreState_get_has_update_order(self)
3877 r"""get_update_order(ScoreState self) -> unsigned int"""
3878 return _IMP_kernel.ScoreState_get_update_order(self)
3880 def handle_set_has_required_score_states(self, tf):
3881 r"""handle_set_has_required_score_states(ScoreState self, bool tf)"""
3882 return _IMP_kernel.ScoreState_handle_set_has_required_score_states(self, tf)
3884 def do_before_evaluate(self):
3885 r"""do_before_evaluate(ScoreState self)"""
3886 return _IMP_kernel.ScoreState_do_before_evaluate(self)
3888 def do_after_evaluate(self, accpt):
3889 r"""do_after_evaluate(ScoreState self, DerivativeAccumulator accpt)"""
3890 return _IMP_kernel.ScoreState_do_after_evaluate(self, accpt)
3891 __swig_destroy__ = _IMP_kernel.delete_ScoreState
3894 r"""__str__(ScoreState self) -> std::string"""
3895 return _IMP_kernel.ScoreState___str__(self)
3898 r"""__repr__(ScoreState self) -> std::string"""
3899 return _IMP_kernel.ScoreState___repr__(self)
3903 return _object_cast_to_ScoreState(o)
3906 def do_show(self, out):
3911 return _object_cast_to_ScoreState(o)
3913 def __disown__(self):
3915 _IMP_kernel.disown_ScoreState(self)
3916 return weakref.proxy(self)
3919 r"""do_destroy(ScoreState self)"""
3920 return _IMP_kernel.ScoreState_do_destroy(self)
3922 def do_get_inputs(self):
3923 r"""do_get_inputs(ScoreState self) -> IMP::ModelObjectsTemp"""
3924 return _IMP_kernel.ScoreState_do_get_inputs(self)
3926 def do_get_outputs(self):
3927 r"""do_get_outputs(ScoreState self) -> IMP::ModelObjectsTemp"""
3928 return _IMP_kernel.ScoreState_do_get_outputs(self)
3930 def do_get_interactions(self):
3931 r"""do_get_interactions(ScoreState self) -> IMP::ModelObjectsTemps"""
3932 return _IMP_kernel.ScoreState_do_get_interactions(self)
3935 _IMP_kernel.ScoreState_swigregister(ScoreState)
3938 r"""get_update_order(IMP::ScoreStatesTemp input) -> IMP::ScoreStatesTemp"""
3939 return _IMP_kernel.get_update_order(input)
3940 class Constraint(ScoreState):
3941 r"""Proxy of C++ IMP::Constraint class."""
3943 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
3945 def __init__(self, *args):
3947 __init__(Constraint self, Model m, std::string name="Constraint %1%") -> Constraint
3948 __init__(Constraint self) -> Constraint
3950 if self.__class__ == Constraint:
3954 _IMP_kernel.Constraint_swiginit(self, _IMP_kernel.new_Constraint(_self, *args))
3956 if self.__class__ != Constraint:
3957 _director_objects.register(self)
3962 def do_update_attributes(self):
3963 r"""do_update_attributes(Constraint self)"""
3964 return _IMP_kernel.Constraint_do_update_attributes(self)
3966 def do_update_derivatives(self, da):
3967 r"""do_update_derivatives(Constraint self, DerivativeAccumulator da)"""
3968 return _IMP_kernel.Constraint_do_update_derivatives(self, da)
3970 def do_before_evaluate(self):
3971 r"""do_before_evaluate(Constraint self)"""
3972 return _IMP_kernel.Constraint_do_before_evaluate(self)
3974 def do_after_evaluate(self, da):
3975 r"""do_after_evaluate(Constraint self, DerivativeAccumulator da)"""
3976 return _IMP_kernel.Constraint_do_after_evaluate(self, da)
3977 __swig_destroy__ = _IMP_kernel.delete_Constraint
3980 r"""__str__(Constraint self) -> std::string"""
3981 return _IMP_kernel.Constraint___str__(self)
3984 r"""__repr__(Constraint self) -> std::string"""
3985 return _IMP_kernel.Constraint___repr__(self)
3989 return _object_cast_to_Constraint(o)
3992 def do_show(self, out):
3997 return _object_cast_to_Constraint(o)
3999 def __disown__(self):
4001 _IMP_kernel.disown_Constraint(self)
4002 return weakref.proxy(self)
4005 r"""do_destroy(Constraint self)"""
4006 return _IMP_kernel.Constraint_do_destroy(self)
4008 def do_get_inputs(self):
4009 r"""do_get_inputs(Constraint self) -> IMP::ModelObjectsTemp"""
4010 return _IMP_kernel.Constraint_do_get_inputs(self)
4012 def do_get_outputs(self):
4013 r"""do_get_outputs(Constraint self) -> IMP::ModelObjectsTemp"""
4014 return _IMP_kernel.Constraint_do_get_outputs(self)
4016 def do_get_interactions(self):
4017 r"""do_get_interactions(Constraint self) -> IMP::ModelObjectsTemps"""
4018 return _IMP_kernel.Constraint_do_get_interactions(self)
4021 _IMP_kernel.Constraint_swigregister(Constraint)
4022 class Container(ModelObject):
4023 r"""Proxy of C++ IMP::Container class."""
4025 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4027 def __init__(self, *args):
4029 __init__(Container self, Model m, std::string name="Container %1%") -> Container
4030 __init__(Container self) -> Container
4032 if self.__class__ == Container:
4036 _IMP_kernel.Container_swiginit(self, _IMP_kernel.new_Container(_self, *args))
4038 if self.__class__ != Container:
4039 _director_objects.register(self)
4044 def do_get_contents_hash(self):
4045 r"""do_get_contents_hash(Container self) -> std::size_t"""
4046 return _IMP_kernel.Container_do_get_contents_hash(self)
4048 def get_all_possible_indexes(self):
4049 r"""get_all_possible_indexes(Container self) -> IMP::ParticleIndexes"""
4050 return _IMP_kernel.Container_get_all_possible_indexes(self)
4052 def get_contents_hash(self):
4053 r"""get_contents_hash(Container self) -> std::size_t"""
4054 return _IMP_kernel.Container_get_contents_hash(self)
4056 def do_get_outputs(self):
4057 r"""do_get_outputs(Container self) -> IMP::ModelObjectsTemp"""
4058 return _IMP_kernel.Container_do_get_outputs(self)
4060 def get_is_decomposable(self):
4061 r"""get_is_decomposable(Container self) -> bool"""
4062 return _IMP_kernel.Container_get_is_decomposable(self)
4064 def validate_readable(self):
4065 r"""validate_readable(Container self)"""
4066 return _IMP_kernel.Container_validate_readable(self)
4068 def validate_writable(self):
4069 r"""validate_writable(Container self)"""
4070 return _IMP_kernel.Container_validate_writable(self)
4072 def set_is_readable(self, tf):
4073 r"""set_is_readable(Container self, bool tf)"""
4074 return _IMP_kernel.Container_set_is_readable(self, tf)
4076 def set_is_writable(self, tf):
4077 r"""set_is_writable(Container self, bool tf)"""
4078 return _IMP_kernel.Container_set_is_writable(self, tf)
4079 __swig_destroy__ = _IMP_kernel.delete_Container
4082 r"""__str__(Container self) -> std::string"""
4083 return _IMP_kernel.Container___str__(self)
4086 r"""__repr__(Container self) -> std::string"""
4087 return _IMP_kernel.Container___repr__(self)
4091 return _object_cast_to_Container(o)
4094 def do_show(self, out):
4099 return _object_cast_to_Container(o)
4101 def __disown__(self):
4103 _IMP_kernel.disown_Container(self)
4104 return weakref.proxy(self)
4107 r"""do_destroy(Container self)"""
4108 return _IMP_kernel.Container_do_destroy(self)
4110 def handle_set_has_required_score_states(self, arg0):
4111 r"""handle_set_has_required_score_states(Container self, bool arg0)"""
4112 return _IMP_kernel.Container_handle_set_has_required_score_states(self, arg0)
4114 def do_get_inputs(self):
4115 r"""do_get_inputs(Container self) -> IMP::ModelObjectsTemp"""
4116 return _IMP_kernel.Container_do_get_inputs(self)
4118 def do_get_interactions(self):
4119 r"""do_get_interactions(Container self) -> IMP::ModelObjectsTemps"""
4120 return _IMP_kernel.Container_do_get_interactions(self)
4123 _IMP_kernel.Container_swigregister(Container)
4124 class RestraintInfo(
Object):
4125 r"""Proxy of C++ IMP::RestraintInfo class."""
4127 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4129 def __init__(self, *args):
4130 r"""__init__(RestraintInfo self, std::string name="RestraintInfo %1%") -> RestraintInfo"""
4131 _IMP_kernel.RestraintInfo_swiginit(self, _IMP_kernel.new_RestraintInfo(*args))
4134 r"""clear(RestraintInfo self)"""
4135 return _IMP_kernel.RestraintInfo_clear(self)
4137 def add_int(self, key, value):
4138 r"""add_int(RestraintInfo self, std::string key, int value)"""
4139 return _IMP_kernel.RestraintInfo_add_int(self, key, value)
4141 def get_number_of_int(self):
4142 r"""get_number_of_int(RestraintInfo self) -> unsigned int"""
4143 return _IMP_kernel.RestraintInfo_get_number_of_int(self)
4145 def get_int_key(self, i):
4146 r"""get_int_key(RestraintInfo self, unsigned int i) -> std::string"""
4147 return _IMP_kernel.RestraintInfo_get_int_key(self, i)
4149 def get_int_value(self, i):
4150 r"""get_int_value(RestraintInfo self, unsigned int i) -> int"""
4151 return _IMP_kernel.RestraintInfo_get_int_value(self, i)
4153 def add_float(self, key, value):
4154 r"""add_float(RestraintInfo self, std::string key, double value)"""
4155 return _IMP_kernel.RestraintInfo_add_float(self, key, value)
4157 def get_number_of_float(self):
4158 r"""get_number_of_float(RestraintInfo self) -> unsigned int"""
4159 return _IMP_kernel.RestraintInfo_get_number_of_float(self)
4161 def get_float_key(self, i):
4162 r"""get_float_key(RestraintInfo self, unsigned int i) -> std::string"""
4163 return _IMP_kernel.RestraintInfo_get_float_key(self, i)
4165 def get_float_value(self, i):
4166 r"""get_float_value(RestraintInfo self, unsigned int i) -> double"""
4167 return _IMP_kernel.RestraintInfo_get_float_value(self, i)
4169 def add_string(self, key, value):
4170 r"""add_string(RestraintInfo self, std::string key, std::string value)"""
4171 return _IMP_kernel.RestraintInfo_add_string(self, key, value)
4173 def get_number_of_string(self):
4174 r"""get_number_of_string(RestraintInfo self) -> unsigned int"""
4175 return _IMP_kernel.RestraintInfo_get_number_of_string(self)
4177 def get_string_key(self, i):
4178 r"""get_string_key(RestraintInfo self, unsigned int i) -> std::string"""
4179 return _IMP_kernel.RestraintInfo_get_string_key(self, i)
4181 def get_string_value(self, i):
4182 r"""get_string_value(RestraintInfo self, unsigned int i) -> std::string"""
4183 return _IMP_kernel.RestraintInfo_get_string_value(self, i)
4185 def add_filename(self, key, value):
4186 r"""add_filename(RestraintInfo self, std::string key, std::string value)"""
4187 return _IMP_kernel.RestraintInfo_add_filename(self, key, value)
4189 def get_number_of_filename(self):
4190 r"""get_number_of_filename(RestraintInfo self) -> unsigned int"""
4191 return _IMP_kernel.RestraintInfo_get_number_of_filename(self)
4193 def get_filename_key(self, i):
4194 r"""get_filename_key(RestraintInfo self, unsigned int i) -> std::string"""
4195 return _IMP_kernel.RestraintInfo_get_filename_key(self, i)
4197 def get_filename_value(self, i):
4198 r"""get_filename_value(RestraintInfo self, unsigned int i) -> std::string"""
4199 return _IMP_kernel.RestraintInfo_get_filename_value(self, i)
4201 def add_floats(self, key, value):
4202 r"""add_floats(RestraintInfo self, std::string key, IMP::Floats value)"""
4203 return _IMP_kernel.RestraintInfo_add_floats(self, key, value)
4205 def get_number_of_floats(self):
4206 r"""get_number_of_floats(RestraintInfo self) -> unsigned int"""
4207 return _IMP_kernel.RestraintInfo_get_number_of_floats(self)
4209 def get_floats_key(self, i):
4210 r"""get_floats_key(RestraintInfo self, unsigned int i) -> std::string"""
4211 return _IMP_kernel.RestraintInfo_get_floats_key(self, i)
4213 def get_floats_value(self, i):
4214 r"""get_floats_value(RestraintInfo self, unsigned int i) -> IMP::Floats"""
4215 return _IMP_kernel.RestraintInfo_get_floats_value(self, i)
4217 def add_ints(self, key, value):
4218 r"""add_ints(RestraintInfo self, std::string key, IMP::Ints value)"""
4219 return _IMP_kernel.RestraintInfo_add_ints(self, key, value)
4221 def get_number_of_ints(self):
4222 r"""get_number_of_ints(RestraintInfo self) -> unsigned int"""
4223 return _IMP_kernel.RestraintInfo_get_number_of_ints(self)
4225 def get_ints_key(self, i):
4226 r"""get_ints_key(RestraintInfo self, unsigned int i) -> std::string"""
4227 return _IMP_kernel.RestraintInfo_get_ints_key(self, i)
4229 def get_ints_value(self, i):
4230 r"""get_ints_value(RestraintInfo self, unsigned int i) -> IMP::Ints"""
4231 return _IMP_kernel.RestraintInfo_get_ints_value(self, i)
4233 def add_strings(self, key, value):
4234 r"""add_strings(RestraintInfo self, std::string key, IMP::Strings value)"""
4235 return _IMP_kernel.RestraintInfo_add_strings(self, key, value)
4237 def get_number_of_strings(self):
4238 r"""get_number_of_strings(RestraintInfo self) -> unsigned int"""
4239 return _IMP_kernel.RestraintInfo_get_number_of_strings(self)
4241 def get_strings_key(self, i):
4242 r"""get_strings_key(RestraintInfo self, unsigned int i) -> std::string"""
4243 return _IMP_kernel.RestraintInfo_get_strings_key(self, i)
4245 def get_strings_value(self, i):
4246 r"""get_strings_value(RestraintInfo self, unsigned int i) -> IMP::Strings"""
4247 return _IMP_kernel.RestraintInfo_get_strings_value(self, i)
4249 def add_filenames(self, key, value):
4250 r"""add_filenames(RestraintInfo self, std::string key, IMP::Strings value)"""
4251 return _IMP_kernel.RestraintInfo_add_filenames(self, key, value)
4253 def get_number_of_filenames(self):
4254 r"""get_number_of_filenames(RestraintInfo self) -> unsigned int"""
4255 return _IMP_kernel.RestraintInfo_get_number_of_filenames(self)
4257 def get_filenames_key(self, i):
4258 r"""get_filenames_key(RestraintInfo self, unsigned int i) -> std::string"""
4259 return _IMP_kernel.RestraintInfo_get_filenames_key(self, i)
4261 def get_filenames_value(self, i):
4262 r"""get_filenames_value(RestraintInfo self, unsigned int i) -> IMP::Strings"""
4263 return _IMP_kernel.RestraintInfo_get_filenames_value(self, i)
4265 def add_particle_indexes(self, key, value):
4266 r"""add_particle_indexes(RestraintInfo self, std::string key, IMP::ParticleIndexes value)"""
4267 return _IMP_kernel.RestraintInfo_add_particle_indexes(self, key, value)
4269 def get_number_of_particle_indexes(self):
4270 r"""get_number_of_particle_indexes(RestraintInfo self) -> unsigned int"""
4271 return _IMP_kernel.RestraintInfo_get_number_of_particle_indexes(self)
4273 def get_particle_indexes_key(self, i):
4274 r"""get_particle_indexes_key(RestraintInfo self, unsigned int i) -> std::string"""
4275 return _IMP_kernel.RestraintInfo_get_particle_indexes_key(self, i)
4277 def get_particle_indexes_value(self, i):
4278 r"""get_particle_indexes_value(RestraintInfo self, unsigned int i) -> IMP::ParticleIndexes"""
4279 return _IMP_kernel.RestraintInfo_get_particle_indexes_value(self, i)
4282 r"""get_version_info(RestraintInfo self) -> VersionInfo"""
4283 return _IMP_kernel.RestraintInfo_get_version_info(self)
4284 __swig_destroy__ = _IMP_kernel.delete_RestraintInfo
4287 r"""__str__(RestraintInfo self) -> std::string"""
4288 return _IMP_kernel.RestraintInfo___str__(self)
4291 r"""__repr__(RestraintInfo self) -> std::string"""
4292 return _IMP_kernel.RestraintInfo___repr__(self)
4296 return _object_cast_to_RestraintInfo(o)
4300 _IMP_kernel.RestraintInfo_swigregister(RestraintInfo)
4301 class Restraint(ModelObject):
4302 r"""Proxy of C++ IMP::Restraint class."""
4304 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4306 def __init__(self, *args):
4308 __init__(Restraint self, Model m, std::string name) -> Restraint
4309 __init__(Restraint self) -> Restraint
4311 if self.__class__ == Restraint:
4315 _IMP_kernel.Restraint_swiginit(self, _IMP_kernel.new_Restraint(_self, *args))
4317 if self.__class__ != Restraint:
4318 _director_objects.register(self)
4323 def get_score(self):
4324 r"""get_score(Restraint self) -> double"""
4325 return _IMP_kernel.Restraint_get_score(self)
4327 def evaluate(self, calc_derivs):
4328 r"""evaluate(Restraint self, bool calc_derivs) -> double"""
4329 return _IMP_kernel.Restraint_evaluate(self, calc_derivs)
4331 def evaluate_moved(self, calc_derivs, moved_pis, reset_pis):
4332 r"""evaluate_moved(Restraint self, bool calc_derivs, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
4333 return _IMP_kernel.Restraint_evaluate_moved(self, calc_derivs, moved_pis, reset_pis)
4335 def evaluate_moved_if_below(self, calc_derivatives, moved_pis, reset_pis, max):
4336 r"""evaluate_moved_if_below(Restraint self, bool calc_derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
4337 return _IMP_kernel.Restraint_evaluate_moved_if_below(self, calc_derivatives, moved_pis, reset_pis, max)
4339 def evaluate_moved_if_good(self, calc_derivatives, moved_pis, reset_pis):
4340 r"""evaluate_moved_if_good(Restraint self, bool calc_derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
4341 return _IMP_kernel.Restraint_evaluate_moved_if_good(self, calc_derivatives, moved_pis, reset_pis)
4343 def evaluate_if_good(self, calc_derivatives):
4344 r"""evaluate_if_good(Restraint self, bool calc_derivatives) -> double"""
4345 return _IMP_kernel.Restraint_evaluate_if_good(self, calc_derivatives)
4347 def evaluate_if_below(self, calc_derivatives, max):
4348 r"""evaluate_if_below(Restraint self, bool calc_derivatives, double max) -> double"""
4349 return _IMP_kernel.Restraint_evaluate_if_below(self, calc_derivatives, max)
4351 def unprotected_evaluate(self, da):
4352 r"""unprotected_evaluate(Restraint self, DerivativeAccumulator da) -> double"""
4353 return _IMP_kernel.Restraint_unprotected_evaluate(self, da)
4355 def unprotected_evaluate_moved(self, da, moved_pis, reset_pis):
4356 r"""unprotected_evaluate_moved(Restraint self, DerivativeAccumulator da, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
4357 return _IMP_kernel.Restraint_unprotected_evaluate_moved(self, da, moved_pis, reset_pis)
4359 def unprotected_evaluate_if_good(self, da, max):
4360 r"""unprotected_evaluate_if_good(Restraint self, DerivativeAccumulator da, double max) -> double"""
4361 return _IMP_kernel.Restraint_unprotected_evaluate_if_good(self, da, max)
4363 def unprotected_evaluate_if_below(self, da, max):
4364 r"""unprotected_evaluate_if_below(Restraint self, DerivativeAccumulator da, double max) -> double"""
4365 return _IMP_kernel.Restraint_unprotected_evaluate_if_below(self, da, max)
4367 def unprotected_evaluate_moved_if_below(self, da, moved_pis, reset_pis, max):
4368 r"""unprotected_evaluate_moved_if_below(Restraint self, DerivativeAccumulator da, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
4369 return _IMP_kernel.Restraint_unprotected_evaluate_moved_if_below(self, da, moved_pis, reset_pis, max)
4371 def unprotected_evaluate_moved_if_good(self, da, moved_pis, reset_pis, max):
4372 r"""unprotected_evaluate_moved_if_good(Restraint self, DerivativeAccumulator da, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
4373 return _IMP_kernel.Restraint_unprotected_evaluate_moved_if_good(self, da, moved_pis, reset_pis, max)
4375 def get_static_info(self):
4376 r"""get_static_info(Restraint self) -> RestraintInfo"""
4377 return _IMP_kernel.Restraint_get_static_info(self)
4379 def get_dynamic_info(self):
4380 r"""get_dynamic_info(Restraint self) -> RestraintInfo"""
4381 return _IMP_kernel.Restraint_get_dynamic_info(self)
4383 def add_score_and_derivatives(self, sa):
4384 r"""add_score_and_derivatives(Restraint self, ScoreAccumulator sa)"""
4385 return _IMP_kernel.Restraint_add_score_and_derivatives(self, sa)
4387 def add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
4388 r"""add_score_and_derivatives_moved(Restraint self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
4389 return _IMP_kernel.Restraint_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
4392 r"""create_decomposition(Restraint self) -> Restraint"""
4393 return _IMP_kernel.Restraint_create_decomposition(self)
4395 def create_current_decomposition(self):
4396 r"""create_current_decomposition(Restraint self) -> Restraint"""
4397 return _IMP_kernel.Restraint_create_current_decomposition(self)
4399 def set_weight(self, weight):
4400 r"""set_weight(Restraint self, IMP::Float weight)"""
4401 return _IMP_kernel.Restraint_set_weight(self, weight)
4403 def get_weight(self):
4404 r"""get_weight(Restraint self) -> IMP::Float"""
4405 return _IMP_kernel.Restraint_get_weight(self)
4407 def get_maximum_score(self):
4408 r"""get_maximum_score(Restraint self) -> double"""
4409 return _IMP_kernel.Restraint_get_maximum_score(self)
4411 def set_maximum_score(self, s):
4412 r"""set_maximum_score(Restraint self, double s)"""
4413 return _IMP_kernel.Restraint_set_maximum_score(self, s)
4416 r"""create_scoring_function(Restraint self, double weight=1.0, double max=NO_MAX) -> ScoringFunction"""
4417 return _IMP_kernel.Restraint_create_scoring_function(self, *args)
4419 def set_last_score(self, s):
4420 r"""set_last_score(Restraint self, double s)"""
4421 return _IMP_kernel.Restraint_set_last_score(self, s)
4423 def set_last_last_score(self, s):
4424 r"""set_last_last_score(Restraint self, double s)"""
4425 return _IMP_kernel.Restraint_set_last_last_score(self, s)
4427 def get_last_score(self):
4428 r"""get_last_score(Restraint self) -> double"""
4429 return _IMP_kernel.Restraint_get_last_score(self)
4431 def get_last_last_score(self):
4432 r"""get_last_last_score(Restraint self) -> double"""
4433 return _IMP_kernel.Restraint_get_last_last_score(self)
4435 def get_is_aggregate(self):
4436 r"""get_is_aggregate(Restraint self) -> bool"""
4437 return _IMP_kernel.Restraint_get_is_aggregate(self)
4439 def get_was_good(self):
4440 r"""get_was_good(Restraint self) -> bool"""
4441 return _IMP_kernel.Restraint_get_was_good(self)
4442 __swig_destroy__ = _IMP_kernel.delete_Restraint
4444 def do_create_decomposition(self):
4445 r"""do_create_decomposition(Restraint self) -> IMP::Restraints"""
4446 return _IMP_kernel.Restraint_do_create_decomposition(self)
4448 def do_create_current_decomposition(self):
4449 r"""do_create_current_decomposition(Restraint self) -> IMP::Restraints"""
4450 return _IMP_kernel.Restraint_do_create_current_decomposition(self)
4452 def do_add_score_and_derivatives(self, sa):
4453 r"""do_add_score_and_derivatives(Restraint self, ScoreAccumulator sa)"""
4454 return _IMP_kernel.Restraint_do_add_score_and_derivatives(self, sa)
4456 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
4457 r"""do_add_score_and_derivatives_moved(Restraint self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
4458 return _IMP_kernel.Restraint_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
4460 def do_get_outputs(self):
4461 r"""do_get_outputs(Restraint self) -> IMP::ModelObjectsTemp"""
4462 return _IMP_kernel.Restraint_do_get_outputs(self)
4463 is_aggregate_ = property(_IMP_kernel.Restraint_is_aggregate__get, _IMP_kernel.Restraint_is_aggregate__set, doc=
r"""is_aggregate_ : bool""")
4466 r"""__str__(Restraint self) -> std::string"""
4467 return _IMP_kernel.Restraint___str__(self)
4470 r"""__repr__(Restraint self) -> std::string"""
4471 return _IMP_kernel.Restraint___repr__(self)
4475 return _object_cast_to_Restraint(o)
4478 def do_show(self, out):
4483 return _object_cast_to_Restraint(o)
4486 def _wrap_jax(self, score_func, keys=None):
4487 """Create the return value for _get_jax.
4488 Use this method in _get_jax() to wrap the JAX scoring function
4489 with other model- and restraint-specific information.
4491 @param score_func A function implemented using JAX that takes
4492 a single argument (the current model state) and returns
4493 the score of the restraint.
4494 @param keys If given, a set of IMP::Key objects describing Model
4495 attributes (other than xyz and radius) that the restraint
4496 uses. For example, a restraint that uses electrostatic charge
4497 would pass IMP::atom::Charged::get_charge_key() here.
4499 from IMP._jax_util
import JaxRestraintInfo
4500 return JaxRestraintInfo(m=self.get_model(), score_func=score_func,
4501 weight=self.get_weight(), keys=keys)
4504 """Return a JAX implementation of this Restraint.
4505 Implement this method in a Restraint subclass to provide
4506 an equivalent function using [JAX](https://docs.jax.dev/)
4507 that scores the current model state. See also _wrap_jax.
4509 raise NotImplementedError(f
"No JAX implementation for {self}")
4511 def __disown__(self):
4513 _IMP_kernel.disown_Restraint(self)
4514 return weakref.proxy(self)
4517 r"""do_destroy(Restraint self)"""
4518 return _IMP_kernel.Restraint_do_destroy(self)
4520 def handle_set_has_required_score_states(self, arg0):
4521 r"""handle_set_has_required_score_states(Restraint self, bool arg0)"""
4522 return _IMP_kernel.Restraint_handle_set_has_required_score_states(self, arg0)
4524 def do_get_inputs(self):
4525 r"""do_get_inputs(Restraint self) -> IMP::ModelObjectsTemp"""
4526 return _IMP_kernel.Restraint_do_get_inputs(self)
4528 def do_get_interactions(self):
4529 r"""do_get_interactions(Restraint self) -> IMP::ModelObjectsTemps"""
4530 return _IMP_kernel.Restraint_do_get_interactions(self)
4533 _IMP_kernel.Restraint_swigregister(Restraint)
4534 class _RestraintsAdaptor(_InputAdaptor):
4535 r"""Proxy of C++ IMP::RestraintsAdaptor class."""
4537 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4538 __repr__ = _swig_repr
4540 def __init__(self, *args):
4542 __init__(_RestraintsAdaptor self) -> _RestraintsAdaptor
4543 __init__(_RestraintsAdaptor self, IMP::Restraints const & sf) -> _RestraintsAdaptor
4544 __init__(_RestraintsAdaptor self, IMP::RestraintsTemp const & sf) -> _RestraintsAdaptor
4545 __init__(_RestraintsAdaptor self, Restraint sf) -> _RestraintsAdaptor
4547 _IMP_kernel._RestraintsAdaptor_swiginit(self, _IMP_kernel.new__RestraintsAdaptor(*args))
4548 __swig_destroy__ = _IMP_kernel.delete__RestraintsAdaptor
4551 _IMP_kernel._RestraintsAdaptor_swigregister(_RestraintsAdaptor)
4552 class RestraintSet(Restraint):
4553 r"""Proxy of C++ IMP::RestraintSet class."""
