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""")
4465 def _wrap_jax(self, score_func):
4466 """Use in _get_jax() to wrap the JAX scoring function with other
4467 model- and restraint-specific information"""
4468 from IMP._jax_util
import JaxInfo
4469 return JaxInfo(m=self.get_model(), score_func=score_func,
4470 weight=self.get_weight())
4474 r"""__str__(Restraint self) -> std::string"""
4475 return _IMP_kernel.Restraint___str__(self)
4478 r"""__repr__(Restraint self) -> std::string"""
4479 return _IMP_kernel.Restraint___repr__(self)
4483 return _object_cast_to_Restraint(o)
4486 def do_show(self, out):
4491 return _object_cast_to_Restraint(o)
4493 def __disown__(self):
4495 _IMP_kernel.disown_Restraint(self)
4496 return weakref.proxy(self)
4499 r"""do_destroy(Restraint self)"""
4500 return _IMP_kernel.Restraint_do_destroy(self)
4502 def handle_set_has_required_score_states(self, arg0):
4503 r"""handle_set_has_required_score_states(Restraint self, bool arg0)"""
4504 return _IMP_kernel.Restraint_handle_set_has_required_score_states(self, arg0)
4506 def do_get_inputs(self):
4507 r"""do_get_inputs(Restraint self) -> IMP::ModelObjectsTemp"""
4508 return _IMP_kernel.Restraint_do_get_inputs(self)
4510 def do_get_interactions(self):
4511 r"""do_get_interactions(Restraint self) -> IMP::ModelObjectsTemps"""
4512 return _IMP_kernel.Restraint_do_get_interactions(self)
4515 _IMP_kernel.Restraint_swigregister(Restraint)
4516 class _RestraintsAdaptor(_InputAdaptor):
4517 r"""Proxy of C++ IMP::RestraintsAdaptor class."""
4519 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4520 __repr__ = _swig_repr
4522 def __init__(self, *args):
4524 __init__(_RestraintsAdaptor self) -> _RestraintsAdaptor
4525 __init__(_RestraintsAdaptor self, IMP::Restraints const & sf) -> _RestraintsAdaptor
4526 __init__(_RestraintsAdaptor self, IMP::RestraintsTemp const & sf) -> _RestraintsAdaptor
4527 __init__(_RestraintsAdaptor self, Restraint sf) -> _RestraintsAdaptor
4529 _IMP_kernel._RestraintsAdaptor_swiginit(self, _IMP_kernel.new__RestraintsAdaptor(*args))
4530 __swig_destroy__ = _IMP_kernel.delete__RestraintsAdaptor
4533 _IMP_kernel._RestraintsAdaptor_swigregister(_RestraintsAdaptor)
4534 class RestraintSet(Restraint):
4535 r"""Proxy of C++ IMP::RestraintSet class."""
4537 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4539 def __init__(self, *args):
4541 __init__(RestraintSet self, Model m, double weight, std::string const & name="RestraintSet %1%") -> RestraintSet
4542 __init__(RestraintSet self, Model m, std::string const & name="RestraintSet %1%") -> RestraintSet
4543 __init__(RestraintSet self, IMP::RestraintsTemp const & rs, double weight, std::string const & name="RestraintSet %1%") -> RestraintSet
4544 __init__(RestraintSet self) -> RestraintSet
4546 if self.__class__ == RestraintSet:
4550 _IMP_kernel.RestraintSet_swiginit(self, _IMP_kernel.new_RestraintSet(_self, *args))
4552 if self.__class__ != RestraintSet:
4553 _director_objects.register(self)
4558 def unprotected_evaluate(self, da):
4559 r"""unprotected_evaluate(RestraintSet self, DerivativeAccumulator da) -> double"""
4560 return _IMP_kernel.RestraintSet_unprotected_evaluate(self, da)
4562 def get_type_name(self):
4563 r"""get_type_name(RestraintSet self) -> std::string"""
4564 return _IMP_kernel.RestraintSet_get_type_name(self)
4567 r"""get_version_info(RestraintSet self) -> VersionInfo"""
4568 return _IMP_kernel.RestraintSet_get_version_info(self)
4569 __swig_destroy__ = _IMP_kernel.delete_RestraintSet
4570 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)
4571 def __set_restraints(self, obj): _list_util.set_varlist(self.restraints, obj)
4572 def __del_restraints(self): _list_util.del_varlist(self.restraints)
4573 restraints = property(__get_restraints, __set_restraints, __del_restraints, doc=
"List of ##ucnames")
4575 def remove_restraint(self, d):
4576 r"""remove_restraint(RestraintSet self, Restraint d)"""
4577 return _IMP_kernel.RestraintSet_remove_restraint(self, d)
4579 def _python_index_restraint(self, d, start, stop):
4580 r"""_python_index_restraint(RestraintSet self, Restraint d, unsigned int start, unsigned int stop) -> unsigned int"""
4581 return _IMP_kernel.RestraintSet__python_index_restraint(self, d, start, stop)
4583 def remove_restraints(self, d):
4584 r"""remove_restraints(RestraintSet self, IMP::Restraints const & d)"""
4585 return _IMP_kernel.RestraintSet_remove_restraints(self, d)
4587 def set_restraints(self, ps):
4588 r"""set_restraints(RestraintSet self, IMP::Restraints const & ps)"""
4589 return _IMP_kernel.RestraintSet_set_restraints(self, ps)
4591 def set_restraints_order(self, objs):
4592 r"""set_restraints_order(RestraintSet self, IMP::Restraints const & objs)"""
4593 return _IMP_kernel.RestraintSet_set_restraints_order(self, objs)
4596 r"""add_restraint(RestraintSet self, Restraint obj) -> unsigned int"""
4597 return _IMP_kernel.RestraintSet_add_restraint(self, obj)
4600 r"""add_restraints(RestraintSet self, IMP::Restraints const & objs)"""
4601 return _IMP_kernel.RestraintSet_add_restraints(self, objs)
4603 def clear_restraints(self):
4604 r"""clear_restraints(RestraintSet self)"""
4605 return _IMP_kernel.RestraintSet_clear_restraints(self)
4607 def get_number_of_restraints(self):
4608 r"""get_number_of_restraints(RestraintSet self) -> unsigned int"""
4609 return _IMP_kernel.RestraintSet_get_number_of_restraints(self)
4611 def get_has_restraints(self):
4612 r"""get_has_restraints(RestraintSet self) -> bool"""
4613 return _IMP_kernel.RestraintSet_get_has_restraints(self)
4615 def get_restraint(self, i):
4616 r"""get_restraint(RestraintSet self, unsigned int i) -> Restraint"""
4617 return _IMP_kernel.RestraintSet_get_restraint(self, i)
4619 def get_restraints(self):
4620 r"""get_restraints(RestraintSet self) -> IMP::Restraints"""
4621 return _IMP_kernel.RestraintSet_get_restraints(self)
4623 def erase_restraint(self, i):
4624 r"""erase_restraint(RestraintSet self, unsigned int i)"""
4625 return _IMP_kernel.RestraintSet_erase_restraint(self, i)
4627 def reserve_restraints(self, sz):
4628 r"""reserve_restraints(RestraintSet self, unsigned int sz)"""
4629 return _IMP_kernel.RestraintSet_reserve_restraints(self, sz)
4631 def get_non_sets_and_sets(self):
4632 r"""get_non_sets_and_sets(RestraintSet self) -> std::pair< IMP::RestraintsTemp,IMP::RestraintSetsTemp >"""
4633 return _IMP_kernel.RestraintSet_get_non_sets_and_sets(self)
4635 def do_get_inputs(self):
4636 r"""do_get_inputs(RestraintSet self) -> IMP::ModelObjectsTemp"""
4637 return _IMP_kernel.RestraintSet_do_get_inputs(self)
4640 r"""create_scoring_function(RestraintSet self, double weight=1.0, double max=std::numeric_limits< double >::max()) -> ScoringFunction"""
4641 return _IMP_kernel.RestraintSet_create_scoring_function(self, *args)
4643 def get_last_score(self):
4644 r"""get_last_score(RestraintSet self) -> double"""
4645 return _IMP_kernel.RestraintSet_get_last_score(self)
4648 r"""__str__(RestraintSet self) -> std::string"""
4649 return _IMP_kernel.RestraintSet___str__(self)
4652 r"""__repr__(RestraintSet self) -> std::string"""
4653 return _IMP_kernel.RestraintSet___repr__(self)
4657 return _object_cast_to_RestraintSet(o)
4660 def do_show(self, out):
4665 return _object_cast_to_RestraintSet(o)
4668 def _get_as_binary(self):
4669 r"""_get_as_binary(RestraintSet self) -> PyObject *"""
4670 return _IMP_kernel.RestraintSet__get_as_binary(self)
4672 def _set_from_binary(self, p):
4673 r"""_set_from_binary(RestraintSet self, PyObject * p)"""
4674 return _IMP_kernel.RestraintSet__set_from_binary(self, p)
4676 def __getstate__(self):
4677 p = self._get_as_binary()
4678 if len(self.__dict__) > 1:
4679 d = self.__dict__.copy()
4684 def __setstate__(self, p):
4685 if not hasattr(self,
'this'):
4687 if isinstance(p, tuple):
4689 self.__dict__.update(d)
4690 return self._set_from_binary(p)
4692 def __disown__(self):
4694 _IMP_kernel.disown_RestraintSet(self)
4695 return weakref.proxy(self)
4698 r"""do_destroy(RestraintSet self)"""
4699 return _IMP_kernel.RestraintSet_do_destroy(self)
4701 def handle_set_has_required_score_states(self, arg0):
4702 r"""handle_set_has_required_score_states(RestraintSet self, bool arg0)"""
4703 return _IMP_kernel.RestraintSet_handle_set_has_required_score_states(self, arg0)
4705 def do_get_outputs(self):
4706 r"""do_get_outputs(RestraintSet self) -> IMP::ModelObjectsTemp"""
4707 return _IMP_kernel.RestraintSet_do_get_outputs(self)
4709 def do_get_interactions(self):
4710 r"""do_get_interactions(RestraintSet self) -> IMP::ModelObjectsTemps"""
4711 return _IMP_kernel.RestraintSet_do_get_interactions(self)
4713 def do_create_decomposition(self):
4714 r"""do_create_decomposition(RestraintSet self) -> IMP::Restraints"""
4715 return _IMP_kernel.RestraintSet_do_create_decomposition(self)
4717 def do_create_current_decomposition(self):
4718 r"""do_create_current_decomposition(RestraintSet self) -> IMP::Restraints"""
4719 return _IMP_kernel.RestraintSet_do_create_current_decomposition(self)
4721 def do_add_score_and_derivatives(self, sa):
4722 r"""do_add_score_and_derivatives(RestraintSet self, ScoreAccumulator sa)"""
4723 return _IMP_kernel.RestraintSet_do_add_score_and_derivatives(self, sa)
4725 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis):
4726 r"""do_add_score_and_derivatives_moved(RestraintSet self, ScoreAccumulator sa, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
4727 return _IMP_kernel.RestraintSet_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis)
4730 _IMP_kernel.RestraintSet_swigregister(RestraintSet)
4732 def get_restraints(rs):
4733 r"""get_restraints(IMP::RestraintsTemp const & rs) -> IMP::RestraintsTemp"""
4734 return _IMP_kernel.get_restraints(rs)
4736 def _check_particle(p, a):
4737 if (
not p.get_is_active()):
4738 raise ValueError(
"Inactive Particle")
4739 if (type(a)() == a):
4740 raise IndexError(
"Cannot use default Index")
4741 if (
not p.has_attribute(a)):
4742 raise IndexError(
"Particle does not have attribute")
4744 class Particle(ModelObject):
4745 r"""Proxy of C++ IMP::Particle class."""
4747 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
4750 r"""get_version_info(Particle self) -> VersionInfo"""
4751 return _IMP_kernel.Particle_get_version_info(self)
4752 __swig_destroy__ = _IMP_kernel.delete_Particle
4754 def __init__(self, *args):
4756 __init__(Particle self, Model m, std::string name) -> Particle
4757 __init__(Particle self, Model m) -> Particle
4758 __init__(Particle self) -> Particle
4760 _IMP_kernel.Particle_swiginit(self, _IMP_kernel.new_Particle(*args))
4762 def get_float_keys(self):
4763 r"""get_float_keys(Particle self) -> IMP::FloatKeys"""
4764 return _IMP_kernel.Particle_get_float_keys(self)
4766 def get_floats_keys(self):
4767 r"""get_floats_keys(Particle self) -> IMP::FloatsKeys"""
4768 return _IMP_kernel.Particle_get_floats_keys(self)
4770 def get_int_keys(self):
4771 r"""get_int_keys(Particle self) -> IMP::IntKeys"""
4772 return _IMP_kernel.Particle_get_int_keys(self)
4774 def get_ints_keys(self):
4775 r"""get_ints_keys(Particle self) -> IMP::IntsKeys"""
4776 return _IMP_kernel.Particle_get_ints_keys(self)
4778 def get_string_keys(self):
4779 r"""get_string_keys(Particle self) -> IMP::StringKeys"""
4780 return _IMP_kernel.Particle_get_string_keys(self)
4782 def get_object_keys(self):
4783 r"""get_object_keys(Particle self) -> IMP::ObjectKeys"""
4784 return _IMP_kernel.Particle_get_object_keys(self)
4786 def add_cache_attribute(self, *args):
4788 add_cache_attribute(Particle self, FloatKey name, IMP::Float value)
4789 add_cache_attribute(Particle self, FloatsKey name, IMP::Floats value)
4790 add_cache_attribute(Particle self, IntKey name, IMP::Int value)
4791 add_cache_attribute(Particle self, IntsKey name, IMP::Ints value)
4792 add_cache_attribute(Particle self, StringKey name, IMP::String value)
4793 add_cache_attribute(Particle self, ObjectKey name, Object value)
4794 add_cache_attribute(Particle self, IMP::WeakObjectKey name, Object value)
4796 return _IMP_kernel.Particle_add_cache_attribute(self, *args)
4798 def get_weak_object_keys(self):
4799 r"""get_weak_object_keys(Particle self) -> IMP::WeakObjectKeys"""
4800 return _IMP_kernel.Particle_get_weak_object_keys(self)
4802 def add_to_derivative(self, key, value, da):
4803 r"""add_to_derivative(Particle self, FloatKey key, IMP::Float value, DerivativeAccumulator da)"""
4804 return _IMP_kernel.Particle_add_to_derivative(self, key, value, da)
4806 def set_is_optimized(self, k, tf):
4807 r"""set_is_optimized(Particle self, FloatKey k, bool tf)"""
4808 return _IMP_kernel.Particle_set_is_optimized(self, k, tf)
4810 def get_is_optimized(self, k):
4811 r"""get_is_optimized(Particle self, FloatKey k) -> bool"""
4812 return _IMP_kernel.Particle_get_is_optimized(self, k)
4814 def get_derivative(self, k):
4815 r"""get_derivative(Particle self, FloatKey k) -> IMP::Float"""
4816 return _IMP_kernel.Particle_get_derivative(self, k)
4818 def add_attribute(self, *args):
4820 add_attribute(Particle self, FloatKey name, IMP::Float initial_value)
4821 add_attribute(Particle self, FloatsKey name, IMP::Floats initial_value)
4822 add_attribute(Particle self, IntKey name, IMP::Int initial_value)
4823 add_attribute(Particle self, IntsKey name, IMP::Ints initial_value)
4824 add_attribute(Particle self, StringKey name, IMP::String initial_value)
4825 add_attribute(Particle self, ObjectKey name, Object initial_value)
4826 add_attribute(Particle self, IMP::WeakObjectKey name, Object initial_value)
4827 add_attribute(Particle self, SparseStringKey name, IMP::String initial_value)
4828 add_attribute(Particle self, SparseIntKey name, IMP::Int initial_value)
4829 add_attribute(Particle self, SparseFloatKey name, IMP::Float initial_value)
4830 add_attribute(Particle self, SparseParticleIndexKey name, ParticleIndex initial_value)
4831 add_attribute(Particle self, FloatKey name, IMP::Float const initial_value, bool optimized)
4832 add_attribute(Particle self, ParticleIndexKey k, Particle v)
4834 return _IMP_kernel.Particle_add_attribute(self, *args)
4836 def has_attribute(self, *args):
4838 has_attribute(Particle self, FloatKey name) -> bool
4839 has_attribute(Particle self, FloatsKey name) -> bool
4840 has_attribute(Particle self, IntKey name) -> bool
4841 has_attribute(Particle self, IntsKey name) -> bool
4842 has_attribute(Particle self, StringKey name) -> bool
4843 has_attribute(Particle self, ObjectKey name) -> bool
4844 has_attribute(Particle self, IMP::WeakObjectKey name) -> bool
4845 has_attribute(Particle self, SparseStringKey name) -> bool
4846 has_attribute(Particle self, SparseIntKey name) -> bool
4847 has_attribute(Particle self, SparseFloatKey name) -> bool
4848 has_attribute(Particle self, SparseParticleIndexKey name) -> bool
4849 has_attribute(Particle self, ParticleIndexKey k) -> bool
4851 return _IMP_kernel.Particle_has_attribute(self, *args)
4853 def set_value(self, *args):
4855 set_value(Particle self, FloatKey name, IMP::Float value)
4856 set_value(Particle self, FloatsKey name, IMP::Floats value)
4857 set_value(Particle self, IntKey name, IMP::Int value)
4858 set_value(Particle self, IntsKey name, IMP::Ints value)
4859 set_value(Particle self, StringKey name, IMP::String value)
4860 set_value(Particle self, ObjectKey name, Object value)
4861 set_value(Particle self, IMP::WeakObjectKey name, Object value)
4862 set_value(Particle self, SparseStringKey name, IMP::String value)
4863 set_value(Particle self, SparseIntKey name, IMP::Int value)
4864 set_value(Particle self, SparseFloatKey name, IMP::Float value)
4865 set_value(Particle self, SparseParticleIndexKey name, ParticleIndex value)
4866 set_value(Particle self, ParticleIndexKey k, Particle v)
4868 return _IMP_kernel.Particle_set_value(self, *args)
4870 def get_value(self, *args):
4872 get_value(Particle self, FloatKey name) -> IMP::Float
4873 get_value(Particle self, FloatsKey name) -> IMP::Floats
4874 get_value(Particle self, IntKey name) -> IMP::Int
4875 get_value(Particle self, IntsKey name) -> IMP::Ints
4876 get_value(Particle self, StringKey name) -> IMP::String
4877 get_value(Particle self, ObjectKey name) -> Object
4878 get_value(Particle self, IMP::WeakObjectKey name) -> Object
4879 get_value(Particle self, SparseStringKey name) -> IMP::String
4880 get_value(Particle self, SparseIntKey name) -> IMP::Int
4881 get_value(Particle self, SparseFloatKey name) -> IMP::Float
4882 get_value(Particle self, SparseParticleIndexKey name) -> ParticleIndex
4883 get_value(Particle self, ParticleIndexKey k) -> Particle
4885 return _IMP_kernel.Particle_get_value(self, *args)
4887 def remove_attribute(self, *args):
4889 remove_attribute(Particle self, FloatKey name)
4890 remove_attribute(Particle self, FloatsKey name)
4891 remove_attribute(Particle self, IntKey name)
4892 remove_attribute(Particle self, IntsKey name)
4893 remove_attribute(Particle self, StringKey name)
4894 remove_attribute(Particle self, ObjectKey name)
4895 remove_attribute(Particle self, IMP::WeakObjectKey name)
4896 remove_attribute(Particle self, SparseStringKey name)
4897 remove_attribute(Particle self, SparseIntKey name)
4898 remove_attribute(Particle self, SparseFloatKey name)
4899 remove_attribute(Particle self, SparseParticleIndexKey name)
4900 remove_attribute(Particle self, ParticleIndexKey k)
4902 return _IMP_kernel.Particle_remove_attribute(self, *args)
4904 def get_particle_keys(self):
4905 r"""get_particle_keys(Particle self) -> IMP::ParticleIndexKeys"""
4906 return _IMP_kernel.Particle_get_particle_keys(self)
4908 def show(self, *args):
4909 r"""show(Particle self, _ostream out=std::cout)"""
4910 return _IMP_kernel.Particle_show(self, *args)
4912 def get_is_active(self):
4913 r"""get_is_active(Particle self) -> bool"""
4914 return _IMP_kernel.Particle_get_is_active(self)
4917 r"""get_index(Particle self) -> ParticleIndex"""
4918 return _IMP_kernel.Particle_get_index(self)
4920 def __eq__(self, *args):
4922 __eq__(Particle self, Particle o) -> bool
4923 __eq__(Particle self, Decorator d) -> bool
4925 return _IMP_kernel.Particle___eq__(self, *args)
4927 def __ne__(self, *args):
4929 __ne__(Particle self, Particle o) -> bool
4930 __ne__(Particle self, Decorator d) -> bool
4932 return _IMP_kernel.Particle___ne__(self, *args)
4934 def __le__(self, *args):
4936 __le__(Particle self, Particle o) -> bool
4937 __le__(Particle self, Decorator d) -> bool
4939 return _IMP_kernel.Particle___le__(self, *args)
4941 def __lt__(self, *args):
4943 __lt__(Particle self, Particle o) -> bool
4944 __lt__(Particle self, Decorator d) -> bool
4946 return _IMP_kernel.Particle___lt__(self, *args)
4948 def __ge__(self, *args):
4950 __ge__(Particle self, Particle o) -> bool
4951 __ge__(Particle self, Decorator d) -> bool
4953 return _IMP_kernel.Particle___ge__(self, *args)
4955 def __gt__(self, *args):
4957 __gt__(Particle self, Particle o) -> bool
4958 __gt__(Particle self, Decorator d) -> bool
4960 return _IMP_kernel.Particle___gt__(self, *args)
4962 __hash__ = ModelObject.__hash__
4966 r"""__str__(Particle self) -> std::string"""
4967 return _IMP_kernel.Particle___str__(self)
4970 r"""__repr__(Particle self) -> std::string"""
4971 return _IMP_kernel.Particle___repr__(self)
4975 return _object_cast_to_Particle(o)
4978 def _get_as_binary(self):
4979 r"""_get_as_binary(Particle self) -> PyObject *"""
4980 return _IMP_kernel.Particle__get_as_binary(self)
4982 def _set_from_binary(self, p):
4983 r"""_set_from_binary(Particle self, PyObject * p)"""
4984 return _IMP_kernel.Particle__set_from_binary(self, p)
4986 def __getstate__(self):
4987 p = self._get_as_binary()
4988 if len(self.__dict__) > 1:
4989 d = self.__dict__.copy()
4994 def __setstate__(self, p):
4995 if not hasattr(self,
'this'):
4997 if isinstance(p, tuple):
4999 self.__dict__.update(d)
5000 return self._set_from_binary(p)
5004 _IMP_kernel.Particle_swigregister(Particle)
5005 class _ParticleAdaptor(_InputAdaptor):
5006 r"""Proxy of C++ IMP::ParticleAdaptor class."""