4555 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4557 def __init__(self, *args):
4559 __init__(RestraintSet self, Model m, double weight, std::string const & name="RestraintSet %1%") -> RestraintSet
4560 __init__(RestraintSet self, Model m, std::string const & name="RestraintSet %1%") -> RestraintSet
4561 __init__(RestraintSet self, IMP::RestraintsTemp const & rs, double weight, std::string const & name="RestraintSet %1%") -> RestraintSet
4562 __init__(RestraintSet self) -> RestraintSet
4564 if self.__class__ == RestraintSet:
4568 _IMP_kernel.RestraintSet_swiginit(self, _IMP_kernel.new_RestraintSet(_self, *args))
4570 if self.__class__ != RestraintSet:
4571 _director_objects.register(self)
4576 def unprotected_evaluate(self, da):
4577 r"""unprotected_evaluate(RestraintSet self, DerivativeAccumulator da) -> double"""
4578 return _IMP_kernel.RestraintSet_unprotected_evaluate(self, da)
4580 def get_type_name(self):
4581 r"""get_type_name(RestraintSet self) -> std::string"""
4582 return _IMP_kernel.RestraintSet_get_type_name(self)
4585 r"""get_version_info(RestraintSet self) -> VersionInfo"""
4586 return _IMP_kernel.RestraintSet_get_version_info(self)
4587 __swig_destroy__ = _IMP_kernel.delete_RestraintSet
4588 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)
4589 def __set_restraints(self, obj): _list_util.set_varlist(self.restraints, obj)
4590 def __del_restraints(self): _list_util.del_varlist(self.restraints)
4591 restraints = property(__get_restraints, __set_restraints, __del_restraints, doc=
"List of ##ucnames")
4593 def remove_restraint(self, d):
4594 r"""remove_restraint(RestraintSet self, Restraint d)"""
4595 return _IMP_kernel.RestraintSet_remove_restraint(self, d)
4597 def _python_index_restraint(self, d, start, stop):
4598 r"""_python_index_restraint(RestraintSet self, Restraint d, unsigned int start, unsigned int stop) -> unsigned int"""
4599 return _IMP_kernel.RestraintSet__python_index_restraint(self, d, start, stop)
4601 def remove_restraints(self, d):
4602 r"""remove_restraints(RestraintSet self, IMP::Restraints const & d)"""
4603 return _IMP_kernel.RestraintSet_remove_restraints(self, d)
4605 def set_restraints(self, ps):
4606 r"""set_restraints(RestraintSet self, IMP::Restraints const & ps)"""
4607 return _IMP_kernel.RestraintSet_set_restraints(self, ps)
4609 def set_restraints_order(self, objs):
4610 r"""set_restraints_order(RestraintSet self, IMP::Restraints const & objs)"""
4611 return _IMP_kernel.RestraintSet_set_restraints_order(self, objs)
4614 r"""add_restraint(RestraintSet self, Restraint obj) -> unsigned int"""
4615 return _IMP_kernel.RestraintSet_add_restraint(self, obj)
4618 r"""add_restraints(RestraintSet self, IMP::Restraints const & objs)"""
4619 return _IMP_kernel.RestraintSet_add_restraints(self, objs)
4621 def clear_restraints(self):
4622 r"""clear_restraints(RestraintSet self)"""
4623 return _IMP_kernel.RestraintSet_clear_restraints(self)
4625 def get_number_of_restraints(self):
4626 r"""get_number_of_restraints(RestraintSet self) -> unsigned int"""
4627 return _IMP_kernel.RestraintSet_get_number_of_restraints(self)
4629 def get_has_restraints(self):
4630 r"""get_has_restraints(RestraintSet self) -> bool"""
4631 return _IMP_kernel.RestraintSet_get_has_restraints(self)
4633 def get_restraint(self, i):
4634 r"""get_restraint(RestraintSet self, unsigned int i) -> Restraint"""
4635 return _IMP_kernel.RestraintSet_get_restraint(self, i)
4637 def get_restraints(self):
4638 r"""get_restraints(RestraintSet self) -> IMP::Restraints"""
4639 return _IMP_kernel.RestraintSet_get_restraints(self)
4641 def erase_restraint(self, i):
4642 r"""erase_restraint(RestraintSet self, unsigned int i)"""
4643 return _IMP_kernel.RestraintSet_erase_restraint(self, i)
4645 def reserve_restraints(self, sz):
4646 r"""reserve_restraints(RestraintSet self, unsigned int sz)"""
4647 return _IMP_kernel.RestraintSet_reserve_restraints(self, sz)
4649 def get_non_sets_and_sets(self):
4650 r"""get_non_sets_and_sets(RestraintSet self) -> std::pair< IMP::RestraintsTemp,IMP::RestraintSetsTemp >"""
4651 return _IMP_kernel.RestraintSet_get_non_sets_and_sets(self)
4653 def do_get_inputs(self):
4654 r"""do_get_inputs(RestraintSet self) -> IMP::ModelObjectsTemp"""
4655 return _IMP_kernel.RestraintSet_do_get_inputs(self)
4658 r"""create_scoring_function(RestraintSet self, double weight=1.0, double max=std::numeric_limits< double >::max()) -> ScoringFunction"""
4659 return _IMP_kernel.RestraintSet_create_scoring_function(self, *args)
4661 def get_last_score(self):
4662 r"""get_last_score(RestraintSet self) -> double"""
4663 return _IMP_kernel.RestraintSet_get_last_score(self)
4666 r"""__str__(RestraintSet self) -> std::string"""
4667 return _IMP_kernel.RestraintSet___str__(self)
4670 r"""__repr__(RestraintSet self) -> std::string"""
4671 return _IMP_kernel.RestraintSet___repr__(self)
4675 return _object_cast_to_RestraintSet(o)
4678 def do_show(self, out):
4683 return _object_cast_to_RestraintSet(o)
4686 def _get_as_binary(self):
4687 r"""_get_as_binary(RestraintSet self) -> PyObject *"""
4688 return _IMP_kernel.RestraintSet__get_as_binary(self)
4690 def _set_from_binary(self, p):
4691 r"""_set_from_binary(RestraintSet self, PyObject * p)"""
4692 return _IMP_kernel.RestraintSet__set_from_binary(self, p)
4694 def __getstate__(self):
4695 p = self._get_as_binary()
4696 if len(self.__dict__) > 1:
4697 d = self.__dict__.copy()
4702 def __setstate__(self, p):
4703 if not hasattr(self,
'this'):
4705 if isinstance(p, tuple):
4707 self.__dict__.update(d)
4708 return self._set_from_binary(p)
4710 def __disown__(self):
4712 _IMP_kernel.disown_RestraintSet(self)
4713 return weakref.proxy(self)
4716 r"""do_destroy(RestraintSet self)"""
4717 return _IMP_kernel.RestraintSet_do_destroy(self)
4719 def handle_set_has_required_score_states(self, arg0):
4720 r"""handle_set_has_required_score_states(RestraintSet self, bool arg0)"""
4721 return _IMP_kernel.RestraintSet_handle_set_has_required_score_states(self, arg0)
4723 def do_get_outputs(self):
4724 r"""do_get_outputs(RestraintSet self) -> IMP::ModelObjectsTemp"""
4725 return _IMP_kernel.RestraintSet_do_get_outputs(self)
4727 def do_get_interactions(self):
4728 r"""do_get_interactions(RestraintSet self) -> IMP::ModelObjectsTemps"""
4729 return _IMP_kernel.RestraintSet_do_get_interactions(self)
4731 def do_create_decomposition(self):
4732 r"""do_create_decomposition(RestraintSet self) -> IMP::Restraints"""
4733 return _IMP_kernel.RestraintSet_do_create_decomposition(self)
4735 def do_create_current_decomposition(self):
4736 r"""do_create_current_decomposition(RestraintSet self) -> IMP::Restraints"""
4737 return _IMP_kernel.RestraintSet_do_create_current_decomposition(self)
4739 def do_add_score_and_derivatives(self, sa):
4740 r"""do_add_score_and_derivatives(RestraintSet self, ScoreAccumulator sa)"""
4741 return _IMP_kernel.RestraintSet_do_add_score_and_derivatives(self, sa)
4743 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
4744 r"""do_add_score_and_derivatives_moved(RestraintSet self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
4745 return _IMP_kernel.RestraintSet_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
4748 _IMP_kernel.RestraintSet_swigregister(RestraintSet)
4750 def get_restraints(rs):
4751 r"""get_restraints(IMP::RestraintsTemp const & rs) -> IMP::RestraintsTemp"""
4752 return _IMP_kernel.get_restraints(rs)
4754 def _check_particle(p, a):
4755 if (
not p.get_is_active()):
4756 raise ValueError(
"Inactive Particle")
4757 if (type(a)() == a):
4758 raise IndexError(
"Cannot use default Index")
4759 if (
not p.has_attribute(a)):
4760 raise IndexError(
"Particle does not have attribute")
4762 class Particle(ModelObject):
4763 r"""Proxy of C++ IMP::Particle class."""
4765 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4768 r"""get_version_info(Particle self) -> VersionInfo"""
4769 return _IMP_kernel.Particle_get_version_info(self)
4770 __swig_destroy__ = _IMP_kernel.delete_Particle
4772 def __init__(self, *args):
4774 __init__(Particle self, Model m, std::string name) -> Particle
4775 __init__(Particle self, Model m) -> Particle
4776 __init__(Particle self) -> Particle
4778 _IMP_kernel.Particle_swiginit(self, _IMP_kernel.new_Particle(*args))
4780 def get_float_keys(self):
4781 r"""get_float_keys(Particle self) -> IMP::FloatKeys"""
4782 return _IMP_kernel.Particle_get_float_keys(self)
4784 def get_floats_keys(self):
4785 r"""get_floats_keys(Particle self) -> IMP::FloatsKeys"""
4786 return _IMP_kernel.Particle_get_floats_keys(self)
4788 def get_int_keys(self):
4789 r"""get_int_keys(Particle self) -> IMP::IntKeys"""
4790 return _IMP_kernel.Particle_get_int_keys(self)
4792 def get_ints_keys(self):
4793 r"""get_ints_keys(Particle self) -> IMP::IntsKeys"""
4794 return _IMP_kernel.Particle_get_ints_keys(self)
4796 def get_string_keys(self):
4797 r"""get_string_keys(Particle self) -> IMP::StringKeys"""
4798 return _IMP_kernel.Particle_get_string_keys(self)
4800 def get_object_keys(self):
4801 r"""get_object_keys(Particle self) -> IMP::ObjectKeys"""
4802 return _IMP_kernel.Particle_get_object_keys(self)
4804 def add_cache_attribute(self, *args):
4806 add_cache_attribute(Particle self, FloatKey name, IMP::Float value)
4807 add_cache_attribute(Particle self, FloatsKey name, IMP::Floats value)
4808 add_cache_attribute(Particle self, IntKey name, IMP::Int value)
4809 add_cache_attribute(Particle self, IntsKey name, IMP::Ints value)
4810 add_cache_attribute(Particle self, StringKey name, IMP::String value)
4811 add_cache_attribute(Particle self, ObjectKey name, Object value)
4812 add_cache_attribute(Particle self, IMP::WeakObjectKey name, Object value)
4814 return _IMP_kernel.Particle_add_cache_attribute(self, *args)
4816 def get_weak_object_keys(self):
4817 r"""get_weak_object_keys(Particle self) -> IMP::WeakObjectKeys"""
4818 return _IMP_kernel.Particle_get_weak_object_keys(self)
4820 def add_to_derivative(self, key, value, da):
4821 r"""add_to_derivative(Particle self, FloatKey key, IMP::Float value, DerivativeAccumulator da)"""
4822 return _IMP_kernel.Particle_add_to_derivative(self, key, value, da)
4824 def set_is_optimized(self, k, tf):
4825 r"""set_is_optimized(Particle self, FloatKey k, bool tf)"""
4826 return _IMP_kernel.Particle_set_is_optimized(self, k, tf)
4828 def get_is_optimized(self, k):
4829 r"""get_is_optimized(Particle self, FloatKey k) -> bool"""
4830 return _IMP_kernel.Particle_get_is_optimized(self, k)
4832 def get_derivative(self, k):
4833 r"""get_derivative(Particle self, FloatKey k) -> IMP::Float"""
4834 return _IMP_kernel.Particle_get_derivative(self, k)
4836 def add_attribute(self, *args):
4838 add_attribute(Particle self, FloatKey name, IMP::Float initial_value)
4839 add_attribute(Particle self, FloatsKey name, IMP::Floats initial_value)
4840 add_attribute(Particle self, IntKey name, IMP::Int initial_value)
4841 add_attribute(Particle self, IntsKey name, IMP::Ints initial_value)
4842 add_attribute(Particle self, StringKey name, IMP::String initial_value)
4843 add_attribute(Particle self, ObjectKey name, Object initial_value)
4844 add_attribute(Particle self, IMP::WeakObjectKey name, Object initial_value)
4845 add_attribute(Particle self, SparseStringKey name, IMP::String initial_value)
4846 add_attribute(Particle self, SparseIntKey name, IMP::Int initial_value)
4847 add_attribute(Particle self, SparseFloatKey name, IMP::Float initial_value)
4848 add_attribute(Particle self, SparseParticleIndexKey name, ParticleIndex initial_value)
4849 add_attribute(Particle self, FloatKey name, IMP::Float const initial_value, bool optimized)
4850 add_attribute(Particle self, ParticleIndexKey k, Particle v)
4852 return _IMP_kernel.Particle_add_attribute(self, *args)
4854 def has_attribute(self, *args):
4856 has_attribute(Particle self, FloatKey name) -> bool
4857 has_attribute(Particle self, FloatsKey name) -> bool
4858 has_attribute(Particle self, IntKey name) -> bool
4859 has_attribute(Particle self, IntsKey name) -> bool
4860 has_attribute(Particle self, StringKey name) -> bool
4861 has_attribute(Particle self, ObjectKey name) -> bool
4862 has_attribute(Particle self, IMP::WeakObjectKey name) -> bool
4863 has_attribute(Particle self, SparseStringKey name) -> bool
4864 has_attribute(Particle self, SparseIntKey name) -> bool
4865 has_attribute(Particle self, SparseFloatKey name) -> bool
4866 has_attribute(Particle self, SparseParticleIndexKey name) -> bool
4867 has_attribute(Particle self, ParticleIndexKey k) -> bool
4869 return _IMP_kernel.Particle_has_attribute(self, *args)
4871 def set_value(self, *args):
4873 set_value(Particle self, FloatKey name, IMP::Float value)
4874 set_value(Particle self, FloatsKey name, IMP::Floats value)
4875 set_value(Particle self, IntKey name, IMP::Int value)
4876 set_value(Particle self, IntsKey name, IMP::Ints value)
4877 set_value(Particle self, StringKey name, IMP::String value)
4878 set_value(Particle self, ObjectKey name, Object value)
4879 set_value(Particle self, IMP::WeakObjectKey name, Object value)
4880 set_value(Particle self, SparseStringKey name, IMP::String value)
4881 set_value(Particle self, SparseIntKey name, IMP::Int value)
4882 set_value(Particle self, SparseFloatKey name, IMP::Float value)
4883 set_value(Particle self, SparseParticleIndexKey name, ParticleIndex value)
4884 set_value(Particle self, ParticleIndexKey k, Particle v)
4886 return _IMP_kernel.Particle_set_value(self, *args)
4888 def get_value(self, *args):
4890 get_value(Particle self, FloatKey name) -> IMP::Float
4891 get_value(Particle self, FloatsKey name) -> IMP::Floats
4892 get_value(Particle self, IntKey name) -> IMP::Int
4893 get_value(Particle self, IntsKey name) -> IMP::Ints
4894 get_value(Particle self, StringKey name) -> IMP::String
4895 get_value(Particle self, ObjectKey name) -> Object
4896 get_value(Particle self, IMP::WeakObjectKey name) -> Object
4897 get_value(Particle self, SparseStringKey name) -> IMP::String
4898 get_value(Particle self, SparseIntKey name) -> IMP::Int
4899 get_value(Particle self, SparseFloatKey name) -> IMP::Float
4900 get_value(Particle self, SparseParticleIndexKey name) -> ParticleIndex
4901 get_value(Particle self, ParticleIndexKey k) -> Particle
4903 return _IMP_kernel.Particle_get_value(self, *args)
4905 def remove_attribute(self, *args):
4907 remove_attribute(Particle self, FloatKey name)
4908 remove_attribute(Particle self, FloatsKey name)
4909 remove_attribute(Particle self, IntKey name)
4910 remove_attribute(Particle self, IntsKey name)
4911 remove_attribute(Particle self, StringKey name)
4912 remove_attribute(Particle self, ObjectKey name)
4913 remove_attribute(Particle self, IMP::WeakObjectKey name)
4914 remove_attribute(Particle self, SparseStringKey name)
4915 remove_attribute(Particle self, SparseIntKey name)
4916 remove_attribute(Particle self, SparseFloatKey name)
4917 remove_attribute(Particle self, SparseParticleIndexKey name)
4918 remove_attribute(Particle self, ParticleIndexKey k)
4920 return _IMP_kernel.Particle_remove_attribute(self, *args)
4922 def get_particle_keys(self):
4923 r"""get_particle_keys(Particle self) -> IMP::ParticleIndexKeys"""
4924 return _IMP_kernel.Particle_get_particle_keys(self)
4926 def show(self, *args):
4927 r"""show(Particle self, _ostream out=std::cout)"""
4928 return _IMP_kernel.Particle_show(self, *args)
4930 def get_is_active(self):
4931 r"""get_is_active(Particle self) -> bool"""
4932 return _IMP_kernel.Particle_get_is_active(self)
4935 r"""get_index(Particle self) -> ParticleIndex"""
4936 return _IMP_kernel.Particle_get_index(self)
4938 def __eq__(self, *args):
4940 __eq__(Particle self, Particle o) -> bool
4941 __eq__(Particle self, Decorator d) -> bool
4943 return _IMP_kernel.Particle___eq__(self, *args)
4945 def __ne__(self, *args):
4947 __ne__(Particle self, Particle o) -> bool
4948 __ne__(Particle self, Decorator d) -> bool
4950 return _IMP_kernel.Particle___ne__(self, *args)
4952 def __le__(self, *args):
4954 __le__(Particle self, Particle o) -> bool
4955 __le__(Particle self, Decorator d) -> bool
4957 return _IMP_kernel.Particle___le__(self, *args)
4959 def __lt__(self, *args):
4961 __lt__(Particle self, Particle o) -> bool
4962 __lt__(Particle self, Decorator d) -> bool
4964 return _IMP_kernel.Particle___lt__(self, *args)
4966 def __ge__(self, *args):
4968 __ge__(Particle self, Particle o) -> bool
4969 __ge__(Particle self, Decorator d) -> bool
4971 return _IMP_kernel.Particle___ge__(self, *args)
4973 def __gt__(self, *args):
4975 __gt__(Particle self, Particle o) -> bool
4976 __gt__(Particle self, Decorator d) -> bool
4978 return _IMP_kernel.Particle___gt__(self, *args)
4980 __hash__ = ModelObject.__hash__
4984 r"""__str__(Particle self) -> std::string"""
4985 return _IMP_kernel.Particle___str__(self)
4988 r"""__repr__(Particle self) -> std::string"""
4989 return _IMP_kernel.Particle___repr__(self)
4993 return _object_cast_to_Particle(o)
4996 def _get_as_binary(self):
4997 r"""_get_as_binary(Particle self) -> PyObject *"""
4998 return _IMP_kernel.Particle__get_as_binary(self)
5000 def _set_from_binary(self, p):
5001 r"""_set_from_binary(Particle self, PyObject * p)"""
5002 return _IMP_kernel.Particle__set_from_binary(self, p)
5004 def __getstate__(self):
5005 p = self._get_as_binary()
5006 if len(self.__dict__) > 1:
5007 d = self.__dict__.copy()
5012 def __setstate__(self, p):
5013 if not hasattr(self,
'this'):
5015 if isinstance(p, tuple):
5017 self.__dict__.update(d)
5018 return self._set_from_binary(p)
5022 _IMP_kernel.Particle_swigregister(Particle)
5023 class _ParticleAdaptor(_InputAdaptor):
5024 r"""Proxy of C++ IMP::ParticleAdaptor class."""
5026 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5027 __repr__ = _swig_repr
5029 def __init__(self, *args):
5031 __init__(_ParticleAdaptor self) -> _ParticleAdaptor
5032 __init__(_ParticleAdaptor self, Particle p) -> _ParticleAdaptor
5033 __init__(_ParticleAdaptor self, Decorator d) -> _ParticleAdaptor
5035 _IMP_kernel._ParticleAdaptor_swiginit(self, _IMP_kernel.new__ParticleAdaptor(*args))
5037 def get_model(self):
5038 r"""get_model(_ParticleAdaptor self) -> Model"""
5039 return _IMP_kernel._ParticleAdaptor_get_model(self)
5041 def get_particle_index(self):
5042 r"""get_particle_index(_ParticleAdaptor self) -> ParticleIndex"""
5043 return _IMP_kernel._ParticleAdaptor_get_particle_index(self)
5044 __swig_destroy__ = _IMP_kernel.delete__ParticleAdaptor
5047 _IMP_kernel._ParticleAdaptor_swigregister(_ParticleAdaptor)
5048 class _DependencyGraphVertexIndex(object):
5049 r"""Proxy of C++ IMP::DependencyGraphVertexIndex class."""
5051 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5052 __repr__ = _swig_repr
5055 r"""__init__(_DependencyGraphVertexIndex self) -> _DependencyGraphVertexIndex"""
5056 _IMP_kernel._DependencyGraphVertexIndex_swiginit(self, _IMP_kernel.new__DependencyGraphVertexIndex())
5057 __swig_destroy__ = _IMP_kernel.delete__DependencyGraphVertexIndex
5060 _IMP_kernel._DependencyGraphVertexIndex_swigregister(_DependencyGraphVertexIndex)
5062 def show_as_graphviz(name, out):
5063 r"""show_as_graphviz(IMP::DependencyGraph const & name, TextOutput out)"""
5064 return _IMP_kernel.show_as_graphviz(name, out)
5066 def get_vertex_index(g):
5067 r"""get_vertex_index(IMP::DependencyGraph const & g) -> _DependencyGraphVertexIndex"""
5068 return _IMP_kernel.get_vertex_index(g)
5071 r"""get_dependency_graph(Model m) -> IMP::DependencyGraph"""
5072 return _IMP_kernel.get_dependency_graph(m)
5075 r"""get_pruned_dependency_graph(Model m) -> IMP::DependencyGraph"""
5076 return _IMP_kernel.get_pruned_dependency_graph(m)
5078 def get_dependent_particles(p, all, dg, index):
5079 r"""get_dependent_particles(ModelObject p, IMP::ModelObjectsTemp const & all, IMP::DependencyGraph const & dg, _DependencyGraphVertexIndex index) -> IMP::ParticlesTemp"""
5080 return _IMP_kernel.get_dependent_particles(p, all, dg, index)
5082 def get_required_score_states(*args):
5084 get_required_score_states(IMP::ModelObjectsTemp const & mos, IMP::ScoreStatesTemp exclude=IMP::ScoreStatesTemp()) -> IMP::ScoreStatesTemp
5085 get_required_score_states(ModelObject p, IMP::ModelObjectsTemp const & all, IMP::DependencyGraph const & dg, _DependencyGraphVertexIndex index) -> IMP::ScoreStatesTemp
5086 get_required_score_states(Model m, ParticleIndex pi) -> IMP::ScoreStatesTemp
5088 return _IMP_kernel.get_required_score_states(*args)
5089 class ScoringFunction(ModelObject):
5090 r"""Proxy of C++ IMP::ScoringFunction class."""
5092 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5094 def do_add_score_and_derivatives(self, sa, ss):
5095 r"""do_add_score_and_derivatives(ScoringFunction self, ScoreAccumulator sa, IMP::ScoreStatesTemp const & ss)"""
5096 return _IMP_kernel.ScoringFunction_do_add_score_and_derivatives(self, sa, ss)
5098 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss):
5099 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)"""
5100 return _IMP_kernel.ScoringFunction_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss)
5102 def get_score_accumulator_if_below(self, deriv, max):
5103 r"""get_score_accumulator_if_below(ScoringFunction self, bool deriv, double max) -> ScoreAccumulator"""
5104 return _IMP_kernel.ScoringFunction_get_score_accumulator_if_below(self, deriv, max)
5106 def get_score_accumulator_if_good(self, deriv):
5107 r"""get_score_accumulator_if_good(ScoringFunction self, bool deriv) -> ScoreAccumulator"""
5108 return _IMP_kernel.ScoringFunction_get_score_accumulator_if_good(self, deriv)
5110 def get_score_accumulator(self, deriv):
5111 r"""get_score_accumulator(ScoringFunction self, bool deriv) -> ScoreAccumulator"""
5112 return _IMP_kernel.ScoringFunction_get_score_accumulator(self, deriv)
5114 def __init__(self, *args):
5116 __init__(ScoringFunction self, Model m, std::string name) -> ScoringFunction
5117 __init__(ScoringFunction self) -> ScoringFunction
5119 if self.__class__ == ScoringFunction:
5123 _IMP_kernel.ScoringFunction_swiginit(self, _IMP_kernel.new_ScoringFunction(_self, *args))
5125 if self.__class__ != ScoringFunction:
5126 _director_objects.register(self)
5131 def do_get_outputs(self):
5132 r"""do_get_outputs(ScoringFunction self) -> IMP::ModelObjectsTemp"""
5133 return _IMP_kernel.ScoringFunction_do_get_outputs(self)
5135 def evaluate(self, derivatives):
5136 r"""evaluate(ScoringFunction self, bool derivatives) -> double"""
5137 return _IMP_kernel.ScoringFunction_evaluate(self, derivatives)
5139 def evaluate_if_good(self, derivatives):
5140 r"""evaluate_if_good(ScoringFunction self, bool derivatives) -> double"""
5141 return _IMP_kernel.ScoringFunction_evaluate_if_good(self, derivatives)
5143 def evaluate_if_below(self, derivatives, max):
5144 r"""evaluate_if_below(ScoringFunction self, bool derivatives, double max) -> double"""
5145 return _IMP_kernel.ScoringFunction_evaluate_if_below(self, derivatives, max)
5147 def evaluate_moved(self, derivatives, moved_pis, reset_pis):
5148 r"""evaluate_moved(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
5149 return _IMP_kernel.ScoringFunction_evaluate_moved(self, derivatives, moved_pis, reset_pis)
5151 def evaluate_moved_if_below(self, derivatives, moved_pis, reset_pis, max):
5152 r"""evaluate_moved_if_below(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
5153 return _IMP_kernel.ScoringFunction_evaluate_moved_if_below(self, derivatives, moved_pis, reset_pis, max)
5155 def evaluate_moved_if_good(self, derivatives, moved_pis, reset_pis):
5156 r"""evaluate_moved_if_good(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
5157 return _IMP_kernel.ScoringFunction_evaluate_moved_if_good(self, derivatives, moved_pis, reset_pis)
5159 def get_had_good_score(self):
5160 r"""get_had_good_score(ScoringFunction self) -> bool"""
5161 return _IMP_kernel.ScoringFunction_get_had_good_score(self)
5163 def get_last_score(self):
5164 r"""get_last_score(ScoringFunction self) -> double"""
5165 return _IMP_kernel.ScoringFunction_get_last_score(self)
5168 r"""create_restraints(ScoringFunction self) -> IMP::Restraints"""
5169 return _IMP_kernel.ScoringFunction_create_restraints(self)
5172 r"""__str__(ScoringFunction self) -> std::string"""
5173 return _IMP_kernel.ScoringFunction___str__(self)
5176 r"""__repr__(ScoringFunction self) -> std::string"""
5177 return _IMP_kernel.ScoringFunction___repr__(self)
5181 return _object_cast_to_ScoringFunction(o)
5184 def do_show(self, out):
5189 return _object_cast_to_ScoringFunction(o)
5193 raise NotImplementedError(f
"No JAX implementation for {self}")
5195 __swig_destroy__ = _IMP_kernel.delete_ScoringFunction
5196 def __disown__(self):
5198 _IMP_kernel.disown_ScoringFunction(self)
5199 return weakref.proxy(self)
5202 r"""do_destroy(ScoringFunction self)"""
5203 return _IMP_kernel.ScoringFunction_do_destroy(self)
5205 def handle_set_has_required_score_states(self, arg0):
5206 r"""handle_set_has_required_score_states(ScoringFunction self, bool arg0)"""
5207 return _IMP_kernel.ScoringFunction_handle_set_has_required_score_states(self, arg0)
5209 def do_get_inputs(self):
5210 r"""do_get_inputs(ScoringFunction self) -> IMP::ModelObjectsTemp"""
5211 return _IMP_kernel.ScoringFunction_do_get_inputs(self)
5213 def do_get_interactions(self):
5214 r"""do_get_interactions(ScoringFunction self) -> IMP::ModelObjectsTemps"""
5215 return _IMP_kernel.ScoringFunction_do_get_interactions(self)
5218 _IMP_kernel.ScoringFunction_swigregister(ScoringFunction)
5222 create_decomposition(IMP::RestraintsTemp const & rs) -> IMP::Restraints
5223 create_decomposition(ScoringFunction sf) -> IMP::ScoringFunctions
5225 return _IMP_kernel.create_decomposition(*args)
5226 class _ScoringFunctionAdaptor(_InputAdaptor):
5227 r"""Proxy of C++ IMP::ScoringFunctionAdaptor class."""