5008 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5009 __repr__ = _swig_repr
5011 def __init__(self, *args):
5013 __init__(_ParticleAdaptor self) -> _ParticleAdaptor
5014 __init__(_ParticleAdaptor self, Particle p) -> _ParticleAdaptor
5015 __init__(_ParticleAdaptor self, Decorator d) -> _ParticleAdaptor
5017 _IMP_kernel._ParticleAdaptor_swiginit(self, _IMP_kernel.new__ParticleAdaptor(*args))
5019 def get_model(self):
5020 r"""get_model(_ParticleAdaptor self) -> Model"""
5021 return _IMP_kernel._ParticleAdaptor_get_model(self)
5023 def get_particle_index(self):
5024 r"""get_particle_index(_ParticleAdaptor self) -> ParticleIndex"""
5025 return _IMP_kernel._ParticleAdaptor_get_particle_index(self)
5026 __swig_destroy__ = _IMP_kernel.delete__ParticleAdaptor
5029 _IMP_kernel._ParticleAdaptor_swigregister(_ParticleAdaptor)
5030 class _DependencyGraphVertexIndex(object):
5031 r"""Proxy of C++ IMP::DependencyGraphVertexIndex class."""
5033 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5034 __repr__ = _swig_repr
5037 r"""__init__(_DependencyGraphVertexIndex self) -> _DependencyGraphVertexIndex"""
5038 _IMP_kernel._DependencyGraphVertexIndex_swiginit(self, _IMP_kernel.new__DependencyGraphVertexIndex())
5039 __swig_destroy__ = _IMP_kernel.delete__DependencyGraphVertexIndex
5042 _IMP_kernel._DependencyGraphVertexIndex_swigregister(_DependencyGraphVertexIndex)
5044 def show_as_graphviz(name, out):
5045 r"""show_as_graphviz(IMP::DependencyGraph const & name, TextOutput out)"""
5046 return _IMP_kernel.show_as_graphviz(name, out)
5048 def get_vertex_index(g):
5049 r"""get_vertex_index(IMP::DependencyGraph const & g) -> _DependencyGraphVertexIndex"""
5050 return _IMP_kernel.get_vertex_index(g)
5053 r"""get_dependency_graph(Model m) -> IMP::DependencyGraph"""
5054 return _IMP_kernel.get_dependency_graph(m)
5057 r"""get_pruned_dependency_graph(Model m) -> IMP::DependencyGraph"""
5058 return _IMP_kernel.get_pruned_dependency_graph(m)
5060 def get_dependent_particles(p, all, dg, index):
5061 r"""get_dependent_particles(ModelObject p, IMP::ModelObjectsTemp const & all, IMP::DependencyGraph const & dg, _DependencyGraphVertexIndex index) -> IMP::ParticlesTemp"""
5062 return _IMP_kernel.get_dependent_particles(p, all, dg, index)
5064 def get_required_score_states(*args):
5066 get_required_score_states(IMP::ModelObjectsTemp const & mos, IMP::ScoreStatesTemp exclude=IMP::ScoreStatesTemp()) -> IMP::ScoreStatesTemp
5067 get_required_score_states(ModelObject p, IMP::ModelObjectsTemp const & all, IMP::DependencyGraph const & dg, _DependencyGraphVertexIndex index) -> IMP::ScoreStatesTemp
5068 get_required_score_states(Model m, ParticleIndex pi) -> IMP::ScoreStatesTemp
5070 return _IMP_kernel.get_required_score_states(*args)
5071 class ScoringFunction(ModelObject):
5072 r"""Proxy of C++ IMP::ScoringFunction class."""
5074 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5076 def do_add_score_and_derivatives(self, sa, ss):
5077 r"""do_add_score_and_derivatives(ScoringFunction self, ScoreAccumulator sa, IMP::ScoreStatesTemp const & ss)"""
5078 return _IMP_kernel.ScoringFunction_do_add_score_and_derivatives(self, sa, ss)
5080 def do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss):
5081 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)"""
5082 return _IMP_kernel.ScoringFunction_do_add_score_and_derivatives_moved(self, sa, moved_pis, reset_pis, ss)
5084 def get_score_accumulator_if_below(self, deriv, max):
5085 r"""get_score_accumulator_if_below(ScoringFunction self, bool deriv, double max) -> ScoreAccumulator"""
5086 return _IMP_kernel.ScoringFunction_get_score_accumulator_if_below(self, deriv, max)
5088 def get_score_accumulator_if_good(self, deriv):
5089 r"""get_score_accumulator_if_good(ScoringFunction self, bool deriv) -> ScoreAccumulator"""
5090 return _IMP_kernel.ScoringFunction_get_score_accumulator_if_good(self, deriv)
5092 def get_score_accumulator(self, deriv):
5093 r"""get_score_accumulator(ScoringFunction self, bool deriv) -> ScoreAccumulator"""
5094 return _IMP_kernel.ScoringFunction_get_score_accumulator(self, deriv)
5096 def __init__(self, *args):
5098 __init__(ScoringFunction self, Model m, std::string name) -> ScoringFunction
5099 __init__(ScoringFunction self) -> ScoringFunction
5101 if self.__class__ == ScoringFunction:
5105 _IMP_kernel.ScoringFunction_swiginit(self, _IMP_kernel.new_ScoringFunction(_self, *args))
5107 if self.__class__ != ScoringFunction:
5108 _director_objects.register(self)
5113 def do_get_outputs(self):
5114 r"""do_get_outputs(ScoringFunction self) -> IMP::ModelObjectsTemp"""
5115 return _IMP_kernel.ScoringFunction_do_get_outputs(self)
5117 def evaluate(self, derivatives):
5118 r"""evaluate(ScoringFunction self, bool derivatives) -> double"""
5119 return _IMP_kernel.ScoringFunction_evaluate(self, derivatives)
5121 def evaluate_if_good(self, derivatives):
5122 r"""evaluate_if_good(ScoringFunction self, bool derivatives) -> double"""
5123 return _IMP_kernel.ScoringFunction_evaluate_if_good(self, derivatives)
5125 def evaluate_if_below(self, derivatives, max):
5126 r"""evaluate_if_below(ScoringFunction self, bool derivatives, double max) -> double"""
5127 return _IMP_kernel.ScoringFunction_evaluate_if_below(self, derivatives, max)
5129 def evaluate_moved(self, derivatives, moved_pis, reset_pis):
5130 r"""evaluate_moved(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
5131 return _IMP_kernel.ScoringFunction_evaluate_moved(self, derivatives, moved_pis, reset_pis)
5133 def evaluate_moved_if_below(self, derivatives, moved_pis, reset_pis, max):
5134 r"""evaluate_moved_if_below(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis, double max) -> double"""
5135 return _IMP_kernel.ScoringFunction_evaluate_moved_if_below(self, derivatives, moved_pis, reset_pis, max)
5137 def evaluate_moved_if_good(self, derivatives, moved_pis, reset_pis):
5138 r"""evaluate_moved_if_good(ScoringFunction self, bool derivatives, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis) -> double"""
5139 return _IMP_kernel.ScoringFunction_evaluate_moved_if_good(self, derivatives, moved_pis, reset_pis)
5141 def get_had_good_score(self):
5142 r"""get_had_good_score(ScoringFunction self) -> bool"""
5143 return _IMP_kernel.ScoringFunction_get_had_good_score(self)
5145 def get_last_score(self):
5146 r"""get_last_score(ScoringFunction self) -> double"""
5147 return _IMP_kernel.ScoringFunction_get_last_score(self)
5150 r"""create_restraints(ScoringFunction self) -> IMP::Restraints"""
5151 return _IMP_kernel.ScoringFunction_create_restraints(self)
5154 r"""__str__(ScoringFunction self) -> std::string"""
5155 return _IMP_kernel.ScoringFunction___str__(self)
5158 r"""__repr__(ScoringFunction self) -> std::string"""
5159 return _IMP_kernel.ScoringFunction___repr__(self)
5163 return _object_cast_to_ScoringFunction(o)
5166 def do_show(self, out):
5171 return _object_cast_to_ScoringFunction(o)
5173 __swig_destroy__ = _IMP_kernel.delete_ScoringFunction
5174 def __disown__(self):
5176 _IMP_kernel.disown_ScoringFunction(self)
5177 return weakref.proxy(self)
5180 r"""do_destroy(ScoringFunction self)"""
5181 return _IMP_kernel.ScoringFunction_do_destroy(self)
5183 def handle_set_has_required_score_states(self, arg0):
5184 r"""handle_set_has_required_score_states(ScoringFunction self, bool arg0)"""
5185 return _IMP_kernel.ScoringFunction_handle_set_has_required_score_states(self, arg0)
5187 def do_get_inputs(self):
5188 r"""do_get_inputs(ScoringFunction self) -> IMP::ModelObjectsTemp"""
5189 return _IMP_kernel.ScoringFunction_do_get_inputs(self)
5191 def do_get_interactions(self):
5192 r"""do_get_interactions(ScoringFunction self) -> IMP::ModelObjectsTemps"""
5193 return _IMP_kernel.ScoringFunction_do_get_interactions(self)
5196 _IMP_kernel.ScoringFunction_swigregister(ScoringFunction)
5200 create_decomposition(IMP::RestraintsTemp const & rs) -> IMP::Restraints
5201 create_decomposition(ScoringFunction sf) -> IMP::ScoringFunctions
5203 return _IMP_kernel.create_decomposition(*args)
5204 class _ScoringFunctionAdaptor(_InputAdaptor):
5205 r"""Proxy of C++ IMP::ScoringFunctionAdaptor class."""
5207 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5208 __repr__ = _swig_repr
5210 def __init__(self, *args):
5212 __init__(_ScoringFunctionAdaptor self) -> _ScoringFunctionAdaptor
5213 __init__(_ScoringFunctionAdaptor self, ScoringFunction sf) -> _ScoringFunctionAdaptor
5214 __init__(_ScoringFunctionAdaptor self, IMP::RestraintsTemp const & sf) -> _ScoringFunctionAdaptor
5215 __init__(_ScoringFunctionAdaptor self, IMP::Restraints const & sf) -> _ScoringFunctionAdaptor
5216 __init__(_ScoringFunctionAdaptor self, Restraint sf) -> _ScoringFunctionAdaptor
5218 _IMP_kernel._ScoringFunctionAdaptor_swiginit(self, _IMP_kernel.new__ScoringFunctionAdaptor(*args))
5219 __swig_destroy__ = _IMP_kernel.delete__ScoringFunctionAdaptor
5222 _IMP_kernel._ScoringFunctionAdaptor_swigregister(_ScoringFunctionAdaptor)
5225 r"""show_restraint_hierarchy(_ScoringFunctionAdaptor rs, _ostream out=std::cout)"""
5226 return _IMP_kernel.show_restraint_hierarchy(*args)
5227 class Undecorator(
Object):
5228 r"""Proxy of C++ IMP::Undecorator class."""
5230 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5232 def __init__(self, m, name):
5233 r"""__init__(Undecorator self, Model m, std::string name) -> Undecorator"""
5234 if self.__class__ == Undecorator:
5238 _IMP_kernel.Undecorator_swiginit(self, _IMP_kernel.new_Undecorator(_self, m, name))
5240 if self.__class__ != Undecorator:
5241 _director_objects.register(self)
5246 def teardown(self, pi):
5247 r"""teardown(Undecorator self, ParticleIndex pi)"""
5248 return _IMP_kernel.Undecorator_teardown(self, pi)
5251 r"""__str__(Undecorator self) -> std::string"""
5252 return _IMP_kernel.Undecorator___str__(self)
5255 r"""__repr__(Undecorator self) -> std::string"""
5256 return _IMP_kernel.Undecorator___repr__(self)
5260 return _object_cast_to_Undecorator(o)
5263 def do_show(self, out):
5268 return _object_cast_to_Undecorator(o)
5270 __swig_destroy__ = _IMP_kernel.delete_Undecorator
5271 def __disown__(self):
5273 _IMP_kernel.disown_Undecorator(self)
5274 return weakref.proxy(self)
5277 r"""do_destroy(Undecorator self)"""
5278 return _IMP_kernel.Undecorator_do_destroy(self)
5281 _IMP_kernel.Undecorator_swigregister(Undecorator)
5283 r"""Proxy of C++ IMP::Model class."""
5285 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5287 def __init__(self, *args):
5288 r"""__init__(Model self, std::string name="Model %1%") -> Model"""
5289 _IMP_kernel.Model_swiginit(self, _IMP_kernel.new_Model(*args))
5291 if self
not in _models_set:
5292 _models_set.add(self)
5297 def clear_particle_caches(self, pi):
5298 r"""clear_particle_caches(Model self, ParticleIndex pi)"""
5299 return _IMP_kernel.Model_clear_particle_caches(self, pi)
5302 r"""add_particle(Model self, std::string name) -> ParticleIndex"""
5303 return _IMP_kernel.Model_add_particle(self, name)
5305 def get_particle_name(self, pi):
5306 r"""get_particle_name(Model self, ParticleIndex pi) -> std::string"""
5307 return _IMP_kernel.Model_get_particle_name(self, pi)
5309 def add_undecorator(self, pi, d):
5310 r"""add_undecorator(Model self, ParticleIndex pi, Undecorator d)"""
5311 return _IMP_kernel.Model_add_undecorator(self, pi, d)
5313 def get_dependent_restraints_uncached(self, pi):
5314 r"""get_dependent_restraints_uncached(Model self, ParticleIndex pi) -> IMP::RestraintsTemp"""
5315 return _IMP_kernel.Model_get_dependent_restraints_uncached(self, pi)
5317 def get_dependent_particles_uncached(self, pi):
5318 r"""get_dependent_particles_uncached(Model self, ParticleIndex pi) -> IMP::ParticlesTemp"""
5319 return _IMP_kernel.Model_get_dependent_particles_uncached(self, pi)
5321 def get_dependent_score_states_uncached(self, pi):
5322 r"""get_dependent_score_states_uncached(Model self, ParticleIndex pi) -> IMP::ScoreStatesTemp"""
5323 return _IMP_kernel.Model_get_dependent_score_states_uncached(self, pi)
5324 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)
5325 def __set_score_states(self, obj): _list_util.set_varlist(self.score_states, obj)
5326 def __del_score_states(self): _list_util.del_varlist(self.score_states)
5327 score_states = property(__get_score_states, __set_score_states, __del_score_states, doc=
"List of ##ucnames")
5329 def remove_score_state(self, d):
5330 r"""remove_score_state(Model self, ScoreState d)"""
5331 return _IMP_kernel.Model_remove_score_state(self, d)
5333 def _python_index_score_state(self, d, start, stop):
5334 r"""_python_index_score_state(Model self, ScoreState d, unsigned int start, unsigned int stop) -> unsigned int"""
5335 return _IMP_kernel.Model__python_index_score_state(self, d, start, stop)
5337 def remove_score_states(self, d):
5338 r"""remove_score_states(Model self, IMP::ScoreStates const & d)"""
5339 return _IMP_kernel.Model_remove_score_states(self, d)
5341 def set_score_states(self, ps):
5342 r"""set_score_states(Model self, IMP::ScoreStates const & ps)"""
5343 return _IMP_kernel.Model_set_score_states(self, ps)
5345 def set_score_states_order(self, objs):
5346 r"""set_score_states_order(Model self, IMP::ScoreStates const & objs)"""
5347 return _IMP_kernel.Model_set_score_states_order(self, objs)
5349 def add_score_state(self, obj):
5350 r"""add_score_state(Model self, ScoreState obj) -> unsigned int"""
5351 return _IMP_kernel.Model_add_score_state(self, obj)
5353 def add_score_states(self, objs):
5354 r"""add_score_states(Model self, IMP::ScoreStates const & objs)"""
5355 return _IMP_kernel.Model_add_score_states(self, objs)
5357 def clear_score_states(self):
5358 r"""clear_score_states(Model self)"""
5359 return _IMP_kernel.Model_clear_score_states(self)
5361 def get_number_of_score_states(self):
5362 r"""get_number_of_score_states(Model self) -> unsigned int"""
5363 return _IMP_kernel.Model_get_number_of_score_states(self)
5365 def get_has_score_states(self):
5366 r"""get_has_score_states(Model self) -> bool"""
5367 return _IMP_kernel.Model_get_has_score_states(self)
5369 def get_score_state(self, i):
5370 r"""get_score_state(Model self, unsigned int i) -> ScoreState"""
5371 return _IMP_kernel.Model_get_score_state(self, i)
5373 def get_score_states(self):
5374 r"""get_score_states(Model self) -> IMP::ScoreStates"""
5375 return _IMP_kernel.Model_get_score_states(self)
5377 def erase_score_state(self, i):
5378 r"""erase_score_state(Model self, unsigned int i)"""
5379 return _IMP_kernel.Model_erase_score_state(self, i)
5381 def reserve_score_states(self, sz):
5382 r"""reserve_score_states(Model self, unsigned int sz)"""
5383 return _IMP_kernel.Model_reserve_score_states(self, sz)
5386 r"""update(Model self)"""
5387 return _IMP_kernel.Model_update(self)
5389 def add_cache_attribute(self, *args):
5391 add_cache_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
5392 add_cache_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
5393 add_cache_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
5394 add_cache_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, IMP::algebra::Vector3D value)
5395 add_cache_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
5396 add_cache_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
5397 add_cache_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
5398 add_cache_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
5399 add_cache_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
5400 add_cache_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
5402 return _IMP_kernel.Model_add_cache_attribute(self, *args)
5404 def add_attribute(self, *args):
5406 add_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
5407 add_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
5408 add_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
5409 add_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, IMP::algebra::Vector3D value)
5410 add_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
5411 add_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
5412 add_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
5413 add_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
5414 add_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
5415 add_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
5416 add_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle, IMP::String value)
5417 add_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle, IMP::Int value)
5418 add_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle, IMP::Float value)
5419 add_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
5421 return _IMP_kernel.Model_add_attribute(self, *args)
5423 def remove_attribute(self, *args):
5425 remove_attribute(Model self, FloatKey attribute_key, ParticleIndex particle)
5426 remove_attribute(Model self, IntKey attribute_key, ParticleIndex particle)
5427 remove_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle)
5428 remove_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle)
5429 remove_attribute(Model self, IntsKey attribute_key, ParticleIndex particle)
5430 remove_attribute(Model self, StringKey attribute_key, ParticleIndex particle)
5431 remove_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle)
5432 remove_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle)
5433 remove_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle)
5434 remove_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle)
5435 remove_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle)
5436 remove_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle)
5437 remove_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle)
5438 remove_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle)
5440 return _IMP_kernel.Model_remove_attribute(self, *args)
5442 def get_has_attribute(self, *args):
5444 get_has_attribute(Model self, FloatKey attribute_key, ParticleIndex particle) -> bool
5445 get_has_attribute(Model self, IntKey attribute_key, ParticleIndex particle) -> bool
5446 get_has_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle) -> bool
5447 get_has_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle) -> bool
5448 get_has_attribute(Model self, IntsKey attribute_key, ParticleIndex particle) -> bool
5449 get_has_attribute(Model self, StringKey attribute_key, ParticleIndex particle) -> bool
5450 get_has_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle) -> bool
5451 get_has_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle) -> bool
5452 get_has_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle) -> bool
5453 get_has_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle) -> bool
5454 get_has_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle) -> bool
5455 get_has_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle) -> bool