5229 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5230 __repr__ = _swig_repr
5232 def __init__(self, *args):
5234 __init__(_ScoringFunctionAdaptor self) -> _ScoringFunctionAdaptor
5235 __init__(_ScoringFunctionAdaptor self, ScoringFunction sf) -> _ScoringFunctionAdaptor
5236 __init__(_ScoringFunctionAdaptor self, IMP::RestraintsTemp const & sf) -> _ScoringFunctionAdaptor
5237 __init__(_ScoringFunctionAdaptor self, IMP::Restraints const & sf) -> _ScoringFunctionAdaptor
5238 __init__(_ScoringFunctionAdaptor self, Restraint sf) -> _ScoringFunctionAdaptor
5240 _IMP_kernel._ScoringFunctionAdaptor_swiginit(self, _IMP_kernel.new__ScoringFunctionAdaptor(*args))
5241 __swig_destroy__ = _IMP_kernel.delete__ScoringFunctionAdaptor
5244 _IMP_kernel._ScoringFunctionAdaptor_swigregister(_ScoringFunctionAdaptor)
5247 r"""show_restraint_hierarchy(_ScoringFunctionAdaptor rs, _ostream out=std::cout)"""
5248 return _IMP_kernel.show_restraint_hierarchy(*args)
5249 class Undecorator(
Object):
5250 r"""Proxy of C++ IMP::Undecorator class."""
5252 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5254 def __init__(self, m, name):
5255 r"""__init__(Undecorator self, Model m, std::string name) -> Undecorator"""
5256 if self.__class__ == Undecorator:
5260 _IMP_kernel.Undecorator_swiginit(self, _IMP_kernel.new_Undecorator(_self, m, name))
5262 if self.__class__ != Undecorator:
5263 _director_objects.register(self)
5268 def teardown(self, pi):
5269 r"""teardown(Undecorator self, ParticleIndex pi)"""
5270 return _IMP_kernel.Undecorator_teardown(self, pi)
5273 r"""__str__(Undecorator self) -> std::string"""
5274 return _IMP_kernel.Undecorator___str__(self)
5277 r"""__repr__(Undecorator self) -> std::string"""
5278 return _IMP_kernel.Undecorator___repr__(self)
5282 return _object_cast_to_Undecorator(o)
5285 def do_show(self, out):
5290 return _object_cast_to_Undecorator(o)
5292 __swig_destroy__ = _IMP_kernel.delete_Undecorator
5293 def __disown__(self):
5295 _IMP_kernel.disown_Undecorator(self)
5296 return weakref.proxy(self)
5299 r"""do_destroy(Undecorator self)"""
5300 return _IMP_kernel.Undecorator_do_destroy(self)
5303 _IMP_kernel.Undecorator_swigregister(Undecorator)
5305 r"""Proxy of C++ IMP::Model class."""
5307 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5309 def __init__(self, *args):
5310 r"""__init__(Model self, std::string name="Model %1%") -> Model"""
5311 _IMP_kernel.Model_swiginit(self, _IMP_kernel.new_Model(*args))
5313 if self
not in _models_set:
5314 _models_set.add(self)
5319 def clear_particle_caches(self, pi):
5320 r"""clear_particle_caches(Model self, ParticleIndex pi)"""
5321 return _IMP_kernel.Model_clear_particle_caches(self, pi)
5324 r"""add_particle(Model self, std::string name) -> ParticleIndex"""
5325 return _IMP_kernel.Model_add_particle(self, name)
5327 def get_particle_name(self, pi):
5328 r"""get_particle_name(Model self, ParticleIndex pi) -> std::string"""
5329 return _IMP_kernel.Model_get_particle_name(self, pi)
5331 def add_undecorator(self, pi, d):
5332 r"""add_undecorator(Model self, ParticleIndex pi, Undecorator d)"""
5333 return _IMP_kernel.Model_add_undecorator(self, pi, d)
5335 def get_dependent_restraints_uncached(self, pi):
5336 r"""get_dependent_restraints_uncached(Model self, ParticleIndex pi) -> IMP::RestraintsTemp"""
5337 return _IMP_kernel.Model_get_dependent_restraints_uncached(self, pi)
5339 def get_dependent_particles_uncached(self, pi):
5340 r"""get_dependent_particles_uncached(Model self, ParticleIndex pi) -> IMP::ParticlesTemp"""
5341 return _IMP_kernel.Model_get_dependent_particles_uncached(self, pi)
5343 def get_dependent_score_states_uncached(self, pi):
5344 r"""get_dependent_score_states_uncached(Model self, ParticleIndex pi) -> IMP::ScoreStatesTemp"""
5345 return _IMP_kernel.Model_get_dependent_score_states_uncached(self, pi)
5346 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)
5347 def __set_score_states(self, obj): _list_util.set_varlist(self.score_states, obj)
5348 def __del_score_states(self): _list_util.del_varlist(self.score_states)
5349 score_states = property(__get_score_states, __set_score_states, __del_score_states, doc=
"List of ##ucnames")
5351 def remove_score_state(self, d):
5352 r"""remove_score_state(Model self, ScoreState d)"""
5353 return _IMP_kernel.Model_remove_score_state(self, d)
5355 def _python_index_score_state(self, d, start, stop):
5356 r"""_python_index_score_state(Model self, ScoreState d, unsigned int start, unsigned int stop) -> unsigned int"""
5357 return _IMP_kernel.Model__python_index_score_state(self, d, start, stop)
5359 def remove_score_states(self, d):
5360 r"""remove_score_states(Model self, IMP::ScoreStates const & d)"""
5361 return _IMP_kernel.Model_remove_score_states(self, d)
5363 def set_score_states(self, ps):
5364 r"""set_score_states(Model self, IMP::ScoreStates const & ps)"""
5365 return _IMP_kernel.Model_set_score_states(self, ps)
5367 def set_score_states_order(self, objs):
5368 r"""set_score_states_order(Model self, IMP::ScoreStates const & objs)"""
5369 return _IMP_kernel.Model_set_score_states_order(self, objs)
5371 def add_score_state(self, obj):
5372 r"""add_score_state(Model self, ScoreState obj) -> unsigned int"""
5373 return _IMP_kernel.Model_add_score_state(self, obj)
5375 def add_score_states(self, objs):
5376 r"""add_score_states(Model self, IMP::ScoreStates const & objs)"""
5377 return _IMP_kernel.Model_add_score_states(self, objs)
5379 def clear_score_states(self):
5380 r"""clear_score_states(Model self)"""
5381 return _IMP_kernel.Model_clear_score_states(self)
5383 def get_number_of_score_states(self):
5384 r"""get_number_of_score_states(Model self) -> unsigned int"""
5385 return _IMP_kernel.Model_get_number_of_score_states(self)
5387 def get_has_score_states(self):
5388 r"""get_has_score_states(Model self) -> bool"""
5389 return _IMP_kernel.Model_get_has_score_states(self)
5391 def get_score_state(self, i):
5392 r"""get_score_state(Model self, unsigned int i) -> ScoreState"""
5393 return _IMP_kernel.Model_get_score_state(self, i)
5395 def get_score_states(self):
5396 r"""get_score_states(Model self) -> IMP::ScoreStates"""
5397 return _IMP_kernel.Model_get_score_states(self)
5399 def erase_score_state(self, i):
5400 r"""erase_score_state(Model self, unsigned int i)"""
5401 return _IMP_kernel.Model_erase_score_state(self, i)
5403 def reserve_score_states(self, sz):
5404 r"""reserve_score_states(Model self, unsigned int sz)"""
5405 return _IMP_kernel.Model_reserve_score_states(self, sz)
5408 r"""update(Model self)"""
5409 return _IMP_kernel.Model_update(self)
5411 def add_cache_attribute(self, *args):
5413 add_cache_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
5414 add_cache_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
5415 add_cache_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
5416 add_cache_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, IMP::algebra::Vector3D value)
5417 add_cache_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
5418 add_cache_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
5419 add_cache_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
5420 add_cache_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
5421 add_cache_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
5422 add_cache_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
5424 return _IMP_kernel.Model_add_cache_attribute(self, *args)
5426 def add_attribute(self, *args):
5428 add_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
5429 add_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
5430 add_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
5431 add_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, IMP::algebra::Vector3D value)
5432 add_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
5433 add_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
5434 add_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
5435 add_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
5436 add_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
5437 add_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
5438 add_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle, IMP::String value)
5439 add_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle, IMP::Int value)
5440 add_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle, IMP::Float value)
5441 add_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
5443 return _IMP_kernel.Model_add_attribute(self, *args)
5445 def remove_attribute(self, *args):
5447 remove_attribute(Model self, FloatKey attribute_key, ParticleIndex particle)
5448 remove_attribute(Model self, IntKey attribute_key, ParticleIndex particle)
5449 remove_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle)
5450 remove_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle)
5451 remove_attribute(Model self, IntsKey attribute_key, ParticleIndex particle)
5452 remove_attribute(Model self, StringKey attribute_key, ParticleIndex particle)
5453 remove_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle)
5454 remove_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle)
5455 remove_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle)
5456 remove_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle)
5457 remove_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle)
5458 remove_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle)
5459 remove_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle)
5460 remove_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle)
5462 return _IMP_kernel.Model_remove_attribute(self, *args)
5464 def get_has_attribute(self, *args):
5466 get_has_attribute(Model self, FloatKey attribute_key, ParticleIndex particle) -> bool
5467 get_has_attribute(Model self, IntKey attribute_key, ParticleIndex particle) -> bool
5468 get_has_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle) -> bool
5469 get_has_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle) -> bool
5470 get_has_attribute(Model self, IntsKey attribute_key, ParticleIndex particle) -> bool
5471 get_has_attribute(Model self, StringKey attribute_key, ParticleIndex particle) -> bool
5472 get_has_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle) -> bool
5473 get_has_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle) -> bool
5474 get_has_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle) -> bool
5475 get_has_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle) -> bool
5476 get_has_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle) -> bool
5477 get_has_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle) -> bool
5478 get_has_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle) -> bool
5479 get_has_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle) -> bool
5481 return _IMP_kernel.Model_get_has_attribute(self, *args)
5483 def set_attribute(self, *args):
5485 set_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
5486 set_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
5487 set_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
5488 set_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, IMP::algebra::Vector3D value)
5489 set_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
5490 set_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
5491 set_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
5492 set_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
5493 set_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
5494 set_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
5495 set_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle, IMP::String value)
5496 set_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle, IMP::Int value)
5497 set_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle, IMP::Float value)
5498 set_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
5500 return _IMP_kernel.Model_set_attribute(self, *args)
5502 def get_attribute(self, *args):
5504 get_attribute(Model self, FloatKey attribute_key, ParticleIndex particle) -> IMP::Float
5505 get_attribute(Model self, IntKey attribute_key, ParticleIndex particle) -> IMP::Int
5506 get_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle) -> IMP::Floats
5507 get_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle) -> IMP::algebra::Vector3D
5508 get_attribute(Model self, IntsKey attribute_key, ParticleIndex particle) -> IMP::Ints
5509 get_attribute(Model self, StringKey attribute_key, ParticleIndex particle) -> IMP::String
5510 get_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle) -> IMP::ParticleIndexes
5511 get_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle) -> ParticleIndex
5512 get_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle) -> Object
5513 get_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle) -> Object
5514 get_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle) -> IMP::String
5515 get_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle) -> IMP::Int
5516 get_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle) -> IMP::Float
5517 get_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle) -> ParticleIndex
5519 return _IMP_kernel.Model_get_attribute(self, *args)
5521 def set_is_optimized(self, arg2, arg3, arg4):
5522 r"""set_is_optimized(Model self, FloatKey arg2, ParticleIndex arg3, bool arg4)"""
5523 return _IMP_kernel.Model_set_is_optimized(self, arg2, arg3, arg4)
5525 def add_to_derivative(self, k, particle, v, da):
5526 r"""add_to_derivative(Model self, FloatKey k, ParticleIndex particle, double v, DerivativeAccumulator da)"""
5527 return _IMP_kernel.Model_add_to_derivative(self, k, particle, v, da)
5529 def get_particle(self, p):
5530 r"""get_particle(Model self, ParticleIndex p) -> Particle"""
5531 return _IMP_kernel.Model_get_particle(self, p)
5533 def get_has_particle(self, p):
5534 r"""get_has_particle(Model self, ParticleIndex p) -> bool"""
5535 return _IMP_kernel.Model_get_has_particle(self, p)
5538 r"""get_particle_indexes(Model self) -> IMP::ParticleIndexes"""
5539 return _IMP_kernel.Model_get_particle_indexes(self)
5541 def get_model_objects(self):
5542 r"""get_model_objects(Model self) -> IMP::ModelObjectsTemp"""
5543 return _IMP_kernel.Model_get_model_objects(self)
5545 def remove_particle(self, pi):
5546 r"""remove_particle(Model self, ParticleIndex pi)"""
5547 return _IMP_kernel.Model_remove_particle(self, pi)
5549 def add_data(self, mk, o):
5550 r"""add_data(Model self, ModelKey mk, Object o)"""
5551 return _IMP_kernel.Model_add_data(self, mk, o)
5553 def get_data(self, mk):
5554 r"""get_data(Model self, ModelKey mk) -> Object"""
5555 return _IMP_kernel.Model_get_data(self, mk)
5557 def remove_data(self, mk):
5558 r"""remove_data(Model self, ModelKey mk)"""
5559 return _IMP_kernel.Model_remove_data(self, mk)
5561 def get_has_data(self, mk):
5562 r"""get_has_data(Model self, ModelKey mk) -> bool"""
5563 return _IMP_kernel.Model_get_has_data(self, mk)
5566 r"""get_age(Model self) -> unsigned int"""
5567 return _IMP_kernel.Model_get_age(self)
5569 def get_trigger_last_updated(self, tk):
5570 r"""get_trigger_last_updated(Model self, TriggerKey tk) -> unsigned int"""
5571 return _IMP_kernel.Model_get_trigger_last_updated(self, tk)
5573 def set_trigger_updated(self, tk):
5574 r"""set_trigger_updated(Model self, TriggerKey tk)"""
5575 return _IMP_kernel.Model_set_trigger_updated(self, tk)
5577 def get_dependencies_updated(self):
5578 r"""get_dependencies_updated(Model self) -> unsigned int"""
5579 return _IMP_kernel.Model_get_dependencies_updated(self)
5581 def get_removed_particles_attributes_age(self):
5582 r"""get_removed_particles_attributes_age(Model self) -> unsigned int"""
5583 return _IMP_kernel.Model_get_removed_particles_attributes_age(self)
5585 def save_dependencies(self):
5586 r"""save_dependencies(Model self)"""
5587 return _IMP_kernel.Model_save_dependencies(self)
5589 def restore_dependencies(self):
5590 r"""restore_dependencies(Model self)"""
5591 return _IMP_kernel.Model_restore_dependencies(self)
5593 def get_particles_size(self):
5594 r"""get_particles_size(Model self) -> unsigned int"""
5595 return _IMP_kernel.Model_get_particles_size(self)
5597 def get_unique_id(self):
5598 r"""get_unique_id(Model self) -> uint32_t"""
5599 return _IMP_kernel.Model_get_unique_id(self)
5602 def get_by_unique_id(id):
5603 r"""get_by_unique_id(uint32_t id) -> Model"""
5604 return _IMP_kernel.Model_get_by_unique_id(id)
5607 r"""get_version_info(Model self) -> VersionInfo"""
5608 return _IMP_kernel.Model_get_version_info(self)
5609 __swig_destroy__ = _IMP_kernel.delete_Model
5611 r"""__del__(Model self)"""
5613 _director_objects.cleanup()
5620 r"""do_destroy(Model self)"""
5621 return _IMP_kernel.Model_do_destroy(self)
5624 r"""__str__(Model self) -> std::string"""
5625 return _IMP_kernel.Model___str__(self)
5628 r"""__repr__(Model self) -> std::string"""
5629 return _IMP_kernel.Model___repr__(self)
5633 return _object_cast_to_Model(o)
5636 def _get_as_binary(self):
5637 r"""_get_as_binary(Model self) -> PyObject *"""
5638 return _IMP_kernel.Model__get_as_binary(self)
5640 def _set_from_binary(self, p):
5641 r"""_set_from_binary(Model self, PyObject * p)"""
5642 return _IMP_kernel.Model__set_from_binary(self, p)
5644 def __getstate__(self):
5645 p = self._get_as_binary()
5646 if len(self.__dict__) > 1:
5647 d = self.__dict__.copy()
5652 def __setstate__(self, p):
5653 if not hasattr(self,
'this'):
5655 if isinstance(p, tuple):
5657 self.__dict__.update(d)
5658 return self._set_from_binary(p)
5662 """Get the model's attribute array for IntKey k as a NumPy array.
5663 The array is indexed by ParticleIndex; particles that don't have
5664 this attribute will either be off the end of the array or will have
5666 This is a NumPy view that shares memory with the Model. Thus,
5667 any changes to values in this list will be reflected in the Model.
5668 Also, if the Model attribute array moves in memory (e.g. if particles
5669 or attributes are added) this array will be invalidated, so it is
5670 unsafe to keep it around long term.
5671 If read_only is set True, values in the array cannot be changed.
5673 return _get_ints_numpy(self, k, self, read_only)
5676 """Get the model's attribute array for any type of Key
5677 k as a NumPy array. See Model::get_ints_numpy() for more details."""
5678 _numpy_meth_map = {IntKey: _get_ints_numpy,
5679 FloatKey: _get_floats_numpy,
5680 Vector3DKey: _get_vector3ds_numpy}
5681 return _numpy_meth_map[type(k)](self, k, self, read_only)
5684 """Get the model's attribute array for FloatKey k as a NumPy array.
5685 See Model::get_ints_numpy() for more details."""
5686 return _get_floats_numpy(self, k, self, read_only)
5689 """Get the model's attribute derivatives array for FloatKey k
5690 as a NumPy array. See Model::get_ints_numpy() for more details."""
5691 return _get_derivatives_numpy(self, k, self, read_only)
5694 """Get the model's attribute array for Vector3DKey k as a NumPy array.
5695 See Model::get_ints_numpy() for more details."""
5696 return _get_vector3ds_numpy(self, k, self, read_only)
5699 """Get the model's XYZR attribute arrays as NumPy arrays.
5700 The attribute arrays for Cartesian coordinates and radii are
5701 stored separately from those for other FloatKeys. This function
5702 returns a tuple of two NumPy arrays, the first of coordinates and
5703 the second of radii. See Model::get_ints_numpy() for more details."""
5704 return _get_spheres_numpy(self, self, read_only)
5707 """Get the model's XYZR attribute derivatives arrays as NumPy arrays.
5708 See Model::get_ints_numpy() for more details."""
5709 return _get_sphere_derivatives_numpy(self, self, read_only)
5713 _IMP_kernel.Model_swigregister(Model)
5715 r"""Proxy of C++ IMP::Decorator class."""
5717 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5718 __repr__ = _swig_repr
5720 def __init__(self, p):
5721 r"""__init__(Decorator self, _ParticleAdaptor p) -> Decorator"""
5722 _IMP_kernel.Decorator_swiginit(self, _IMP_kernel.new_Decorator(p))
5724 def __ne__(self, o):
5725 r"""__ne__(Decorator self, Object o) -> bool"""
5726 return _IMP_kernel.Decorator___ne__(self, o)
5728 def __lt__(self, o):
5729 r"""__lt__(Decorator self, Object o) -> bool"""
5730 return _IMP_kernel.Decorator___lt__(self, o)
5732 def __gt__(self, o):
5733 r"""__gt__(Decorator self, Object o) -> bool"""
5734 return _IMP_kernel.Decorator___gt__(self, o)
5736 def __ge__(self, o):
5737 r"""__ge__(Decorator self, Object o) -> bool"""
5738 return _IMP_kernel.Decorator___ge__(self, o)
5740 def __le__(self, o):
5741 r"""__le__(Decorator self, Object o) -> bool"""
5742 return _IMP_kernel.Decorator___le__(self, o)
5745 r"""get_particle(Decorator self) -> Particle"""
5746 return _IMP_kernel.Decorator_get_particle(self)
5748 def get_particle_index(self):
5749 r"""get_particle_index(Decorator self) -> ParticleIndex"""
5750 return _IMP_kernel.Decorator_get_particle_index(self)
5752 def get_model(self):
5753 m = _IMP_kernel.Decorator_get_model(self)
5754 if m
in _models_set:
5755 m = _models_set_get(m)
5760 def get_is_valid(self):
5761 r"""get_is_valid(Decorator self) -> bool"""
5762 return _IMP_kernel.Decorator_get_is_valid(self)
5765 r"""__hash__(Decorator self) -> std::size_t"""
5766 return _IMP_kernel.Decorator___hash__(self)
5768 def __eq__(self, *args):
5770 __eq__(Decorator self, Object o) -> bool
5771 __eq__(Decorator self, Decorator o) -> bool
5772 __eq__(Decorator self, Particle o) -> bool
5774 return _IMP_kernel.Decorator___eq__(self, *args)
5777 r"""__bool__(Decorator self) -> bool"""
5778 return _IMP_kernel.Decorator___bool__(self)
5779 __swig_destroy__ = _IMP_kernel.delete_Decorator
5782 _IMP_kernel.Decorator_swigregister(Decorator)
5784 def check_particle(m, pi):
5785 r"""check_particle(Model m, ParticleIndex pi)"""
5786 return _IMP_kernel.check_particle(m, pi)
5788 r"""Proxy of C++ IMP::UnaryFunction class."""
5790 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5792 def __init__(self, *args):
5793 r"""__init__(UnaryFunction self, std::string name="UnaryFunction%1%") -> UnaryFunction"""
5794 if self.__class__ == UnaryFunction:
5798 _IMP_kernel.UnaryFunction_swiginit(self, _IMP_kernel.new_UnaryFunction(_self, *args))
5800 if self.__class__ != UnaryFunction:
5801 _director_objects.register(self)
5806 def evaluate(self, feature):
5807 r"""evaluate(UnaryFunction self, double feature) -> double"""
5808 return _IMP_kernel.UnaryFunction_evaluate(self, feature)
5810 def evaluate_with_derivative(self, feature):
5811 r"""evaluate_with_derivative(UnaryFunction self, double feature) -> IMP::DerivativePair"""
5812 return _IMP_kernel.UnaryFunction_evaluate_with_derivative(self, feature)
5813 __swig_destroy__ = _IMP_kernel.delete_UnaryFunction
5816 r"""__str__(UnaryFunction self) -> std::string"""
5817 return _IMP_kernel.UnaryFunction___str__(self)
5820 r"""__repr__(UnaryFunction self) -> std::string"""
5821 return _IMP_kernel.UnaryFunction___repr__(self)
5825 return _object_cast_to_UnaryFunction(o)
5828 def do_show(self, out):
5833 return _object_cast_to_UnaryFunction(o)
5837 """Return a JAX implementation of this UnaryFunction.
5838 Implement this method in a UnaryFunction subclass to provide
5839 an equivalent function using [JAX](https://docs.jax.dev/)
5840 that scores the provided feature value.
5842 raise NotImplementedError(f
"No JAX implementation for {self}")
5844 def __disown__(self):
5846 _IMP_kernel.disown_UnaryFunction(self)
5847 return weakref.proxy(self)
5850 r"""do_destroy(UnaryFunction self)"""
5851 return _IMP_kernel.UnaryFunction_do_destroy(self)
5854 _IMP_kernel.UnaryFunction_swigregister(UnaryFunction)
5856 r"""Proxy of C++ IMP::OptimizerState class."""
5858 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5860 def __init__(self, *args):
5862 __init__(OptimizerState self, Model m, std::string name) -> OptimizerState
5863 __init__(OptimizerState self) -> OptimizerState
5865 if self.__class__ == OptimizerState:
5869 _IMP_kernel.OptimizerState_swiginit(self, _IMP_kernel.new_OptimizerState(_self, *args))
5871 if self.__class__ != OptimizerState:
5872 _director_objects.register(self)
5878 r"""update(OptimizerState self)"""
5879 return _IMP_kernel.OptimizerState_update(self)
5881 def set_is_optimizing(self, arg0):
5882 r"""set_is_optimizing(OptimizerState self, bool arg0)"""
5883 return _IMP_kernel.OptimizerState_set_is_optimizing(self, arg0)
5885 def get_optimizer(self):
5886 r"""get_optimizer(OptimizerState self) -> Optimizer"""
5887 return _IMP_kernel.OptimizerState_get_optimizer(self)
5889 def set_period(self, p):
5890 r"""set_period(OptimizerState self, unsigned int p)"""
5891 return _IMP_kernel.OptimizerState_set_period(self, p)
5893 def get_period(self):
5894 r"""get_period(OptimizerState self) -> unsigned int"""
5895 return _IMP_kernel.OptimizerState_get_period(self)
5898 r"""reset(OptimizerState self)"""
5899 return _IMP_kernel.OptimizerState_reset(self)
5901 def update_always(self):
5902 r"""update_always(OptimizerState self)"""
5903 return _IMP_kernel.OptimizerState_update_always(self)
5905 def get_number_of_updates(self):
5906 r"""get_number_of_updates(OptimizerState self) -> unsigned int"""
5907 return _IMP_kernel.OptimizerState_get_number_of_updates(self)
5909 def set_number_of_updates(self, n):
5910 r"""set_number_of_updates(OptimizerState self, unsigned int n)"""
5911 return _IMP_kernel.OptimizerState_set_number_of_updates(self, n)
5912 __swig_destroy__ = _IMP_kernel.delete_OptimizerState
5914 def do_update(self, arg0):
5915 r"""do_update(OptimizerState self, unsigned int arg0)"""
5916 return _IMP_kernel.OptimizerState_do_update(self, arg0)
5918 def do_set_is_optimizing(self, arg0):
5919 r"""do_set_is_optimizing(OptimizerState self, bool arg0)"""
5920 return _IMP_kernel.OptimizerState_do_set_is_optimizing(self, arg0)
5922 def do_get_inputs(self):
5923 r"""do_get_inputs(OptimizerState self) -> IMP::ModelObjectsTemp"""
5924 return _IMP_kernel.OptimizerState_do_get_inputs(self)
5926 def do_get_outputs(self):
5927 r"""do_get_outputs(OptimizerState self) -> IMP::ModelObjectsTemp"""
5928 return _IMP_kernel.OptimizerState_do_get_outputs(self)
5931 r"""__str__(OptimizerState self) -> std::string"""
5932 return _IMP_kernel.OptimizerState___str__(self)
5935 r"""__repr__(OptimizerState self) -> std::string"""
5936 return _IMP_kernel.OptimizerState___repr__(self)
5940 return _object_cast_to_OptimizerState(o)
5943 def do_show(self, out):
5948 return _object_cast_to_OptimizerState(o)
5950 def __disown__(self):
5952 _IMP_kernel.disown_OptimizerState(self)
5953 return weakref.proxy(self)
5956 r"""do_destroy(OptimizerState self)"""
5957 return _IMP_kernel.OptimizerState_do_destroy(self)
5959 def handle_set_has_required_score_states(self, arg0):
5960 r"""handle_set_has_required_score_states(OptimizerState self, bool arg0)"""
5961 return _IMP_kernel.OptimizerState_handle_set_has_required_score_states(self, arg0)
5963 def do_get_interactions(self):
5964 r"""do_get_interactions(OptimizerState self) -> IMP::ModelObjectsTemps"""
5965 return _IMP_kernel.OptimizerState_do_get_interactions(self)
5968 _IMP_kernel.OptimizerState_swigregister(OptimizerState)
5970 r"""Proxy of C++ IMP::Refiner class."""