5456 get_has_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle) -> bool
5457 get_has_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle) -> bool
5459 return _IMP_kernel.Model_get_has_attribute(self, *args)
5461 def set_attribute(self, *args):
5463 set_attribute(Model self, FloatKey attribute_key, ParticleIndex particle, IMP::Float value)
5464 set_attribute(Model self, IntKey attribute_key, ParticleIndex particle, IMP::Int value)
5465 set_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle, IMP::Floats value)
5466 set_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle, IMP::algebra::Vector3D value)
5467 set_attribute(Model self, IntsKey attribute_key, ParticleIndex particle, IMP::Ints value)
5468 set_attribute(Model self, StringKey attribute_key, ParticleIndex particle, IMP::String value)
5469 set_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle, IMP::ParticleIndexes value)
5470 set_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
5471 set_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle, Object value)
5472 set_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle, Object value)
5473 set_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle, IMP::String value)
5474 set_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle, IMP::Int value)
5475 set_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle, IMP::Float value)
5476 set_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle, ParticleIndex value)
5478 return _IMP_kernel.Model_set_attribute(self, *args)
5480 def get_attribute(self, *args):
5482 get_attribute(Model self, FloatKey attribute_key, ParticleIndex particle) -> IMP::Float
5483 get_attribute(Model self, IntKey attribute_key, ParticleIndex particle) -> IMP::Int
5484 get_attribute(Model self, FloatsKey attribute_key, ParticleIndex particle) -> IMP::Floats
5485 get_attribute(Model self, Vector3DKey attribute_key, ParticleIndex particle) -> IMP::algebra::Vector3D
5486 get_attribute(Model self, IntsKey attribute_key, ParticleIndex particle) -> IMP::Ints
5487 get_attribute(Model self, StringKey attribute_key, ParticleIndex particle) -> IMP::String
5488 get_attribute(Model self, ParticleIndexesKey attribute_key, ParticleIndex particle) -> IMP::ParticleIndexes
5489 get_attribute(Model self, ParticleIndexKey attribute_key, ParticleIndex particle) -> ParticleIndex
5490 get_attribute(Model self, ObjectKey attribute_key, ParticleIndex particle) -> Object
5491 get_attribute(Model self, IMP::WeakObjectKey attribute_key, ParticleIndex particle) -> Object
5492 get_attribute(Model self, SparseStringKey attribute_key, ParticleIndex particle) -> IMP::String
5493 get_attribute(Model self, SparseIntKey attribute_key, ParticleIndex particle) -> IMP::Int
5494 get_attribute(Model self, SparseFloatKey attribute_key, ParticleIndex particle) -> IMP::Float
5495 get_attribute(Model self, SparseParticleIndexKey attribute_key, ParticleIndex particle) -> ParticleIndex
5497 return _IMP_kernel.Model_get_attribute(self, *args)
5499 def set_is_optimized(self, arg2, arg3, arg4):
5500 r"""set_is_optimized(Model self, FloatKey arg2, ParticleIndex arg3, bool arg4)"""
5501 return _IMP_kernel.Model_set_is_optimized(self, arg2, arg3, arg4)
5503 def add_to_derivative(self, k, particle, v, da):
5504 r"""add_to_derivative(Model self, FloatKey k, ParticleIndex particle, double v, DerivativeAccumulator da)"""
5505 return _IMP_kernel.Model_add_to_derivative(self, k, particle, v, da)
5507 def get_particle(self, p):
5508 r"""get_particle(Model self, ParticleIndex p) -> Particle"""
5509 return _IMP_kernel.Model_get_particle(self, p)
5511 def get_has_particle(self, p):
5512 r"""get_has_particle(Model self, ParticleIndex p) -> bool"""
5513 return _IMP_kernel.Model_get_has_particle(self, p)
5516 r"""get_particle_indexes(Model self) -> IMP::ParticleIndexes"""
5517 return _IMP_kernel.Model_get_particle_indexes(self)
5519 def get_model_objects(self):
5520 r"""get_model_objects(Model self) -> IMP::ModelObjectsTemp"""
5521 return _IMP_kernel.Model_get_model_objects(self)
5523 def remove_particle(self, pi):
5524 r"""remove_particle(Model self, ParticleIndex pi)"""
5525 return _IMP_kernel.Model_remove_particle(self, pi)
5527 def add_data(self, mk, o):
5528 r"""add_data(Model self, ModelKey mk, Object o)"""
5529 return _IMP_kernel.Model_add_data(self, mk, o)
5531 def get_data(self, mk):
5532 r"""get_data(Model self, ModelKey mk) -> Object"""
5533 return _IMP_kernel.Model_get_data(self, mk)
5535 def remove_data(self, mk):
5536 r"""remove_data(Model self, ModelKey mk)"""
5537 return _IMP_kernel.Model_remove_data(self, mk)
5539 def get_has_data(self, mk):
5540 r"""get_has_data(Model self, ModelKey mk) -> bool"""
5541 return _IMP_kernel.Model_get_has_data(self, mk)
5544 r"""get_age(Model self) -> unsigned int"""
5545 return _IMP_kernel.Model_get_age(self)
5547 def get_trigger_last_updated(self, tk):
5548 r"""get_trigger_last_updated(Model self, TriggerKey tk) -> unsigned int"""
5549 return _IMP_kernel.Model_get_trigger_last_updated(self, tk)
5551 def set_trigger_updated(self, tk):
5552 r"""set_trigger_updated(Model self, TriggerKey tk)"""
5553 return _IMP_kernel.Model_set_trigger_updated(self, tk)
5555 def get_dependencies_updated(self):
5556 r"""get_dependencies_updated(Model self) -> unsigned int"""
5557 return _IMP_kernel.Model_get_dependencies_updated(self)
5559 def get_removed_particles_attributes_age(self):
5560 r"""get_removed_particles_attributes_age(Model self) -> unsigned int"""
5561 return _IMP_kernel.Model_get_removed_particles_attributes_age(self)
5563 def save_dependencies(self):
5564 r"""save_dependencies(Model self)"""
5565 return _IMP_kernel.Model_save_dependencies(self)
5567 def restore_dependencies(self):
5568 r"""restore_dependencies(Model self)"""
5569 return _IMP_kernel.Model_restore_dependencies(self)
5571 def get_particles_size(self):
5572 r"""get_particles_size(Model self) -> unsigned int"""
5573 return _IMP_kernel.Model_get_particles_size(self)
5575 def get_unique_id(self):
5576 r"""get_unique_id(Model self) -> uint32_t"""
5577 return _IMP_kernel.Model_get_unique_id(self)
5580 def get_by_unique_id(id):
5581 r"""get_by_unique_id(uint32_t id) -> Model"""
5582 return _IMP_kernel.Model_get_by_unique_id(id)
5585 r"""get_version_info(Model self) -> VersionInfo"""
5586 return _IMP_kernel.Model_get_version_info(self)
5587 __swig_destroy__ = _IMP_kernel.delete_Model
5589 r"""__del__(Model self)"""
5591 _director_objects.cleanup()
5598 r"""do_destroy(Model self)"""
5599 return _IMP_kernel.Model_do_destroy(self)
5602 r"""__str__(Model self) -> std::string"""
5603 return _IMP_kernel.Model___str__(self)
5606 r"""__repr__(Model self) -> std::string"""
5607 return _IMP_kernel.Model___repr__(self)
5611 return _object_cast_to_Model(o)
5614 def _get_as_binary(self):
5615 r"""_get_as_binary(Model self) -> PyObject *"""
5616 return _IMP_kernel.Model__get_as_binary(self)
5618 def _set_from_binary(self, p):
5619 r"""_set_from_binary(Model self, PyObject * p)"""
5620 return _IMP_kernel.Model__set_from_binary(self, p)
5622 def __getstate__(self):
5623 p = self._get_as_binary()
5624 if len(self.__dict__) > 1:
5625 d = self.__dict__.copy()
5630 def __setstate__(self, p):
5631 if not hasattr(self,
'this'):
5633 if isinstance(p, tuple):
5635 self.__dict__.update(d)
5636 return self._set_from_binary(p)
5640 """Get the model's attribute array for IntKey k as a NumPy array.
5641 The array is indexed by ParticleIndex; particles that don't have
5642 this attribute will either be off the end of the array or will have
5644 This is a NumPy view that shares memory with the Model. Thus,
5645 any changes to values in this list will be reflected in the Model.
5646 Also, if the Model attribute array moves in memory (e.g. if particles
5647 or attributes are added) this array will be invalidated, so it is
5648 unsafe to keep it around long term.
5649 If read_only is set True, values in the array cannot be changed.
5651 return _get_ints_numpy(self, k, self, read_only)
5654 """Get the model's attribute array for FloatKey k as a NumPy array.
5655 See Model::get_ints_numpy() for more details."""
5656 return _get_floats_numpy(self, k, self, read_only)
5659 """Get the model's attribute derivatives array for FloatKey k
5660 as a NumPy array. See Model::get_ints_numpy() for more details."""
5661 return _get_derivatives_numpy(self, k, self, read_only)
5664 """Get the model's attribute array for Vector3DKey k as a NumPy array.
5665 See Model::get_ints_numpy() for more details."""
5666 return _get_vector3ds_numpy(self, k, self, read_only)
5669 """Get the model's XYZR attribute arrays as NumPy arrays.
5670 The attribute arrays for Cartesian coordinates and radii are
5671 stored separately from those for other FloatKeys. This function
5672 returns a tuple of two NumPy arrays, the first of coordinates and
5673 the second of radii. See Model::get_ints_numpy() for more details."""
5674 return _get_spheres_numpy(self, self, read_only)
5677 """Get the model's XYZR attribute derivatives arrays as NumPy arrays.
5678 See Model::get_ints_numpy() for more details."""
5679 return _get_sphere_derivatives_numpy(self, self, read_only)
5683 _IMP_kernel.Model_swigregister(Model)
5685 r"""Proxy of C++ IMP::Decorator class."""
5687 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5688 __repr__ = _swig_repr
5690 def __init__(self, p):
5691 r"""__init__(Decorator self, _ParticleAdaptor p) -> Decorator"""
5692 _IMP_kernel.Decorator_swiginit(self, _IMP_kernel.new_Decorator(p))
5694 def __ne__(self, o):
5695 r"""__ne__(Decorator self, Object o) -> bool"""
5696 return _IMP_kernel.Decorator___ne__(self, o)
5698 def __lt__(self, o):
5699 r"""__lt__(Decorator self, Object o) -> bool"""
5700 return _IMP_kernel.Decorator___lt__(self, o)
5702 def __gt__(self, o):
5703 r"""__gt__(Decorator self, Object o) -> bool"""
5704 return _IMP_kernel.Decorator___gt__(self, o)
5706 def __ge__(self, o):
5707 r"""__ge__(Decorator self, Object o) -> bool"""
5708 return _IMP_kernel.Decorator___ge__(self, o)
5710 def __le__(self, o):
5711 r"""__le__(Decorator self, Object o) -> bool"""
5712 return _IMP_kernel.Decorator___le__(self, o)
5715 r"""get_particle(Decorator self) -> Particle"""
5716 return _IMP_kernel.Decorator_get_particle(self)
5718 def get_particle_index(self):
5719 r"""get_particle_index(Decorator self) -> ParticleIndex"""
5720 return _IMP_kernel.Decorator_get_particle_index(self)
5722 def get_model(self):
5723 m = _IMP_kernel.Decorator_get_model(self)
5724 if m
in _models_set:
5725 m = _models_set_get(m)
5730 def get_is_valid(self):
5731 r"""get_is_valid(Decorator self) -> bool"""
5732 return _IMP_kernel.Decorator_get_is_valid(self)
5735 r"""__hash__(Decorator self) -> std::size_t"""
5736 return _IMP_kernel.Decorator___hash__(self)
5738 def __eq__(self, *args):
5740 __eq__(Decorator self, Object o) -> bool
5741 __eq__(Decorator self, Decorator o) -> bool
5742 __eq__(Decorator self, Particle o) -> bool
5744 return _IMP_kernel.Decorator___eq__(self, *args)
5747 r"""__bool__(Decorator self) -> bool"""
5748 return _IMP_kernel.Decorator___bool__(self)
5749 __swig_destroy__ = _IMP_kernel.delete_Decorator
5752 _IMP_kernel.Decorator_swigregister(Decorator)
5754 def check_particle(m, pi):
5755 r"""check_particle(Model m, ParticleIndex pi)"""
5756 return _IMP_kernel.check_particle(m, pi)
5758 r"""Proxy of C++ IMP::UnaryFunction class."""
5760 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5762 def __init__(self, *args):
5763 r"""__init__(UnaryFunction self, std::string name="UnaryFunction%1%") -> UnaryFunction"""
5764 if self.__class__ == UnaryFunction:
5768 _IMP_kernel.UnaryFunction_swiginit(self, _IMP_kernel.new_UnaryFunction(_self, *args))
5770 if self.__class__ != UnaryFunction:
5771 _director_objects.register(self)
5776 def evaluate(self, feature):
5777 r"""evaluate(UnaryFunction self, double feature) -> double"""
5778 return _IMP_kernel.UnaryFunction_evaluate(self, feature)
5780 def evaluate_with_derivative(self, feature):
5781 r"""evaluate_with_derivative(UnaryFunction self, double feature) -> IMP::DerivativePair"""
5782 return _IMP_kernel.UnaryFunction_evaluate_with_derivative(self, feature)
5783 __swig_destroy__ = _IMP_kernel.delete_UnaryFunction
5786 r"""__str__(UnaryFunction self) -> std::string"""
5787 return _IMP_kernel.UnaryFunction___str__(self)
5790 r"""__repr__(UnaryFunction self) -> std::string"""
5791 return _IMP_kernel.UnaryFunction___repr__(self)
5795 return _object_cast_to_UnaryFunction(o)
5798 def do_show(self, out):
5803 return _object_cast_to_UnaryFunction(o)
5805 def __disown__(self):
5807 _IMP_kernel.disown_UnaryFunction(self)
5808 return weakref.proxy(self)
5811 r"""do_destroy(UnaryFunction self)"""
5812 return _IMP_kernel.UnaryFunction_do_destroy(self)
5815 _IMP_kernel.UnaryFunction_swigregister(UnaryFunction)
5817 r"""Proxy of C++ IMP::OptimizerState class."""
5819 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5821 def __init__(self, *args):
5823 __init__(OptimizerState self, Model m, std::string name) -> OptimizerState
5824 __init__(OptimizerState self) -> OptimizerState
5826 if self.__class__ == OptimizerState:
5830 _IMP_kernel.OptimizerState_swiginit(self, _IMP_kernel.new_OptimizerState(_self, *args))
5832 if self.__class__ != OptimizerState:
5833 _director_objects.register(self)
5839 r"""update(OptimizerState self)"""
5840 return _IMP_kernel.OptimizerState_update(self)
5842 def set_is_optimizing(self, arg0):
5843 r"""set_is_optimizing(OptimizerState self, bool arg0)"""
5844 return _IMP_kernel.OptimizerState_set_is_optimizing(self, arg0)
5846 def get_optimizer(self):
5847 r"""get_optimizer(OptimizerState self) -> Optimizer"""
5848 return _IMP_kernel.OptimizerState_get_optimizer(self)
5850 def set_period(self, p):
5851 r"""set_period(OptimizerState self, unsigned int p)"""
5852 return _IMP_kernel.OptimizerState_set_period(self, p)
5854 def get_period(self):
5855 r"""get_period(OptimizerState self) -> unsigned int"""
5856 return _IMP_kernel.OptimizerState_get_period(self)
5859 r"""reset(OptimizerState self)"""
5860 return _IMP_kernel.OptimizerState_reset(self)
5862 def update_always(self):
5863 r"""update_always(OptimizerState self)"""
5864 return _IMP_kernel.OptimizerState_update_always(self)
5866 def get_number_of_updates(self):
5867 r"""get_number_of_updates(OptimizerState self) -> unsigned int"""
5868 return _IMP_kernel.OptimizerState_get_number_of_updates(self)
5870 def set_number_of_updates(self, n):
5871 r"""set_number_of_updates(OptimizerState self, unsigned int n)"""
5872 return _IMP_kernel.OptimizerState_set_number_of_updates(self, n)
5873 __swig_destroy__ = _IMP_kernel.delete_OptimizerState
5875 def do_update(self, arg0):
5876 r"""do_update(OptimizerState self, unsigned int arg0)"""
5877 return _IMP_kernel.OptimizerState_do_update(self, arg0)
5879 def do_set_is_optimizing(self, arg0):
5880 r"""do_set_is_optimizing(OptimizerState self, bool arg0)"""
5881 return _IMP_kernel.OptimizerState_do_set_is_optimizing(self, arg0)
5883 def do_get_inputs(self):
5884 r"""do_get_inputs(OptimizerState self) -> IMP::ModelObjectsTemp"""
5885 return _IMP_kernel.OptimizerState_do_get_inputs(self)
5887 def do_get_outputs(self):
5888 r"""do_get_outputs(OptimizerState self) -> IMP::ModelObjectsTemp"""
5889 return _IMP_kernel.OptimizerState_do_get_outputs(self)
5892 r"""__str__(OptimizerState self) -> std::string"""
5893 return _IMP_kernel.OptimizerState___str__(self)
5896 r"""__repr__(OptimizerState self) -> std::string"""
5897 return _IMP_kernel.OptimizerState___repr__(self)
5901 return _object_cast_to_OptimizerState(o)
5904 def do_show(self, out):
5909 return _object_cast_to_OptimizerState(o)
5911 def __disown__(self):
5913 _IMP_kernel.disown_OptimizerState(self)
5914 return weakref.proxy(self)
5917 r"""do_destroy(OptimizerState self)"""
5918 return _IMP_kernel.OptimizerState_do_destroy(self)
5920 def handle_set_has_required_score_states(self, arg0):
5921 r"""handle_set_has_required_score_states(OptimizerState self, bool arg0)"""
5922 return _IMP_kernel.OptimizerState_handle_set_has_required_score_states(self, arg0)
5924 def do_get_interactions(self):
5925 r"""do_get_interactions(OptimizerState self) -> IMP::ModelObjectsTemps"""
5926 return _IMP_kernel.OptimizerState_do_get_interactions(self)
5929 _IMP_kernel.OptimizerState_swigregister(OptimizerState)
5931 r"""Proxy of C++ IMP::Refiner class."""
5933 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
5935 def __init__(self, *args):
5936 r"""__init__(Refiner self, std::string name="Refiner %1%", bool is_by_ref=False) -> Refiner"""
5937 if self.__class__ == Refiner:
5941 _IMP_kernel.Refiner_swiginit(self, _IMP_kernel.new_Refiner(_self, *args))
5943 if self.__class__ != Refiner:
5944 _director_objects.register(self)
5949 def get_can_refine(self, arg0):
5950 r"""get_can_refine(Refiner self, Particle arg0) -> bool"""
5951 return _IMP_kernel.Refiner_get_can_refine(self, arg0)
5953 def get_refined_indexes(self, m, pi):
5954 r"""get_refined_indexes(Refiner self, Model m, ParticleIndex pi) -> IMP::ParticleIndexes"""
5955 return _IMP_kernel.Refiner_get_refined_indexes(self, m, pi)
5957 def get_refined_indexes_by_ref(self, m, pi):
5958 r"""get_refined_indexes_by_ref(Refiner self, Model m, ParticleIndex pi) -> IMP::ParticleIndexes const &"""
5959 return _IMP_kernel.Refiner_get_refined_indexes_by_ref(self, m, pi)
5961 def get_is_by_ref_supported(self):
5962 r"""get_is_by_ref_supported(Refiner self) -> bool"""
5963 return _IMP_kernel.Refiner_get_is_by_ref_supported(self)
5965 def get_refined(self, *args):
5967 get_refined(Refiner self, Particle a) -> IMP::ParticlesTemp const
5968 get_refined(Refiner self, Particle a, unsigned int i) -> Particle
5970 return _IMP_kernel.Refiner_get_refined(self, *args)
5972 def get_number_of_refined(self, a):
5973 r"""get_number_of_refined(Refiner self, Particle a) -> unsigned int"""
5974 return _IMP_kernel.Refiner_get_number_of_refined(self, a)
5977 r"""__str__(Refiner self) -> std::string"""
5978 return _IMP_kernel.Refiner___str__(self)
5981 r"""__repr__(Refiner self) -> std::string"""
5982 return _IMP_kernel.Refiner___repr__(self)
5986 return _object_cast_to_Refiner(o)
5989 def do_show(self, out):
5994 return _object_cast_to_Refiner(o)
5996 __swig_destroy__ = _IMP_kernel.delete_Refiner
5997 def __disown__(self):
5999 _IMP_kernel.disown_Refiner(self)
6000 return weakref.proxy(self)
6002 def do_get_inputs(self, m, pis):
6003 r"""do_get_inputs(Refiner self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6004 return _IMP_kernel.Refiner_do_get_inputs(self, m, pis)
6007 r"""do_destroy(Refiner self)"""
6008 return _IMP_kernel.Refiner_do_destroy(self)
6011 _IMP_kernel.Refiner_swigregister(Refiner)
6013 r"""Proxy of C++ IMP::Optimizer class."""