5972 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5974 def __init__(self, *args):
5975 r"""__init__(Refiner self, std::string name="Refiner %1%", bool is_by_ref=False) -> Refiner"""
5976 if self.__class__ == Refiner:
5980 _IMP_kernel.Refiner_swiginit(self, _IMP_kernel.new_Refiner(_self, *args))
5982 if self.__class__ != Refiner:
5983 _director_objects.register(self)
5988 def get_can_refine(self, arg0):
5989 r"""get_can_refine(Refiner self, Particle arg0) -> bool"""
5990 return _IMP_kernel.Refiner_get_can_refine(self, arg0)
5992 def get_refined_indexes(self, m, pi):
5993 r"""get_refined_indexes(Refiner self, Model m, ParticleIndex pi) -> IMP::ParticleIndexes"""
5994 return _IMP_kernel.Refiner_get_refined_indexes(self, m, pi)
5996 def get_refined_indexes_by_ref(self, m, pi):
5997 r"""get_refined_indexes_by_ref(Refiner self, Model m, ParticleIndex pi) -> IMP::ParticleIndexes const &"""
5998 return _IMP_kernel.Refiner_get_refined_indexes_by_ref(self, m, pi)
6000 def get_is_by_ref_supported(self):
6001 r"""get_is_by_ref_supported(Refiner self) -> bool"""
6002 return _IMP_kernel.Refiner_get_is_by_ref_supported(self)
6004 def get_refined(self, *args):
6006 get_refined(Refiner self, Particle a) -> IMP::ParticlesTemp const
6007 get_refined(Refiner self, Particle a, unsigned int i) -> Particle
6009 return _IMP_kernel.Refiner_get_refined(self, *args)
6011 def get_number_of_refined(self, a):
6012 r"""get_number_of_refined(Refiner self, Particle a) -> unsigned int"""
6013 return _IMP_kernel.Refiner_get_number_of_refined(self, a)
6016 r"""__str__(Refiner self) -> std::string"""
6017 return _IMP_kernel.Refiner___str__(self)
6020 r"""__repr__(Refiner self) -> std::string"""
6021 return _IMP_kernel.Refiner___repr__(self)
6025 return _object_cast_to_Refiner(o)
6028 def do_show(self, out):
6033 return _object_cast_to_Refiner(o)
6035 __swig_destroy__ = _IMP_kernel.delete_Refiner
6036 def __disown__(self):
6038 _IMP_kernel.disown_Refiner(self)
6039 return weakref.proxy(self)
6041 def do_get_inputs(self, m, pis):
6042 r"""do_get_inputs(Refiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6043 return _IMP_kernel.Refiner_do_get_inputs(self, m, pis)
6046 r"""do_destroy(Refiner self)"""
6047 return _IMP_kernel.Refiner_do_destroy(self)
6050 _IMP_kernel.Refiner_swigregister(Refiner)
6052 r"""Proxy of C++ IMP::Optimizer class."""
6054 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6056 def set_is_optimizing_states(self, tf):
6057 r"""set_is_optimizing_states(Optimizer self, bool tf)"""
6058 return _IMP_kernel.Optimizer_set_is_optimizing_states(self, tf)
6060 def get_optimizer_state_inputs(self):
6061 r"""get_optimizer_state_inputs(Optimizer self) -> IMP::ModelObjectsTemp"""
6062 return _IMP_kernel.Optimizer_get_optimizer_state_inputs(self)
6064 def do_get_inputs(self):
6065 r"""do_get_inputs(Optimizer self) -> IMP::ModelObjectsTemp"""
6066 return _IMP_kernel.Optimizer_do_get_inputs(self)
6068 def do_get_outputs(self):
6069 r"""do_get_outputs(Optimizer self) -> IMP::ModelObjectsTemp"""
6070 return _IMP_kernel.Optimizer_do_get_outputs(self)
6072 def __init__(self, *args):
6074 __init__(Optimizer self, Model m, std::string name="Optimizer %1%") -> Optimizer
6075 __init__(Optimizer self) -> Optimizer
6077 if self.__class__ == Optimizer:
6081 _IMP_kernel.Optimizer_swiginit(self, _IMP_kernel.new_Optimizer(_self, *args))
6083 if self.__class__ != Optimizer:
6084 _director_objects.register(self)
6089 def optimize(self, max_steps):
6090 r"""optimize(Optimizer self, unsigned int max_steps) -> double"""
6091 return _IMP_kernel.Optimizer_optimize(self, max_steps)
6093 def set_stop_on_good_score(self, tf):
6094 r"""set_stop_on_good_score(Optimizer self, bool tf)"""
6095 return _IMP_kernel.Optimizer_set_stop_on_good_score(self, tf)
6097 def get_stop_on_good_score(self):
6098 r"""get_stop_on_good_score(Optimizer self) -> bool"""
6099 return _IMP_kernel.Optimizer_get_stop_on_good_score(self)
6101 def get_last_score(self):
6102 r"""get_last_score(Optimizer self) -> double"""
6103 return _IMP_kernel.Optimizer_get_last_score(self)
6105 def get_scoring_function(self):
6106 r"""get_scoring_function(Optimizer self) -> ScoringFunction"""
6107 return _IMP_kernel.Optimizer_get_scoring_function(self)
6108 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)
6109 def __set_optimizer_states(self, obj): _list_util.set_varlist(self.optimizer_states, obj)
6110 def __del_optimizer_states(self): _list_util.del_varlist(self.optimizer_states)
6111 optimizer_states = property(__get_optimizer_states, __set_optimizer_states, __del_optimizer_states, doc=
"List of ##ucnames")
6113 def remove_optimizer_state(self, d):
6114 r"""remove_optimizer_state(Optimizer self, OptimizerState d)"""
6115 return _IMP_kernel.Optimizer_remove_optimizer_state(self, d)
6117 def _python_index_optimizer_state(self, d, start, stop):
6118 r"""_python_index_optimizer_state(Optimizer self, OptimizerState d, unsigned int start, unsigned int stop) -> unsigned int"""
6119 return _IMP_kernel.Optimizer__python_index_optimizer_state(self, d, start, stop)
6121 def remove_optimizer_states(self, d):
6122 r"""remove_optimizer_states(Optimizer self, IMP::OptimizerStates const & d)"""
6123 return _IMP_kernel.Optimizer_remove_optimizer_states(self, d)
6125 def set_optimizer_states(self, ps):
6126 r"""set_optimizer_states(Optimizer self, IMP::OptimizerStates const & ps)"""
6127 return _IMP_kernel.Optimizer_set_optimizer_states(self, ps)
6129 def set_optimizer_states_order(self, objs):
6130 r"""set_optimizer_states_order(Optimizer self, IMP::OptimizerStates const & objs)"""
6131 return _IMP_kernel.Optimizer_set_optimizer_states_order(self, objs)
6133 def add_optimizer_state(self, obj):
6134 r"""add_optimizer_state(Optimizer self, OptimizerState obj) -> unsigned int"""
6135 return _IMP_kernel.Optimizer_add_optimizer_state(self, obj)
6137 def add_optimizer_states(self, objs):
6138 r"""add_optimizer_states(Optimizer self, IMP::OptimizerStates const & objs)"""
6139 return _IMP_kernel.Optimizer_add_optimizer_states(self, objs)
6141 def clear_optimizer_states(self):
6142 r"""clear_optimizer_states(Optimizer self)"""
6143 return _IMP_kernel.Optimizer_clear_optimizer_states(self)
6145 def get_number_of_optimizer_states(self):
6146 r"""get_number_of_optimizer_states(Optimizer self) -> unsigned int"""
6147 return _IMP_kernel.Optimizer_get_number_of_optimizer_states(self)
6149 def get_has_optimizer_states(self):
6150 r"""get_has_optimizer_states(Optimizer self) -> bool"""
6151 return _IMP_kernel.Optimizer_get_has_optimizer_states(self)
6153 def get_optimizer_state(self, i):
6154 r"""get_optimizer_state(Optimizer self, unsigned int i) -> OptimizerState"""
6155 return _IMP_kernel.Optimizer_get_optimizer_state(self, i)
6157 def get_optimizer_states(self):
6158 r"""get_optimizer_states(Optimizer self) -> IMP::OptimizerStates"""
6159 return _IMP_kernel.Optimizer_get_optimizer_states(self)
6161 def erase_optimizer_state(self, i):
6162 r"""erase_optimizer_state(Optimizer self, unsigned int i)"""
6163 return _IMP_kernel.Optimizer_erase_optimizer_state(self, i)
6165 def reserve_optimizer_states(self, sz):
6166 r"""reserve_optimizer_states(Optimizer self, unsigned int sz)"""
6167 return _IMP_kernel.Optimizer_reserve_optimizer_states(self, sz)
6169 def set_scoring_function(self, sf):
6170 r"""set_scoring_function(Optimizer self, _ScoringFunctionAdaptor sf)"""
6171 return _IMP_kernel.Optimizer_set_scoring_function(self, sf)
6172 __swig_destroy__ = _IMP_kernel.delete_Optimizer
6174 r"""__del__(Optimizer self)"""
6176 _director_objects.cleanup()
6182 def do_optimize(self, ns):
6183 r"""do_optimize(Optimizer self, unsigned int ns) -> double"""
6184 return _IMP_kernel.Optimizer_do_optimize(self, ns)
6186 def update_states(self):
6187 r"""update_states(Optimizer self)"""
6188 return _IMP_kernel.Optimizer_update_states(self)
6191 r"""__str__(Optimizer self) -> std::string"""
6192 return _IMP_kernel.Optimizer___str__(self)
6195 r"""__repr__(Optimizer self) -> std::string"""
6196 return _IMP_kernel.Optimizer___repr__(self)
6200 return _object_cast_to_Optimizer(o)
6203 def do_show(self, out):
6208 return _object_cast_to_Optimizer(o)
6210 def __disown__(self):
6212 _IMP_kernel.disown_Optimizer(self)
6213 return weakref.proxy(self)
6216 r"""do_destroy(Optimizer self)"""
6217 return _IMP_kernel.Optimizer_do_destroy(self)
6219 def handle_set_has_required_score_states(self, arg0):
6220 r"""handle_set_has_required_score_states(Optimizer self, bool arg0)"""
6221 return _IMP_kernel.Optimizer_handle_set_has_required_score_states(self, arg0)
6223 def do_get_interactions(self):
6224 r"""do_get_interactions(Optimizer self) -> IMP::ModelObjectsTemps"""
6225 return _IMP_kernel.Optimizer_do_get_interactions(self)
6228 _IMP_kernel.Optimizer_swigregister(Optimizer)
6230 r"""Proxy of C++ IMP::AttributeOptimizer class."""
6232 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6234 def __init__(self, *args):
6236 __init__(AttributeOptimizer self, Model m, std::string name="Optimizer %1%") -> AttributeOptimizer
6237 __init__(AttributeOptimizer self) -> AttributeOptimizer
6239 if self.__class__ == AttributeOptimizer:
6243 _IMP_kernel.AttributeOptimizer_swiginit(self, _IMP_kernel.new_AttributeOptimizer(_self, *args))
6245 if self.__class__ != AttributeOptimizer:
6246 _director_objects.register(self)
6251 def get_optimized_attributes(self):
6252 r"""get_optimized_attributes(AttributeOptimizer self) -> IMP::FloatIndexes"""
6253 return _IMP_kernel.AttributeOptimizer_get_optimized_attributes(self)
6255 def set_value(self, fi, v):
6256 r"""set_value(AttributeOptimizer self, FloatIndex fi, double v)"""
6257 return _IMP_kernel.AttributeOptimizer_set_value(self, fi, v)
6259 def get_value(self, fi):
6260 r"""get_value(AttributeOptimizer self, FloatIndex fi) -> IMP::Float"""
6261 return _IMP_kernel.AttributeOptimizer_get_value(self, fi)
6263 def get_derivative(self, fi):
6264 r"""get_derivative(AttributeOptimizer self, FloatIndex fi) -> IMP::Float"""
6265 return _IMP_kernel.AttributeOptimizer_get_derivative(self, fi)
6267 def get_width(self, k):
6268 r"""get_width(AttributeOptimizer self, FloatKey k) -> double"""
6269 return _IMP_kernel.AttributeOptimizer_get_width(self, k)
6271 def set_scaled_value(self, fi, v):
6272 r"""set_scaled_value(AttributeOptimizer self, FloatIndex fi, IMP::Float v)"""
6273 return _IMP_kernel.AttributeOptimizer_set_scaled_value(self, fi, v)
6275 def get_scaled_value(self, fi):
6276 r"""get_scaled_value(AttributeOptimizer self, FloatIndex fi) -> double"""
6277 return _IMP_kernel.AttributeOptimizer_get_scaled_value(self, fi)
6279 def get_scaled_derivative(self, fi):
6280 r"""get_scaled_derivative(AttributeOptimizer self, FloatIndex fi) -> double"""
6281 return _IMP_kernel.AttributeOptimizer_get_scaled_derivative(self, fi)
6283 def clear_range_cache(self):
6284 r"""clear_range_cache(AttributeOptimizer self)"""
6285 return _IMP_kernel.AttributeOptimizer_clear_range_cache(self)
6288 r"""__str__(AttributeOptimizer self) -> std::string"""
6289 return _IMP_kernel.AttributeOptimizer___str__(self)
6292 r"""__repr__(AttributeOptimizer self) -> std::string"""
6293 return _IMP_kernel.AttributeOptimizer___repr__(self)
6297 return _object_cast_to_AttributeOptimizer(o)
6300 def do_show(self, out):
6305 return _object_cast_to_AttributeOptimizer(o)
6307 __swig_destroy__ = _IMP_kernel.delete_AttributeOptimizer
6308 def __disown__(self):
6310 _IMP_kernel.disown_AttributeOptimizer(self)
6311 return weakref.proxy(self)
6314 r"""do_destroy(AttributeOptimizer self)"""
6315 return _IMP_kernel.AttributeOptimizer_do_destroy(self)
6317 def handle_set_has_required_score_states(self, arg0):
6318 r"""handle_set_has_required_score_states(AttributeOptimizer self, bool arg0)"""
6319 return _IMP_kernel.AttributeOptimizer_handle_set_has_required_score_states(self, arg0)
6321 def do_get_inputs(self):
6322 r"""do_get_inputs(AttributeOptimizer self) -> IMP::ModelObjectsTemp"""
6323 return _IMP_kernel.AttributeOptimizer_do_get_inputs(self)
6325 def do_get_outputs(self):
6326 r"""do_get_outputs(AttributeOptimizer self) -> IMP::ModelObjectsTemp"""
6327 return _IMP_kernel.AttributeOptimizer_do_get_outputs(self)
6329 def do_get_interactions(self):
6330 r"""do_get_interactions(AttributeOptimizer self) -> IMP::ModelObjectsTemps"""
6331 return _IMP_kernel.AttributeOptimizer_do_get_interactions(self)
6333 def do_optimize(self, ns):
6334 r"""do_optimize(AttributeOptimizer self, unsigned int ns) -> double"""
6335 return _IMP_kernel.AttributeOptimizer_do_optimize(self, ns)
6338 _IMP_kernel.AttributeOptimizer_swigregister(AttributeOptimizer)
6340 r"""Proxy of C++ IMP::ConfigurationSet class."""
6342 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6344 def __init__(self, *args):
6345 r"""__init__(ConfigurationSet self, Model m, std::string name="ConfigurationSet %1%") -> ConfigurationSet"""
6346 _IMP_kernel.ConfigurationSet_swiginit(self, _IMP_kernel.new_ConfigurationSet(*args))
6348 def save_configuration(self):
6349 r"""save_configuration(ConfigurationSet self)"""
6350 return _IMP_kernel.ConfigurationSet_save_configuration(self)
6352 def get_number_of_configurations(self):
6353 r"""get_number_of_configurations(ConfigurationSet self) -> unsigned int"""
6354 return _IMP_kernel.ConfigurationSet_get_number_of_configurations(self)
6356 def load_configuration(self, i):
6357 r"""load_configuration(ConfigurationSet self, int i)"""
6358 return _IMP_kernel.ConfigurationSet_load_configuration(self, i)
6360 def remove_configuration(self, i):
6361 r"""remove_configuration(ConfigurationSet self, unsigned int i)"""
6362 return _IMP_kernel.ConfigurationSet_remove_configuration(self, i)
6364 def get_model(self):
6365 r"""get_model(ConfigurationSet self) -> Model"""
6366 return _IMP_kernel.ConfigurationSet_get_model(self)
6369 r"""get_version_info(ConfigurationSet self) -> VersionInfo"""
6370 return _IMP_kernel.ConfigurationSet_get_version_info(self)
6371 __swig_destroy__ = _IMP_kernel.delete_ConfigurationSet
6374 r"""__str__(ConfigurationSet self) -> std::string"""
6375 return _IMP_kernel.ConfigurationSet___str__(self)
6378 r"""__repr__(ConfigurationSet self) -> std::string"""
6379 return _IMP_kernel.ConfigurationSet___repr__(self)
6383 return _object_cast_to_ConfigurationSet(o)
6387 _IMP_kernel.ConfigurationSet_swigregister(ConfigurationSet)
6389 r"""Proxy of C++ IMP::SaveToConfigurationSetOptimizerState class."""
6391 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6393 def __init__(self, cs):
6394 r"""__init__(SaveToConfigurationSetOptimizerState self, ConfigurationSet cs) -> SaveToConfigurationSetOptimizerState"""
6395 _IMP_kernel.SaveToConfigurationSetOptimizerState_swiginit(self, _IMP_kernel.new_SaveToConfigurationSetOptimizerState(cs))
6398 r"""get_version_info(SaveToConfigurationSetOptimizerState self) -> VersionInfo"""
6399 return _IMP_kernel.SaveToConfigurationSetOptimizerState_get_version_info(self)
6400 __swig_destroy__ = _IMP_kernel.delete_SaveToConfigurationSetOptimizerState
6403 r"""__str__(SaveToConfigurationSetOptimizerState self) -> std::string"""
6404 return _IMP_kernel.SaveToConfigurationSetOptimizerState___str__(self)
6407 r"""__repr__(SaveToConfigurationSetOptimizerState self) -> std::string"""
6408 return _IMP_kernel.SaveToConfigurationSetOptimizerState___repr__(self)
6412 return _object_cast_to_SaveToConfigurationSetOptimizerState(o)
6416 _IMP_kernel.SaveToConfigurationSetOptimizerState_swigregister(SaveToConfigurationSetOptimizerState)
6418 r"""Proxy of C++ IMP::Configuration class."""
6420 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6422 def __init__(self, *args):
6424 __init__(Configuration self, Model m, std::string name="Configuration %1%") -> Configuration
6425 __init__(Configuration self, Model m, Configuration base, std::string name="Configuration %1%") -> Configuration
6427 _IMP_kernel.Configuration_swiginit(self, _IMP_kernel.new_Configuration(*args))
6429 def load_configuration(self):
6430 r"""load_configuration(Configuration self)"""
6431 return _IMP_kernel.Configuration_load_configuration(self)
6433 def swap_configuration(self):
6434 r"""swap_configuration(Configuration self)"""
6435 return _IMP_kernel.Configuration_swap_configuration(self)
6438 r"""get_version_info(Configuration self) -> VersionInfo"""
6439 return _IMP_kernel.Configuration_get_version_info(self)
6440 __swig_destroy__ = _IMP_kernel.delete_Configuration
6443 r"""__str__(Configuration self) -> std::string"""
6444 return _IMP_kernel.Configuration___str__(self)
6447 r"""__repr__(Configuration self) -> std::string"""
6448 return _IMP_kernel.Configuration___repr__(self)
6452 return _object_cast_to_Configuration(o)
6456 _IMP_kernel.Configuration_swigregister(Configuration)
6458 r"""Proxy of C++ IMP::Sampler class."""
6460 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6462 def __init__(self, *args):
6463 r"""__init__(Sampler self, Model m, std::string name="Sampler %1%") -> Sampler"""
6464 if self.__class__ == Sampler:
6468 _IMP_kernel.Sampler_swiginit(self, _IMP_kernel.new_Sampler(_self, *args))
6470 if self.__class__ != Sampler:
6471 _director_objects.register(self)
6476 def create_sample(self):
6477 r"""create_sample(Sampler self) -> ConfigurationSet"""
6478 return _IMP_kernel.Sampler_create_sample(self)
6480 def get_scoring_function(self):
6481 r"""get_scoring_function(Sampler self) -> ScoringFunction"""
6482 return _IMP_kernel.Sampler_get_scoring_function(self)
6484 def set_scoring_function(self, sf):
6485 r"""set_scoring_function(Sampler self, _ScoringFunctionAdaptor sf)"""
6486 return _IMP_kernel.Sampler_set_scoring_function(self, sf)
6488 def get_model(self):
6489 r"""get_model(Sampler self) -> Model"""
6490 return _IMP_kernel.Sampler_get_model(self)
6492 def do_sample(self):
6493 r"""do_sample(Sampler self) -> ConfigurationSet"""
6494 return _IMP_kernel.Sampler_do_sample(self)
6495 __swig_destroy__ = _IMP_kernel.delete_Sampler
6498 r"""__str__(Sampler self) -> std::string"""
6499 return _IMP_kernel.Sampler___str__(self)
6502 r"""__repr__(Sampler self) -> std::string"""
6503 return _IMP_kernel.Sampler___repr__(self)
6507 return _object_cast_to_Sampler(o)
6510 def do_show(self, out):
6515 return _object_cast_to_Sampler(o)
6517 def __disown__(self):
6519 _IMP_kernel.disown_Sampler(self)
6520 return weakref.proxy(self)
6523 r"""do_destroy(Sampler self)"""
6524 return _IMP_kernel.Sampler_do_destroy(self)
6527 _IMP_kernel.Sampler_swigregister(Sampler)
6529 r"""Proxy of C++ IMP::PairModifier class."""
6531 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6533 def __init__(self, *args):
6534 r"""__init__(PairModifier self, std::string name="PairModifier %1%") -> PairModifier"""
6535 if self.__class__ == PairModifier:
6539 _IMP_kernel.PairModifier_swiginit(self, _IMP_kernel.new_PairModifier(_self, *args))
6541 if self.__class__ != PairModifier:
6542 _director_objects.register(self)
6547 def apply_index(self, m, v):
6548 r"""apply_index(PairModifier self, Model m, IMP::ParticleIndexPair const & v)"""
6549 return _IMP_kernel.PairModifier_apply_index(self, m, v)
6551 def apply_indexes(self, m, o, lower_bound, upper_bound):
6552 r"""apply_indexes(PairModifier self, Model m, IMP::ParticleIndexPairs const & o, unsigned int lower_bound, unsigned int upper_bound)"""
6553 return _IMP_kernel.PairModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
6555 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
6556 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)"""
6557 return _IMP_kernel.PairModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
6560 r"""__str__(PairModifier self) -> std::string"""
6561 return _IMP_kernel.PairModifier___str__(self)
6564 r"""__repr__(PairModifier self) -> std::string"""
6565 return _IMP_kernel.PairModifier___repr__(self)
6569 return _object_cast_to_PairModifier(o)
6572 def do_show(self, out):
6577 return _object_cast_to_PairModifier(o)
6579 __swig_destroy__ = _IMP_kernel.delete_PairModifier
6580 def __disown__(self):
6582 _IMP_kernel.disown_PairModifier(self)
6583 return weakref.proxy(self)
6585 def do_get_inputs(self, m, pis):
6586 r"""do_get_inputs(PairModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6587 return _IMP_kernel.PairModifier_do_get_inputs(self, m, pis)
6589 def do_get_outputs(self, m, pis):
6590 r"""do_get_outputs(PairModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6591 return _IMP_kernel.PairModifier_do_get_outputs(self, m, pis)
6594 r"""do_destroy(PairModifier self)"""
6595 return _IMP_kernel.PairModifier_do_destroy(self)
6598 _IMP_kernel.PairModifier_swigregister(PairModifier)
6600 r"""Proxy of C++ IMP::PairScore class."""
6602 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6604 def __init__(self, *args):
6605 r"""__init__(PairScore self, std::string name="PairScore %1%") -> PairScore"""
6606 if self.__class__ == PairScore:
6610 _IMP_kernel.PairScore_swiginit(self, _IMP_kernel.new_PairScore(_self, *args))
6612 if self.__class__ != PairScore:
6613 _director_objects.register(self)
6618 def evaluate_index(self, m, vt, da):
6619 r"""evaluate_index(PairScore self, Model m, IMP::ParticleIndexPair const & vt, DerivativeAccumulator da) -> double"""
6620 return _IMP_kernel.PairScore_evaluate_index(self, m, vt, da)
6622 def check_indexes(self, m, pis):
6623 r"""check_indexes(PairScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
6624 return _IMP_kernel.PairScore_check_indexes(self, m, pis)
6626 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
6627 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"""
6628 return _IMP_kernel.PairScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
6630 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
6631 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"""
6632 return _IMP_kernel.PairScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
6634 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
6635 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"""
6636 return _IMP_kernel.PairScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
6638 def evaluate_if_good_index(self, m, vt, da, max):
6639 r"""evaluate_if_good_index(PairScore self, Model m, IMP::ParticleIndexPair const & vt, DerivativeAccumulator da, double max) -> double"""
6640 return _IMP_kernel.PairScore_evaluate_if_good_index(self, m, vt, da, max)
6642 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
6643 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"""
6644 return _IMP_kernel.PairScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
6646 def create_current_decomposition(self, m, vt):
6647 r"""create_current_decomposition(PairScore self, Model m, IMP::ParticleIndexPair const & vt) -> IMP::Restraints"""
6648 return _IMP_kernel.PairScore_create_current_decomposition(self, m, vt)
6650 def do_create_current_decomposition(self, m, vt):
6651 r"""do_create_current_decomposition(PairScore self, Model m, IMP::ParticleIndexPair const & vt) -> IMP::Restraints"""
6652 return _IMP_kernel.PairScore_do_create_current_decomposition(self, m, vt)
6653 __swig_destroy__ = _IMP_kernel.delete_PairScore
6656 r"""__str__(PairScore self) -> std::string"""
6657 return _IMP_kernel.PairScore___str__(self)
6660 r"""__repr__(PairScore self) -> std::string"""
6661 return _IMP_kernel.PairScore___repr__(self)
6665 return _object_cast_to_PairScore(o)
6668 def do_show(self, out):
6673 return _object_cast_to_PairScore(o)
6676 def _wrap_jax(self, score_func, keys=None):
6677 """Create the return value for _get_jax.
6678 Use this method in _get_jax() to wrap the JAX scoring function
6679 with other score-specific information.
6681 @param score_func A function implemented using JAX that takes
6682 two arguments (the current model state, and the
6683 ParticlePairIndexes to act on) and returns the total
6684 score (for all indexes).
6685 @param keys Model attributes used by the PairScore.
6686 See IMP::Restraint::_wrap_jax.
6688 from IMP._jax_util
import JaxScoreInfo
6689 return JaxScoreInfo(score_func=score_func, keys=keys)
6692 """Return a JAX implementation of this PairScore.
6693 Implement this method in a PairScore subclass to provide
6694 an equivalent function using [JAX](https://docs.jax.dev/)
6695 that scores the current model state with a given set of
6696 ParticlePairIndexes. See also _wrap_jax.
6698 raise NotImplementedError(f
"No JAX implementation for {self}")
6700 def __disown__(self):
6702 _IMP_kernel.disown_PairScore(self)
6703 return weakref.proxy(self)
6705 def do_get_inputs(self, m, pis):
6706 r"""do_get_inputs(PairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6707 return _IMP_kernel.PairScore_do_get_inputs(self, m, pis)
6710 r"""do_destroy(PairScore self)"""
6711 return _IMP_kernel.PairScore_do_destroy(self)
6714 _IMP_kernel.PairScore_swigregister(PairScore)
6716 r"""Proxy of C++ IMP::PairPredicate class."""
6718 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6720 def __init__(self, *args):
6721 r"""__init__(PairPredicate self, std::string name="PairPredicate %1%") -> PairPredicate"""
6722 if self.__class__ == PairPredicate:
6726 _IMP_kernel.PairPredicate_swiginit(self, _IMP_kernel.new_PairPredicate(_self, *args))
6728 if self.__class__ != PairPredicate:
6729 _director_objects.register(self)
6734 def setup_for_get_value_index_in_batch(self, arg0):
6735 r"""setup_for_get_value_index_in_batch(PairPredicate self, Model arg0)"""
6736 return _IMP_kernel.PairPredicate_setup_for_get_value_index_in_batch(self, arg0)
6738 def get_value_index_in_batch(self, m, vt):
6739 r"""get_value_index_in_batch(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int"""
6740 return _IMP_kernel.PairPredicate_get_value_index_in_batch(self, m, vt)
6742 def __call__(self, m, vt):
6743 r"""__call__(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int"""
6744 return _IMP_kernel.PairPredicate___call__(self, m, vt)
6746 def get_value_index(self, *args):
6748 get_value_index(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int
6749 get_value_index(PairPredicate self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6751 return _IMP_kernel.PairPredicate_get_value_index(self, *args)
6752 __swig_destroy__ = _IMP_kernel.delete_PairPredicate
6755 r"""__str__(PairPredicate self) -> std::string"""
6756 return _IMP_kernel.PairPredicate___str__(self)
6759 r"""__repr__(PairPredicate self) -> std::string"""
6760 return _IMP_kernel.PairPredicate___repr__(self)
6764 return _object_cast_to_PairPredicate(o)
6767 def do_show(self, out):
6772 return _object_cast_to_PairPredicate(o)
6774 def __disown__(self):
6776 _IMP_kernel.disown_PairPredicate(self)
6777 return weakref.proxy(self)
6779 def do_get_inputs(self, m, pis):
6780 r"""do_get_inputs(PairPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6781 return _IMP_kernel.PairPredicate_do_get_inputs(self, m, pis)
6784 r"""do_destroy(PairPredicate self)"""
6785 return _IMP_kernel.PairPredicate_do_destroy(self)
6788 _IMP_kernel.PairPredicate_swigregister(PairPredicate)
6790 r"""Proxy of C++ IMP::PairContainer class."""
6792 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6794 def apply_generic(self, m):
6795 r"""apply_generic(PairContainer self, PairModifier m)"""
6796 return _IMP_kernel.PairContainer_apply_generic(self, m)
6798 def apply_generic_moved(self, m, moved_pis, reset_pis):
6799 r"""apply_generic_moved(PairContainer self, PairModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
6800 return _IMP_kernel.PairContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
6802 def apply(self, sm):
6803 r"""apply(PairContainer self, PairModifier sm)"""
6804 return _IMP_kernel.PairContainer_apply(self, sm)
6806 def apply_moved(self, sm, moved_pis, reset_pis):
6807 r"""apply_moved(PairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
6808 return _IMP_kernel.PairContainer_apply_moved(self, sm, moved_pis, reset_pis)
6810 def get_range_indexes(self):
6811 r"""get_range_indexes(PairContainer self) -> IMP::ParticleIndexPairs"""
6812 return _IMP_kernel.PairContainer_get_range_indexes(self)
6814 def get_contents(self):
6815 r"""get_contents(PairContainer self) -> IMP::ParticleIndexPairs const &"""
6816 return _IMP_kernel.PairContainer_get_contents(self)
6819 r"""get_indexes(PairContainer self) -> IMP::ParticleIndexPairs"""
6820 return _IMP_kernel.PairContainer_get_indexes(self)
6822 def get(self, *args):
6824 get(PairContainer self) -> IMP::ParticlePairsTemp
6825 get(PairContainer self, unsigned int i) -> IMP::ParticlePair
6827 return _IMP_kernel.PairContainer_get(self, *args)
6829 def get_number(self):
6830 r"""get_number(PairContainer self) -> unsigned int"""
6831 return _IMP_kernel.PairContainer_get_number(self)
6833 def __init__(self, *args):
6835 __init__(PairContainer self, Model m, std::string name="PairContainer %1%") -> PairContainer
6836 __init__(PairContainer self) -> PairContainer
6838 if self.__class__ == PairContainer:
6842 _IMP_kernel.PairContainer_swiginit(self, _IMP_kernel.new_PairContainer(_self, *args))
6844 if self.__class__ != PairContainer:
6845 _director_objects.register(self)
6850 def do_apply(self, sm):
6851 r"""do_apply(PairContainer self, PairModifier sm)"""
6852 return _IMP_kernel.PairContainer_do_apply(self, sm)
6854 def do_apply_moved(self, sm, moved_pis, reset_pis):
6855 r"""do_apply_moved(PairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
6856 return _IMP_kernel.PairContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
6858 def do_get_provides_access(self):
6859 r"""do_get_provides_access(PairContainer self) -> bool"""
6860 return _IMP_kernel.PairContainer_do_get_provides_access(self)
6861 __swig_destroy__ = _IMP_kernel.delete_PairContainer
6864 r"""__str__(PairContainer self) -> std::string"""
6865 return _IMP_kernel.PairContainer___str__(self)
6868 r"""__repr__(PairContainer self) -> std::string"""
6869 return _IMP_kernel.PairContainer___repr__(self)
6873 return _object_cast_to_PairContainer(o)
6876 def do_show(self, out):
6881 return _object_cast_to_PairContainer(o)
6883 def __disown__(self):
6885 _IMP_kernel.disown_PairContainer(self)
6886 return weakref.proxy(self)
6889 r"""do_destroy(PairContainer self)"""
6890 return _IMP_kernel.PairContainer_do_destroy(self)
6892 def handle_set_has_required_score_states(self, arg0):
6893 r"""handle_set_has_required_score_states(PairContainer self, bool arg0)"""
6894 return _IMP_kernel.PairContainer_handle_set_has_required_score_states(self, arg0)
6896 def do_get_inputs(self):
6897 r"""do_get_inputs(PairContainer self) -> IMP::ModelObjectsTemp"""
6898 return _IMP_kernel.PairContainer_do_get_inputs(self)
6900 def do_get_interactions(self):
6901 r"""do_get_interactions(PairContainer self) -> IMP::ModelObjectsTemps"""
6902 return _IMP_kernel.PairContainer_do_get_interactions(self)
6904 def do_get_contents_hash(self):
6905 r"""do_get_contents_hash(PairContainer self) -> std::size_t"""
6906 return _IMP_kernel.PairContainer_do_get_contents_hash(self)
6909 _IMP_kernel.PairContainer_swigregister(PairContainer)
6910 class _PairContainerAdaptor(_InputAdaptor):
6911 r"""Proxy of C++ IMP::PairContainerAdaptor class."""
6913 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6914 __repr__ = _swig_repr
6916 def __init__(self, *args):
6918 __init__(_PairContainerAdaptor self) -> _PairContainerAdaptor
6919 __init__(_PairContainerAdaptor self, PairContainer c) -> _PairContainerAdaptor
6920 __init__(_PairContainerAdaptor self, IMP::ParticlePairsTemp const & t) -> _PairContainerAdaptor
6922 _IMP_kernel._PairContainerAdaptor_swiginit(self, _IMP_kernel.new__PairContainerAdaptor(*args))
6924 def set_name_if_default(self, name):
6925 r"""set_name_if_default(_PairContainerAdaptor self, std::string name)"""
6926 return _IMP_kernel._PairContainerAdaptor_set_name_if_default(self, name)
6927 __swig_destroy__ = _IMP_kernel.delete__PairContainerAdaptor
6930 _IMP_kernel._PairContainerAdaptor_swigregister(_PairContainerAdaptor)
6932 r"""Proxy of C++ IMP::QuadModifier class."""
6934 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6936 def __init__(self, *args):
6937 r"""__init__(QuadModifier self, std::string name="QuadModifier %1%") -> QuadModifier"""
6938 if self.__class__ == QuadModifier:
6942 _IMP_kernel.QuadModifier_swiginit(self, _IMP_kernel.new_QuadModifier(_self, *args))
6944 if self.__class__ != QuadModifier:
6945 _director_objects.register(self)
6950 def apply_index(self, m, v):
6951 r"""apply_index(QuadModifier self, Model m, IMP::ParticleIndexQuad const & v)"""
6952 return _IMP_kernel.QuadModifier_apply_index(self, m, v)
6954 def apply_indexes(self, m, o, lower_bound, upper_bound):
6955 r"""apply_indexes(QuadModifier self, Model m, IMP::ParticleIndexQuads const & o, unsigned int lower_bound, unsigned int upper_bound)"""
6956 return _IMP_kernel.QuadModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
6958 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
6959 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)"""
6960 return _IMP_kernel.QuadModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
6963 r"""__str__(QuadModifier self) -> std::string"""
6964 return _IMP_kernel.QuadModifier___str__(self)
6967 r"""__repr__(QuadModifier self) -> std::string"""
6968 return _IMP_kernel.QuadModifier___repr__(self)
6972 return _object_cast_to_QuadModifier(o)
6975 def do_show(self, out):
6980 return _object_cast_to_QuadModifier(o)
6982 __swig_destroy__ = _IMP_kernel.delete_QuadModifier
6983 def __disown__(self):
6985 _IMP_kernel.disown_QuadModifier(self)
6986 return weakref.proxy(self)
6988 def do_get_inputs(self, m, pis):
6989 r"""do_get_inputs(QuadModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6990 return _IMP_kernel.QuadModifier_do_get_inputs(self, m, pis)
6992 def do_get_outputs(self, m, pis):
6993 r"""do_get_outputs(QuadModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6994 return _IMP_kernel.QuadModifier_do_get_outputs(self, m, pis)
6997 r"""do_destroy(QuadModifier self)"""
6998 return _IMP_kernel.QuadModifier_do_destroy(self)
7001 _IMP_kernel.QuadModifier_swigregister(QuadModifier)
7003 r"""Proxy of C++ IMP::QuadScore class."""
7005 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7007 def __init__(self, *args):
7008 r"""__init__(QuadScore self, std::string name="QuadScore %1%") -> QuadScore"""
7009 if self.__class__ == QuadScore:
7013 _IMP_kernel.QuadScore_swiginit(self, _IMP_kernel.new_QuadScore(_self, *args))
7015 if self.__class__ != QuadScore:
7016 _director_objects.register(self)
7021 def evaluate_index(self, m, vt, da):
7022 r"""evaluate_index(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt, DerivativeAccumulator da) -> double"""
7023 return _IMP_kernel.QuadScore_evaluate_index(self, m, vt, da)
7025 def check_indexes(self, m, pis):
7026 r"""check_indexes(QuadScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
7027 return _IMP_kernel.QuadScore_check_indexes(self, m, pis)
7029 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
7030 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"""
7031 return _IMP_kernel.QuadScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
7033 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7034 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"""
7035 return _IMP_kernel.QuadScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
7037 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
7038 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"""
7039 return _IMP_kernel.QuadScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
7041 def evaluate_if_good_index(self, m, vt, da, max):
7042 r"""evaluate_if_good_index(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt, DerivativeAccumulator da, double max) -> double"""
7043 return _IMP_kernel.QuadScore_evaluate_if_good_index(self, m, vt, da, max)
7045 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7046 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"""
7047 return _IMP_kernel.QuadScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
7049 def create_current_decomposition(self, m, vt):
7050 r"""create_current_decomposition(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt) -> IMP::Restraints"""
7051 return _IMP_kernel.QuadScore_create_current_decomposition(self, m, vt)
7053 def do_create_current_decomposition(self, m, vt):
7054 r"""do_create_current_decomposition(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt) -> IMP::Restraints"""
7055 return _IMP_kernel.QuadScore_do_create_current_decomposition(self, m, vt)
7056 __swig_destroy__ = _IMP_kernel.delete_QuadScore
7059 r"""__str__(QuadScore self) -> std::string"""
7060 return _IMP_kernel.QuadScore___str__(self)
7063 r"""__repr__(QuadScore self) -> std::string"""
7064 return _IMP_kernel.QuadScore___repr__(self)
7068 return _object_cast_to_QuadScore(o)
7071 def do_show(self, out):
7076 return _object_cast_to_QuadScore(o)
7078 def __disown__(self):
7080 _IMP_kernel.disown_QuadScore(self)
7081 return weakref.proxy(self)
7083 def do_get_inputs(self, m, pis):
7084 r"""do_get_inputs(QuadScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7085 return _IMP_kernel.QuadScore_do_get_inputs(self, m, pis)
7088 r"""do_destroy(QuadScore self)"""
7089 return _IMP_kernel.QuadScore_do_destroy(self)
7092 _IMP_kernel.QuadScore_swigregister(QuadScore)
7094 r"""Proxy of C++ IMP::QuadPredicate class."""
7096 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7098 def __init__(self, *args):
7099 r"""__init__(QuadPredicate self, std::string name="QuadPredicate %1%") -> QuadPredicate"""
7100 if self.__class__ == QuadPredicate:
7104 _IMP_kernel.QuadPredicate_swiginit(self, _IMP_kernel.new_QuadPredicate(_self, *args))
7106 if self.__class__ != QuadPredicate:
7107 _director_objects.register(self)
7112 def setup_for_get_value_index_in_batch(self, arg0):
7113 r"""setup_for_get_value_index_in_batch(QuadPredicate self, Model arg0)"""
7114 return _IMP_kernel.QuadPredicate_setup_for_get_value_index_in_batch(self, arg0)
7116 def get_value_index_in_batch(self, m, vt):
7117 r"""get_value_index_in_batch(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int"""
7118 return _IMP_kernel.QuadPredicate_get_value_index_in_batch(self, m, vt)
7120 def __call__(self, m, vt):
7121 r"""__call__(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int"""
7122 return _IMP_kernel.QuadPredicate___call__(self, m, vt)
7124 def get_value_index(self, *args):
7126 get_value_index(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int
7127 get_value_index(QuadPredicate self, Model m, IMP::ParticleIndexQuads const & o) -> IMP::Ints
7129 return _IMP_kernel.QuadPredicate_get_value_index(self, *args)
7130 __swig_destroy__ = _IMP_kernel.delete_QuadPredicate
7133 r"""__str__(QuadPredicate self) -> std::string"""
7134 return _IMP_kernel.QuadPredicate___str__(self)
7137 r"""__repr__(QuadPredicate self) -> std::string"""
7138 return _IMP_kernel.QuadPredicate___repr__(self)
7142 return _object_cast_to_QuadPredicate(o)
7145 def do_show(self, out):
7150 return _object_cast_to_QuadPredicate(o)
7152 def __disown__(self):
7154 _IMP_kernel.disown_QuadPredicate(self)
7155 return weakref.proxy(self)
7157 def do_get_inputs(self, m, pis):
7158 r"""do_get_inputs(QuadPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7159 return _IMP_kernel.QuadPredicate_do_get_inputs(self, m, pis)
7162 r"""do_destroy(QuadPredicate self)"""
7163 return _IMP_kernel.QuadPredicate_do_destroy(self)
7166 _IMP_kernel.QuadPredicate_swigregister(QuadPredicate)
7168 r"""Proxy of C++ IMP::QuadContainer class."""
7170 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7172 def apply_generic(self, m):
7173 r"""apply_generic(QuadContainer self, QuadModifier m)"""
7174 return _IMP_kernel.QuadContainer_apply_generic(self, m)
7176 def apply_generic_moved(self, m, moved_pis, reset_pis):
7177 r"""apply_generic_moved(QuadContainer self, QuadModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7178 return _IMP_kernel.QuadContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
7180 def apply(self, sm):
7181 r"""apply(QuadContainer self, QuadModifier sm)"""
7182 return _IMP_kernel.QuadContainer_apply(self, sm)
7184 def apply_moved(self, sm, moved_pis, reset_pis):
7185 r"""apply_moved(QuadContainer self, QuadModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7186 return _IMP_kernel.QuadContainer_apply_moved(self, sm, moved_pis, reset_pis)
7188 def get_range_indexes(self):
7189 r"""get_range_indexes(QuadContainer self) -> IMP::ParticleIndexQuads"""
7190 return _IMP_kernel.QuadContainer_get_range_indexes(self)
7192 def get_contents(self):
7193 r"""get_contents(QuadContainer self) -> IMP::ParticleIndexQuads const &"""
7194 return _IMP_kernel.QuadContainer_get_contents(self)
7197 r"""get_indexes(QuadContainer self) -> IMP::ParticleIndexQuads"""
7198 return _IMP_kernel.QuadContainer_get_indexes(self)
7200 def get(self, *args):
7202 get(QuadContainer self) -> IMP::ParticleQuadsTemp
7203 get(QuadContainer self, unsigned int i) -> IMP::ParticleQuad
7205 return _IMP_kernel.QuadContainer_get(self, *args)
7207 def get_number(self):
7208 r"""get_number(QuadContainer self) -> unsigned int"""
7209 return _IMP_kernel.QuadContainer_get_number(self)
7211 def __init__(self, *args):
7213 __init__(QuadContainer self, Model m, std::string name="QuadContainer %1%") -> QuadContainer
7214 __init__(QuadContainer self) -> QuadContainer
7216 if self.__class__ == QuadContainer:
7220 _IMP_kernel.QuadContainer_swiginit(self, _IMP_kernel.new_QuadContainer(_self, *args))
7222 if self.__class__ != QuadContainer:
7223 _director_objects.register(self)
7228 def do_apply(self, sm):
7229 r"""do_apply(QuadContainer self, QuadModifier sm)"""
7230 return _IMP_kernel.QuadContainer_do_apply(self, sm)
7232 def do_apply_moved(self, sm, moved_pis, reset_pis):
7233 r"""do_apply_moved(QuadContainer self, QuadModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7234 return _IMP_kernel.QuadContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
7236 def do_get_provides_access(self):
7237 r"""do_get_provides_access(QuadContainer self) -> bool"""
7238 return _IMP_kernel.QuadContainer_do_get_provides_access(self)
7239 __swig_destroy__ = _IMP_kernel.delete_QuadContainer
7242 r"""__str__(QuadContainer self) -> std::string"""
7243 return _IMP_kernel.QuadContainer___str__(self)
7246 r"""__repr__(QuadContainer self) -> std::string"""
7247 return _IMP_kernel.QuadContainer___repr__(self)
7251 return _object_cast_to_QuadContainer(o)
7254 def do_show(self, out):
7259 return _object_cast_to_QuadContainer(o)
7261 def __disown__(self):
7263 _IMP_kernel.disown_QuadContainer(self)
7264 return weakref.proxy(self)
7267 r"""do_destroy(QuadContainer self)"""
7268 return _IMP_kernel.QuadContainer_do_destroy(self)
7270 def handle_set_has_required_score_states(self, arg0):
7271 r"""handle_set_has_required_score_states(QuadContainer self, bool arg0)"""
7272 return _IMP_kernel.QuadContainer_handle_set_has_required_score_states(self, arg0)
7274 def do_get_inputs(self):
7275 r"""do_get_inputs(QuadContainer self) -> IMP::ModelObjectsTemp"""
7276 return _IMP_kernel.QuadContainer_do_get_inputs(self)
7278 def do_get_interactions(self):
7279 r"""do_get_interactions(QuadContainer self) -> IMP::ModelObjectsTemps"""
7280 return _IMP_kernel.QuadContainer_do_get_interactions(self)
7282 def do_get_contents_hash(self):
7283 r"""do_get_contents_hash(QuadContainer self) -> std::size_t"""
7284 return _IMP_kernel.QuadContainer_do_get_contents_hash(self)
7287 _IMP_kernel.QuadContainer_swigregister(QuadContainer)
7288 class _QuadContainerAdaptor(_InputAdaptor):
7289 r"""Proxy of C++ IMP::QuadContainerAdaptor class."""
7291 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7292 __repr__ = _swig_repr
7294 def __init__(self, *args):
7296 __init__(_QuadContainerAdaptor self) -> _QuadContainerAdaptor
7297 __init__(_QuadContainerAdaptor self, QuadContainer c) -> _QuadContainerAdaptor
7298 __init__(_QuadContainerAdaptor self, IMP::ParticleQuadsTemp const & t) -> _QuadContainerAdaptor
7300 _IMP_kernel._QuadContainerAdaptor_swiginit(self, _IMP_kernel.new__QuadContainerAdaptor(*args))
7302 def set_name_if_default(self, name):
7303 r"""set_name_if_default(_QuadContainerAdaptor self, std::string name)"""
7304 return _IMP_kernel._QuadContainerAdaptor_set_name_if_default(self, name)
7305 __swig_destroy__ = _IMP_kernel.delete__QuadContainerAdaptor
7308 _IMP_kernel._QuadContainerAdaptor_swigregister(_QuadContainerAdaptor)
7310 r"""Proxy of C++ IMP::SingletonModifier class."""
7312 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7314 def __init__(self, *args):
7315 r"""__init__(SingletonModifier self, std::string name="SingletonModifier %1%") -> SingletonModifier"""
7316 if self.__class__ == SingletonModifier:
7320 _IMP_kernel.SingletonModifier_swiginit(self, _IMP_kernel.new_SingletonModifier(_self, *args))
7322 if self.__class__ != SingletonModifier:
7323 _director_objects.register(self)
7328 def apply_index(self, m, v):
7329 r"""apply_index(SingletonModifier self, Model m, ParticleIndex v)"""
7330 return _IMP_kernel.SingletonModifier_apply_index(self, m, v)
7332 def apply_indexes(self, m, o, lower_bound, upper_bound):
7333 r"""apply_indexes(SingletonModifier self, Model m, IMP::ParticleIndexes const & o, unsigned int lower_bound, unsigned int upper_bound)"""
7334 return _IMP_kernel.SingletonModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
7336 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
7337 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)"""
7338 return _IMP_kernel.SingletonModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
7341 r"""__str__(SingletonModifier self) -> std::string"""
7342 return _IMP_kernel.SingletonModifier___str__(self)
7345 r"""__repr__(SingletonModifier self) -> std::string"""
7346 return _IMP_kernel.SingletonModifier___repr__(self)
7350 return _object_cast_to_SingletonModifier(o)
7353 def do_show(self, out):
7358 return _object_cast_to_SingletonModifier(o)
7360 __swig_destroy__ = _IMP_kernel.delete_SingletonModifier
7361 def __disown__(self):
7363 _IMP_kernel.disown_SingletonModifier(self)
7364 return weakref.proxy(self)
7366 def do_get_inputs(self, m, pis):
7367 r"""do_get_inputs(SingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7368 return _IMP_kernel.SingletonModifier_do_get_inputs(self, m, pis)
7370 def do_get_outputs(self, m, pis):
7371 r"""do_get_outputs(SingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7372 return _IMP_kernel.SingletonModifier_do_get_outputs(self, m, pis)
7375 r"""do_destroy(SingletonModifier self)"""
7376 return _IMP_kernel.SingletonModifier_do_destroy(self)
7379 _IMP_kernel.SingletonModifier_swigregister(SingletonModifier)
7381 r"""Proxy of C++ IMP::SingletonScore class."""
7383 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7385 def __init__(self, *args):
7386 r"""__init__(SingletonScore self, std::string name="SingletonScore %1%") -> SingletonScore"""
7387 if self.__class__ == SingletonScore:
7391 _IMP_kernel.SingletonScore_swiginit(self, _IMP_kernel.new_SingletonScore(_self, *args))
7393 if self.__class__ != SingletonScore:
7394 _director_objects.register(self)
7399 def evaluate_index(self, m, vt, da):
7400 r"""evaluate_index(SingletonScore self, Model m, ParticleIndex vt, DerivativeAccumulator da) -> double"""
7401 return _IMP_kernel.SingletonScore_evaluate_index(self, m, vt, da)
7403 def check_indexes(self, m, pis):
7404 r"""check_indexes(SingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
7405 return _IMP_kernel.SingletonScore_check_indexes(self, m, pis)
7407 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
7408 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"""
7409 return _IMP_kernel.SingletonScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
7411 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7412 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"""
7413 return _IMP_kernel.SingletonScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
7415 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
7416 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"""
7417 return _IMP_kernel.SingletonScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
7419 def evaluate_if_good_index(self, m, vt, da, max):
7420 r"""evaluate_if_good_index(SingletonScore self, Model m, ParticleIndex vt, DerivativeAccumulator da, double max) -> double"""
7421 return _IMP_kernel.SingletonScore_evaluate_if_good_index(self, m, vt, da, max)
7423 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7424 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"""
7425 return _IMP_kernel.SingletonScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
7427 def create_current_decomposition(self, m, vt):
7428 r"""create_current_decomposition(SingletonScore self, Model m, ParticleIndex vt) -> IMP::Restraints"""
7429 return _IMP_kernel.SingletonScore_create_current_decomposition(self, m, vt)
7431 def do_create_current_decomposition(self, m, vt):
7432 r"""do_create_current_decomposition(SingletonScore self, Model m, ParticleIndex vt) -> IMP::Restraints"""
7433 return _IMP_kernel.SingletonScore_do_create_current_decomposition(self, m, vt)
7434 __swig_destroy__ = _IMP_kernel.delete_SingletonScore
7437 r"""__str__(SingletonScore self) -> std::string"""
7438 return _IMP_kernel.SingletonScore___str__(self)
7441 r"""__repr__(SingletonScore self) -> std::string"""
7442 return _IMP_kernel.SingletonScore___repr__(self)
7446 return _object_cast_to_SingletonScore(o)
7449 def do_show(self, out):
7454 return _object_cast_to_SingletonScore(o)
7457 def _wrap_jax(self, score_func, keys=None):
7458 """See IMP::PairScore::_wrap_jax"""
7459 from IMP._jax_util
import JaxScoreInfo
7460 return JaxScoreInfo(score_func=score_func, keys=keys)
7463 """See IMP::PairScore::_get_jax"""
7464 raise NotImplementedError(f
"No JAX implementation for {self}")
7466 def __disown__(self):
7468 _IMP_kernel.disown_SingletonScore(self)
7469 return weakref.proxy(self)
7471 def do_get_inputs(self, m, pis):
7472 r"""do_get_inputs(SingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7473 return _IMP_kernel.SingletonScore_do_get_inputs(self, m, pis)
7476 r"""do_destroy(SingletonScore self)"""
7477 return _IMP_kernel.SingletonScore_do_destroy(self)
7480 _IMP_kernel.SingletonScore_swigregister(SingletonScore)
7482 r"""Proxy of C++ IMP::SingletonPredicate class."""
7484 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7486 def __init__(self, *args):
7487 r"""__init__(SingletonPredicate self, std::string name="SingletonPredicate %1%") -> SingletonPredicate"""
7488 if self.__class__ == SingletonPredicate:
7492 _IMP_kernel.SingletonPredicate_swiginit(self, _IMP_kernel.new_SingletonPredicate(_self, *args))
7494 if self.__class__ != SingletonPredicate:
7495 _director_objects.register(self)
7500 def setup_for_get_value_index_in_batch(self, arg0):
7501 r"""setup_for_get_value_index_in_batch(SingletonPredicate self, Model arg0)"""
7502 return _IMP_kernel.SingletonPredicate_setup_for_get_value_index_in_batch(self, arg0)
7504 def get_value_index_in_batch(self, m, vt):
7505 r"""get_value_index_in_batch(SingletonPredicate self, Model m, ParticleIndex vt) -> int"""
7506 return _IMP_kernel.SingletonPredicate_get_value_index_in_batch(self, m, vt)
7508 def __call__(self, m, vt):
7509 r"""__call__(SingletonPredicate self, Model m, ParticleIndex vt) -> int"""
7510 return _IMP_kernel.SingletonPredicate___call__(self, m, vt)
7512 def get_value_index(self, *args):
7514 get_value_index(SingletonPredicate self, Model m, ParticleIndex vt) -> int
7515 get_value_index(SingletonPredicate self, Model m, IMP::ParticleIndexes const & o) -> IMP::Ints
7517 return _IMP_kernel.SingletonPredicate_get_value_index(self, *args)
7518 __swig_destroy__ = _IMP_kernel.delete_SingletonPredicate
7521 r"""__str__(SingletonPredicate self) -> std::string"""
7522 return _IMP_kernel.SingletonPredicate___str__(self)
7525 r"""__repr__(SingletonPredicate self) -> std::string"""
7526 return _IMP_kernel.SingletonPredicate___repr__(self)
7530 return _object_cast_to_SingletonPredicate(o)
7533 def do_show(self, out):
7538 return _object_cast_to_SingletonPredicate(o)
7540 def __disown__(self):
7542 _IMP_kernel.disown_SingletonPredicate(self)
7543 return weakref.proxy(self)
7545 def do_get_inputs(self, m, pis):
7546 r"""do_get_inputs(SingletonPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7547 return _IMP_kernel.SingletonPredicate_do_get_inputs(self, m, pis)
7550 r"""do_destroy(SingletonPredicate self)"""
7551 return _IMP_kernel.SingletonPredicate_do_destroy(self)
7554 _IMP_kernel.SingletonPredicate_swigregister(SingletonPredicate)
7556 r"""Proxy of C++ IMP::SingletonContainer class."""