6015 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6017 def set_is_optimizing_states(self, tf):
6018 r"""set_is_optimizing_states(Optimizer self, bool tf)"""
6019 return _IMP_kernel.Optimizer_set_is_optimizing_states(self, tf)
6021 def get_optimizer_state_inputs(self):
6022 r"""get_optimizer_state_inputs(Optimizer self) -> IMP::ModelObjectsTemp"""
6023 return _IMP_kernel.Optimizer_get_optimizer_state_inputs(self)
6025 def do_get_inputs(self):
6026 r"""do_get_inputs(Optimizer self) -> IMP::ModelObjectsTemp"""
6027 return _IMP_kernel.Optimizer_do_get_inputs(self)
6029 def do_get_outputs(self):
6030 r"""do_get_outputs(Optimizer self) -> IMP::ModelObjectsTemp"""
6031 return _IMP_kernel.Optimizer_do_get_outputs(self)
6033 def __init__(self, *args):
6035 __init__(Optimizer self, Model m, std::string name="Optimizer %1%") -> Optimizer
6036 __init__(Optimizer self) -> Optimizer
6038 if self.__class__ == Optimizer:
6042 _IMP_kernel.Optimizer_swiginit(self, _IMP_kernel.new_Optimizer(_self, *args))
6044 if self.__class__ != Optimizer:
6045 _director_objects.register(self)
6050 def optimize(self, max_steps):
6051 r"""optimize(Optimizer self, unsigned int max_steps) -> double"""
6052 return _IMP_kernel.Optimizer_optimize(self, max_steps)
6054 def set_stop_on_good_score(self, tf):
6055 r"""set_stop_on_good_score(Optimizer self, bool tf)"""
6056 return _IMP_kernel.Optimizer_set_stop_on_good_score(self, tf)
6058 def get_stop_on_good_score(self):
6059 r"""get_stop_on_good_score(Optimizer self) -> bool"""
6060 return _IMP_kernel.Optimizer_get_stop_on_good_score(self)
6062 def get_last_score(self):
6063 r"""get_last_score(Optimizer self) -> double"""
6064 return _IMP_kernel.Optimizer_get_last_score(self)
6066 def get_scoring_function(self):
6067 r"""get_scoring_function(Optimizer self) -> ScoringFunction"""
6068 return _IMP_kernel.Optimizer_get_scoring_function(self)
6069 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)
6070 def __set_optimizer_states(self, obj): _list_util.set_varlist(self.optimizer_states, obj)
6071 def __del_optimizer_states(self): _list_util.del_varlist(self.optimizer_states)
6072 optimizer_states = property(__get_optimizer_states, __set_optimizer_states, __del_optimizer_states, doc=
"List of ##ucnames")
6074 def remove_optimizer_state(self, d):
6075 r"""remove_optimizer_state(Optimizer self, OptimizerState d)"""
6076 return _IMP_kernel.Optimizer_remove_optimizer_state(self, d)
6078 def _python_index_optimizer_state(self, d, start, stop):
6079 r"""_python_index_optimizer_state(Optimizer self, OptimizerState d, unsigned int start, unsigned int stop) -> unsigned int"""
6080 return _IMP_kernel.Optimizer__python_index_optimizer_state(self, d, start, stop)
6082 def remove_optimizer_states(self, d):
6083 r"""remove_optimizer_states(Optimizer self, IMP::OptimizerStates const & d)"""
6084 return _IMP_kernel.Optimizer_remove_optimizer_states(self, d)
6086 def set_optimizer_states(self, ps):
6087 r"""set_optimizer_states(Optimizer self, IMP::OptimizerStates const & ps)"""
6088 return _IMP_kernel.Optimizer_set_optimizer_states(self, ps)
6090 def set_optimizer_states_order(self, objs):
6091 r"""set_optimizer_states_order(Optimizer self, IMP::OptimizerStates const & objs)"""
6092 return _IMP_kernel.Optimizer_set_optimizer_states_order(self, objs)
6094 def add_optimizer_state(self, obj):
6095 r"""add_optimizer_state(Optimizer self, OptimizerState obj) -> unsigned int"""
6096 return _IMP_kernel.Optimizer_add_optimizer_state(self, obj)
6098 def add_optimizer_states(self, objs):
6099 r"""add_optimizer_states(Optimizer self, IMP::OptimizerStates const & objs)"""
6100 return _IMP_kernel.Optimizer_add_optimizer_states(self, objs)
6102 def clear_optimizer_states(self):
6103 r"""clear_optimizer_states(Optimizer self)"""
6104 return _IMP_kernel.Optimizer_clear_optimizer_states(self)
6106 def get_number_of_optimizer_states(self):
6107 r"""get_number_of_optimizer_states(Optimizer self) -> unsigned int"""
6108 return _IMP_kernel.Optimizer_get_number_of_optimizer_states(self)
6110 def get_has_optimizer_states(self):
6111 r"""get_has_optimizer_states(Optimizer self) -> bool"""
6112 return _IMP_kernel.Optimizer_get_has_optimizer_states(self)
6114 def get_optimizer_state(self, i):
6115 r"""get_optimizer_state(Optimizer self, unsigned int i) -> OptimizerState"""
6116 return _IMP_kernel.Optimizer_get_optimizer_state(self, i)
6118 def get_optimizer_states(self):
6119 r"""get_optimizer_states(Optimizer self) -> IMP::OptimizerStates"""
6120 return _IMP_kernel.Optimizer_get_optimizer_states(self)
6122 def erase_optimizer_state(self, i):
6123 r"""erase_optimizer_state(Optimizer self, unsigned int i)"""
6124 return _IMP_kernel.Optimizer_erase_optimizer_state(self, i)
6126 def reserve_optimizer_states(self, sz):
6127 r"""reserve_optimizer_states(Optimizer self, unsigned int sz)"""
6128 return _IMP_kernel.Optimizer_reserve_optimizer_states(self, sz)
6130 def set_scoring_function(self, sf):
6131 r"""set_scoring_function(Optimizer self, _ScoringFunctionAdaptor sf)"""
6132 return _IMP_kernel.Optimizer_set_scoring_function(self, sf)
6133 __swig_destroy__ = _IMP_kernel.delete_Optimizer
6135 r"""__del__(Optimizer self)"""
6137 _director_objects.cleanup()
6143 def do_optimize(self, ns):
6144 r"""do_optimize(Optimizer self, unsigned int ns) -> double"""
6145 return _IMP_kernel.Optimizer_do_optimize(self, ns)
6147 def update_states(self):
6148 r"""update_states(Optimizer self)"""
6149 return _IMP_kernel.Optimizer_update_states(self)
6152 r"""__str__(Optimizer self) -> std::string"""
6153 return _IMP_kernel.Optimizer___str__(self)
6156 r"""__repr__(Optimizer self) -> std::string"""
6157 return _IMP_kernel.Optimizer___repr__(self)
6161 return _object_cast_to_Optimizer(o)
6164 def do_show(self, out):
6169 return _object_cast_to_Optimizer(o)
6171 def __disown__(self):
6173 _IMP_kernel.disown_Optimizer(self)
6174 return weakref.proxy(self)
6177 r"""do_destroy(Optimizer self)"""
6178 return _IMP_kernel.Optimizer_do_destroy(self)
6180 def handle_set_has_required_score_states(self, arg0):
6181 r"""handle_set_has_required_score_states(Optimizer self, bool arg0)"""
6182 return _IMP_kernel.Optimizer_handle_set_has_required_score_states(self, arg0)
6184 def do_get_interactions(self):
6185 r"""do_get_interactions(Optimizer self) -> IMP::ModelObjectsTemps"""
6186 return _IMP_kernel.Optimizer_do_get_interactions(self)
6189 _IMP_kernel.Optimizer_swigregister(Optimizer)
6191 r"""Proxy of C++ IMP::AttributeOptimizer class."""
6193 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6195 def __init__(self, *args):
6197 __init__(AttributeOptimizer self, Model m, std::string name="Optimizer %1%") -> AttributeOptimizer
6198 __init__(AttributeOptimizer self) -> AttributeOptimizer
6200 if self.__class__ == AttributeOptimizer:
6204 _IMP_kernel.AttributeOptimizer_swiginit(self, _IMP_kernel.new_AttributeOptimizer(_self, *args))
6206 if self.__class__ != AttributeOptimizer:
6207 _director_objects.register(self)
6212 def get_optimized_attributes(self):
6213 r"""get_optimized_attributes(AttributeOptimizer self) -> IMP::FloatIndexes"""
6214 return _IMP_kernel.AttributeOptimizer_get_optimized_attributes(self)
6216 def set_value(self, fi, v):
6217 r"""set_value(AttributeOptimizer self, FloatIndex fi, double v)"""
6218 return _IMP_kernel.AttributeOptimizer_set_value(self, fi, v)
6220 def get_value(self, fi):
6221 r"""get_value(AttributeOptimizer self, FloatIndex fi) -> IMP::Float"""
6222 return _IMP_kernel.AttributeOptimizer_get_value(self, fi)
6224 def get_derivative(self, fi):
6225 r"""get_derivative(AttributeOptimizer self, FloatIndex fi) -> IMP::Float"""
6226 return _IMP_kernel.AttributeOptimizer_get_derivative(self, fi)
6228 def get_width(self, k):
6229 r"""get_width(AttributeOptimizer self, FloatKey k) -> double"""
6230 return _IMP_kernel.AttributeOptimizer_get_width(self, k)
6232 def set_scaled_value(self, fi, v):
6233 r"""set_scaled_value(AttributeOptimizer self, FloatIndex fi, IMP::Float v)"""
6234 return _IMP_kernel.AttributeOptimizer_set_scaled_value(self, fi, v)
6236 def get_scaled_value(self, fi):
6237 r"""get_scaled_value(AttributeOptimizer self, FloatIndex fi) -> double"""
6238 return _IMP_kernel.AttributeOptimizer_get_scaled_value(self, fi)
6240 def get_scaled_derivative(self, fi):
6241 r"""get_scaled_derivative(AttributeOptimizer self, FloatIndex fi) -> double"""
6242 return _IMP_kernel.AttributeOptimizer_get_scaled_derivative(self, fi)
6244 def clear_range_cache(self):
6245 r"""clear_range_cache(AttributeOptimizer self)"""
6246 return _IMP_kernel.AttributeOptimizer_clear_range_cache(self)
6249 r"""__str__(AttributeOptimizer self) -> std::string"""
6250 return _IMP_kernel.AttributeOptimizer___str__(self)
6253 r"""__repr__(AttributeOptimizer self) -> std::string"""
6254 return _IMP_kernel.AttributeOptimizer___repr__(self)
6258 return _object_cast_to_AttributeOptimizer(o)
6261 def do_show(self, out):
6266 return _object_cast_to_AttributeOptimizer(o)
6268 __swig_destroy__ = _IMP_kernel.delete_AttributeOptimizer
6269 def __disown__(self):
6271 _IMP_kernel.disown_AttributeOptimizer(self)
6272 return weakref.proxy(self)
6275 r"""do_destroy(AttributeOptimizer self)"""
6276 return _IMP_kernel.AttributeOptimizer_do_destroy(self)
6278 def handle_set_has_required_score_states(self, arg0):
6279 r"""handle_set_has_required_score_states(AttributeOptimizer self, bool arg0)"""
6280 return _IMP_kernel.AttributeOptimizer_handle_set_has_required_score_states(self, arg0)
6282 def do_get_inputs(self):
6283 r"""do_get_inputs(AttributeOptimizer self) -> IMP::ModelObjectsTemp"""
6284 return _IMP_kernel.AttributeOptimizer_do_get_inputs(self)
6286 def do_get_outputs(self):
6287 r"""do_get_outputs(AttributeOptimizer self) -> IMP::ModelObjectsTemp"""
6288 return _IMP_kernel.AttributeOptimizer_do_get_outputs(self)
6290 def do_get_interactions(self):
6291 r"""do_get_interactions(AttributeOptimizer self) -> IMP::ModelObjectsTemps"""
6292 return _IMP_kernel.AttributeOptimizer_do_get_interactions(self)
6294 def do_optimize(self, ns):
6295 r"""do_optimize(AttributeOptimizer self, unsigned int ns) -> double"""
6296 return _IMP_kernel.AttributeOptimizer_do_optimize(self, ns)
6299 _IMP_kernel.AttributeOptimizer_swigregister(AttributeOptimizer)
6301 r"""Proxy of C++ IMP::ConfigurationSet class."""
6303 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6305 def __init__(self, *args):
6306 r"""__init__(ConfigurationSet self, Model m, std::string name="ConfigurationSet %1%") -> ConfigurationSet"""
6307 _IMP_kernel.ConfigurationSet_swiginit(self, _IMP_kernel.new_ConfigurationSet(*args))
6309 def save_configuration(self):
6310 r"""save_configuration(ConfigurationSet self)"""
6311 return _IMP_kernel.ConfigurationSet_save_configuration(self)
6313 def get_number_of_configurations(self):
6314 r"""get_number_of_configurations(ConfigurationSet self) -> unsigned int"""
6315 return _IMP_kernel.ConfigurationSet_get_number_of_configurations(self)
6317 def load_configuration(self, i):
6318 r"""load_configuration(ConfigurationSet self, int i)"""
6319 return _IMP_kernel.ConfigurationSet_load_configuration(self, i)
6321 def remove_configuration(self, i):
6322 r"""remove_configuration(ConfigurationSet self, unsigned int i)"""
6323 return _IMP_kernel.ConfigurationSet_remove_configuration(self, i)
6325 def get_model(self):
6326 r"""get_model(ConfigurationSet self) -> Model"""
6327 return _IMP_kernel.ConfigurationSet_get_model(self)
6330 r"""get_version_info(ConfigurationSet self) -> VersionInfo"""
6331 return _IMP_kernel.ConfigurationSet_get_version_info(self)
6332 __swig_destroy__ = _IMP_kernel.delete_ConfigurationSet
6335 r"""__str__(ConfigurationSet self) -> std::string"""
6336 return _IMP_kernel.ConfigurationSet___str__(self)
6339 r"""__repr__(ConfigurationSet self) -> std::string"""
6340 return _IMP_kernel.ConfigurationSet___repr__(self)
6344 return _object_cast_to_ConfigurationSet(o)
6348 _IMP_kernel.ConfigurationSet_swigregister(ConfigurationSet)
6350 r"""Proxy of C++ IMP::SaveToConfigurationSetOptimizerState class."""
6352 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6354 def __init__(self, cs):
6355 r"""__init__(SaveToConfigurationSetOptimizerState self, ConfigurationSet cs) -> SaveToConfigurationSetOptimizerState"""
6356 _IMP_kernel.SaveToConfigurationSetOptimizerState_swiginit(self, _IMP_kernel.new_SaveToConfigurationSetOptimizerState(cs))
6359 r"""get_version_info(SaveToConfigurationSetOptimizerState self) -> VersionInfo"""
6360 return _IMP_kernel.SaveToConfigurationSetOptimizerState_get_version_info(self)
6361 __swig_destroy__ = _IMP_kernel.delete_SaveToConfigurationSetOptimizerState
6364 r"""__str__(SaveToConfigurationSetOptimizerState self) -> std::string"""
6365 return _IMP_kernel.SaveToConfigurationSetOptimizerState___str__(self)
6368 r"""__repr__(SaveToConfigurationSetOptimizerState self) -> std::string"""
6369 return _IMP_kernel.SaveToConfigurationSetOptimizerState___repr__(self)
6373 return _object_cast_to_SaveToConfigurationSetOptimizerState(o)
6377 _IMP_kernel.SaveToConfigurationSetOptimizerState_swigregister(SaveToConfigurationSetOptimizerState)
6379 r"""Proxy of C++ IMP::Configuration class."""
6381 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6383 def __init__(self, *args):
6385 __init__(Configuration self, Model m, std::string name="Configuration %1%") -> Configuration
6386 __init__(Configuration self, Model m, Configuration base, std::string name="Configuration %1%") -> Configuration
6388 _IMP_kernel.Configuration_swiginit(self, _IMP_kernel.new_Configuration(*args))
6390 def load_configuration(self):
6391 r"""load_configuration(Configuration self)"""
6392 return _IMP_kernel.Configuration_load_configuration(self)
6394 def swap_configuration(self):
6395 r"""swap_configuration(Configuration self)"""
6396 return _IMP_kernel.Configuration_swap_configuration(self)
6399 r"""get_version_info(Configuration self) -> VersionInfo"""
6400 return _IMP_kernel.Configuration_get_version_info(self)
6401 __swig_destroy__ = _IMP_kernel.delete_Configuration
6404 r"""__str__(Configuration self) -> std::string"""
6405 return _IMP_kernel.Configuration___str__(self)
6408 r"""__repr__(Configuration self) -> std::string"""
6409 return _IMP_kernel.Configuration___repr__(self)
6413 return _object_cast_to_Configuration(o)
6417 _IMP_kernel.Configuration_swigregister(Configuration)
6419 r"""Proxy of C++ IMP::Sampler class."""
6421 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6423 def __init__(self, *args):
6424 r"""__init__(Sampler self, Model m, std::string name="Sampler %1%") -> Sampler"""
6425 if self.__class__ == Sampler:
6429 _IMP_kernel.Sampler_swiginit(self, _IMP_kernel.new_Sampler(_self, *args))
6431 if self.__class__ != Sampler:
6432 _director_objects.register(self)
6437 def create_sample(self):
6438 r"""create_sample(Sampler self) -> ConfigurationSet"""
6439 return _IMP_kernel.Sampler_create_sample(self)
6441 def get_scoring_function(self):
6442 r"""get_scoring_function(Sampler self) -> ScoringFunction"""
6443 return _IMP_kernel.Sampler_get_scoring_function(self)
6445 def set_scoring_function(self, sf):
6446 r"""set_scoring_function(Sampler self, _ScoringFunctionAdaptor sf)"""
6447 return _IMP_kernel.Sampler_set_scoring_function(self, sf)
6449 def get_model(self):
6450 r"""get_model(Sampler self) -> Model"""
6451 return _IMP_kernel.Sampler_get_model(self)
6453 def do_sample(self):
6454 r"""do_sample(Sampler self) -> ConfigurationSet"""
6455 return _IMP_kernel.Sampler_do_sample(self)
6456 __swig_destroy__ = _IMP_kernel.delete_Sampler
6459 r"""__str__(Sampler self) -> std::string"""
6460 return _IMP_kernel.Sampler___str__(self)
6463 r"""__repr__(Sampler self) -> std::string"""
6464 return _IMP_kernel.Sampler___repr__(self)
6468 return _object_cast_to_Sampler(o)
6471 def do_show(self, out):
6476 return _object_cast_to_Sampler(o)
6478 def __disown__(self):
6480 _IMP_kernel.disown_Sampler(self)
6481 return weakref.proxy(self)
6484 r"""do_destroy(Sampler self)"""
6485 return _IMP_kernel.Sampler_do_destroy(self)
6488 _IMP_kernel.Sampler_swigregister(Sampler)
6490 r"""Proxy of C++ IMP::PairModifier class."""
6492 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6494 def __init__(self, *args):
6495 r"""__init__(PairModifier self, std::string name="PairModifier %1%") -> PairModifier"""
6496 if self.__class__ == PairModifier:
6500 _IMP_kernel.PairModifier_swiginit(self, _IMP_kernel.new_PairModifier(_self, *args))
6502 if self.__class__ != PairModifier:
6503 _director_objects.register(self)
6508 def apply_index(self, m, v):
6509 r"""apply_index(PairModifier self, Model m, IMP::ParticleIndexPair const & v)"""
6510 return _IMP_kernel.PairModifier_apply_index(self, m, v)
6512 def apply_indexes(self, m, o, lower_bound, upper_bound):
6513 r"""apply_indexes(PairModifier self, Model m, IMP::ParticleIndexPairs const & o, unsigned int lower_bound, unsigned int upper_bound)"""
6514 return _IMP_kernel.PairModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
6516 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
6517 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)"""
6518 return _IMP_kernel.PairModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
6521 r"""__str__(PairModifier self) -> std::string"""
6522 return _IMP_kernel.PairModifier___str__(self)
6525 r"""__repr__(PairModifier self) -> std::string"""
6526 return _IMP_kernel.PairModifier___repr__(self)
6530 return _object_cast_to_PairModifier(o)
6533 def do_show(self, out):
6538 return _object_cast_to_PairModifier(o)
6540 __swig_destroy__ = _IMP_kernel.delete_PairModifier
6541 def __disown__(self):
6543 _IMP_kernel.disown_PairModifier(self)
6544 return weakref.proxy(self)
6546 def do_get_inputs(self, m, pis):
6547 r"""do_get_inputs(PairModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6548 return _IMP_kernel.PairModifier_do_get_inputs(self, m, pis)
6550 def do_get_outputs(self, m, pis):
6551 r"""do_get_outputs(PairModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6552 return _IMP_kernel.PairModifier_do_get_outputs(self, m, pis)
6555 r"""do_destroy(PairModifier self)"""
6556 return _IMP_kernel.PairModifier_do_destroy(self)
6559 _IMP_kernel.PairModifier_swigregister(PairModifier)
6561 r"""Proxy of C++ IMP::PairScore class."""
6563 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6565 def __init__(self, *args):
6566 r"""__init__(PairScore self, std::string name="PairScore %1%") -> PairScore"""
6567 if self.__class__ == PairScore:
6571 _IMP_kernel.PairScore_swiginit(self, _IMP_kernel.new_PairScore(_self, *args))
6573 if self.__class__ != PairScore:
6574 _director_objects.register(self)
6579 def evaluate_index(self, m, vt, da):
6580 r"""evaluate_index(PairScore self, Model m, IMP::ParticleIndexPair const & vt, DerivativeAccumulator da) -> double"""
6581 return _IMP_kernel.PairScore_evaluate_index(self, m, vt, da)
6583 def check_indexes(self, m, pis):
6584 r"""check_indexes(PairScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
6585 return _IMP_kernel.PairScore_check_indexes(self, m, pis)
6587 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
6588 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"""
6589 return _IMP_kernel.PairScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
6591 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
6592 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"""
6593 return _IMP_kernel.PairScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
6595 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
6596 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"""
6597 return _IMP_kernel.PairScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
6599 def evaluate_if_good_index(self, m, vt, da, max):
6600 r"""evaluate_if_good_index(PairScore self, Model m, IMP::ParticleIndexPair const & vt, DerivativeAccumulator da, double max) -> double"""
6601 return _IMP_kernel.PairScore_evaluate_if_good_index(self, m, vt, da, max)
6603 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
6604 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"""
6605 return _IMP_kernel.PairScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
6607 def create_current_decomposition(self, m, vt):
6608 r"""create_current_decomposition(PairScore self, Model m, IMP::ParticleIndexPair const & vt) -> IMP::Restraints"""
6609 return _IMP_kernel.PairScore_create_current_decomposition(self, m, vt)
6611 def do_create_current_decomposition(self, m, vt):
6612 r"""do_create_current_decomposition(PairScore self, Model m, IMP::ParticleIndexPair const & vt) -> IMP::Restraints"""
6613 return _IMP_kernel.PairScore_do_create_current_decomposition(self, m, vt)
6614 __swig_destroy__ = _IMP_kernel.delete_PairScore
6617 r"""__str__(PairScore self) -> std::string"""
6618 return _IMP_kernel.PairScore___str__(self)
6621 r"""__repr__(PairScore self) -> std::string"""
6622 return _IMP_kernel.PairScore___repr__(self)
6626 return _object_cast_to_PairScore(o)
6629 def do_show(self, out):
6634 return _object_cast_to_PairScore(o)
6636 def __disown__(self):
6638 _IMP_kernel.disown_PairScore(self)
6639 return weakref.proxy(self)
6641 def do_get_inputs(self, m, pis):
6642 r"""do_get_inputs(PairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6643 return _IMP_kernel.PairScore_do_get_inputs(self, m, pis)
6646 r"""do_destroy(PairScore self)"""
6647 return _IMP_kernel.PairScore_do_destroy(self)
6650 _IMP_kernel.PairScore_swigregister(PairScore)
6652 r"""Proxy of C++ IMP::PairPredicate class."""
6654 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6656 def __init__(self, *args):
6657 r"""__init__(PairPredicate self, std::string name="PairPredicate %1%") -> PairPredicate"""
6658 if self.__class__ == PairPredicate:
6662 _IMP_kernel.PairPredicate_swiginit(self, _IMP_kernel.new_PairPredicate(_self, *args))
6664 if self.__class__ != PairPredicate:
6665 _director_objects.register(self)
6670 def setup_for_get_value_index_in_batch(self, arg0):
6671 r"""setup_for_get_value_index_in_batch(PairPredicate self, Model arg0)"""
6672 return _IMP_kernel.PairPredicate_setup_for_get_value_index_in_batch(self, arg0)
6674 def get_value_index_in_batch(self, m, vt):
6675 r"""get_value_index_in_batch(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int"""
6676 return _IMP_kernel.PairPredicate_get_value_index_in_batch(self, m, vt)
6678 def __call__(self, m, vt):
6679 r"""__call__(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int"""
6680 return _IMP_kernel.PairPredicate___call__(self, m, vt)
6682 def get_value_index(self, *args):
6684 get_value_index(PairPredicate self, Model m, IMP::ParticleIndexPair const & vt) -> int
6685 get_value_index(PairPredicate self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
6687 return _IMP_kernel.PairPredicate_get_value_index(self, *args)
6688 __swig_destroy__ = _IMP_kernel.delete_PairPredicate
6691 r"""__str__(PairPredicate self) -> std::string"""
6692 return _IMP_kernel.PairPredicate___str__(self)
6695 r"""__repr__(PairPredicate self) -> std::string"""
6696 return _IMP_kernel.PairPredicate___repr__(self)
6700 return _object_cast_to_PairPredicate(o)
6703 def do_show(self, out):
6708 return _object_cast_to_PairPredicate(o)
6710 def __disown__(self):
6712 _IMP_kernel.disown_PairPredicate(self)
6713 return weakref.proxy(self)
6715 def do_get_inputs(self, m, pis):
6716 r"""do_get_inputs(PairPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6717 return _IMP_kernel.PairPredicate_do_get_inputs(self, m, pis)
6720 r"""do_destroy(PairPredicate self)"""
6721 return _IMP_kernel.PairPredicate_do_destroy(self)
6724 _IMP_kernel.PairPredicate_swigregister(PairPredicate)
6726 r"""Proxy of C++ IMP::PairContainer class."""
6728 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6730 def apply_generic(self, m):
6731 r"""apply_generic(PairContainer self, PairModifier m)"""
6732 return _IMP_kernel.PairContainer_apply_generic(self, m)
6734 def apply_generic_moved(self, m, moved_pis, reset_pis):
6735 r"""apply_generic_moved(PairContainer self, PairModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
6736 return _IMP_kernel.PairContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
6738 def apply(self, sm):
6739 r"""apply(PairContainer self, PairModifier sm)"""
6740 return _IMP_kernel.PairContainer_apply(self, sm)
6742 def apply_moved(self, sm, moved_pis, reset_pis):
6743 r"""apply_moved(PairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
6744 return _IMP_kernel.PairContainer_apply_moved(self, sm, moved_pis, reset_pis)
6746 def get_range_indexes(self):
6747 r"""get_range_indexes(PairContainer self) -> IMP::ParticleIndexPairs"""
6748 return _IMP_kernel.PairContainer_get_range_indexes(self)
6750 def get_contents(self):
6751 r"""get_contents(PairContainer self) -> IMP::ParticleIndexPairs const &"""
6752 return _IMP_kernel.PairContainer_get_contents(self)
6755 r"""get_indexes(PairContainer self) -> IMP::ParticleIndexPairs"""
6756 return _IMP_kernel.PairContainer_get_indexes(self)
6758 def get(self, *args):
6760 get(PairContainer self) -> IMP::ParticlePairsTemp
6761 get(PairContainer self, unsigned int i) -> IMP::ParticlePair
6763 return _IMP_kernel.PairContainer_get(self, *args)
6765 def get_number(self):
6766 r"""get_number(PairContainer self) -> unsigned int"""
6767 return _IMP_kernel.PairContainer_get_number(self)
6769 def __init__(self, *args):
6771 __init__(PairContainer self, Model m, std::string name="PairContainer %1%") -> PairContainer
6772 __init__(PairContainer self) -> PairContainer
6774 if self.__class__ == PairContainer:
6778 _IMP_kernel.PairContainer_swiginit(self, _IMP_kernel.new_PairContainer(_self, *args))
6780 if self.__class__ != PairContainer:
6781 _director_objects.register(self)
6786 def do_apply(self, sm):
6787 r"""do_apply(PairContainer self, PairModifier sm)"""
6788 return _IMP_kernel.PairContainer_do_apply(self, sm)
6790 def do_apply_moved(self, sm, moved_pis, reset_pis):
6791 r"""do_apply_moved(PairContainer self, PairModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
6792 return _IMP_kernel.PairContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
6794 def do_get_provides_access(self):
6795 r"""do_get_provides_access(PairContainer self) -> bool"""
6796 return _IMP_kernel.PairContainer_do_get_provides_access(self)
6797 __swig_destroy__ = _IMP_kernel.delete_PairContainer
6800 r"""__str__(PairContainer self) -> std::string"""
6801 return _IMP_kernel.PairContainer___str__(self)
6804 r"""__repr__(PairContainer self) -> std::string"""
6805 return _IMP_kernel.PairContainer___repr__(self)
6809 return _object_cast_to_PairContainer(o)
6812 def do_show(self, out):
6817 return _object_cast_to_PairContainer(o)
6819 def __disown__(self):
6821 _IMP_kernel.disown_PairContainer(self)
6822 return weakref.proxy(self)
6825 r"""do_destroy(PairContainer self)"""
6826 return _IMP_kernel.PairContainer_do_destroy(self)
6828 def handle_set_has_required_score_states(self, arg0):
6829 r"""handle_set_has_required_score_states(PairContainer self, bool arg0)"""
6830 return _IMP_kernel.PairContainer_handle_set_has_required_score_states(self, arg0)
6832 def do_get_inputs(self):
6833 r"""do_get_inputs(PairContainer self) -> IMP::ModelObjectsTemp"""
6834 return _IMP_kernel.PairContainer_do_get_inputs(self)
6836 def do_get_interactions(self):
6837 r"""do_get_interactions(PairContainer self) -> IMP::ModelObjectsTemps"""
6838 return _IMP_kernel.PairContainer_do_get_interactions(self)
6840 def do_get_contents_hash(self):
6841 r"""do_get_contents_hash(PairContainer self) -> std::size_t"""
6842 return _IMP_kernel.PairContainer_do_get_contents_hash(self)
6845 _IMP_kernel.PairContainer_swigregister(PairContainer)
6846 class _PairContainerAdaptor(_InputAdaptor):
6847 r"""Proxy of C++ IMP::PairContainerAdaptor class."""
6849 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6850 __repr__ = _swig_repr
6852 def __init__(self, *args):
6854 __init__(_PairContainerAdaptor self) -> _PairContainerAdaptor
6855 __init__(_PairContainerAdaptor self, PairContainer c) -> _PairContainerAdaptor
6856 __init__(_PairContainerAdaptor self, IMP::ParticlePairsTemp const & t) -> _PairContainerAdaptor
6858 _IMP_kernel._PairContainerAdaptor_swiginit(self, _IMP_kernel.new__PairContainerAdaptor(*args))
6860 def set_name_if_default(self, name):
6861 r"""set_name_if_default(_PairContainerAdaptor self, std::string name)"""
6862 return _IMP_kernel._PairContainerAdaptor_set_name_if_default(self, name)
6863 __swig_destroy__ = _IMP_kernel.delete__PairContainerAdaptor
6866 _IMP_kernel._PairContainerAdaptor_swigregister(_PairContainerAdaptor)
6868 r"""Proxy of C++ IMP::QuadModifier class."""
6870 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6872 def __init__(self, *args):
6873 r"""__init__(QuadModifier self, std::string name="QuadModifier %1%") -> QuadModifier"""
6874 if self.__class__ == QuadModifier:
6878 _IMP_kernel.QuadModifier_swiginit(self, _IMP_kernel.new_QuadModifier(_self, *args))
6880 if self.__class__ != QuadModifier:
6881 _director_objects.register(self)
6886 def apply_index(self, m, v):
6887 r"""apply_index(QuadModifier self, Model m, IMP::ParticleIndexQuad const & v)"""
6888 return _IMP_kernel.QuadModifier_apply_index(self, m, v)
6890 def apply_indexes(self, m, o, lower_bound, upper_bound):
6891 r"""apply_indexes(QuadModifier self, Model m, IMP::ParticleIndexQuads const & o, unsigned int lower_bound, unsigned int upper_bound)"""
6892 return _IMP_kernel.QuadModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
6894 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
6895 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)"""
6896 return _IMP_kernel.QuadModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
6899 r"""__str__(QuadModifier self) -> std::string"""
6900 return _IMP_kernel.QuadModifier___str__(self)
6903 r"""__repr__(QuadModifier self) -> std::string"""
6904 return _IMP_kernel.QuadModifier___repr__(self)
6908 return _object_cast_to_QuadModifier(o)
6911 def do_show(self, out):
6916 return _object_cast_to_QuadModifier(o)
6918 __swig_destroy__ = _IMP_kernel.delete_QuadModifier
6919 def __disown__(self):
6921 _IMP_kernel.disown_QuadModifier(self)
6922 return weakref.proxy(self)
6924 def do_get_inputs(self, m, pis):
6925 r"""do_get_inputs(QuadModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6926 return _IMP_kernel.QuadModifier_do_get_inputs(self, m, pis)
6928 def do_get_outputs(self, m, pis):
6929 r"""do_get_outputs(QuadModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
6930 return _IMP_kernel.QuadModifier_do_get_outputs(self, m, pis)
6933 r"""do_destroy(QuadModifier self)"""
6934 return _IMP_kernel.QuadModifier_do_destroy(self)
6937 _IMP_kernel.QuadModifier_swigregister(QuadModifier)
6939 r"""Proxy of C++ IMP::QuadScore class."""
6941 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
6943 def __init__(self, *args):
6944 r"""__init__(QuadScore self, std::string name="QuadScore %1%") -> QuadScore"""
6945 if self.__class__ == QuadScore:
6949 _IMP_kernel.QuadScore_swiginit(self, _IMP_kernel.new_QuadScore(_self, *args))
6951 if self.__class__ != QuadScore:
6952 _director_objects.register(self)
6957 def evaluate_index(self, m, vt, da):
6958 r"""evaluate_index(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt, DerivativeAccumulator da) -> double"""
6959 return _IMP_kernel.QuadScore_evaluate_index(self, m, vt, da)
6961 def check_indexes(self, m, pis):
6962 r"""check_indexes(QuadScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
6963 return _IMP_kernel.QuadScore_check_indexes(self, m, pis)
6965 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
6966 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"""
6967 return _IMP_kernel.QuadScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
6969 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
6970 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"""
6971 return _IMP_kernel.QuadScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
6973 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
6974 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"""
6975 return _IMP_kernel.QuadScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
6977 def evaluate_if_good_index(self, m, vt, da, max):
6978 r"""evaluate_if_good_index(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt, DerivativeAccumulator da, double max) -> double"""
6979 return _IMP_kernel.QuadScore_evaluate_if_good_index(self, m, vt, da, max)
6981 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
6982 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"""
6983 return _IMP_kernel.QuadScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
6985 def create_current_decomposition(self, m, vt):
6986 r"""create_current_decomposition(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt) -> IMP::Restraints"""
6987 return _IMP_kernel.QuadScore_create_current_decomposition(self, m, vt)
6989 def do_create_current_decomposition(self, m, vt):
6990 r"""do_create_current_decomposition(QuadScore self, Model m, IMP::ParticleIndexQuad const & vt) -> IMP::Restraints"""
6991 return _IMP_kernel.QuadScore_do_create_current_decomposition(self, m, vt)
6992 __swig_destroy__ = _IMP_kernel.delete_QuadScore
6995 r"""__str__(QuadScore self) -> std::string"""
6996 return _IMP_kernel.QuadScore___str__(self)
6999 r"""__repr__(QuadScore self) -> std::string"""
7000 return _IMP_kernel.QuadScore___repr__(self)
7004 return _object_cast_to_QuadScore(o)
7007 def do_show(self, out):
7012 return _object_cast_to_QuadScore(o)
7014 def __disown__(self):
7016 _IMP_kernel.disown_QuadScore(self)
7017 return weakref.proxy(self)
7019 def do_get_inputs(self, m, pis):
7020 r"""do_get_inputs(QuadScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7021 return _IMP_kernel.QuadScore_do_get_inputs(self, m, pis)
7024 r"""do_destroy(QuadScore self)"""
7025 return _IMP_kernel.QuadScore_do_destroy(self)
7028 _IMP_kernel.QuadScore_swigregister(QuadScore)
7030 r"""Proxy of C++ IMP::QuadPredicate class."""
7032 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7034 def __init__(self, *args):
7035 r"""__init__(QuadPredicate self, std::string name="QuadPredicate %1%") -> QuadPredicate"""
7036 if self.__class__ == QuadPredicate:
7040 _IMP_kernel.QuadPredicate_swiginit(self, _IMP_kernel.new_QuadPredicate(_self, *args))
7042 if self.__class__ != QuadPredicate:
7043 _director_objects.register(self)
7048 def setup_for_get_value_index_in_batch(self, arg0):
7049 r"""setup_for_get_value_index_in_batch(QuadPredicate self, Model arg0)"""
7050 return _IMP_kernel.QuadPredicate_setup_for_get_value_index_in_batch(self, arg0)
7052 def get_value_index_in_batch(self, m, vt):
7053 r"""get_value_index_in_batch(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int"""
7054 return _IMP_kernel.QuadPredicate_get_value_index_in_batch(self, m, vt)
7056 def __call__(self, m, vt):
7057 r"""__call__(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int"""
7058 return _IMP_kernel.QuadPredicate___call__(self, m, vt)
7060 def get_value_index(self, *args):
7062 get_value_index(QuadPredicate self, Model m, IMP::ParticleIndexQuad const & vt) -> int
7063 get_value_index(QuadPredicate self, Model m, IMP::ParticleIndexQuads const & o) -> IMP::Ints
7065 return _IMP_kernel.QuadPredicate_get_value_index(self, *args)
7066 __swig_destroy__ = _IMP_kernel.delete_QuadPredicate
7069 r"""__str__(QuadPredicate self) -> std::string"""
7070 return _IMP_kernel.QuadPredicate___str__(self)
7073 r"""__repr__(QuadPredicate self) -> std::string"""
7074 return _IMP_kernel.QuadPredicate___repr__(self)
7078 return _object_cast_to_QuadPredicate(o)
7081 def do_show(self, out):
7086 return _object_cast_to_QuadPredicate(o)
7088 def __disown__(self):
7090 _IMP_kernel.disown_QuadPredicate(self)
7091 return weakref.proxy(self)
7093 def do_get_inputs(self, m, pis):
7094 r"""do_get_inputs(QuadPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7095 return _IMP_kernel.QuadPredicate_do_get_inputs(self, m, pis)
7098 r"""do_destroy(QuadPredicate self)"""
7099 return _IMP_kernel.QuadPredicate_do_destroy(self)
7102 _IMP_kernel.QuadPredicate_swigregister(QuadPredicate)
7104 r"""Proxy of C++ IMP::QuadContainer class."""