7558 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7560 def apply_generic(self, m):
7561 r"""apply_generic(SingletonContainer self, SingletonModifier m)"""
7562 return _IMP_kernel.SingletonContainer_apply_generic(self, m)
7564 def apply_generic_moved(self, m, moved_pis, reset_pis):
7565 r"""apply_generic_moved(SingletonContainer self, SingletonModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7566 return _IMP_kernel.SingletonContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
7568 def apply(self, sm):
7569 r"""apply(SingletonContainer self, SingletonModifier sm)"""
7570 return _IMP_kernel.SingletonContainer_apply(self, sm)
7572 def apply_moved(self, sm, moved_pis, reset_pis):
7573 r"""apply_moved(SingletonContainer self, SingletonModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7574 return _IMP_kernel.SingletonContainer_apply_moved(self, sm, moved_pis, reset_pis)
7576 def get_range_indexes(self):
7577 r"""get_range_indexes(SingletonContainer self) -> IMP::ParticleIndexes"""
7578 return _IMP_kernel.SingletonContainer_get_range_indexes(self)
7580 def get_contents(self):
7581 r"""get_contents(SingletonContainer self) -> IMP::ParticleIndexes const &"""
7582 return _IMP_kernel.SingletonContainer_get_contents(self)
7585 r"""get_indexes(SingletonContainer self) -> IMP::ParticleIndexes"""
7586 return _IMP_kernel.SingletonContainer_get_indexes(self)
7588 def get(self, *args):
7590 get(SingletonContainer self) -> IMP::ParticlesTemp
7591 get(SingletonContainer self, unsigned int i) -> Particle
7593 return _IMP_kernel.SingletonContainer_get(self, *args)
7595 def get_number(self):
7596 r"""get_number(SingletonContainer self) -> unsigned int"""
7597 return _IMP_kernel.SingletonContainer_get_number(self)
7599 def __init__(self, *args):
7601 __init__(SingletonContainer self, Model m, std::string name="SingletonContainer %1%") -> SingletonContainer
7602 __init__(SingletonContainer self) -> SingletonContainer
7604 if self.__class__ == SingletonContainer:
7608 _IMP_kernel.SingletonContainer_swiginit(self, _IMP_kernel.new_SingletonContainer(_self, *args))
7610 if self.__class__ != SingletonContainer:
7611 _director_objects.register(self)
7616 def do_apply(self, sm):
7617 r"""do_apply(SingletonContainer self, SingletonModifier sm)"""
7618 return _IMP_kernel.SingletonContainer_do_apply(self, sm)
7620 def do_apply_moved(self, sm, moved_pis, reset_pis):
7621 r"""do_apply_moved(SingletonContainer self, SingletonModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7622 return _IMP_kernel.SingletonContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
7624 def do_get_provides_access(self):
7625 r"""do_get_provides_access(SingletonContainer self) -> bool"""
7626 return _IMP_kernel.SingletonContainer_do_get_provides_access(self)
7627 __swig_destroy__ = _IMP_kernel.delete_SingletonContainer
7630 r"""__str__(SingletonContainer self) -> std::string"""
7631 return _IMP_kernel.SingletonContainer___str__(self)
7634 r"""__repr__(SingletonContainer self) -> std::string"""
7635 return _IMP_kernel.SingletonContainer___repr__(self)
7639 return _object_cast_to_SingletonContainer(o)
7642 def do_show(self, out):
7647 return _object_cast_to_SingletonContainer(o)
7649 def __disown__(self):
7651 _IMP_kernel.disown_SingletonContainer(self)
7652 return weakref.proxy(self)
7655 r"""do_destroy(SingletonContainer self)"""
7656 return _IMP_kernel.SingletonContainer_do_destroy(self)
7658 def handle_set_has_required_score_states(self, arg0):
7659 r"""handle_set_has_required_score_states(SingletonContainer self, bool arg0)"""
7660 return _IMP_kernel.SingletonContainer_handle_set_has_required_score_states(self, arg0)
7662 def do_get_inputs(self):
7663 r"""do_get_inputs(SingletonContainer self) -> IMP::ModelObjectsTemp"""
7664 return _IMP_kernel.SingletonContainer_do_get_inputs(self)
7666 def do_get_interactions(self):
7667 r"""do_get_interactions(SingletonContainer self) -> IMP::ModelObjectsTemps"""
7668 return _IMP_kernel.SingletonContainer_do_get_interactions(self)
7670 def do_get_contents_hash(self):
7671 r"""do_get_contents_hash(SingletonContainer self) -> std::size_t"""
7672 return _IMP_kernel.SingletonContainer_do_get_contents_hash(self)
7675 _IMP_kernel.SingletonContainer_swigregister(SingletonContainer)
7676 class _SingletonContainerAdaptor(_InputAdaptor):
7677 r"""Proxy of C++ IMP::SingletonContainerAdaptor class."""
7679 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7680 __repr__ = _swig_repr
7682 def __init__(self, *args):
7684 __init__(_SingletonContainerAdaptor self) -> _SingletonContainerAdaptor
7685 __init__(_SingletonContainerAdaptor self, SingletonContainer c) -> _SingletonContainerAdaptor
7686 __init__(_SingletonContainerAdaptor self, IMP::ParticlesTemp const & t) -> _SingletonContainerAdaptor
7688 _IMP_kernel._SingletonContainerAdaptor_swiginit(self, _IMP_kernel.new__SingletonContainerAdaptor(*args))
7690 def set_name_if_default(self, name):
7691 r"""set_name_if_default(_SingletonContainerAdaptor self, std::string name)"""
7692 return _IMP_kernel._SingletonContainerAdaptor_set_name_if_default(self, name)
7693 __swig_destroy__ = _IMP_kernel.delete__SingletonContainerAdaptor
7696 _IMP_kernel._SingletonContainerAdaptor_swigregister(_SingletonContainerAdaptor)
7698 r"""Proxy of C++ IMP::TripletModifier class."""
7700 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7702 def __init__(self, *args):
7703 r"""__init__(TripletModifier self, std::string name="TripletModifier %1%") -> TripletModifier"""
7704 if self.__class__ == TripletModifier:
7708 _IMP_kernel.TripletModifier_swiginit(self, _IMP_kernel.new_TripletModifier(_self, *args))
7710 if self.__class__ != TripletModifier:
7711 _director_objects.register(self)
7716 def apply_index(self, m, v):
7717 r"""apply_index(TripletModifier self, Model m, IMP::ParticleIndexTriplet const & v)"""
7718 return _IMP_kernel.TripletModifier_apply_index(self, m, v)
7720 def apply_indexes(self, m, o, lower_bound, upper_bound):
7721 r"""apply_indexes(TripletModifier self, Model m, IMP::ParticleIndexTriplets const & o, unsigned int lower_bound, unsigned int upper_bound)"""
7722 return _IMP_kernel.TripletModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
7724 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
7725 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)"""
7726 return _IMP_kernel.TripletModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
7729 r"""__str__(TripletModifier self) -> std::string"""
7730 return _IMP_kernel.TripletModifier___str__(self)
7733 r"""__repr__(TripletModifier self) -> std::string"""
7734 return _IMP_kernel.TripletModifier___repr__(self)
7738 return _object_cast_to_TripletModifier(o)
7741 def do_show(self, out):
7746 return _object_cast_to_TripletModifier(o)
7748 __swig_destroy__ = _IMP_kernel.delete_TripletModifier
7749 def __disown__(self):
7751 _IMP_kernel.disown_TripletModifier(self)
7752 return weakref.proxy(self)
7754 def do_get_inputs(self, m, pis):
7755 r"""do_get_inputs(TripletModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7756 return _IMP_kernel.TripletModifier_do_get_inputs(self, m, pis)
7758 def do_get_outputs(self, m, pis):
7759 r"""do_get_outputs(TripletModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7760 return _IMP_kernel.TripletModifier_do_get_outputs(self, m, pis)
7763 r"""do_destroy(TripletModifier self)"""
7764 return _IMP_kernel.TripletModifier_do_destroy(self)
7767 _IMP_kernel.TripletModifier_swigregister(TripletModifier)
7769 r"""Proxy of C++ IMP::TripletScore class."""
7771 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7773 def __init__(self, *args):
7774 r"""__init__(TripletScore self, std::string name="TripletScore %1%") -> TripletScore"""
7775 if self.__class__ == TripletScore:
7779 _IMP_kernel.TripletScore_swiginit(self, _IMP_kernel.new_TripletScore(_self, *args))
7781 if self.__class__ != TripletScore:
7782 _director_objects.register(self)
7787 def evaluate_index(self, m, vt, da):
7788 r"""evaluate_index(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt, DerivativeAccumulator da) -> double"""
7789 return _IMP_kernel.TripletScore_evaluate_index(self, m, vt, da)
7791 def check_indexes(self, m, pis):
7792 r"""check_indexes(TripletScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
7793 return _IMP_kernel.TripletScore_check_indexes(self, m, pis)
7795 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
7796 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"""
7797 return _IMP_kernel.TripletScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
7799 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7800 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"""
7801 return _IMP_kernel.TripletScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
7803 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
7804 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"""
7805 return _IMP_kernel.TripletScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
7807 def evaluate_if_good_index(self, m, vt, da, max):
7808 r"""evaluate_if_good_index(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt, DerivativeAccumulator da, double max) -> double"""
7809 return _IMP_kernel.TripletScore_evaluate_if_good_index(self, m, vt, da, max)
7811 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7812 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"""
7813 return _IMP_kernel.TripletScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
7815 def create_current_decomposition(self, m, vt):
7816 r"""create_current_decomposition(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt) -> IMP::Restraints"""
7817 return _IMP_kernel.TripletScore_create_current_decomposition(self, m, vt)
7819 def do_create_current_decomposition(self, m, vt):
7820 r"""do_create_current_decomposition(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt) -> IMP::Restraints"""
7821 return _IMP_kernel.TripletScore_do_create_current_decomposition(self, m, vt)
7822 __swig_destroy__ = _IMP_kernel.delete_TripletScore
7825 r"""__str__(TripletScore self) -> std::string"""
7826 return _IMP_kernel.TripletScore___str__(self)
7829 r"""__repr__(TripletScore self) -> std::string"""
7830 return _IMP_kernel.TripletScore___repr__(self)
7834 return _object_cast_to_TripletScore(o)
7837 def do_show(self, out):
7842 return _object_cast_to_TripletScore(o)
7844 def __disown__(self):
7846 _IMP_kernel.disown_TripletScore(self)
7847 return weakref.proxy(self)
7849 def do_get_inputs(self, m, pis):
7850 r"""do_get_inputs(TripletScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7851 return _IMP_kernel.TripletScore_do_get_inputs(self, m, pis)
7854 r"""do_destroy(TripletScore self)"""
7855 return _IMP_kernel.TripletScore_do_destroy(self)
7858 _IMP_kernel.TripletScore_swigregister(TripletScore)
7860 r"""Proxy of C++ IMP::TripletPredicate class."""
7862 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7864 def __init__(self, *args):
7865 r"""__init__(TripletPredicate self, std::string name="TripletPredicate %1%") -> TripletPredicate"""
7866 if self.__class__ == TripletPredicate:
7870 _IMP_kernel.TripletPredicate_swiginit(self, _IMP_kernel.new_TripletPredicate(_self, *args))
7872 if self.__class__ != TripletPredicate:
7873 _director_objects.register(self)
7878 def setup_for_get_value_index_in_batch(self, arg0):
7879 r"""setup_for_get_value_index_in_batch(TripletPredicate self, Model arg0)"""
7880 return _IMP_kernel.TripletPredicate_setup_for_get_value_index_in_batch(self, arg0)
7882 def get_value_index_in_batch(self, m, vt):
7883 r"""get_value_index_in_batch(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int"""
7884 return _IMP_kernel.TripletPredicate_get_value_index_in_batch(self, m, vt)
7886 def __call__(self, m, vt):
7887 r"""__call__(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int"""
7888 return _IMP_kernel.TripletPredicate___call__(self, m, vt)
7890 def get_value_index(self, *args):
7892 get_value_index(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int
7893 get_value_index(TripletPredicate self, Model m, IMP::ParticleIndexTriplets const & o) -> IMP::Ints
7895 return _IMP_kernel.TripletPredicate_get_value_index(self, *args)
7896 __swig_destroy__ = _IMP_kernel.delete_TripletPredicate
7899 r"""__str__(TripletPredicate self) -> std::string"""
7900 return _IMP_kernel.TripletPredicate___str__(self)
7903 r"""__repr__(TripletPredicate self) -> std::string"""
7904 return _IMP_kernel.TripletPredicate___repr__(self)
7908 return _object_cast_to_TripletPredicate(o)
7911 def do_show(self, out):
7916 return _object_cast_to_TripletPredicate(o)
7918 def __disown__(self):
7920 _IMP_kernel.disown_TripletPredicate(self)
7921 return weakref.proxy(self)
7923 def do_get_inputs(self, m, pis):
7924 r"""do_get_inputs(TripletPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7925 return _IMP_kernel.TripletPredicate_do_get_inputs(self, m, pis)
7928 r"""do_destroy(TripletPredicate self)"""
7929 return _IMP_kernel.TripletPredicate_do_destroy(self)
7932 _IMP_kernel.TripletPredicate_swigregister(TripletPredicate)
7934 r"""Proxy of C++ IMP::TripletContainer class."""
7936 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7938 def apply_generic(self, m):
7939 r"""apply_generic(TripletContainer self, TripletModifier m)"""
7940 return _IMP_kernel.TripletContainer_apply_generic(self, m)
7942 def apply_generic_moved(self, m, moved_pis, reset_pis):
7943 r"""apply_generic_moved(TripletContainer self, TripletModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7944 return _IMP_kernel.TripletContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
7946 def apply(self, sm):
7947 r"""apply(TripletContainer self, TripletModifier sm)"""
7948 return _IMP_kernel.TripletContainer_apply(self, sm)
7950 def apply_moved(self, sm, moved_pis, reset_pis):
7951 r"""apply_moved(TripletContainer self, TripletModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7952 return _IMP_kernel.TripletContainer_apply_moved(self, sm, moved_pis, reset_pis)
7954 def get_range_indexes(self):
7955 r"""get_range_indexes(TripletContainer self) -> IMP::ParticleIndexTriplets"""
7956 return _IMP_kernel.TripletContainer_get_range_indexes(self)
7958 def get_contents(self):
7959 r"""get_contents(TripletContainer self) -> IMP::ParticleIndexTriplets const &"""
7960 return _IMP_kernel.TripletContainer_get_contents(self)
7963 r"""get_indexes(TripletContainer self) -> IMP::ParticleIndexTriplets"""
7964 return _IMP_kernel.TripletContainer_get_indexes(self)
7966 def get(self, *args):
7968 get(TripletContainer self) -> IMP::ParticleTripletsTemp
7969 get(TripletContainer self, unsigned int i) -> IMP::ParticleTriplet
7971 return _IMP_kernel.TripletContainer_get(self, *args)
7973 def get_number(self):
7974 r"""get_number(TripletContainer self) -> unsigned int"""
7975 return _IMP_kernel.TripletContainer_get_number(self)
7977 def __init__(self, *args):
7979 __init__(TripletContainer self, Model m, std::string name="TripletContainer %1%") -> TripletContainer
7980 __init__(TripletContainer self) -> TripletContainer
7982 if self.__class__ == TripletContainer:
7986 _IMP_kernel.TripletContainer_swiginit(self, _IMP_kernel.new_TripletContainer(_self, *args))
7988 if self.__class__ != TripletContainer:
7989 _director_objects.register(self)
7994 def do_apply(self, sm):
7995 r"""do_apply(TripletContainer self, TripletModifier sm)"""
7996 return _IMP_kernel.TripletContainer_do_apply(self, sm)
7998 def do_apply_moved(self, sm, moved_pis, reset_pis):
7999 r"""do_apply_moved(TripletContainer self, TripletModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
8000 return _IMP_kernel.TripletContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
8002 def do_get_provides_access(self):
8003 r"""do_get_provides_access(TripletContainer self) -> bool"""
8004 return _IMP_kernel.TripletContainer_do_get_provides_access(self)
8005 __swig_destroy__ = _IMP_kernel.delete_TripletContainer
8008 r"""__str__(TripletContainer self) -> std::string"""
8009 return _IMP_kernel.TripletContainer___str__(self)
8012 r"""__repr__(TripletContainer self) -> std::string"""
8013 return _IMP_kernel.TripletContainer___repr__(self)
8017 return _object_cast_to_TripletContainer(o)
8020 def do_show(self, out):
8025 return _object_cast_to_TripletContainer(o)
8027 def __disown__(self):
8029 _IMP_kernel.disown_TripletContainer(self)
8030 return weakref.proxy(self)
8033 r"""do_destroy(TripletContainer self)"""
8034 return _IMP_kernel.TripletContainer_do_destroy(self)
8036 def handle_set_has_required_score_states(self, arg0):
8037 r"""handle_set_has_required_score_states(TripletContainer self, bool arg0)"""
8038 return _IMP_kernel.TripletContainer_handle_set_has_required_score_states(self, arg0)
8040 def do_get_inputs(self):
8041 r"""do_get_inputs(TripletContainer self) -> IMP::ModelObjectsTemp"""
8042 return _IMP_kernel.TripletContainer_do_get_inputs(self)
8044 def do_get_interactions(self):
8045 r"""do_get_interactions(TripletContainer self) -> IMP::ModelObjectsTemps"""
8046 return _IMP_kernel.TripletContainer_do_get_interactions(self)
8048 def do_get_contents_hash(self):
8049 r"""do_get_contents_hash(TripletContainer self) -> std::size_t"""
8050 return _IMP_kernel.TripletContainer_do_get_contents_hash(self)
8053 _IMP_kernel.TripletContainer_swigregister(TripletContainer)
8054 class _TripletContainerAdaptor(_InputAdaptor):
8055 r"""Proxy of C++ IMP::TripletContainerAdaptor class."""
8057 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8058 __repr__ = _swig_repr
8060 def __init__(self, *args):
8062 __init__(_TripletContainerAdaptor self) -> _TripletContainerAdaptor
8063 __init__(_TripletContainerAdaptor self, TripletContainer c) -> _TripletContainerAdaptor
8064 __init__(_TripletContainerAdaptor self, IMP::ParticleTripletsTemp const & t) -> _TripletContainerAdaptor
8066 _IMP_kernel._TripletContainerAdaptor_swiginit(self, _IMP_kernel.new__TripletContainerAdaptor(*args))
8068 def set_name_if_default(self, name):
8069 r"""set_name_if_default(_TripletContainerAdaptor self, std::string name)"""
8070 return _IMP_kernel._TripletContainerAdaptor_set_name_if_default(self, name)
8071 __swig_destroy__ = _IMP_kernel.delete__TripletContainerAdaptor
8074 _IMP_kernel._TripletContainerAdaptor_swigregister(_TripletContainerAdaptor)
8077 r"""write_particles_to_buffer(IMP::ParticlesTemp const & particles, IMP::FloatKeys const & keys) -> IMP::Vector< char,std::allocator< char > >"""
8078 return _IMP_kernel.write_particles_to_buffer(particles, keys)
8081 r"""read_particles_from_buffer(IMP::Vector< char,std::allocator< char > > const & buffer, IMP::ParticlesTemp const & particles, IMP::FloatKeys const & keys)"""
8082 return _IMP_kernel.read_particles_from_buffer(buffer, particles, keys)
8085 r"""get_particles(Model m, IMP::ParticleIndexes const & ps) -> IMP::ParticlesTemp"""
8086 return _IMP_kernel.get_particles(m, ps)
8090 get_indexes(IMP::ParticlesTemp const & ps) -> IMP::ParticleIndexes
8091 get_indexes(IMP::ParticlePairsTemp const & ps) -> IMP::ParticleIndexPairs
8093 return _IMP_kernel.get_indexes(*args)
8094 class _ParticleIndexAdaptor(object):
8095 r"""Proxy of C++ IMP::ParticleIndexAdaptor class."""
8097 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8098 __repr__ = _swig_repr
8100 def __init__(self, *args):
8102 __init__(_ParticleIndexAdaptor self, Particle p) -> _ParticleIndexAdaptor
8103 __init__(_ParticleIndexAdaptor self, ParticleIndex pi) -> _ParticleIndexAdaptor
8104 __init__(_ParticleIndexAdaptor self, Decorator d) -> _ParticleIndexAdaptor
8106 _IMP_kernel._ParticleIndexAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexAdaptor(*args))
8107 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexAdaptor
8110 _IMP_kernel._ParticleIndexAdaptor_swigregister(_ParticleIndexAdaptor)
8111 class _ParticleIndexesAdaptor(_InputAdaptor):
8112 r"""Proxy of C++ IMP::ParticleIndexesAdaptor class."""
8114 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8115 __repr__ = _swig_repr
8117 def __init__(self, *args):
8119 __init__(_ParticleIndexesAdaptor self, IMP::ParticlesTemp const & ps) -> _ParticleIndexesAdaptor
8120 __init__(_ParticleIndexesAdaptor self, IMP::ParticleIndexes const & pi) -> _ParticleIndexesAdaptor
8121 __init__(_ParticleIndexesAdaptor self) -> _ParticleIndexesAdaptor
8123 _IMP_kernel._ParticleIndexesAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexesAdaptor(*args))
8124 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexesAdaptor
8127 _IMP_kernel._ParticleIndexesAdaptor_swigregister(_ParticleIndexesAdaptor)
8128 class _ParticleIndexPairsAdaptor(object):
8129 r"""Proxy of C++ IMP::ParticleIndexPairsAdaptor class."""
8131 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8132 __repr__ = _swig_repr
8134 def __init__(self, *args):
8136 __init__(_ParticleIndexPairsAdaptor self, IMP::ParticlePairsTemp const & ps) -> _ParticleIndexPairsAdaptor
8137 __init__(_ParticleIndexPairsAdaptor self, IMP::ParticleIndexPairs const & pi) -> _ParticleIndexPairsAdaptor
8138 __init__(_ParticleIndexPairsAdaptor self) -> _ParticleIndexPairsAdaptor
8140 _IMP_kernel._ParticleIndexPairsAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexPairsAdaptor(*args))
8141 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexPairsAdaptor
8144 _IMP_kernel._ParticleIndexPairsAdaptor_swigregister(_ParticleIndexPairsAdaptor)
8146 r"""Proxy of C++ IMP::internal::_ConstRestraint class."""
8148 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8150 def __init__(self, *args):
8152 __init__(_ConstRestraint self, Model m, IMP::ParticleIndexes const & pis, double v) -> _ConstRestraint
8153 __init__(_ConstRestraint self) -> _ConstRestraint
8155 _IMP_kernel._ConstRestraint_swiginit(self, _IMP_kernel.new__ConstRestraint(*args))
8157 def get_value(self):
8158 r"""get_value(_ConstRestraint self) -> double"""
8159 return _IMP_kernel._ConstRestraint_get_value(self)
8161 def do_create_decomposition(self):
8162 r"""do_create_decomposition(_ConstRestraint self) -> IMP::Restraints"""
8163 return _IMP_kernel._ConstRestraint_do_create_decomposition(self)
8165 def do_get_inputs(self):
8166 r"""do_get_inputs(_ConstRestraint self) -> IMP::ModelObjectsTemp"""
8167 return _IMP_kernel._ConstRestraint_do_get_inputs(self)
8170 r"""get_version_info(_ConstRestraint self) -> VersionInfo"""
8171 return _IMP_kernel._ConstRestraint_get_version_info(self)
8172 __swig_destroy__ = _IMP_kernel.delete__ConstRestraint
8175 r"""__str__(_ConstRestraint self) -> std::string"""
8176 return _IMP_kernel._ConstRestraint___str__(self)
8179 r"""__repr__(_ConstRestraint self) -> std::string"""
8180 return _IMP_kernel._ConstRestraint___repr__(self)
8184 return _object_cast_to__ConstRestraint(o)
8187 def _get_as_binary(self):
8188 r"""_get_as_binary(_ConstRestraint self) -> PyObject *"""
8189 return _IMP_kernel._ConstRestraint__get_as_binary(self)
8191 def _set_from_binary(self, p):
8192 r"""_set_from_binary(_ConstRestraint self, PyObject * p)"""
8193 return _IMP_kernel._ConstRestraint__set_from_binary(self, p)
8195 def __getstate__(self):
8196 p = self._get_as_binary()
8197 if len(self.__dict__) > 1:
8198 d = self.__dict__.copy()
8203 def __setstate__(self, p):
8204 if not hasattr(self,
'this'):
8206 if isinstance(p, tuple):
8208 self.__dict__.update(d)
8209 return self._set_from_binary(p)
8213 value = self.get_value()
8215 return self._wrap_jax(
lambda X: value)
8219 _IMP_kernel._ConstRestraint_swigregister(_ConstRestraint)
8221 r"""Proxy of C++ IMP::internal::_ConstSingletonScore class."""
8223 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8225 def __init__(self, *args):
8227 __init__(_ConstSingletonScore self, double v) -> _ConstSingletonScore
8228 __init__(_ConstSingletonScore self) -> _ConstSingletonScore
8230 _IMP_kernel._ConstSingletonScore_swiginit(self, _IMP_kernel.new__ConstSingletonScore(*args))
8232 def do_get_inputs(self, arg2, arg3):
8233 r"""do_get_inputs(_ConstSingletonScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
8234 return _IMP_kernel._ConstSingletonScore_do_get_inputs(self, arg2, arg3)
8236 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
8237 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"""
8238 return _IMP_kernel._ConstSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
8240 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
8241 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"""
8242 return _IMP_kernel._ConstSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
8244 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
8245 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"""
8246 return _IMP_kernel._ConstSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
8248 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
8249 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"""
8250 return _IMP_kernel._ConstSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
8253 r"""get_version_info(_ConstSingletonScore self) -> VersionInfo"""
8254 return _IMP_kernel._ConstSingletonScore_get_version_info(self)
8255 __swig_destroy__ = _IMP_kernel.delete__ConstSingletonScore
8258 r"""__str__(_ConstSingletonScore self) -> std::string"""
8259 return _IMP_kernel._ConstSingletonScore___str__(self)
8262 r"""__repr__(_ConstSingletonScore self) -> std::string"""
8263 return _IMP_kernel._ConstSingletonScore___repr__(self)
8267 return _object_cast_to__ConstSingletonScore(o)
8270 def _get_as_binary(self):
8271 r"""_get_as_binary(_ConstSingletonScore self) -> PyObject *"""
8272 return _IMP_kernel._ConstSingletonScore__get_as_binary(self)
8274 def _set_from_binary(self, p):
8275 r"""_set_from_binary(_ConstSingletonScore self, PyObject * p)"""
8276 return _IMP_kernel._ConstSingletonScore__set_from_binary(self, p)
8278 def __getstate__(self):
8279 p = self._get_as_binary()
8280 if len(self.__dict__) > 1:
8281 d = self.__dict__.copy()
8286 def __setstate__(self, p):
8287 if not hasattr(self,
'this'):
8289 if isinstance(p, tuple):
8291 self.__dict__.update(d)
8292 return self._set_from_binary(p)
8296 _IMP_kernel._ConstSingletonScore_swigregister(_ConstSingletonScore)
8298 r"""Proxy of C++ IMP::internal::_ConstPairScore class."""
8300 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8302 def __init__(self, *args):
8304 __init__(_ConstPairScore self, double v) -> _ConstPairScore
8305 __init__(_ConstPairScore self) -> _ConstPairScore
8307 _IMP_kernel._ConstPairScore_swiginit(self, _IMP_kernel.new__ConstPairScore(*args))
8309 def do_get_inputs(self, arg2, arg3):
8310 r"""do_get_inputs(_ConstPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
8311 return _IMP_kernel._ConstPairScore_do_get_inputs(self, arg2, arg3)
8313 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
8314 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"""
8315 return _IMP_kernel._ConstPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
8317 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
8318 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"""
8319 return _IMP_kernel._ConstPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
8321 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
8322 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"""
8323 return _IMP_kernel._ConstPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
8325 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
8326 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"""
8327 return _IMP_kernel._ConstPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
8330 r"""get_version_info(_ConstPairScore self) -> VersionInfo"""
8331 return _IMP_kernel._ConstPairScore_get_version_info(self)
8332 __swig_destroy__ = _IMP_kernel.delete__ConstPairScore
8335 r"""__str__(_ConstPairScore self) -> std::string"""
8336 return _IMP_kernel._ConstPairScore___str__(self)
8339 r"""__repr__(_ConstPairScore self) -> std::string"""
8340 return _IMP_kernel._ConstPairScore___repr__(self)
8344 return _object_cast_to__ConstPairScore(o)
8347 def _get_as_binary(self):
8348 r"""_get_as_binary(_ConstPairScore self) -> PyObject *"""
8349 return _IMP_kernel._ConstPairScore__get_as_binary(self)
8351 def _set_from_binary(self, p):
8352 r"""_set_from_binary(_ConstPairScore self, PyObject * p)"""
8353 return _IMP_kernel._ConstPairScore__set_from_binary(self, p)
8355 def __getstate__(self):
8356 p = self._get_as_binary()
8357 if len(self.__dict__) > 1:
8358 d = self.__dict__.copy()
8363 def __setstate__(self, p):
8364 if not hasattr(self,
'this'):
8366 if isinstance(p, tuple):
8368 self.__dict__.update(d)
8369 return self._set_from_binary(p)
8373 _IMP_kernel._ConstPairScore_swigregister(_ConstPairScore)
8375 r"""Proxy of C++ IMP::internal::_TrivialDecorator class."""