7106 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7108 def apply_generic(self, m):
7109 r"""apply_generic(QuadContainer self, QuadModifier m)"""
7110 return _IMP_kernel.QuadContainer_apply_generic(self, m)
7112 def apply_generic_moved(self, m, moved_pis, reset_pis):
7113 r"""apply_generic_moved(QuadContainer self, QuadModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7114 return _IMP_kernel.QuadContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
7116 def apply(self, sm):
7117 r"""apply(QuadContainer self, QuadModifier sm)"""
7118 return _IMP_kernel.QuadContainer_apply(self, sm)
7120 def apply_moved(self, sm, moved_pis, reset_pis):
7121 r"""apply_moved(QuadContainer self, QuadModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7122 return _IMP_kernel.QuadContainer_apply_moved(self, sm, moved_pis, reset_pis)
7124 def get_range_indexes(self):
7125 r"""get_range_indexes(QuadContainer self) -> IMP::ParticleIndexQuads"""
7126 return _IMP_kernel.QuadContainer_get_range_indexes(self)
7128 def get_contents(self):
7129 r"""get_contents(QuadContainer self) -> IMP::ParticleIndexQuads const &"""
7130 return _IMP_kernel.QuadContainer_get_contents(self)
7133 r"""get_indexes(QuadContainer self) -> IMP::ParticleIndexQuads"""
7134 return _IMP_kernel.QuadContainer_get_indexes(self)
7136 def get(self, *args):
7138 get(QuadContainer self) -> IMP::ParticleQuadsTemp
7139 get(QuadContainer self, unsigned int i) -> IMP::ParticleQuad
7141 return _IMP_kernel.QuadContainer_get(self, *args)
7143 def get_number(self):
7144 r"""get_number(QuadContainer self) -> unsigned int"""
7145 return _IMP_kernel.QuadContainer_get_number(self)
7147 def __init__(self, *args):
7149 __init__(QuadContainer self, Model m, std::string name="QuadContainer %1%") -> QuadContainer
7150 __init__(QuadContainer self) -> QuadContainer
7152 if self.__class__ == QuadContainer:
7156 _IMP_kernel.QuadContainer_swiginit(self, _IMP_kernel.new_QuadContainer(_self, *args))
7158 if self.__class__ != QuadContainer:
7159 _director_objects.register(self)
7164 def do_apply(self, sm):
7165 r"""do_apply(QuadContainer self, QuadModifier sm)"""
7166 return _IMP_kernel.QuadContainer_do_apply(self, sm)
7168 def do_apply_moved(self, sm, moved_pis, reset_pis):
7169 r"""do_apply_moved(QuadContainer self, QuadModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7170 return _IMP_kernel.QuadContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
7172 def do_get_provides_access(self):
7173 r"""do_get_provides_access(QuadContainer self) -> bool"""
7174 return _IMP_kernel.QuadContainer_do_get_provides_access(self)
7175 __swig_destroy__ = _IMP_kernel.delete_QuadContainer
7178 r"""__str__(QuadContainer self) -> std::string"""
7179 return _IMP_kernel.QuadContainer___str__(self)
7182 r"""__repr__(QuadContainer self) -> std::string"""
7183 return _IMP_kernel.QuadContainer___repr__(self)
7187 return _object_cast_to_QuadContainer(o)
7190 def do_show(self, out):
7195 return _object_cast_to_QuadContainer(o)
7197 def __disown__(self):
7199 _IMP_kernel.disown_QuadContainer(self)
7200 return weakref.proxy(self)
7203 r"""do_destroy(QuadContainer self)"""
7204 return _IMP_kernel.QuadContainer_do_destroy(self)
7206 def handle_set_has_required_score_states(self, arg0):
7207 r"""handle_set_has_required_score_states(QuadContainer self, bool arg0)"""
7208 return _IMP_kernel.QuadContainer_handle_set_has_required_score_states(self, arg0)
7210 def do_get_inputs(self):
7211 r"""do_get_inputs(QuadContainer self) -> IMP::ModelObjectsTemp"""
7212 return _IMP_kernel.QuadContainer_do_get_inputs(self)
7214 def do_get_interactions(self):
7215 r"""do_get_interactions(QuadContainer self) -> IMP::ModelObjectsTemps"""
7216 return _IMP_kernel.QuadContainer_do_get_interactions(self)
7218 def do_get_contents_hash(self):
7219 r"""do_get_contents_hash(QuadContainer self) -> std::size_t"""
7220 return _IMP_kernel.QuadContainer_do_get_contents_hash(self)
7223 _IMP_kernel.QuadContainer_swigregister(QuadContainer)
7224 class _QuadContainerAdaptor(_InputAdaptor):
7225 r"""Proxy of C++ IMP::QuadContainerAdaptor class."""
7227 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7228 __repr__ = _swig_repr
7230 def __init__(self, *args):
7232 __init__(_QuadContainerAdaptor self) -> _QuadContainerAdaptor
7233 __init__(_QuadContainerAdaptor self, QuadContainer c) -> _QuadContainerAdaptor
7234 __init__(_QuadContainerAdaptor self, IMP::ParticleQuadsTemp const & t) -> _QuadContainerAdaptor
7236 _IMP_kernel._QuadContainerAdaptor_swiginit(self, _IMP_kernel.new__QuadContainerAdaptor(*args))
7238 def set_name_if_default(self, name):
7239 r"""set_name_if_default(_QuadContainerAdaptor self, std::string name)"""
7240 return _IMP_kernel._QuadContainerAdaptor_set_name_if_default(self, name)
7241 __swig_destroy__ = _IMP_kernel.delete__QuadContainerAdaptor
7244 _IMP_kernel._QuadContainerAdaptor_swigregister(_QuadContainerAdaptor)
7246 r"""Proxy of C++ IMP::SingletonModifier class."""
7248 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7250 def __init__(self, *args):
7251 r"""__init__(SingletonModifier self, std::string name="SingletonModifier %1%") -> SingletonModifier"""
7252 if self.__class__ == SingletonModifier:
7256 _IMP_kernel.SingletonModifier_swiginit(self, _IMP_kernel.new_SingletonModifier(_self, *args))
7258 if self.__class__ != SingletonModifier:
7259 _director_objects.register(self)
7264 def apply_index(self, m, v):
7265 r"""apply_index(SingletonModifier self, Model m, ParticleIndex v)"""
7266 return _IMP_kernel.SingletonModifier_apply_index(self, m, v)
7268 def apply_indexes(self, m, o, lower_bound, upper_bound):
7269 r"""apply_indexes(SingletonModifier self, Model m, IMP::ParticleIndexes const & o, unsigned int lower_bound, unsigned int upper_bound)"""
7270 return _IMP_kernel.SingletonModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
7272 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
7273 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)"""
7274 return _IMP_kernel.SingletonModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
7277 r"""__str__(SingletonModifier self) -> std::string"""
7278 return _IMP_kernel.SingletonModifier___str__(self)
7281 r"""__repr__(SingletonModifier self) -> std::string"""
7282 return _IMP_kernel.SingletonModifier___repr__(self)
7286 return _object_cast_to_SingletonModifier(o)
7289 def do_show(self, out):
7294 return _object_cast_to_SingletonModifier(o)
7296 __swig_destroy__ = _IMP_kernel.delete_SingletonModifier
7297 def __disown__(self):
7299 _IMP_kernel.disown_SingletonModifier(self)
7300 return weakref.proxy(self)
7302 def do_get_inputs(self, m, pis):
7303 r"""do_get_inputs(SingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7304 return _IMP_kernel.SingletonModifier_do_get_inputs(self, m, pis)
7306 def do_get_outputs(self, m, pis):
7307 r"""do_get_outputs(SingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7308 return _IMP_kernel.SingletonModifier_do_get_outputs(self, m, pis)
7311 r"""do_destroy(SingletonModifier self)"""
7312 return _IMP_kernel.SingletonModifier_do_destroy(self)
7315 _IMP_kernel.SingletonModifier_swigregister(SingletonModifier)
7317 r"""Proxy of C++ IMP::SingletonScore class."""
7319 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7321 def __init__(self, *args):
7322 r"""__init__(SingletonScore self, std::string name="SingletonScore %1%") -> SingletonScore"""
7323 if self.__class__ == SingletonScore:
7327 _IMP_kernel.SingletonScore_swiginit(self, _IMP_kernel.new_SingletonScore(_self, *args))
7329 if self.__class__ != SingletonScore:
7330 _director_objects.register(self)
7335 def evaluate_index(self, m, vt, da):
7336 r"""evaluate_index(SingletonScore self, Model m, ParticleIndex vt, DerivativeAccumulator da) -> double"""
7337 return _IMP_kernel.SingletonScore_evaluate_index(self, m, vt, da)
7339 def check_indexes(self, m, pis):
7340 r"""check_indexes(SingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
7341 return _IMP_kernel.SingletonScore_check_indexes(self, m, pis)
7343 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
7344 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"""
7345 return _IMP_kernel.SingletonScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
7347 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7348 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"""
7349 return _IMP_kernel.SingletonScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
7351 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
7352 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"""
7353 return _IMP_kernel.SingletonScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
7355 def evaluate_if_good_index(self, m, vt, da, max):
7356 r"""evaluate_if_good_index(SingletonScore self, Model m, ParticleIndex vt, DerivativeAccumulator da, double max) -> double"""
7357 return _IMP_kernel.SingletonScore_evaluate_if_good_index(self, m, vt, da, max)
7359 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7360 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"""
7361 return _IMP_kernel.SingletonScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
7363 def create_current_decomposition(self, m, vt):
7364 r"""create_current_decomposition(SingletonScore self, Model m, ParticleIndex vt) -> IMP::Restraints"""
7365 return _IMP_kernel.SingletonScore_create_current_decomposition(self, m, vt)
7367 def do_create_current_decomposition(self, m, vt):
7368 r"""do_create_current_decomposition(SingletonScore self, Model m, ParticleIndex vt) -> IMP::Restraints"""
7369 return _IMP_kernel.SingletonScore_do_create_current_decomposition(self, m, vt)
7370 __swig_destroy__ = _IMP_kernel.delete_SingletonScore
7373 r"""__str__(SingletonScore self) -> std::string"""
7374 return _IMP_kernel.SingletonScore___str__(self)
7377 r"""__repr__(SingletonScore self) -> std::string"""
7378 return _IMP_kernel.SingletonScore___repr__(self)
7382 return _object_cast_to_SingletonScore(o)
7385 def do_show(self, out):
7390 return _object_cast_to_SingletonScore(o)
7392 def __disown__(self):
7394 _IMP_kernel.disown_SingletonScore(self)
7395 return weakref.proxy(self)
7397 def do_get_inputs(self, m, pis):
7398 r"""do_get_inputs(SingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7399 return _IMP_kernel.SingletonScore_do_get_inputs(self, m, pis)
7402 r"""do_destroy(SingletonScore self)"""
7403 return _IMP_kernel.SingletonScore_do_destroy(self)
7406 _IMP_kernel.SingletonScore_swigregister(SingletonScore)
7408 r"""Proxy of C++ IMP::SingletonPredicate class."""
7410 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7412 def __init__(self, *args):
7413 r"""__init__(SingletonPredicate self, std::string name="SingletonPredicate %1%") -> SingletonPredicate"""
7414 if self.__class__ == SingletonPredicate:
7418 _IMP_kernel.SingletonPredicate_swiginit(self, _IMP_kernel.new_SingletonPredicate(_self, *args))
7420 if self.__class__ != SingletonPredicate:
7421 _director_objects.register(self)
7426 def setup_for_get_value_index_in_batch(self, arg0):
7427 r"""setup_for_get_value_index_in_batch(SingletonPredicate self, Model arg0)"""
7428 return _IMP_kernel.SingletonPredicate_setup_for_get_value_index_in_batch(self, arg0)
7430 def get_value_index_in_batch(self, m, vt):
7431 r"""get_value_index_in_batch(SingletonPredicate self, Model m, ParticleIndex vt) -> int"""
7432 return _IMP_kernel.SingletonPredicate_get_value_index_in_batch(self, m, vt)
7434 def __call__(self, m, vt):
7435 r"""__call__(SingletonPredicate self, Model m, ParticleIndex vt) -> int"""
7436 return _IMP_kernel.SingletonPredicate___call__(self, m, vt)
7438 def get_value_index(self, *args):
7440 get_value_index(SingletonPredicate self, Model m, ParticleIndex vt) -> int
7441 get_value_index(SingletonPredicate self, Model m, IMP::ParticleIndexes const & o) -> IMP::Ints
7443 return _IMP_kernel.SingletonPredicate_get_value_index(self, *args)
7444 __swig_destroy__ = _IMP_kernel.delete_SingletonPredicate
7447 r"""__str__(SingletonPredicate self) -> std::string"""
7448 return _IMP_kernel.SingletonPredicate___str__(self)
7451 r"""__repr__(SingletonPredicate self) -> std::string"""
7452 return _IMP_kernel.SingletonPredicate___repr__(self)
7456 return _object_cast_to_SingletonPredicate(o)
7459 def do_show(self, out):
7464 return _object_cast_to_SingletonPredicate(o)
7466 def __disown__(self):
7468 _IMP_kernel.disown_SingletonPredicate(self)
7469 return weakref.proxy(self)
7471 def do_get_inputs(self, m, pis):
7472 r"""do_get_inputs(SingletonPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7473 return _IMP_kernel.SingletonPredicate_do_get_inputs(self, m, pis)
7476 r"""do_destroy(SingletonPredicate self)"""
7477 return _IMP_kernel.SingletonPredicate_do_destroy(self)
7480 _IMP_kernel.SingletonPredicate_swigregister(SingletonPredicate)
7482 r"""Proxy of C++ IMP::SingletonContainer class."""
7484 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7486 def apply_generic(self, m):
7487 r"""apply_generic(SingletonContainer self, SingletonModifier m)"""
7488 return _IMP_kernel.SingletonContainer_apply_generic(self, m)
7490 def apply_generic_moved(self, m, moved_pis, reset_pis):
7491 r"""apply_generic_moved(SingletonContainer self, SingletonModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7492 return _IMP_kernel.SingletonContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
7494 def apply(self, sm):
7495 r"""apply(SingletonContainer self, SingletonModifier sm)"""
7496 return _IMP_kernel.SingletonContainer_apply(self, sm)
7498 def apply_moved(self, sm, moved_pis, reset_pis):
7499 r"""apply_moved(SingletonContainer self, SingletonModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7500 return _IMP_kernel.SingletonContainer_apply_moved(self, sm, moved_pis, reset_pis)
7502 def get_range_indexes(self):
7503 r"""get_range_indexes(SingletonContainer self) -> IMP::ParticleIndexes"""
7504 return _IMP_kernel.SingletonContainer_get_range_indexes(self)
7506 def get_contents(self):
7507 r"""get_contents(SingletonContainer self) -> IMP::ParticleIndexes const &"""
7508 return _IMP_kernel.SingletonContainer_get_contents(self)
7511 r"""get_indexes(SingletonContainer self) -> IMP::ParticleIndexes"""
7512 return _IMP_kernel.SingletonContainer_get_indexes(self)
7514 def get(self, *args):
7516 get(SingletonContainer self) -> IMP::ParticlesTemp
7517 get(SingletonContainer self, unsigned int i) -> Particle
7519 return _IMP_kernel.SingletonContainer_get(self, *args)
7521 def get_number(self):
7522 r"""get_number(SingletonContainer self) -> unsigned int"""
7523 return _IMP_kernel.SingletonContainer_get_number(self)
7525 def __init__(self, *args):
7527 __init__(SingletonContainer self, Model m, std::string name="SingletonContainer %1%") -> SingletonContainer
7528 __init__(SingletonContainer self) -> SingletonContainer
7530 if self.__class__ == SingletonContainer:
7534 _IMP_kernel.SingletonContainer_swiginit(self, _IMP_kernel.new_SingletonContainer(_self, *args))
7536 if self.__class__ != SingletonContainer:
7537 _director_objects.register(self)
7542 def do_apply(self, sm):
7543 r"""do_apply(SingletonContainer self, SingletonModifier sm)"""
7544 return _IMP_kernel.SingletonContainer_do_apply(self, sm)
7546 def do_apply_moved(self, sm, moved_pis, reset_pis):
7547 r"""do_apply_moved(SingletonContainer self, SingletonModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7548 return _IMP_kernel.SingletonContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
7550 def do_get_provides_access(self):
7551 r"""do_get_provides_access(SingletonContainer self) -> bool"""
7552 return _IMP_kernel.SingletonContainer_do_get_provides_access(self)
7553 __swig_destroy__ = _IMP_kernel.delete_SingletonContainer
7556 r"""__str__(SingletonContainer self) -> std::string"""
7557 return _IMP_kernel.SingletonContainer___str__(self)
7560 r"""__repr__(SingletonContainer self) -> std::string"""
7561 return _IMP_kernel.SingletonContainer___repr__(self)
7565 return _object_cast_to_SingletonContainer(o)
7568 def do_show(self, out):
7573 return _object_cast_to_SingletonContainer(o)
7575 def __disown__(self):
7577 _IMP_kernel.disown_SingletonContainer(self)
7578 return weakref.proxy(self)
7581 r"""do_destroy(SingletonContainer self)"""
7582 return _IMP_kernel.SingletonContainer_do_destroy(self)
7584 def handle_set_has_required_score_states(self, arg0):
7585 r"""handle_set_has_required_score_states(SingletonContainer self, bool arg0)"""
7586 return _IMP_kernel.SingletonContainer_handle_set_has_required_score_states(self, arg0)
7588 def do_get_inputs(self):
7589 r"""do_get_inputs(SingletonContainer self) -> IMP::ModelObjectsTemp"""
7590 return _IMP_kernel.SingletonContainer_do_get_inputs(self)
7592 def do_get_interactions(self):
7593 r"""do_get_interactions(SingletonContainer self) -> IMP::ModelObjectsTemps"""
7594 return _IMP_kernel.SingletonContainer_do_get_interactions(self)
7596 def do_get_contents_hash(self):
7597 r"""do_get_contents_hash(SingletonContainer self) -> std::size_t"""
7598 return _IMP_kernel.SingletonContainer_do_get_contents_hash(self)
7601 _IMP_kernel.SingletonContainer_swigregister(SingletonContainer)
7602 class _SingletonContainerAdaptor(_InputAdaptor):
7603 r"""Proxy of C++ IMP::SingletonContainerAdaptor class."""
7605 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7606 __repr__ = _swig_repr
7608 def __init__(self, *args):
7610 __init__(_SingletonContainerAdaptor self) -> _SingletonContainerAdaptor
7611 __init__(_SingletonContainerAdaptor self, SingletonContainer c) -> _SingletonContainerAdaptor
7612 __init__(_SingletonContainerAdaptor self, IMP::ParticlesTemp const & t) -> _SingletonContainerAdaptor
7614 _IMP_kernel._SingletonContainerAdaptor_swiginit(self, _IMP_kernel.new__SingletonContainerAdaptor(*args))
7616 def set_name_if_default(self, name):
7617 r"""set_name_if_default(_SingletonContainerAdaptor self, std::string name)"""
7618 return _IMP_kernel._SingletonContainerAdaptor_set_name_if_default(self, name)
7619 __swig_destroy__ = _IMP_kernel.delete__SingletonContainerAdaptor
7622 _IMP_kernel._SingletonContainerAdaptor_swigregister(_SingletonContainerAdaptor)
7624 r"""Proxy of C++ IMP::TripletModifier class."""
7626 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7628 def __init__(self, *args):
7629 r"""__init__(TripletModifier self, std::string name="TripletModifier %1%") -> TripletModifier"""
7630 if self.__class__ == TripletModifier:
7634 _IMP_kernel.TripletModifier_swiginit(self, _IMP_kernel.new_TripletModifier(_self, *args))
7636 if self.__class__ != TripletModifier:
7637 _director_objects.register(self)
7642 def apply_index(self, m, v):
7643 r"""apply_index(TripletModifier self, Model m, IMP::ParticleIndexTriplet const & v)"""
7644 return _IMP_kernel.TripletModifier_apply_index(self, m, v)
7646 def apply_indexes(self, m, o, lower_bound, upper_bound):
7647 r"""apply_indexes(TripletModifier self, Model m, IMP::ParticleIndexTriplets const & o, unsigned int lower_bound, unsigned int upper_bound)"""
7648 return _IMP_kernel.TripletModifier_apply_indexes(self, m, o, lower_bound, upper_bound)
7650 def apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis):
7651 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)"""
7652 return _IMP_kernel.TripletModifier_apply_indexes_moved(self, m, o, lower_bound, upper_bound, moved_pis, reset_pis)
7655 r"""__str__(TripletModifier self) -> std::string"""
7656 return _IMP_kernel.TripletModifier___str__(self)
7659 r"""__repr__(TripletModifier self) -> std::string"""
7660 return _IMP_kernel.TripletModifier___repr__(self)
7664 return _object_cast_to_TripletModifier(o)
7667 def do_show(self, out):
7672 return _object_cast_to_TripletModifier(o)
7674 __swig_destroy__ = _IMP_kernel.delete_TripletModifier
7675 def __disown__(self):
7677 _IMP_kernel.disown_TripletModifier(self)
7678 return weakref.proxy(self)
7680 def do_get_inputs(self, m, pis):
7681 r"""do_get_inputs(TripletModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7682 return _IMP_kernel.TripletModifier_do_get_inputs(self, m, pis)
7684 def do_get_outputs(self, m, pis):
7685 r"""do_get_outputs(TripletModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7686 return _IMP_kernel.TripletModifier_do_get_outputs(self, m, pis)
7689 r"""do_destroy(TripletModifier self)"""
7690 return _IMP_kernel.TripletModifier_do_destroy(self)
7693 _IMP_kernel.TripletModifier_swigregister(TripletModifier)
7695 r"""Proxy of C++ IMP::TripletScore class."""
7697 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7699 def __init__(self, *args):
7700 r"""__init__(TripletScore self, std::string name="TripletScore %1%") -> TripletScore"""
7701 if self.__class__ == TripletScore:
7705 _IMP_kernel.TripletScore_swiginit(self, _IMP_kernel.new_TripletScore(_self, *args))
7707 if self.__class__ != TripletScore:
7708 _director_objects.register(self)
7713 def evaluate_index(self, m, vt, da):
7714 r"""evaluate_index(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt, DerivativeAccumulator da) -> double"""
7715 return _IMP_kernel.TripletScore_evaluate_index(self, m, vt, da)
7717 def check_indexes(self, m, pis):
7718 r"""check_indexes(TripletScore self, Model m, IMP::ParticleIndexes const & pis) -> bool"""
7719 return _IMP_kernel.TripletScore_check_indexes(self, m, pis)
7721 def evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked=False):
7722 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"""
7723 return _IMP_kernel.TripletScore_evaluate_indexes(self, m, o, da, lower_bound, upper_bound, all_indexes_checked)
7725 def evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked=False):
7726 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"""
7727 return _IMP_kernel.TripletScore_evaluate_indexes_scores(self, m, o, da, lower_bound, upper_bound, score, all_indexes_checked)
7729 def evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked=False):
7730 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"""
7731 return _IMP_kernel.TripletScore_evaluate_indexes_delta(self, m, o, da, indexes, score, all_indexes_checked)
7733 def evaluate_if_good_index(self, m, vt, da, max):
7734 r"""evaluate_if_good_index(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt, DerivativeAccumulator da, double max) -> double"""
7735 return _IMP_kernel.TripletScore_evaluate_if_good_index(self, m, vt, da, max)
7737 def evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked=False):
7738 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"""
7739 return _IMP_kernel.TripletScore_evaluate_if_good_indexes(self, m, o, da, max, lower_bound, upper_bound, all_indexes_checked)
7741 def create_current_decomposition(self, m, vt):
7742 r"""create_current_decomposition(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt) -> IMP::Restraints"""
7743 return _IMP_kernel.TripletScore_create_current_decomposition(self, m, vt)
7745 def do_create_current_decomposition(self, m, vt):
7746 r"""do_create_current_decomposition(TripletScore self, Model m, IMP::ParticleIndexTriplet const & vt) -> IMP::Restraints"""
7747 return _IMP_kernel.TripletScore_do_create_current_decomposition(self, m, vt)
7748 __swig_destroy__ = _IMP_kernel.delete_TripletScore
7751 r"""__str__(TripletScore self) -> std::string"""
7752 return _IMP_kernel.TripletScore___str__(self)
7755 r"""__repr__(TripletScore self) -> std::string"""
7756 return _IMP_kernel.TripletScore___repr__(self)
7760 return _object_cast_to_TripletScore(o)
7763 def do_show(self, out):
7768 return _object_cast_to_TripletScore(o)
7770 def __disown__(self):
7772 _IMP_kernel.disown_TripletScore(self)
7773 return weakref.proxy(self)
7775 def do_get_inputs(self, m, pis):
7776 r"""do_get_inputs(TripletScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7777 return _IMP_kernel.TripletScore_do_get_inputs(self, m, pis)
7780 r"""do_destroy(TripletScore self)"""
7781 return _IMP_kernel.TripletScore_do_destroy(self)
7784 _IMP_kernel.TripletScore_swigregister(TripletScore)
7786 r"""Proxy of C++ IMP::TripletPredicate class."""
7788 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7790 def __init__(self, *args):
7791 r"""__init__(TripletPredicate self, std::string name="TripletPredicate %1%") -> TripletPredicate"""
7792 if self.__class__ == TripletPredicate:
7796 _IMP_kernel.TripletPredicate_swiginit(self, _IMP_kernel.new_TripletPredicate(_self, *args))
7798 if self.__class__ != TripletPredicate:
7799 _director_objects.register(self)
7804 def setup_for_get_value_index_in_batch(self, arg0):
7805 r"""setup_for_get_value_index_in_batch(TripletPredicate self, Model arg0)"""
7806 return _IMP_kernel.TripletPredicate_setup_for_get_value_index_in_batch(self, arg0)
7808 def get_value_index_in_batch(self, m, vt):
7809 r"""get_value_index_in_batch(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int"""
7810 return _IMP_kernel.TripletPredicate_get_value_index_in_batch(self, m, vt)
7812 def __call__(self, m, vt):
7813 r"""__call__(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int"""
7814 return _IMP_kernel.TripletPredicate___call__(self, m, vt)
7816 def get_value_index(self, *args):
7818 get_value_index(TripletPredicate self, Model m, IMP::ParticleIndexTriplet const & vt) -> int
7819 get_value_index(TripletPredicate self, Model m, IMP::ParticleIndexTriplets const & o) -> IMP::Ints
7821 return _IMP_kernel.TripletPredicate_get_value_index(self, *args)
7822 __swig_destroy__ = _IMP_kernel.delete_TripletPredicate
7825 r"""__str__(TripletPredicate self) -> std::string"""
7826 return _IMP_kernel.TripletPredicate___str__(self)
7829 r"""__repr__(TripletPredicate self) -> std::string"""
7830 return _IMP_kernel.TripletPredicate___repr__(self)
7834 return _object_cast_to_TripletPredicate(o)
7837 def do_show(self, out):
7842 return _object_cast_to_TripletPredicate(o)
7844 def __disown__(self):
7846 _IMP_kernel.disown_TripletPredicate(self)
7847 return weakref.proxy(self)
7849 def do_get_inputs(self, m, pis):
7850 r"""do_get_inputs(TripletPredicate self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
7851 return _IMP_kernel.TripletPredicate_do_get_inputs(self, m, pis)
7854 r"""do_destroy(TripletPredicate self)"""
7855 return _IMP_kernel.TripletPredicate_do_destroy(self)
7858 _IMP_kernel.TripletPredicate_swigregister(TripletPredicate)
7860 r"""Proxy of C++ IMP::TripletContainer class."""
7862 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7864 def apply_generic(self, m):
7865 r"""apply_generic(TripletContainer self, TripletModifier m)"""
7866 return _IMP_kernel.TripletContainer_apply_generic(self, m)
7868 def apply_generic_moved(self, m, moved_pis, reset_pis):
7869 r"""apply_generic_moved(TripletContainer self, TripletModifier m, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7870 return _IMP_kernel.TripletContainer_apply_generic_moved(self, m, moved_pis, reset_pis)
7872 def apply(self, sm):
7873 r"""apply(TripletContainer self, TripletModifier sm)"""
7874 return _IMP_kernel.TripletContainer_apply(self, sm)
7876 def apply_moved(self, sm, moved_pis, reset_pis):
7877 r"""apply_moved(TripletContainer self, TripletModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7878 return _IMP_kernel.TripletContainer_apply_moved(self, sm, moved_pis, reset_pis)
7880 def get_range_indexes(self):
7881 r"""get_range_indexes(TripletContainer self) -> IMP::ParticleIndexTriplets"""
7882 return _IMP_kernel.TripletContainer_get_range_indexes(self)
7884 def get_contents(self):
7885 r"""get_contents(TripletContainer self) -> IMP::ParticleIndexTriplets const &"""
7886 return _IMP_kernel.TripletContainer_get_contents(self)
7889 r"""get_indexes(TripletContainer self) -> IMP::ParticleIndexTriplets"""
7890 return _IMP_kernel.TripletContainer_get_indexes(self)
7892 def get(self, *args):
7894 get(TripletContainer self) -> IMP::ParticleTripletsTemp
7895 get(TripletContainer self, unsigned int i) -> IMP::ParticleTriplet
7897 return _IMP_kernel.TripletContainer_get(self, *args)
7899 def get_number(self):
7900 r"""get_number(TripletContainer self) -> unsigned int"""
7901 return _IMP_kernel.TripletContainer_get_number(self)
7903 def __init__(self, *args):
7905 __init__(TripletContainer self, Model m, std::string name="TripletContainer %1%") -> TripletContainer
7906 __init__(TripletContainer self) -> TripletContainer
7908 if self.__class__ == TripletContainer:
7912 _IMP_kernel.TripletContainer_swiginit(self, _IMP_kernel.new_TripletContainer(_self, *args))
7914 if self.__class__ != TripletContainer:
7915 _director_objects.register(self)
7920 def do_apply(self, sm):
7921 r"""do_apply(TripletContainer self, TripletModifier sm)"""
7922 return _IMP_kernel.TripletContainer_do_apply(self, sm)
7924 def do_apply_moved(self, sm, moved_pis, reset_pis):
7925 r"""do_apply_moved(TripletContainer self, TripletModifier sm, IMP::ParticleIndexes const & moved_pis, IMP::ParticleIndexes const & reset_pis)"""
7926 return _IMP_kernel.TripletContainer_do_apply_moved(self, sm, moved_pis, reset_pis)
7928 def do_get_provides_access(self):
7929 r"""do_get_provides_access(TripletContainer self) -> bool"""
7930 return _IMP_kernel.TripletContainer_do_get_provides_access(self)
7931 __swig_destroy__ = _IMP_kernel.delete_TripletContainer
7934 r"""__str__(TripletContainer self) -> std::string"""
7935 return _IMP_kernel.TripletContainer___str__(self)
7938 r"""__repr__(TripletContainer self) -> std::string"""
7939 return _IMP_kernel.TripletContainer___repr__(self)
7943 return _object_cast_to_TripletContainer(o)
7946 def do_show(self, out):
7951 return _object_cast_to_TripletContainer(o)
7953 def __disown__(self):
7955 _IMP_kernel.disown_TripletContainer(self)
7956 return weakref.proxy(self)
7959 r"""do_destroy(TripletContainer self)"""
7960 return _IMP_kernel.TripletContainer_do_destroy(self)
7962 def handle_set_has_required_score_states(self, arg0):
7963 r"""handle_set_has_required_score_states(TripletContainer self, bool arg0)"""
7964 return _IMP_kernel.TripletContainer_handle_set_has_required_score_states(self, arg0)
7966 def do_get_inputs(self):
7967 r"""do_get_inputs(TripletContainer self) -> IMP::ModelObjectsTemp"""
7968 return _IMP_kernel.TripletContainer_do_get_inputs(self)
7970 def do_get_interactions(self):
7971 r"""do_get_interactions(TripletContainer self) -> IMP::ModelObjectsTemps"""
7972 return _IMP_kernel.TripletContainer_do_get_interactions(self)
7974 def do_get_contents_hash(self):
7975 r"""do_get_contents_hash(TripletContainer self) -> std::size_t"""
7976 return _IMP_kernel.TripletContainer_do_get_contents_hash(self)
7979 _IMP_kernel.TripletContainer_swigregister(TripletContainer)
7980 class _TripletContainerAdaptor(_InputAdaptor):
7981 r"""Proxy of C++ IMP::TripletContainerAdaptor class."""
7983 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
7984 __repr__ = _swig_repr
7986 def __init__(self, *args):
7988 __init__(_TripletContainerAdaptor self) -> _TripletContainerAdaptor
7989 __init__(_TripletContainerAdaptor self, TripletContainer c) -> _TripletContainerAdaptor
7990 __init__(_TripletContainerAdaptor self, IMP::ParticleTripletsTemp const & t) -> _TripletContainerAdaptor
7992 _IMP_kernel._TripletContainerAdaptor_swiginit(self, _IMP_kernel.new__TripletContainerAdaptor(*args))
7994 def set_name_if_default(self, name):
7995 r"""set_name_if_default(_TripletContainerAdaptor self, std::string name)"""
7996 return _IMP_kernel._TripletContainerAdaptor_set_name_if_default(self, name)
7997 __swig_destroy__ = _IMP_kernel.delete__TripletContainerAdaptor
8000 _IMP_kernel._TripletContainerAdaptor_swigregister(_TripletContainerAdaptor)
8003 r"""write_particles_to_buffer(IMP::ParticlesTemp const & particles, IMP::FloatKeys const & keys) -> IMP::Vector< char,std::allocator< char > >"""
8004 return _IMP_kernel.write_particles_to_buffer(particles, keys)
8007 r"""read_particles_from_buffer(IMP::Vector< char,std::allocator< char > > const & buffer, IMP::ParticlesTemp const & particles, IMP::FloatKeys const & keys)"""
8008 return _IMP_kernel.read_particles_from_buffer(buffer, particles, keys)
8011 r"""get_particles(Model m, IMP::ParticleIndexes const & ps) -> IMP::ParticlesTemp"""
8012 return _IMP_kernel.get_particles(m, ps)
8016 get_indexes(IMP::ParticlesTemp const & ps) -> IMP::ParticleIndexes
8017 get_indexes(IMP::ParticlePairsTemp const & ps) -> IMP::ParticleIndexPairs
8019 return _IMP_kernel.get_indexes(*args)
8020 class _ParticleIndexAdaptor(object):
8021 r"""Proxy of C++ IMP::ParticleIndexAdaptor class."""
8023 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8024 __repr__ = _swig_repr
8026 def __init__(self, *args):
8028 __init__(_ParticleIndexAdaptor self, Particle p) -> _ParticleIndexAdaptor
8029 __init__(_ParticleIndexAdaptor self, ParticleIndex pi) -> _ParticleIndexAdaptor
8030 __init__(_ParticleIndexAdaptor self, Decorator d) -> _ParticleIndexAdaptor
8032 _IMP_kernel._ParticleIndexAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexAdaptor(*args))
8033 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexAdaptor
8036 _IMP_kernel._ParticleIndexAdaptor_swigregister(_ParticleIndexAdaptor)
8037 class _ParticleIndexesAdaptor(_InputAdaptor):
8038 r"""Proxy of C++ IMP::ParticleIndexesAdaptor class."""
8040 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8041 __repr__ = _swig_repr
8043 def __init__(self, *args):
8045 __init__(_ParticleIndexesAdaptor self, IMP::ParticlesTemp const & ps) -> _ParticleIndexesAdaptor
8046 __init__(_ParticleIndexesAdaptor self, IMP::ParticleIndexes const & pi) -> _ParticleIndexesAdaptor
8047 __init__(_ParticleIndexesAdaptor self) -> _ParticleIndexesAdaptor
8049 _IMP_kernel._ParticleIndexesAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexesAdaptor(*args))
8050 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexesAdaptor
8053 _IMP_kernel._ParticleIndexesAdaptor_swigregister(_ParticleIndexesAdaptor)
8054 class _ParticleIndexPairsAdaptor(object):
8055 r"""Proxy of C++ IMP::ParticleIndexPairsAdaptor 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__(_ParticleIndexPairsAdaptor self, IMP::ParticlePairsTemp const & ps) -> _ParticleIndexPairsAdaptor
8063 __init__(_ParticleIndexPairsAdaptor self, IMP::ParticleIndexPairs const & pi) -> _ParticleIndexPairsAdaptor
8064 __init__(_ParticleIndexPairsAdaptor self) -> _ParticleIndexPairsAdaptor
8066 _IMP_kernel._ParticleIndexPairsAdaptor_swiginit(self, _IMP_kernel.new__ParticleIndexPairsAdaptor(*args))
8067 __swig_destroy__ = _IMP_kernel.delete__ParticleIndexPairsAdaptor
8070 _IMP_kernel._ParticleIndexPairsAdaptor_swigregister(_ParticleIndexPairsAdaptor)
8072 r"""Proxy of C++ IMP::internal::_ConstRestraint class."""
8074 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8076 def __init__(self, *args):
8078 __init__(_ConstRestraint self, Model m, IMP::ParticleIndexes const & pis, double v) -> _ConstRestraint
8079 __init__(_ConstRestraint self) -> _ConstRestraint
8081 _IMP_kernel._ConstRestraint_swiginit(self, _IMP_kernel.new__ConstRestraint(*args))
8083 def get_value(self):
8084 r"""get_value(_ConstRestraint self) -> double"""
8085 return _IMP_kernel._ConstRestraint_get_value(self)
8087 def do_create_decomposition(self):
8088 r"""do_create_decomposition(_ConstRestraint self) -> IMP::Restraints"""
8089 return _IMP_kernel._ConstRestraint_do_create_decomposition(self)
8091 def do_get_inputs(self):
8092 r"""do_get_inputs(_ConstRestraint self) -> IMP::ModelObjectsTemp"""
8093 return _IMP_kernel._ConstRestraint_do_get_inputs(self)
8096 r"""get_version_info(_ConstRestraint self) -> VersionInfo"""
8097 return _IMP_kernel._ConstRestraint_get_version_info(self)
8098 __swig_destroy__ = _IMP_kernel.delete__ConstRestraint
8101 r"""__str__(_ConstRestraint self) -> std::string"""
8102 return _IMP_kernel._ConstRestraint___str__(self)
8105 r"""__repr__(_ConstRestraint self) -> std::string"""
8106 return _IMP_kernel._ConstRestraint___repr__(self)
8110 return _object_cast_to__ConstRestraint(o)
8113 def _get_as_binary(self):
8114 r"""_get_as_binary(_ConstRestraint self) -> PyObject *"""
8115 return _IMP_kernel._ConstRestraint__get_as_binary(self)
8117 def _set_from_binary(self, p):
8118 r"""_set_from_binary(_ConstRestraint self, PyObject * p)"""
8119 return _IMP_kernel._ConstRestraint__set_from_binary(self, p)
8121 def __getstate__(self):
8122 p = self._get_as_binary()
8123 if len(self.__dict__) > 1:
8124 d = self.__dict__.copy()
8129 def __setstate__(self, p):
8130 if not hasattr(self,
'this'):
8132 if isinstance(p, tuple):
8134 self.__dict__.update(d)
8135 return self._set_from_binary(p)
8139 _IMP_kernel._ConstRestraint_swigregister(_ConstRestraint)
8141 r"""Proxy of C++ IMP::internal::_ConstSingletonScore class."""
8143 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8145 def __init__(self, *args):
8147 __init__(_ConstSingletonScore self, double v) -> _ConstSingletonScore
8148 __init__(_ConstSingletonScore self) -> _ConstSingletonScore
8150 _IMP_kernel._ConstSingletonScore_swiginit(self, _IMP_kernel.new__ConstSingletonScore(*args))
8152 def do_get_inputs(self, arg2, arg3):
8153 r"""do_get_inputs(_ConstSingletonScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
8154 return _IMP_kernel._ConstSingletonScore_do_get_inputs(self, arg2, arg3)
8156 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
8157 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"""
8158 return _IMP_kernel._ConstSingletonScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
8160 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
8161 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"""
8162 return _IMP_kernel._ConstSingletonScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
8164 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
8165 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"""
8166 return _IMP_kernel._ConstSingletonScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
8168 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
8169 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"""
8170 return _IMP_kernel._ConstSingletonScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
8173 r"""get_version_info(_ConstSingletonScore self) -> VersionInfo"""
8174 return _IMP_kernel._ConstSingletonScore_get_version_info(self)
8175 __swig_destroy__ = _IMP_kernel.delete__ConstSingletonScore
8178 r"""__str__(_ConstSingletonScore self) -> std::string"""
8179 return _IMP_kernel._ConstSingletonScore___str__(self)
8182 r"""__repr__(_ConstSingletonScore self) -> std::string"""
8183 return _IMP_kernel._ConstSingletonScore___repr__(self)
8187 return _object_cast_to__ConstSingletonScore(o)
8190 def _get_as_binary(self):
8191 r"""_get_as_binary(_ConstSingletonScore self) -> PyObject *"""
8192 return _IMP_kernel._ConstSingletonScore__get_as_binary(self)
8194 def _set_from_binary(self, p):
8195 r"""_set_from_binary(_ConstSingletonScore self, PyObject * p)"""
8196 return _IMP_kernel._ConstSingletonScore__set_from_binary(self, p)
8198 def __getstate__(self):
8199 p = self._get_as_binary()
8200 if len(self.__dict__) > 1:
8201 d = self.__dict__.copy()
8206 def __setstate__(self, p):
8207 if not hasattr(self,
'this'):
8209 if isinstance(p, tuple):
8211 self.__dict__.update(d)
8212 return self._set_from_binary(p)
8216 _IMP_kernel._ConstSingletonScore_swigregister(_ConstSingletonScore)
8218 r"""Proxy of C++ IMP::internal::_ConstPairScore class."""