8377 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8379 def __init__(self, *args):
8381 __init__(_TrivialDecorator self) -> _TrivialDecorator
8382 __init__(_TrivialDecorator self, Model m, ParticleIndex id) -> _TrivialDecorator
8383 __init__(_TrivialDecorator self, _ParticleAdaptor d) -> _TrivialDecorator
8385 _IMP_kernel._TrivialDecorator_swiginit(self, _IMP_kernel.new__TrivialDecorator(*args))
8387 def show(self, *args):
8388 r"""show(_TrivialDecorator self, _ostream out=std::cout)"""
8389 return _IMP_kernel._TrivialDecorator_show(self, *args)
8392 def setup_particle(*args):
8394 setup_particle(Model m, ParticleIndex pi) -> _TrivialDecorator
8395 setup_particle(_ParticleAdaptor pa) -> _TrivialDecorator
8397 return _IMP_kernel._TrivialDecorator_setup_particle(*args)
8400 def get_is_setup(*args):
8402 get_is_setup(_ParticleAdaptor p) -> bool
8403 get_is_setup(Model m, ParticleIndex pi) -> bool
8405 return _IMP_kernel._TrivialDecorator_get_is_setup(*args)
8409 add_attribute(_TrivialDecorator self, FloatKey k, IMP::Float v, bool opt)
8410 add_attribute(_TrivialDecorator self, FloatKey a0, IMP::Float a1)
8411 add_attribute(_TrivialDecorator self, IntKey a0, IMP::Int a1)
8412 add_attribute(_TrivialDecorator self, FloatsKey a0, IMP::Floats a1)
8413 add_attribute(_TrivialDecorator self, IntsKey a0, IMP::Ints a1)
8414 add_attribute(_TrivialDecorator self, StringKey a0, IMP::String a1)
8415 add_attribute(_TrivialDecorator self, ParticleIndexKey a0, Particle a1)
8416 add_attribute(_TrivialDecorator self, ObjectKey a0, Object a1)
8417 add_attribute(_TrivialDecorator self, SparseFloatKey a0, IMP::Float a1)
8418 add_attribute(_TrivialDecorator self, SparseIntKey a0, IMP::Int a1)
8419 add_attribute(_TrivialDecorator self, SparseStringKey a0, IMP::String a1)
8420 add_attribute(_TrivialDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8422 return _IMP_kernel._TrivialDecorator_add_attribute(self, *args)
8424 def get_value(self, *args):
8426 get_value(_TrivialDecorator self, FloatKey a0) -> IMP::Float
8427 get_value(_TrivialDecorator self, IntKey a0) -> IMP::Int
8428 get_value(_TrivialDecorator self, FloatsKey a0) -> IMP::Floats
8429 get_value(_TrivialDecorator self, IntsKey a0) -> IMP::Ints
8430 get_value(_TrivialDecorator self, StringKey a0) -> IMP::String
8431 get_value(_TrivialDecorator self, ParticleIndexKey a0) -> Particle
8432 get_value(_TrivialDecorator self, ObjectKey a0) -> Object
8433 get_value(_TrivialDecorator self, SparseFloatKey a0) -> IMP::Float
8434 get_value(_TrivialDecorator self, SparseIntKey a0) -> IMP::Int
8435 get_value(_TrivialDecorator self, SparseStringKey a0) -> IMP::String
8436 get_value(_TrivialDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
8438 return _IMP_kernel._TrivialDecorator_get_value(self, *args)
8440 def set_value(self, *args):
8442 set_value(_TrivialDecorator self, FloatKey a0, IMP::Float a1)
8443 set_value(_TrivialDecorator self, IntKey a0, IMP::Int a1)
8444 set_value(_TrivialDecorator self, FloatsKey a0, IMP::Floats a1)
8445 set_value(_TrivialDecorator self, IntsKey a0, IMP::Ints a1)
8446 set_value(_TrivialDecorator self, StringKey a0, IMP::String a1)
8447 set_value(_TrivialDecorator self, ParticleIndexKey a0, Particle a1)
8448 set_value(_TrivialDecorator self, ObjectKey a0, Object a1)
8449 set_value(_TrivialDecorator self, SparseFloatKey a0, IMP::Float a1)
8450 set_value(_TrivialDecorator self, SparseIntKey a0, IMP::Int a1)
8451 set_value(_TrivialDecorator self, SparseStringKey a0, IMP::String a1)
8452 set_value(_TrivialDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8454 return _IMP_kernel._TrivialDecorator_set_value(self, *args)
8458 remove_attribute(_TrivialDecorator self, FloatKey a0)
8459 remove_attribute(_TrivialDecorator self, IntKey a0)
8460 remove_attribute(_TrivialDecorator self, FloatsKey a0)
8461 remove_attribute(_TrivialDecorator self, IntsKey a0)
8462 remove_attribute(_TrivialDecorator self, StringKey a0)
8463 remove_attribute(_TrivialDecorator self, ParticleIndexKey a0)
8464 remove_attribute(_TrivialDecorator self, ObjectKey a0)
8465 remove_attribute(_TrivialDecorator self, SparseFloatKey a0)
8466 remove_attribute(_TrivialDecorator self, SparseIntKey a0)
8467 remove_attribute(_TrivialDecorator self, SparseStringKey a0)
8468 remove_attribute(_TrivialDecorator self, SparseParticleIndexKey a0)
8470 return _IMP_kernel._TrivialDecorator_remove_attribute(self, *args)
8472 def has_attribute(self, *args):
8474 has_attribute(_TrivialDecorator self, FloatKey a0) -> bool
8475 has_attribute(_TrivialDecorator self, IntKey a0) -> bool
8476 has_attribute(_TrivialDecorator self, FloatsKey a0) -> bool
8477 has_attribute(_TrivialDecorator self, IntsKey a0) -> bool
8478 has_attribute(_TrivialDecorator self, StringKey a0) -> bool
8479 has_attribute(_TrivialDecorator self, ParticleIndexKey a0) -> bool
8480 has_attribute(_TrivialDecorator self, ObjectKey a0) -> bool
8481 has_attribute(_TrivialDecorator self, SparseFloatKey a0) -> bool
8482 has_attribute(_TrivialDecorator self, SparseIntKey a0) -> bool
8483 has_attribute(_TrivialDecorator self, SparseStringKey a0) -> bool
8484 has_attribute(_TrivialDecorator self, SparseParticleIndexKey a0) -> bool
8486 return _IMP_kernel._TrivialDecorator_has_attribute(self, *args)
8488 def get_derivative(self, a0):
8489 r"""get_derivative(_TrivialDecorator self, FloatKey a0) -> double"""
8490 return _IMP_kernel._TrivialDecorator_get_derivative(self, a0)
8493 r"""get_name(_TrivialDecorator self) -> std::string"""
8494 return _IMP_kernel._TrivialDecorator_get_name(self)
8497 r"""clear_caches(_TrivialDecorator self)"""
8498 return _IMP_kernel._TrivialDecorator_clear_caches(self)
8500 def set_name(self, a0):
8501 r"""set_name(_TrivialDecorator self, std::string a0)"""
8502 return _IMP_kernel._TrivialDecorator_set_name(self, a0)
8505 r"""set_check_level(_TrivialDecorator self, IMP::CheckLevel a0)"""
8506 return _IMP_kernel._TrivialDecorator_set_check_level(self, a0)
8508 def add_to_derivative(self, a0, a1, a2):
8509 r"""add_to_derivative(_TrivialDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8510 return _IMP_kernel._TrivialDecorator_add_to_derivative(self, a0, a1, a2)
8513 r"""set_is_optimized(_TrivialDecorator self, FloatKey a0, bool a1)"""
8514 return _IMP_kernel._TrivialDecorator_set_is_optimized(self, a0, a1)
8516 def get_is_optimized(self, a0):
8517 r"""get_is_optimized(_TrivialDecorator self, FloatKey a0) -> bool"""
8518 return _IMP_kernel._TrivialDecorator_get_is_optimized(self, a0)
8520 def get_check_level(self):
8521 r"""get_check_level(_TrivialDecorator self) -> IMP::CheckLevel"""
8522 return _IMP_kernel._TrivialDecorator_get_check_level(self)
8524 def __eq__(self, *args):
8526 __eq__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8527 __eq__(_TrivialDecorator self, Particle d) -> bool
8529 return _IMP_kernel._TrivialDecorator___eq__(self, *args)
8531 def __ne__(self, *args):
8533 __ne__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8534 __ne__(_TrivialDecorator self, Particle d) -> bool
8536 return _IMP_kernel._TrivialDecorator___ne__(self, *args)
8538 def __le__(self, *args):
8540 __le__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8541 __le__(_TrivialDecorator self, Particle d) -> bool
8543 return _IMP_kernel._TrivialDecorator___le__(self, *args)
8545 def __lt__(self, *args):
8547 __lt__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8548 __lt__(_TrivialDecorator self, Particle d) -> bool
8550 return _IMP_kernel._TrivialDecorator___lt__(self, *args)
8552 def __ge__(self, *args):
8554 __ge__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8555 __ge__(_TrivialDecorator self, Particle d) -> bool
8557 return _IMP_kernel._TrivialDecorator___ge__(self, *args)
8559 def __gt__(self, *args):
8561 __gt__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8562 __gt__(_TrivialDecorator self, Particle d) -> bool
8564 return _IMP_kernel._TrivialDecorator___gt__(self, *args)
8567 r"""__hash__(_TrivialDecorator self) -> std::size_t"""
8568 return _IMP_kernel._TrivialDecorator___hash__(self)
8571 r"""__str__(_TrivialDecorator self) -> std::string"""
8572 return _IMP_kernel._TrivialDecorator___str__(self)
8575 r"""__repr__(_TrivialDecorator self) -> std::string"""
8576 return _IMP_kernel._TrivialDecorator___repr__(self)
8578 def _get_as_binary(self):
8579 r"""_get_as_binary(_TrivialDecorator self) -> PyObject *"""
8580 return _IMP_kernel._TrivialDecorator__get_as_binary(self)
8582 def _set_from_binary(self, p):
8583 r"""_set_from_binary(_TrivialDecorator self, PyObject * p)"""
8584 return _IMP_kernel._TrivialDecorator__set_from_binary(self, p)
8586 def __getstate__(self):
8587 p = self._get_as_binary()
8588 if len(self.__dict__) > 1:
8589 d = self.__dict__.copy()
8594 def __setstate__(self, p):
8595 if not hasattr(self,
'this'):
8597 if isinstance(p, tuple):
8599 self.__dict__.update(d)
8600 return self._set_from_binary(p)
8602 __swig_destroy__ = _IMP_kernel.delete__TrivialDecorator
8605 _IMP_kernel._TrivialDecorator_swigregister(_TrivialDecorator)
8606 class _TrivialDerivedDecorator(_TrivialDecorator):
8607 r"""Proxy of C++ IMP::internal::_TrivialDerivedDecorator class."""
8609 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8611 def __init__(self, *args):
8613 __init__(_TrivialDerivedDecorator self) -> _TrivialDerivedDecorator
8614 __init__(_TrivialDerivedDecorator self, Model m, ParticleIndex id) -> _TrivialDerivedDecorator
8615 __init__(_TrivialDerivedDecorator self, _ParticleAdaptor d) -> _TrivialDerivedDecorator
8617 _IMP_kernel._TrivialDerivedDecorator_swiginit(self, _IMP_kernel.new__TrivialDerivedDecorator(*args))
8619 def show(self, *args):
8620 r"""show(_TrivialDerivedDecorator self, _ostream out=std::cout)"""
8621 return _IMP_kernel._TrivialDerivedDecorator_show(self, *args)
8624 def setup_particle(*args):
8626 setup_particle(Model m, ParticleIndex pi) -> _TrivialDerivedDecorator
8627 setup_particle(_ParticleAdaptor pa) -> _TrivialDerivedDecorator
8629 return _IMP_kernel._TrivialDerivedDecorator_setup_particle(*args)
8632 def get_is_setup(*args):
8634 get_is_setup(_ParticleAdaptor p) -> bool
8635 get_is_setup(Model m, ParticleIndex pi) -> bool
8637 return _IMP_kernel._TrivialDerivedDecorator_get_is_setup(*args)
8641 add_attribute(_TrivialDerivedDecorator self, FloatKey k, IMP::Float v, bool opt)
8642 add_attribute(_TrivialDerivedDecorator self, FloatKey a0, IMP::Float a1)
8643 add_attribute(_TrivialDerivedDecorator self, IntKey a0, IMP::Int a1)
8644 add_attribute(_TrivialDerivedDecorator self, FloatsKey a0, IMP::Floats a1)
8645 add_attribute(_TrivialDerivedDecorator self, IntsKey a0, IMP::Ints a1)
8646 add_attribute(_TrivialDerivedDecorator self, StringKey a0, IMP::String a1)
8647 add_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0, Particle a1)
8648 add_attribute(_TrivialDerivedDecorator self, ObjectKey a0, Object a1)
8649 add_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0, IMP::Float a1)
8650 add_attribute(_TrivialDerivedDecorator self, SparseIntKey a0, IMP::Int a1)
8651 add_attribute(_TrivialDerivedDecorator self, SparseStringKey a0, IMP::String a1)
8652 add_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8654 return _IMP_kernel._TrivialDerivedDecorator_add_attribute(self, *args)
8656 def get_value(self, *args):
8658 get_value(_TrivialDerivedDecorator self, FloatKey a0) -> IMP::Float
8659 get_value(_TrivialDerivedDecorator self, IntKey a0) -> IMP::Int
8660 get_value(_TrivialDerivedDecorator self, FloatsKey a0) -> IMP::Floats
8661 get_value(_TrivialDerivedDecorator self, IntsKey a0) -> IMP::Ints
8662 get_value(_TrivialDerivedDecorator self, StringKey a0) -> IMP::String
8663 get_value(_TrivialDerivedDecorator self, ParticleIndexKey a0) -> Particle
8664 get_value(_TrivialDerivedDecorator self, ObjectKey a0) -> Object
8665 get_value(_TrivialDerivedDecorator self, SparseFloatKey a0) -> IMP::Float
8666 get_value(_TrivialDerivedDecorator self, SparseIntKey a0) -> IMP::Int
8667 get_value(_TrivialDerivedDecorator self, SparseStringKey a0) -> IMP::String
8668 get_value(_TrivialDerivedDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
8670 return _IMP_kernel._TrivialDerivedDecorator_get_value(self, *args)
8672 def set_value(self, *args):
8674 set_value(_TrivialDerivedDecorator self, FloatKey a0, IMP::Float a1)
8675 set_value(_TrivialDerivedDecorator self, IntKey a0, IMP::Int a1)
8676 set_value(_TrivialDerivedDecorator self, FloatsKey a0, IMP::Floats a1)
8677 set_value(_TrivialDerivedDecorator self, IntsKey a0, IMP::Ints a1)
8678 set_value(_TrivialDerivedDecorator self, StringKey a0, IMP::String a1)
8679 set_value(_TrivialDerivedDecorator self, ParticleIndexKey a0, Particle a1)
8680 set_value(_TrivialDerivedDecorator self, ObjectKey a0, Object a1)
8681 set_value(_TrivialDerivedDecorator self, SparseFloatKey a0, IMP::Float a1)
8682 set_value(_TrivialDerivedDecorator self, SparseIntKey a0, IMP::Int a1)
8683 set_value(_TrivialDerivedDecorator self, SparseStringKey a0, IMP::String a1)
8684 set_value(_TrivialDerivedDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8686 return _IMP_kernel._TrivialDerivedDecorator_set_value(self, *args)
8690 remove_attribute(_TrivialDerivedDecorator self, FloatKey a0)
8691 remove_attribute(_TrivialDerivedDecorator self, IntKey a0)
8692 remove_attribute(_TrivialDerivedDecorator self, FloatsKey a0)
8693 remove_attribute(_TrivialDerivedDecorator self, IntsKey a0)
8694 remove_attribute(_TrivialDerivedDecorator self, StringKey a0)
8695 remove_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0)
8696 remove_attribute(_TrivialDerivedDecorator self, ObjectKey a0)
8697 remove_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0)
8698 remove_attribute(_TrivialDerivedDecorator self, SparseIntKey a0)
8699 remove_attribute(_TrivialDerivedDecorator self, SparseStringKey a0)
8700 remove_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0)
8702 return _IMP_kernel._TrivialDerivedDecorator_remove_attribute(self, *args)
8704 def has_attribute(self, *args):
8706 has_attribute(_TrivialDerivedDecorator self, FloatKey a0) -> bool
8707 has_attribute(_TrivialDerivedDecorator self, IntKey a0) -> bool
8708 has_attribute(_TrivialDerivedDecorator self, FloatsKey a0) -> bool
8709 has_attribute(_TrivialDerivedDecorator self, IntsKey a0) -> bool
8710 has_attribute(_TrivialDerivedDecorator self, StringKey a0) -> bool
8711 has_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0) -> bool
8712 has_attribute(_TrivialDerivedDecorator self, ObjectKey a0) -> bool
8713 has_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0) -> bool
8714 has_attribute(_TrivialDerivedDecorator self, SparseIntKey a0) -> bool
8715 has_attribute(_TrivialDerivedDecorator self, SparseStringKey a0) -> bool
8716 has_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0) -> bool
8718 return _IMP_kernel._TrivialDerivedDecorator_has_attribute(self, *args)
8720 def get_derivative(self, a0):
8721 r"""get_derivative(_TrivialDerivedDecorator self, FloatKey a0) -> double"""
8722 return _IMP_kernel._TrivialDerivedDecorator_get_derivative(self, a0)
8725 r"""get_name(_TrivialDerivedDecorator self) -> std::string"""
8726 return _IMP_kernel._TrivialDerivedDecorator_get_name(self)
8729 r"""clear_caches(_TrivialDerivedDecorator self)"""
8730 return _IMP_kernel._TrivialDerivedDecorator_clear_caches(self)
8732 def set_name(self, a0):
8733 r"""set_name(_TrivialDerivedDecorator self, std::string a0)"""
8734 return _IMP_kernel._TrivialDerivedDecorator_set_name(self, a0)
8737 r"""set_check_level(_TrivialDerivedDecorator self, IMP::CheckLevel a0)"""
8738 return _IMP_kernel._TrivialDerivedDecorator_set_check_level(self, a0)
8740 def add_to_derivative(self, a0, a1, a2):
8741 r"""add_to_derivative(_TrivialDerivedDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8742 return _IMP_kernel._TrivialDerivedDecorator_add_to_derivative(self, a0, a1, a2)
8745 r"""set_is_optimized(_TrivialDerivedDecorator self, FloatKey a0, bool a1)"""
8746 return _IMP_kernel._TrivialDerivedDecorator_set_is_optimized(self, a0, a1)
8748 def get_is_optimized(self, a0):
8749 r"""get_is_optimized(_TrivialDerivedDecorator self, FloatKey a0) -> bool"""
8750 return _IMP_kernel._TrivialDerivedDecorator_get_is_optimized(self, a0)
8752 def get_check_level(self):
8753 r"""get_check_level(_TrivialDerivedDecorator self) -> IMP::CheckLevel"""
8754 return _IMP_kernel._TrivialDerivedDecorator_get_check_level(self)
8756 def __eq__(self, *args):
8758 __eq__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8759 __eq__(_TrivialDerivedDecorator self, Particle d) -> bool
8761 return _IMP_kernel._TrivialDerivedDecorator___eq__(self, *args)
8763 def __ne__(self, *args):
8765 __ne__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8766 __ne__(_TrivialDerivedDecorator self, Particle d) -> bool
8768 return _IMP_kernel._TrivialDerivedDecorator___ne__(self, *args)
8770 def __le__(self, *args):
8772 __le__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8773 __le__(_TrivialDerivedDecorator self, Particle d) -> bool
8775 return _IMP_kernel._TrivialDerivedDecorator___le__(self, *args)
8777 def __lt__(self, *args):
8779 __lt__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8780 __lt__(_TrivialDerivedDecorator self, Particle d) -> bool
8782 return _IMP_kernel._TrivialDerivedDecorator___lt__(self, *args)
8784 def __ge__(self, *args):
8786 __ge__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8787 __ge__(_TrivialDerivedDecorator self, Particle d) -> bool
8789 return _IMP_kernel._TrivialDerivedDecorator___ge__(self, *args)
8791 def __gt__(self, *args):
8793 __gt__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8794 __gt__(_TrivialDerivedDecorator self, Particle d) -> bool
8796 return _IMP_kernel._TrivialDerivedDecorator___gt__(self, *args)
8799 r"""__hash__(_TrivialDerivedDecorator self) -> std::size_t"""
8800 return _IMP_kernel._TrivialDerivedDecorator___hash__(self)
8803 r"""__str__(_TrivialDerivedDecorator self) -> std::string"""
8804 return _IMP_kernel._TrivialDerivedDecorator___str__(self)
8807 r"""__repr__(_TrivialDerivedDecorator self) -> std::string"""
8808 return _IMP_kernel._TrivialDerivedDecorator___repr__(self)
8810 def _get_as_binary(self):
8811 r"""_get_as_binary(_TrivialDerivedDecorator self) -> PyObject *"""
8812 return _IMP_kernel._TrivialDerivedDecorator__get_as_binary(self)
8814 def _set_from_binary(self, p):
8815 r"""_set_from_binary(_TrivialDerivedDecorator self, PyObject * p)"""
8816 return _IMP_kernel._TrivialDerivedDecorator__set_from_binary(self, p)
8818 def __getstate__(self):
8819 p = self._get_as_binary()
8820 if len(self.__dict__) > 1:
8821 d = self.__dict__.copy()
8826 def __setstate__(self, p):
8827 if not hasattr(self,
'this'):
8829 if isinstance(p, tuple):
8831 self.__dict__.update(d)
8832 return self._set_from_binary(p)
8834 __swig_destroy__ = _IMP_kernel.delete__TrivialDerivedDecorator
8837 _IMP_kernel._TrivialDerivedDecorator_swigregister(_TrivialDerivedDecorator)
8838 class _TrivialTraitsDecorator(
Decorator):
8839 r"""Proxy of C++ IMP::internal::_TrivialTraitsDecorator class."""
8841 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8843 def get_decorator_traits(self):
8844 r"""get_decorator_traits(_TrivialTraitsDecorator self) -> StringKey"""
8845 return _IMP_kernel._TrivialTraitsDecorator_get_decorator_traits(self)
8848 def get_default_decorator_traits():
8849 r"""get_default_decorator_traits() -> StringKey"""
8850 return _IMP_kernel._TrivialTraitsDecorator_get_default_decorator_traits()
8852 def __init__(self, *args):
8854 __init__(_TrivialTraitsDecorator self) -> _TrivialTraitsDecorator
8855 __init__(_TrivialTraitsDecorator self, Model m, ParticleIndex id, StringKey tr=get_default_key()) -> _TrivialTraitsDecorator
8856 __init__(_TrivialTraitsDecorator self, _ParticleAdaptor d, StringKey tr=get_default_key()) -> _TrivialTraitsDecorator
8858 _IMP_kernel._TrivialTraitsDecorator_swiginit(self, _IMP_kernel.new__TrivialTraitsDecorator(*args))
8860 def show(self, *args):
8861 r"""show(_TrivialTraitsDecorator self, _ostream out=std::cout)"""
8862 return _IMP_kernel._TrivialTraitsDecorator_show(self, *args)
8865 def setup_particle(*args):
8867 setup_particle(Model m, ParticleIndex pi, StringKey tr=IMP::internal::_TrivialTraitsDecorator::get_default_decorator_traits()) -> _TrivialTraitsDecorator
8868 setup_particle(_ParticleAdaptor d, StringKey tr=IMP::internal::_TrivialTraitsDecorator::get_default_decorator_traits()) -> _TrivialTraitsDecorator
8870 return _IMP_kernel._TrivialTraitsDecorator_setup_particle(*args)
8873 def get_is_setup(*args):
8875 get_is_setup(_ParticleAdaptor p, StringKey tr=get_default_key()) -> bool
8876 get_is_setup(Model m, ParticleIndex pi, StringKey k=get_default_key()) -> bool
8878 return _IMP_kernel._TrivialTraitsDecorator_get_is_setup(*args)
8881 def get_default_key():
8882 r"""get_default_key() -> StringKey"""
8883 return _IMP_kernel._TrivialTraitsDecorator_get_default_key()
8887 add_attribute(_TrivialTraitsDecorator self, FloatKey k, IMP::Float v, bool opt)
8888 add_attribute(_TrivialTraitsDecorator self, FloatKey a0, IMP::Float a1)
8889 add_attribute(_TrivialTraitsDecorator self, IntKey a0, IMP::Int a1)
8890 add_attribute(_TrivialTraitsDecorator self, FloatsKey a0, IMP::Floats a1)
8891 add_attribute(_TrivialTraitsDecorator self, IntsKey a0, IMP::Ints a1)
8892 add_attribute(_TrivialTraitsDecorator self, StringKey a0, IMP::String a1)
8893 add_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0, Particle a1)
8894 add_attribute(_TrivialTraitsDecorator self, ObjectKey a0, Object a1)
8895 add_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0, IMP::Float a1)
8896 add_attribute(_TrivialTraitsDecorator self, SparseIntKey a0, IMP::Int a1)
8897 add_attribute(_TrivialTraitsDecorator self, SparseStringKey a0, IMP::String a1)
8898 add_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8900 return _IMP_kernel._TrivialTraitsDecorator_add_attribute(self, *args)
8902 def get_value(self, *args):
8904 get_value(_TrivialTraitsDecorator self, FloatKey a0) -> IMP::Float
8905 get_value(_TrivialTraitsDecorator self, IntKey a0) -> IMP::Int
8906 get_value(_TrivialTraitsDecorator self, FloatsKey a0) -> IMP::Floats
8907 get_value(_TrivialTraitsDecorator self, IntsKey a0) -> IMP::Ints
8908 get_value(_TrivialTraitsDecorator self, StringKey a0) -> IMP::String
8909 get_value(_TrivialTraitsDecorator self, ParticleIndexKey a0) -> Particle
8910 get_value(_TrivialTraitsDecorator self, ObjectKey a0) -> Object
8911 get_value(_TrivialTraitsDecorator self, SparseFloatKey a0) -> IMP::Float
8912 get_value(_TrivialTraitsDecorator self, SparseIntKey a0) -> IMP::Int
8913 get_value(_TrivialTraitsDecorator self, SparseStringKey a0) -> IMP::String
8914 get_value(_TrivialTraitsDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
8916 return _IMP_kernel._TrivialTraitsDecorator_get_value(self, *args)
8918 def set_value(self, *args):
8920 set_value(_TrivialTraitsDecorator self, FloatKey a0, IMP::Float a1)
8921 set_value(_TrivialTraitsDecorator self, IntKey a0, IMP::Int a1)
8922 set_value(_TrivialTraitsDecorator self, FloatsKey a0, IMP::Floats a1)
8923 set_value(_TrivialTraitsDecorator self, IntsKey a0, IMP::Ints a1)
8924 set_value(_TrivialTraitsDecorator self, StringKey a0, IMP::String a1)
8925 set_value(_TrivialTraitsDecorator self, ParticleIndexKey a0, Particle a1)
8926 set_value(_TrivialTraitsDecorator self, ObjectKey a0, Object a1)
8927 set_value(_TrivialTraitsDecorator self, SparseFloatKey a0, IMP::Float a1)
8928 set_value(_TrivialTraitsDecorator self, SparseIntKey a0, IMP::Int a1)
8929 set_value(_TrivialTraitsDecorator self, SparseStringKey a0, IMP::String a1)
8930 set_value(_TrivialTraitsDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8932 return _IMP_kernel._TrivialTraitsDecorator_set_value(self, *args)
8936 remove_attribute(_TrivialTraitsDecorator self, FloatKey a0)
8937 remove_attribute(_TrivialTraitsDecorator self, IntKey a0)
8938 remove_attribute(_TrivialTraitsDecorator self, FloatsKey a0)
8939 remove_attribute(_TrivialTraitsDecorator self, IntsKey a0)
8940 remove_attribute(_TrivialTraitsDecorator self, StringKey a0)
8941 remove_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0)
8942 remove_attribute(_TrivialTraitsDecorator self, ObjectKey a0)
8943 remove_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0)
8944 remove_attribute(_TrivialTraitsDecorator self, SparseIntKey a0)
8945 remove_attribute(_TrivialTraitsDecorator self, SparseStringKey a0)
8946 remove_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0)
8948 return _IMP_kernel._TrivialTraitsDecorator_remove_attribute(self, *args)
8950 def has_attribute(self, *args):
8952 has_attribute(_TrivialTraitsDecorator self, FloatKey a0) -> bool
8953 has_attribute(_TrivialTraitsDecorator self, IntKey a0) -> bool
8954 has_attribute(_TrivialTraitsDecorator self, FloatsKey a0) -> bool
8955 has_attribute(_TrivialTraitsDecorator self, IntsKey a0) -> bool
8956 has_attribute(_TrivialTraitsDecorator self, StringKey a0) -> bool
8957 has_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0) -> bool
8958 has_attribute(_TrivialTraitsDecorator self, ObjectKey a0) -> bool
8959 has_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0) -> bool
8960 has_attribute(_TrivialTraitsDecorator self, SparseIntKey a0) -> bool
8961 has_attribute(_TrivialTraitsDecorator self, SparseStringKey a0) -> bool
8962 has_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0) -> bool
8964 return _IMP_kernel._TrivialTraitsDecorator_has_attribute(self, *args)
8966 def get_derivative(self, a0):
8967 r"""get_derivative(_TrivialTraitsDecorator self, FloatKey a0) -> double"""
8968 return _IMP_kernel._TrivialTraitsDecorator_get_derivative(self, a0)
8971 r"""get_name(_TrivialTraitsDecorator self) -> std::string"""
8972 return _IMP_kernel._TrivialTraitsDecorator_get_name(self)
8975 r"""clear_caches(_TrivialTraitsDecorator self)"""
8976 return _IMP_kernel._TrivialTraitsDecorator_clear_caches(self)
8978 def set_name(self, a0):
8979 r"""set_name(_TrivialTraitsDecorator self, std::string a0)"""
8980 return _IMP_kernel._TrivialTraitsDecorator_set_name(self, a0)
8983 r"""set_check_level(_TrivialTraitsDecorator self, IMP::CheckLevel a0)"""
8984 return _IMP_kernel._TrivialTraitsDecorator_set_check_level(self, a0)
8986 def add_to_derivative(self, a0, a1, a2):
8987 r"""add_to_derivative(_TrivialTraitsDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8988 return _IMP_kernel._TrivialTraitsDecorator_add_to_derivative(self, a0, a1, a2)
8991 r"""set_is_optimized(_TrivialTraitsDecorator self, FloatKey a0, bool a1)"""
8992 return _IMP_kernel._TrivialTraitsDecorator_set_is_optimized(self, a0, a1)
8994 def get_is_optimized(self, a0):
8995 r"""get_is_optimized(_TrivialTraitsDecorator self, FloatKey a0) -> bool"""
8996 return _IMP_kernel._TrivialTraitsDecorator_get_is_optimized(self, a0)
8998 def get_check_level(self):
8999 r"""get_check_level(_TrivialTraitsDecorator self) -> IMP::CheckLevel"""
9000 return _IMP_kernel._TrivialTraitsDecorator_get_check_level(self)
9002 def __eq__(self, *args):
9004 __eq__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
9005 __eq__(_TrivialTraitsDecorator self, Particle d) -> bool
9007 return _IMP_kernel._TrivialTraitsDecorator___eq__(self, *args)
9009 def __ne__(self, *args):
9011 __ne__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
9012 __ne__(_TrivialTraitsDecorator self, Particle d) -> bool
9014 return _IMP_kernel._TrivialTraitsDecorator___ne__(self, *args)
9016 def __le__(self, *args):
9018 __le__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
9019 __le__(_TrivialTraitsDecorator self, Particle d) -> bool
9021 return _IMP_kernel._TrivialTraitsDecorator___le__(self, *args)
9023 def __lt__(self, *args):
9025 __lt__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
9026 __lt__(_TrivialTraitsDecorator self, Particle d) -> bool
9028 return _IMP_kernel._TrivialTraitsDecorator___lt__(self, *args)
9030 def __ge__(self, *args):
9032 __ge__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
9033 __ge__(_TrivialTraitsDecorator self, Particle d) -> bool
9035 return _IMP_kernel._TrivialTraitsDecorator___ge__(self, *args)
9037 def __gt__(self, *args):
9039 __gt__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
9040 __gt__(_TrivialTraitsDecorator self, Particle d) -> bool
9042 return _IMP_kernel._TrivialTraitsDecorator___gt__(self, *args)
9045 r"""__hash__(_TrivialTraitsDecorator self) -> std::size_t"""
9046 return _IMP_kernel._TrivialTraitsDecorator___hash__(self)
9049 r"""__str__(_TrivialTraitsDecorator self) -> std::string"""
9050 return _IMP_kernel._TrivialTraitsDecorator___str__(self)
9053 r"""__repr__(_TrivialTraitsDecorator self) -> std::string"""
9054 return _IMP_kernel._TrivialTraitsDecorator___repr__(self)
9055 __swig_destroy__ = _IMP_kernel.delete__TrivialTraitsDecorator
9058 _IMP_kernel._TrivialTraitsDecorator_swigregister(_TrivialTraitsDecorator)
9060 def __lshift__(*args):
9062 __lshift__(_ostream out, _TrivialDecorator n) -> _ostream
9063 __lshift__(_ostream out, _TrivialDerivedDecorator n) -> _ostream
9064 __lshift__(_ostream out, _TrivialTraitsDecorator n) -> _ostream
9066 return _IMP_kernel.__lshift__(*args)
9068 r"""Proxy of C++ IMP::internal::_ConstOptimizer class."""
9070 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9072 def __init__(self, *args):
9074 __init__(_ConstOptimizer self, Model m) -> _ConstOptimizer
9075 __init__(_ConstOptimizer self) -> _ConstOptimizer
9077 _IMP_kernel._ConstOptimizer_swiginit(self, _IMP_kernel.new__ConstOptimizer(*args))
9079 def do_optimize(self, max_steps):
9080 r"""do_optimize(_ConstOptimizer self, unsigned int max_steps) -> IMP::Float"""
9081 return _IMP_kernel._ConstOptimizer_do_optimize(self, max_steps)
9084 r"""get_version_info(_ConstOptimizer self) -> VersionInfo"""
9085 return _IMP_kernel._ConstOptimizer_get_version_info(self)
9086 __swig_destroy__ = _IMP_kernel.delete__ConstOptimizer
9089 r"""__str__(_ConstOptimizer self) -> std::string"""
9090 return _IMP_kernel._ConstOptimizer___str__(self)
9093 r"""__repr__(_ConstOptimizer self) -> std::string"""
9094 return _IMP_kernel._ConstOptimizer___repr__(self)
9098 return _object_cast_to__ConstOptimizer(o)
9101 def _get_as_binary(self):
9102 r"""_get_as_binary(_ConstOptimizer self) -> PyObject *"""
9103 return _IMP_kernel._ConstOptimizer__get_as_binary(self)
9105 def _set_from_binary(self, p):
9106 r"""_set_from_binary(_ConstOptimizer self, PyObject * p)"""
9107 return _IMP_kernel._ConstOptimizer__set_from_binary(self, p)
9109 def __getstate__(self):
9110 p = self._get_as_binary()
9111 if len(self.__dict__) > 1:
9112 d = self.__dict__.copy()
9117 def __setstate__(self, p):
9118 if not hasattr(self,
'this'):
9120 if isinstance(p, tuple):
9122 self.__dict__.update(d)
9123 return self._set_from_binary(p)
9127 _IMP_kernel._ConstOptimizer_swigregister(_ConstOptimizer)
9130 r"""get_particle(Particle p) -> Particle"""
9131 return _IMP_kernel.get_particle(p)
9133 def _decorator_test(p):
9134 r"""_decorator_test(Particle p)"""
9135 return _IMP_kernel._decorator_test(p)
9137 def _overloaded_decorator(*args):
9139 _overloaded_decorator(_TrivialDecorator a) -> int
9140 _overloaded_decorator(_TrivialDerivedDecorator a) -> int
9142 return _IMP_kernel._overloaded_decorator(*args)
9144 def _take_particles(*args):
9146 _take_particles(IMP::Particles const & ps) -> unsigned int
9147 _take_particles(Model m, IMP::Particles const & ps) -> unsigned int
9148 _take_particles(Model m, IMP::Particles const & ps, TextOutput out) -> unsigned int
9150 return _IMP_kernel._take_particles(*args)
9152 def _give_particles(m):
9153 r"""_give_particles(Model m) -> IMP::Particles const &"""
9154 return _IMP_kernel._give_particles(m)
9156 def _pass_particles(ps):
9157 r"""_pass_particles(IMP::Particles const & ps) -> IMP::Particles const &"""
9158 return _IMP_kernel._pass_particles(ps)
9160 def _pass_particle(ps):
9161 r"""_pass_particle(Particle ps) -> Particle"""
9162 return _IMP_kernel._pass_particle(ps)
9164 def _pass_particle_pair(pp):
9165 r"""_pass_particle_pair(IMP::ParticlePair const & pp) -> IMP::ParticlePair const &"""
9166 return _IMP_kernel._pass_particle_pair(pp)
9168 def _give_particles_copy(m):
9169 r"""_give_particles_copy(Model m) -> IMP::Particles"""
9170 return _IMP_kernel._give_particles_copy(m)
9172 def _pass_float_keys(input):
9173 r"""_pass_float_keys(IMP::FloatKeys const & input) -> IMP::FloatKeys"""
9174 return _IMP_kernel._pass_float_keys(input)
9178 _pass(IMP::Particles const & p) -> IMP::Particles const
9179 _pass(IMP::Restraints const & p) -> IMP::Restraints const &
9181 return _IMP_kernel._pass(*args)
9183 def _pass_decorators(p):
9184 r"""_pass_decorators(IMP::internal::_TrivialDecorators const & p) -> IMP::internal::_TrivialDecorators const &"""
9185 return _IMP_kernel._pass_decorators(p)
9187 def _pass_decorator_traits(p):
9188 r"""_pass_decorator_traits(IMP::internal::_TrivialTraitsDecorators const & p) -> IMP::internal::_TrivialTraitsDecorators const &"""
9189 return _IMP_kernel._pass_decorator_traits(p)
9191 def _pass_particle_pairs(p):
9192 r"""_pass_particle_pairs(IMP::ParticlePairsTemp const & p) -> IMP::ParticlePairsTemp"""
9193 return _IMP_kernel._pass_particle_pairs(p)
9195 def _pass_particle_index_pairs(p):
9196 r"""_pass_particle_index_pairs(IMP::ParticleIndexPairs const & p) -> IMP::ParticleIndexPairs"""
9197 return _IMP_kernel._pass_particle_index_pairs(p)
9199 def _pass_model_objects(p):
9200 r"""_pass_model_objects(IMP::ModelObjectsTemp const & p) -> IMP::ModelObjectsTemp"""
9201 return _IMP_kernel._pass_model_objects(p)
9203 def _pass_particles_temps(ps):
9204 r"""_pass_particles_temps(IMP::ParticlesTemps const & ps) -> IMP::ParticlesTemps"""
9205 return _IMP_kernel._pass_particles_temps(ps)
9207 def _test_overload(*args):
9209 _test_overload(IMP::Particles const & ps) -> int
9210 _test_overload(IMP::Restraints const & ps) -> int
9212 return _IMP_kernel._test_overload(*args)
9214 def _get_range(m, k):
9215 r"""_get_range(Model m, FloatKey k) -> IMP::FloatRange"""
9216 return _IMP_kernel._get_range(m, k)
9218 def _create_particles_from_pdb(name, m):
9219 r"""_create_particles_from_pdb(std::string name, Model m) -> IMP::ParticleIndexes"""
9220 return _IMP_kernel._create_particles_from_pdb(name, m)
9222 r"""Proxy of C++ IMP::internal::_LogPairScore class."""
9224 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9225 __repr__ = _swig_repr
9228 r"""__init__(_LogPairScore self) -> _LogPairScore"""
9229 _IMP_kernel._LogPairScore_swiginit(self, _IMP_kernel.new__LogPairScore())
9231 def do_get_inputs(self, arg2, arg3):
9232 r"""do_get_inputs(_LogPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
9233 return _IMP_kernel._LogPairScore_do_get_inputs(self, arg2, arg3)
9235 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
9236 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"""
9237 return _IMP_kernel._LogPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
9239 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
9240 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"""
9241 return _IMP_kernel._LogPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
9243 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
9244 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"""
9245 return _IMP_kernel._LogPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
9247 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
9248 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"""
9249 return _IMP_kernel._LogPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
9252 r"""get_version_info(_LogPairScore self) -> VersionInfo"""
9253 return _IMP_kernel._LogPairScore_get_version_info(self)
9254 __swig_destroy__ = _IMP_kernel.delete__LogPairScore
9256 def get_particle_pairs(self):
9257 r"""get_particle_pairs(_LogPairScore self) -> IMP::ParticlePairsTemp"""
9258 return _IMP_kernel._LogPairScore_get_particle_pairs(self)
9261 r"""clear(_LogPairScore self)"""
9262 return _IMP_kernel._LogPairScore_clear(self)
9264 def get_contains(self, pp):
9265 r"""get_contains(_LogPairScore self, IMP::ParticlePair const & pp) -> bool"""
9266 return _IMP_kernel._LogPairScore_get_contains(self, pp)
9269 _IMP_kernel._LogPairScore_swigregister(_LogPairScore)
9271 def _overloaded_particles(*args):
9273 _overloaded_particles(Particle arg1)
9274 _overloaded_particles(IMP::Particles const & arg1)
9275 _overloaded_particles(IMP::ParticlesTemp const & arg1)
9276 _overloaded_particles(Model arg1, IMP::ParticleIndexes const & arg2)
9277 _overloaded_particles(IMP::internal::_TrivialDecorators const & arg1)
9278 _overloaded_particles(_TrivialDecorator arg1)
9280 return _IMP_kernel._overloaded_particles(*args)
9281 class _ImplicitParticles(object):
9282 r"""Proxy of C++ IMP::internal::_ImplicitParticles class."""
9284 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9285 __repr__ = _swig_repr
9287 def __init__(self, *args):
9289 __init__(_ImplicitParticles self, Particle arg2) -> _ImplicitParticles
9290 __init__(_ImplicitParticles self, IMP::Particles const & arg2) -> _ImplicitParticles
9291 __init__(_ImplicitParticles self, IMP::ParticlesTemp const & arg2) -> _ImplicitParticles
9292 __init__(_ImplicitParticles self, Model arg2, IMP::ParticleIndexes const & arg3) -> _ImplicitParticles
9293 __init__(_ImplicitParticles self, IMP::internal::_TrivialDecorators const & arg2) -> _ImplicitParticles
9294 __init__(_ImplicitParticles self, _TrivialDecorator arg2) -> _ImplicitParticles
9296 _IMP_kernel._ImplicitParticles_swiginit(self, _IMP_kernel.new__ImplicitParticles(*args))
9297 __swig_destroy__ = _IMP_kernel.delete__ImplicitParticles
9300 _IMP_kernel._ImplicitParticles_swigregister(_ImplicitParticles)
9302 def _implicit_particles(arg1):
9303 r"""_implicit_particles(_ImplicitParticles arg1)"""
9304 return _IMP_kernel._implicit_particles(arg1)
9306 def _take_particle_adaptor(pa):
9307 r"""_take_particle_adaptor(_ParticleAdaptor pa) -> ParticleIndex"""
9308 return _IMP_kernel._take_particle_adaptor(pa)
9310 def _take_particle_indexes_adaptor(pa):
9311 r"""_take_particle_indexes_adaptor(_ParticleIndexesAdaptor pa) -> IMP::ParticleIndexes"""
9312 return _IMP_kernel._take_particle_indexes_adaptor(pa)
9314 r"""Proxy of C++ IMP::ScopedSetAttribute< IMP::FloatKey,IMP::Float > class."""
9316 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9318 def __init__(self, *args):
9320 __init__(ScopedSetFloatAttribute self) -> ScopedSetFloatAttribute
9321 __init__(ScopedSetFloatAttribute self, Particle p, FloatKey key, double const & value) -> ScopedSetFloatAttribute
9323 _IMP_kernel.ScopedSetFloatAttribute_swiginit(self, _IMP_kernel.new_ScopedSetFloatAttribute(*args))
9325 def set(self, p, key, value):
9326 r"""set(ScopedSetFloatAttribute self, Particle p, FloatKey key, double const & value)"""
9327 return _IMP_kernel.ScopedSetFloatAttribute_set(self, p, key, value)
9330 r"""reset(ScopedSetFloatAttribute self)"""
9331 return _IMP_kernel.ScopedSetFloatAttribute_reset(self)
9332 __swig_destroy__ = _IMP_kernel.delete_ScopedSetFloatAttribute
9334 def show(self, *args):
9335 r"""show(ScopedSetFloatAttribute self, _ostream out=std::cout)"""
9336 return _IMP_kernel.ScopedSetFloatAttribute_show(self, *args)
9339 r"""__str__(ScopedSetFloatAttribute self) -> std::string"""
9340 return _IMP_kernel.ScopedSetFloatAttribute___str__(self)
9343 r"""__repr__(ScopedSetFloatAttribute self) -> std::string"""
9344 return _IMP_kernel.ScopedSetFloatAttribute___repr__(self)
9347 _IMP_kernel.ScopedSetFloatAttribute_swigregister(ScopedSetFloatAttribute)
9349 def _get_module_data_path(module, file_name):
9350 r"""_get_module_data_path(std::string module, std::string file_name) -> std::string"""
9351 return _IMP_kernel._get_module_data_path(module, file_name)
9353 def _get_module_example_path(module, file_name):
9354 r"""_get_module_example_path(std::string module, std::string file_name) -> std::string"""
9355 return _IMP_kernel._get_module_example_path(module, file_name)
9364 if sys.platform ==
'win32' and 'IMP_LD_PATH' in os.environ:
9365 dirs = os.environ[
'IMP_LD_PATH'].split(
":")
9366 pathcomps = os.environ[
'PATH'].split(
";")
9368 if d
not in pathcomps:
9369 os.environ[
'PATH'] = d +
';' + os.environ[
'PATH']
9377 """Allow command line tools to easily implement multiple commands.
9378 Typically, an IMP command line tool will use an instance of this class
9379 to provide a consistent interface to multiple distinct commands
9380 from a single binary, rather than providing a potentially large
9381 number of binaries. This is similar to the way a number of common
9382 command line tools outside of IMP function (e.g. Git provides a single
9383 `git` tool which implements multiple commands - `git add`, `git commit`,
9384 `git push` and so on).
9386 Each command is implemented with a Python module of the same name
9387 that can be imported from the module (for example, if `module_name`
9388 is `IMP.foo`, the `bar` command is provided by the `IMP.foo.bar` Python
9389 module, which would usually be found as `modules/foo/pyext/src/bar.py`).
9390 Each such module should have a docstring and a `%main()` method
9391 that takes no arguments (the module should also call its `%main()` method
9392 if it is run directly, i.e. with something like
9393 `if __name__=="__main__": %main()`). The encompassing module
9394 (`IMP.foo` in the example) should define `_all_commands` as a Python
9395 list of all valid commands.
9397 See the `multifit` and `cnmultifit` command line tools for example
9401 def __init__(self, short_help, long_help, module_name):
9403 @param short_help A few words that describe the command line tool.
9404 @param long_help Longer text, used in the `help` command.
9405 @param module_name Name of the module (e.g. `IMP.foo`) that
9406 implements the commands.
9408 self.short_help = short_help
9409 self.long_help = long_help
9410 self.module_name = module_name
9411 self._all_commands = self.import_module()._all_commands
9412 self._progname = os.path.basename(sys.argv[0])
9415 """Call this method to act upon the user-provided command line"""
9416 if len(sys.argv) <= 1:
9417 print(self.short_help +
" Use '%s help' for help." % self._progname)
9419 command = sys.argv[1]
9420 if command
in (
'help',
'--help',
'-h'):
9421 if len(sys.argv) == 3:
9422 self.show_command_help(sys.argv[2])
9425 elif command ==
'--version':
9427 elif command
in self._all_commands:
9428 self.do_command(command)
9430 self.unknown_command(command)
9432 def import_module(self, mod=None):
9433 modname = self.module_name
9435 modname +=
"." + mod
9436 return __import__(modname, {}, {}, [
''])
9438 def unknown_command(self, command):
9439 print(
"Unknown command: '%s'" % command)
9440 print(
"Use '%s help' for help." % self._progname)
9443 def _get_version(self):
9446 def show_version(self):
9447 print(self._progname +
' ' + self._get_version())
9449 def show_help(self):
9450 ver = self._get_version()
9451 print(
"%s, version %s." % (self._progname, ver))
9452 print(self.long_help +
"""
9454 This program is part of IMP, the Integrative Modeling Platform,
9456 For additional information about IMP, see <https://integrativemodeling.org>.
9458 Usage: %s <command> [options] [args]
9461 commands = self._all_commands[:] + [
'help']
9463 cmdlen = max([len(c)
for c
in commands])
9466 doc =
'Get help on using %s.' % self._progname
9468 doc = self.import_module(c).__doc__
or "<no help>"
9469 c +=
' ' * (cmdlen - len(c))
9470 print(
' ' + c +
' ' + doc)
9472 Use "%s help <command>" for detailed help on any command
9473 or "%s --version" to see the version number.""" % (self._progname,
9476 def do_command(self, command):
9477 mod = self.import_module(command)
9478 sys.argv[0] = self._progname +
' ' + command
9482 def show_command_help(self, command):
9483 if command ==
'help':
9485 elif command
in self._all_commands
or command ==
'help':
9486 mod = self.import_module(command)
9487 sys.argv = [self._progname +
' ' + command,
'--help']
9490 self.unknown_command(command)
9497 g = networkx.DiGraph()
9498 if len(ig.get_vertices()) == 0:
9507 return self.p.get_name()
9509 def __call__(self, name):
9510 return self.p.__call__(name)
9512 for vi
in ig.get_vertices():
9513 n = ig.get_vertex_name(vi)
9514 g.add_node(NodeWrapper(n))
9515 for vi
in ig.get_vertices():
9516 n = ig.get_vertex_name(vi)
9517 for ni
in ig.get_out_neighbors(vi):
9518 nn = ig.get_vertex_name(ni)
9519 g.add_edge(NodeWrapper(n), NodeWrapper(nn))
9526 n0 = name.get_name()
9529 n1 = str(n0).replace(
'"',
'')
9530 n2 = n1.replace(
"\n",
'')
9533 from altgraph
import Graph, Dot
9534 graph = Graph.Graph()
9535 for i, v
in enumerate(g.get_vertices()):
9537 for i, v
in enumerate(g.get_vertices()):
9538 for n
in g.get_out_neighbors(v):
9539 graph.add_edge(v, n)
9540 dot = Dot.Dot(graph)
9541 for i, v
in enumerate(g.get_vertices()):
9542 dot.node_style(i, label=clean(g.get_vertex_name(v)))
9550 st = g.get_graphviz_string()
9551 with open(tfn,
"w")
as fh:
9554 print(
"running dot")
9555 sp = subprocess.Popen([
"dot",
"-Tpdf", tfn,
"-o" + tfon])
9559 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")
9562 if platform.system() ==
"Darwin":
9565 cmd = [
"gv",
"acroread",
"xpdf"]
9568 print(
"launching viewer " + c)
9570 subprocess.check_call([c, tfon])
9576 print(
"Could not display file. It is saved at " + tfon)
9586 """Mark a Python module as deprecated.
9587 @note The `module` argument would normally be `__name__`.
9588 @see [deprecation support](@ref deprecation)."""
9590 "Module %s is deprecated. %s\n" % (module, help_message))
9593 """Python decorator to mark a class as deprecated.
9594 @see [deprecation support](@ref deprecation)."""
9596 orig_init = obj.__init__
9599 @functools.wraps(orig_init, (
'__name__',
'__doc__'))
9600 def __init__(obj, *args, **keys):
9602 % (type(obj), help_message))
9603 orig_init(obj, *args, **keys)
9604 obj.__init__ = __init__
9609 """Python decorator to mark a method as deprecated.
9610 @see [deprecation support](@ref deprecation)."""
9611 def out_wrapper(obj):
9612 @functools.wraps(obj)
9613 def wrapper(cls, *args, **keys):
9615 % (obj.__name__, type(cls), help_message))
9616 return obj(cls, *args, **keys)
9621 """Python decorator to mark a function as deprecated.
9622 @see [deprecation support](@ref deprecation)."""
9623 def out_wrapper(obj):
9624 @functools.wraps(obj)
9625 def wrapper(*args, **keys):
9627 % (obj.__name__, help_message))
9628 return obj(*args, **keys)
9632 @contextlib.contextmanager
9634 """Context manager to temporarily allow (or disallow) deprecated code.
9635 @see [deprecation support](@ref deprecation)."""
9642 def _get_all_flags(ntokens):
9643 r"""_get_all_flags(unsigned int ntokens) -> IMP::Strings"""
9644 return _IMP_kernel._get_all_flags(ntokens)
9646 def _print_internal_help(out, description):
9647 r"""_print_internal_help(_ostream out, std::string description)"""
9648 return _IMP_kernel._print_internal_help(out, description)
9654 class _PassThroughAction(argparse.Action):
9655 """Pass an argument through to the IMP Boost parser"""
9656 def __call__(self, parser, namespace, values, option_string=None):
9657 parser._boost_command_line.append(option_string)
9659 parser._boost_command_line.append(values)
9662 if option_string
in (
'-h',
'--help',
'--help_advanced',
'--version'):
9663 parser._handle_boost()
9667 """IMP-specific subclass of argparse.ArgumentParser.
9668 This adds options common to all IMP applications
9669 (see IMP::setup_from_argv()).
9672 def __init__(self, *args, **kwargs):
9674 kwargs[
'add_help'] =
False
9675 super().__init__(*args, **kwargs)
9676 for ntoken
in (0, 1):
9677 flags = _get_all_flags(ntoken)
9679 arg = [
'-h',
'--help']
if f ==
'help' else [
'--' + f]
9680 self.add_argument(*arg, help=argparse.SUPPRESS,
9681 nargs=
None if ntoken
else 0,
9682 action=_PassThroughAction,
9683 default=argparse.SUPPRESS)
9686 """Parse the command line and return optional and positional arguments.
9687 This functions in the same way as the method in the base class
9688 argparse.ArgumentParser, except that it also processes optional
9689 arguments common to all IMP applications (these are not returned
9690 in `args`, but can be obtained in the usual way, e.g. by calling
9691 IMP::get_string_flag()).
9694 self._boost_command_line = [sys.argv[0]]
9696 if len(self._boost_command_line) > 1:
9697 self._handle_boost()
9700 def _get_description(self):
9701 return self.format_help() +
"\nOptions common to all IMP applications:"
9703 def print_help(self, file=None):
9704 _print_internal_help(file
if file
else sys.stdout,
9705 self._get_description())
9707 def _handle_boost(self):
9709 self._get_description(),
9712 class RandomNumberGenerator(object):
9713 r"""Proxy of C++ IMP::RandomNumberGenerator class."""
9715 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9716 __repr__ = _swig_repr
9719 r"""seed(RandomNumberGenerator self, int x)"""
9720 return _IMP_kernel.RandomNumberGenerator_seed(self, x)
9723 r"""__call__(RandomNumberGenerator self) -> int"""
9724 return _IMP_kernel.RandomNumberGenerator___call__(self)
9727 r"""__init__(RandomNumberGenerator self) -> RandomNumberGenerator"""
9728 _IMP_kernel.RandomNumberGenerator_swiginit(self, _IMP_kernel.new_RandomNumberGenerator())
9729 __swig_destroy__ = _IMP_kernel.delete_RandomNumberGenerator
9732 _IMP_kernel.RandomNumberGenerator_swigregister(RandomNumberGenerator)
9736 get_random_float_uniform() -> float
9737 get_random_float_uniform(float min, float max) -> float
9739 return _IMP_kernel.get_random_float_uniform(*args)
9743 get_random_double_uniform() -> double
9744 get_random_double_uniform(double min, double max) -> double
9746 return _IMP_kernel.get_random_double_uniform(*args)
9748 def get_random_floats_normal(n, mean=0.0, stddev=1.0):
9749 r"""get_random_floats_normal(unsigned int n, float mean=0.0, float stddev=1.0) -> IMP::Vector< float,std::allocator< float > >"""
9750 return _IMP_kernel.get_random_floats_normal(n, mean, stddev)
9752 def get_random_doubles_normal(n, mean=0.0, stddev=1.0):
9753 r"""get_random_doubles_normal(unsigned int n, double mean=0.0, double stddev=1.0) -> IMP::Vector< double,std::allocator< double > >"""
9754 return _IMP_kernel.get_random_doubles_normal(n, mean, stddev)
9756 def get_random_floats_uniform(n):
9757 r"""get_random_floats_uniform(unsigned int n) -> IMP::Vector< float,std::allocator< float > >"""
9758 return _IMP_kernel.get_random_floats_uniform(n)
9760 def get_random_doubles_uniform(n):
9761 r"""get_random_doubles_uniform(unsigned int n) -> IMP::Vector< double,std::allocator< double > >"""
9762 return _IMP_kernel.get_random_doubles_uniform(n)
9765 r"""get_random_seed() -> boost::uint64_t"""
9766 return _IMP_kernel.get_random_seed()
9768 def _get_derivatives_numpy(m, k, m_pyobj, read_only):
9769 r"""_get_derivatives_numpy(Model m, FloatKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9770 return _IMP_kernel._get_derivatives_numpy(m, k, m_pyobj, read_only)
9772 def _get_floats_numpy(m, k, m_pyobj, read_only):
9773 r"""_get_floats_numpy(Model m, FloatKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9774 return _IMP_kernel._get_floats_numpy(m, k, m_pyobj, read_only)
9776 def _get_ints_numpy(m, k, m_pyobj, read_only):
9777 r"""_get_ints_numpy(Model m, IntKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9778 return _IMP_kernel._get_ints_numpy(m, k, m_pyobj, read_only)
9780 def _get_vector3ds_numpy(m, k, m_pyobj, read_only):
9781 r"""_get_vector3ds_numpy(Model m, Vector3DKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9782 return _IMP_kernel._get_vector3ds_numpy(m, k, m_pyobj, read_only)
9784 def _get_spheres_numpy(m, m_pyobj, read_only):
9785 r"""_get_spheres_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9786 return _IMP_kernel._get_spheres_numpy(m, m_pyobj, read_only)
9788 def _get_sphere_derivatives_numpy(m, m_pyobj, read_only):
9789 r"""_get_sphere_derivatives_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9790 return _IMP_kernel._get_sphere_derivatives_numpy(m, m_pyobj, read_only)
9794 ParticleIndex = numpy.intc
9799 def get_module_name():
9800 r"""get_module_name() -> std::string const"""
9801 return _IMP_kernel.get_module_name()
9804 r"""get_module_version() -> std::string const"""
9805 return _IMP_kernel.get_module_version()
9808 r"""get_example_path(std::string fname) -> std::string"""
9809 return _IMP_kernel.get_example_path(fname)
9812 r"""get_data_path(std::string fname) -> std::string"""
9813 return _IMP_kernel.get_data_path(fname)
9815 from .
import _version_check
9820 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.
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.
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.
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)
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< 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.
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)
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)
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.
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.
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 FloatKey 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.
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.
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)
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.
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.