8220 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8222 def __init__(self, *args):
8224 __init__(_ConstPairScore self, double v) -> _ConstPairScore
8225 __init__(_ConstPairScore self) -> _ConstPairScore
8227 _IMP_kernel._ConstPairScore_swiginit(self, _IMP_kernel.new__ConstPairScore(*args))
8229 def do_get_inputs(self, arg2, arg3):
8230 r"""do_get_inputs(_ConstPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
8231 return _IMP_kernel._ConstPairScore_do_get_inputs(self, arg2, arg3)
8233 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
8234 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"""
8235 return _IMP_kernel._ConstPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
8237 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
8238 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"""
8239 return _IMP_kernel._ConstPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
8241 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
8242 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"""
8243 return _IMP_kernel._ConstPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
8245 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
8246 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"""
8247 return _IMP_kernel._ConstPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
8250 r"""get_version_info(_ConstPairScore self) -> VersionInfo"""
8251 return _IMP_kernel._ConstPairScore_get_version_info(self)
8252 __swig_destroy__ = _IMP_kernel.delete__ConstPairScore
8255 r"""__str__(_ConstPairScore self) -> std::string"""
8256 return _IMP_kernel._ConstPairScore___str__(self)
8259 r"""__repr__(_ConstPairScore self) -> std::string"""
8260 return _IMP_kernel._ConstPairScore___repr__(self)
8264 return _object_cast_to__ConstPairScore(o)
8267 def _get_as_binary(self):
8268 r"""_get_as_binary(_ConstPairScore self) -> PyObject *"""
8269 return _IMP_kernel._ConstPairScore__get_as_binary(self)
8271 def _set_from_binary(self, p):
8272 r"""_set_from_binary(_ConstPairScore self, PyObject * p)"""
8273 return _IMP_kernel._ConstPairScore__set_from_binary(self, p)
8275 def __getstate__(self):
8276 p = self._get_as_binary()
8277 if len(self.__dict__) > 1:
8278 d = self.__dict__.copy()
8283 def __setstate__(self, p):
8284 if not hasattr(self,
'this'):
8286 if isinstance(p, tuple):
8288 self.__dict__.update(d)
8289 return self._set_from_binary(p)
8293 _IMP_kernel._ConstPairScore_swigregister(_ConstPairScore)
8295 r"""Proxy of C++ IMP::internal::_TrivialDecorator class."""
8297 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8299 def __init__(self, *args):
8301 __init__(_TrivialDecorator self) -> _TrivialDecorator
8302 __init__(_TrivialDecorator self, Model m, ParticleIndex id) -> _TrivialDecorator
8303 __init__(_TrivialDecorator self, _ParticleAdaptor d) -> _TrivialDecorator
8305 _IMP_kernel._TrivialDecorator_swiginit(self, _IMP_kernel.new__TrivialDecorator(*args))
8307 def show(self, *args):
8308 r"""show(_TrivialDecorator self, _ostream out=std::cout)"""
8309 return _IMP_kernel._TrivialDecorator_show(self, *args)
8312 def setup_particle(*args):
8314 setup_particle(Model m, ParticleIndex pi) -> _TrivialDecorator
8315 setup_particle(_ParticleAdaptor pa) -> _TrivialDecorator
8317 return _IMP_kernel._TrivialDecorator_setup_particle(*args)
8320 def get_is_setup(*args):
8322 get_is_setup(_ParticleAdaptor p) -> bool
8323 get_is_setup(Model m, ParticleIndex pi) -> bool
8325 return _IMP_kernel._TrivialDecorator_get_is_setup(*args)
8329 add_attribute(_TrivialDecorator self, FloatKey k, IMP::Float v, bool opt)
8330 add_attribute(_TrivialDecorator self, FloatKey a0, IMP::Float a1)
8331 add_attribute(_TrivialDecorator self, IntKey a0, IMP::Int a1)
8332 add_attribute(_TrivialDecorator self, FloatsKey a0, IMP::Floats a1)
8333 add_attribute(_TrivialDecorator self, IntsKey a0, IMP::Ints a1)
8334 add_attribute(_TrivialDecorator self, StringKey a0, IMP::String a1)
8335 add_attribute(_TrivialDecorator self, ParticleIndexKey a0, Particle a1)
8336 add_attribute(_TrivialDecorator self, ObjectKey a0, Object a1)
8337 add_attribute(_TrivialDecorator self, SparseFloatKey a0, IMP::Float a1)
8338 add_attribute(_TrivialDecorator self, SparseIntKey a0, IMP::Int a1)
8339 add_attribute(_TrivialDecorator self, SparseStringKey a0, IMP::String a1)
8340 add_attribute(_TrivialDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8342 return _IMP_kernel._TrivialDecorator_add_attribute(self, *args)
8344 def get_value(self, *args):
8346 get_value(_TrivialDecorator self, FloatKey a0) -> IMP::Float
8347 get_value(_TrivialDecorator self, IntKey a0) -> IMP::Int
8348 get_value(_TrivialDecorator self, FloatsKey a0) -> IMP::Floats
8349 get_value(_TrivialDecorator self, IntsKey a0) -> IMP::Ints
8350 get_value(_TrivialDecorator self, StringKey a0) -> IMP::String
8351 get_value(_TrivialDecorator self, ParticleIndexKey a0) -> Particle
8352 get_value(_TrivialDecorator self, ObjectKey a0) -> Object
8353 get_value(_TrivialDecorator self, SparseFloatKey a0) -> IMP::Float
8354 get_value(_TrivialDecorator self, SparseIntKey a0) -> IMP::Int
8355 get_value(_TrivialDecorator self, SparseStringKey a0) -> IMP::String
8356 get_value(_TrivialDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
8358 return _IMP_kernel._TrivialDecorator_get_value(self, *args)
8360 def set_value(self, *args):
8362 set_value(_TrivialDecorator self, FloatKey a0, IMP::Float a1)
8363 set_value(_TrivialDecorator self, IntKey a0, IMP::Int a1)
8364 set_value(_TrivialDecorator self, FloatsKey a0, IMP::Floats a1)
8365 set_value(_TrivialDecorator self, IntsKey a0, IMP::Ints a1)
8366 set_value(_TrivialDecorator self, StringKey a0, IMP::String a1)
8367 set_value(_TrivialDecorator self, ParticleIndexKey a0, Particle a1)
8368 set_value(_TrivialDecorator self, ObjectKey a0, Object a1)
8369 set_value(_TrivialDecorator self, SparseFloatKey a0, IMP::Float a1)
8370 set_value(_TrivialDecorator self, SparseIntKey a0, IMP::Int a1)
8371 set_value(_TrivialDecorator self, SparseStringKey a0, IMP::String a1)
8372 set_value(_TrivialDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8374 return _IMP_kernel._TrivialDecorator_set_value(self, *args)
8378 remove_attribute(_TrivialDecorator self, FloatKey a0)
8379 remove_attribute(_TrivialDecorator self, IntKey a0)
8380 remove_attribute(_TrivialDecorator self, FloatsKey a0)
8381 remove_attribute(_TrivialDecorator self, IntsKey a0)
8382 remove_attribute(_TrivialDecorator self, StringKey a0)
8383 remove_attribute(_TrivialDecorator self, ParticleIndexKey a0)
8384 remove_attribute(_TrivialDecorator self, ObjectKey a0)
8385 remove_attribute(_TrivialDecorator self, SparseFloatKey a0)
8386 remove_attribute(_TrivialDecorator self, SparseIntKey a0)
8387 remove_attribute(_TrivialDecorator self, SparseStringKey a0)
8388 remove_attribute(_TrivialDecorator self, SparseParticleIndexKey a0)
8390 return _IMP_kernel._TrivialDecorator_remove_attribute(self, *args)
8392 def has_attribute(self, *args):
8394 has_attribute(_TrivialDecorator self, FloatKey a0) -> bool
8395 has_attribute(_TrivialDecorator self, IntKey a0) -> bool
8396 has_attribute(_TrivialDecorator self, FloatsKey a0) -> bool
8397 has_attribute(_TrivialDecorator self, IntsKey a0) -> bool
8398 has_attribute(_TrivialDecorator self, StringKey a0) -> bool
8399 has_attribute(_TrivialDecorator self, ParticleIndexKey a0) -> bool
8400 has_attribute(_TrivialDecorator self, ObjectKey a0) -> bool
8401 has_attribute(_TrivialDecorator self, SparseFloatKey a0) -> bool
8402 has_attribute(_TrivialDecorator self, SparseIntKey a0) -> bool
8403 has_attribute(_TrivialDecorator self, SparseStringKey a0) -> bool
8404 has_attribute(_TrivialDecorator self, SparseParticleIndexKey a0) -> bool
8406 return _IMP_kernel._TrivialDecorator_has_attribute(self, *args)
8408 def get_derivative(self, a0):
8409 r"""get_derivative(_TrivialDecorator self, FloatKey a0) -> double"""
8410 return _IMP_kernel._TrivialDecorator_get_derivative(self, a0)
8413 r"""get_name(_TrivialDecorator self) -> std::string"""
8414 return _IMP_kernel._TrivialDecorator_get_name(self)
8417 r"""clear_caches(_TrivialDecorator self)"""
8418 return _IMP_kernel._TrivialDecorator_clear_caches(self)
8420 def set_name(self, a0):
8421 r"""set_name(_TrivialDecorator self, std::string a0)"""
8422 return _IMP_kernel._TrivialDecorator_set_name(self, a0)
8425 r"""set_check_level(_TrivialDecorator self, IMP::CheckLevel a0)"""
8426 return _IMP_kernel._TrivialDecorator_set_check_level(self, a0)
8428 def add_to_derivative(self, a0, a1, a2):
8429 r"""add_to_derivative(_TrivialDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8430 return _IMP_kernel._TrivialDecorator_add_to_derivative(self, a0, a1, a2)
8433 r"""set_is_optimized(_TrivialDecorator self, FloatKey a0, bool a1)"""
8434 return _IMP_kernel._TrivialDecorator_set_is_optimized(self, a0, a1)
8436 def get_is_optimized(self, a0):
8437 r"""get_is_optimized(_TrivialDecorator self, FloatKey a0) -> bool"""
8438 return _IMP_kernel._TrivialDecorator_get_is_optimized(self, a0)
8440 def get_check_level(self):
8441 r"""get_check_level(_TrivialDecorator self) -> IMP::CheckLevel"""
8442 return _IMP_kernel._TrivialDecorator_get_check_level(self)
8444 def __eq__(self, *args):
8446 __eq__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8447 __eq__(_TrivialDecorator self, Particle d) -> bool
8449 return _IMP_kernel._TrivialDecorator___eq__(self, *args)
8451 def __ne__(self, *args):
8453 __ne__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8454 __ne__(_TrivialDecorator self, Particle d) -> bool
8456 return _IMP_kernel._TrivialDecorator___ne__(self, *args)
8458 def __le__(self, *args):
8460 __le__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8461 __le__(_TrivialDecorator self, Particle d) -> bool
8463 return _IMP_kernel._TrivialDecorator___le__(self, *args)
8465 def __lt__(self, *args):
8467 __lt__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8468 __lt__(_TrivialDecorator self, Particle d) -> bool
8470 return _IMP_kernel._TrivialDecorator___lt__(self, *args)
8472 def __ge__(self, *args):
8474 __ge__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8475 __ge__(_TrivialDecorator self, Particle d) -> bool
8477 return _IMP_kernel._TrivialDecorator___ge__(self, *args)
8479 def __gt__(self, *args):
8481 __gt__(_TrivialDecorator self, _TrivialDecorator o) -> bool
8482 __gt__(_TrivialDecorator self, Particle d) -> bool
8484 return _IMP_kernel._TrivialDecorator___gt__(self, *args)
8487 r"""__hash__(_TrivialDecorator self) -> std::size_t"""
8488 return _IMP_kernel._TrivialDecorator___hash__(self)
8491 r"""__str__(_TrivialDecorator self) -> std::string"""
8492 return _IMP_kernel._TrivialDecorator___str__(self)
8495 r"""__repr__(_TrivialDecorator self) -> std::string"""
8496 return _IMP_kernel._TrivialDecorator___repr__(self)
8498 def _get_as_binary(self):
8499 r"""_get_as_binary(_TrivialDecorator self) -> PyObject *"""
8500 return _IMP_kernel._TrivialDecorator__get_as_binary(self)
8502 def _set_from_binary(self, p):
8503 r"""_set_from_binary(_TrivialDecorator self, PyObject * p)"""
8504 return _IMP_kernel._TrivialDecorator__set_from_binary(self, p)
8506 def __getstate__(self):
8507 p = self._get_as_binary()
8508 if len(self.__dict__) > 1:
8509 d = self.__dict__.copy()
8514 def __setstate__(self, p):
8515 if not hasattr(self,
'this'):
8517 if isinstance(p, tuple):
8519 self.__dict__.update(d)
8520 return self._set_from_binary(p)
8522 __swig_destroy__ = _IMP_kernel.delete__TrivialDecorator
8525 _IMP_kernel._TrivialDecorator_swigregister(_TrivialDecorator)
8526 class _TrivialDerivedDecorator(_TrivialDecorator):
8527 r"""Proxy of C++ IMP::internal::_TrivialDerivedDecorator class."""
8529 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8531 def __init__(self, *args):
8533 __init__(_TrivialDerivedDecorator self) -> _TrivialDerivedDecorator
8534 __init__(_TrivialDerivedDecorator self, Model m, ParticleIndex id) -> _TrivialDerivedDecorator
8535 __init__(_TrivialDerivedDecorator self, _ParticleAdaptor d) -> _TrivialDerivedDecorator
8537 _IMP_kernel._TrivialDerivedDecorator_swiginit(self, _IMP_kernel.new__TrivialDerivedDecorator(*args))
8539 def show(self, *args):
8540 r"""show(_TrivialDerivedDecorator self, _ostream out=std::cout)"""
8541 return _IMP_kernel._TrivialDerivedDecorator_show(self, *args)
8544 def setup_particle(*args):
8546 setup_particle(Model m, ParticleIndex pi) -> _TrivialDerivedDecorator
8547 setup_particle(_ParticleAdaptor pa) -> _TrivialDerivedDecorator
8549 return _IMP_kernel._TrivialDerivedDecorator_setup_particle(*args)
8552 def get_is_setup(*args):
8554 get_is_setup(_ParticleAdaptor p) -> bool
8555 get_is_setup(Model m, ParticleIndex pi) -> bool
8557 return _IMP_kernel._TrivialDerivedDecorator_get_is_setup(*args)
8561 add_attribute(_TrivialDerivedDecorator self, FloatKey k, IMP::Float v, bool opt)
8562 add_attribute(_TrivialDerivedDecorator self, FloatKey a0, IMP::Float a1)
8563 add_attribute(_TrivialDerivedDecorator self, IntKey a0, IMP::Int a1)
8564 add_attribute(_TrivialDerivedDecorator self, FloatsKey a0, IMP::Floats a1)
8565 add_attribute(_TrivialDerivedDecorator self, IntsKey a0, IMP::Ints a1)
8566 add_attribute(_TrivialDerivedDecorator self, StringKey a0, IMP::String a1)
8567 add_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0, Particle a1)
8568 add_attribute(_TrivialDerivedDecorator self, ObjectKey a0, Object a1)
8569 add_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0, IMP::Float a1)
8570 add_attribute(_TrivialDerivedDecorator self, SparseIntKey a0, IMP::Int a1)
8571 add_attribute(_TrivialDerivedDecorator self, SparseStringKey a0, IMP::String a1)
8572 add_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8574 return _IMP_kernel._TrivialDerivedDecorator_add_attribute(self, *args)
8576 def get_value(self, *args):
8578 get_value(_TrivialDerivedDecorator self, FloatKey a0) -> IMP::Float
8579 get_value(_TrivialDerivedDecorator self, IntKey a0) -> IMP::Int
8580 get_value(_TrivialDerivedDecorator self, FloatsKey a0) -> IMP::Floats
8581 get_value(_TrivialDerivedDecorator self, IntsKey a0) -> IMP::Ints
8582 get_value(_TrivialDerivedDecorator self, StringKey a0) -> IMP::String
8583 get_value(_TrivialDerivedDecorator self, ParticleIndexKey a0) -> Particle
8584 get_value(_TrivialDerivedDecorator self, ObjectKey a0) -> Object
8585 get_value(_TrivialDerivedDecorator self, SparseFloatKey a0) -> IMP::Float
8586 get_value(_TrivialDerivedDecorator self, SparseIntKey a0) -> IMP::Int
8587 get_value(_TrivialDerivedDecorator self, SparseStringKey a0) -> IMP::String
8588 get_value(_TrivialDerivedDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
8590 return _IMP_kernel._TrivialDerivedDecorator_get_value(self, *args)
8592 def set_value(self, *args):
8594 set_value(_TrivialDerivedDecorator self, FloatKey a0, IMP::Float a1)
8595 set_value(_TrivialDerivedDecorator self, IntKey a0, IMP::Int a1)
8596 set_value(_TrivialDerivedDecorator self, FloatsKey a0, IMP::Floats a1)
8597 set_value(_TrivialDerivedDecorator self, IntsKey a0, IMP::Ints a1)
8598 set_value(_TrivialDerivedDecorator self, StringKey a0, IMP::String a1)
8599 set_value(_TrivialDerivedDecorator self, ParticleIndexKey a0, Particle a1)
8600 set_value(_TrivialDerivedDecorator self, ObjectKey a0, Object a1)
8601 set_value(_TrivialDerivedDecorator self, SparseFloatKey a0, IMP::Float a1)
8602 set_value(_TrivialDerivedDecorator self, SparseIntKey a0, IMP::Int a1)
8603 set_value(_TrivialDerivedDecorator self, SparseStringKey a0, IMP::String a1)
8604 set_value(_TrivialDerivedDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8606 return _IMP_kernel._TrivialDerivedDecorator_set_value(self, *args)
8610 remove_attribute(_TrivialDerivedDecorator self, FloatKey a0)
8611 remove_attribute(_TrivialDerivedDecorator self, IntKey a0)
8612 remove_attribute(_TrivialDerivedDecorator self, FloatsKey a0)
8613 remove_attribute(_TrivialDerivedDecorator self, IntsKey a0)
8614 remove_attribute(_TrivialDerivedDecorator self, StringKey a0)
8615 remove_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0)
8616 remove_attribute(_TrivialDerivedDecorator self, ObjectKey a0)
8617 remove_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0)
8618 remove_attribute(_TrivialDerivedDecorator self, SparseIntKey a0)
8619 remove_attribute(_TrivialDerivedDecorator self, SparseStringKey a0)
8620 remove_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0)
8622 return _IMP_kernel._TrivialDerivedDecorator_remove_attribute(self, *args)
8624 def has_attribute(self, *args):
8626 has_attribute(_TrivialDerivedDecorator self, FloatKey a0) -> bool
8627 has_attribute(_TrivialDerivedDecorator self, IntKey a0) -> bool
8628 has_attribute(_TrivialDerivedDecorator self, FloatsKey a0) -> bool
8629 has_attribute(_TrivialDerivedDecorator self, IntsKey a0) -> bool
8630 has_attribute(_TrivialDerivedDecorator self, StringKey a0) -> bool
8631 has_attribute(_TrivialDerivedDecorator self, ParticleIndexKey a0) -> bool
8632 has_attribute(_TrivialDerivedDecorator self, ObjectKey a0) -> bool
8633 has_attribute(_TrivialDerivedDecorator self, SparseFloatKey a0) -> bool
8634 has_attribute(_TrivialDerivedDecorator self, SparseIntKey a0) -> bool
8635 has_attribute(_TrivialDerivedDecorator self, SparseStringKey a0) -> bool
8636 has_attribute(_TrivialDerivedDecorator self, SparseParticleIndexKey a0) -> bool
8638 return _IMP_kernel._TrivialDerivedDecorator_has_attribute(self, *args)
8640 def get_derivative(self, a0):
8641 r"""get_derivative(_TrivialDerivedDecorator self, FloatKey a0) -> double"""
8642 return _IMP_kernel._TrivialDerivedDecorator_get_derivative(self, a0)
8645 r"""get_name(_TrivialDerivedDecorator self) -> std::string"""
8646 return _IMP_kernel._TrivialDerivedDecorator_get_name(self)
8649 r"""clear_caches(_TrivialDerivedDecorator self)"""
8650 return _IMP_kernel._TrivialDerivedDecorator_clear_caches(self)
8652 def set_name(self, a0):
8653 r"""set_name(_TrivialDerivedDecorator self, std::string a0)"""
8654 return _IMP_kernel._TrivialDerivedDecorator_set_name(self, a0)
8657 r"""set_check_level(_TrivialDerivedDecorator self, IMP::CheckLevel a0)"""
8658 return _IMP_kernel._TrivialDerivedDecorator_set_check_level(self, a0)
8660 def add_to_derivative(self, a0, a1, a2):
8661 r"""add_to_derivative(_TrivialDerivedDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8662 return _IMP_kernel._TrivialDerivedDecorator_add_to_derivative(self, a0, a1, a2)
8665 r"""set_is_optimized(_TrivialDerivedDecorator self, FloatKey a0, bool a1)"""
8666 return _IMP_kernel._TrivialDerivedDecorator_set_is_optimized(self, a0, a1)
8668 def get_is_optimized(self, a0):
8669 r"""get_is_optimized(_TrivialDerivedDecorator self, FloatKey a0) -> bool"""
8670 return _IMP_kernel._TrivialDerivedDecorator_get_is_optimized(self, a0)
8672 def get_check_level(self):
8673 r"""get_check_level(_TrivialDerivedDecorator self) -> IMP::CheckLevel"""
8674 return _IMP_kernel._TrivialDerivedDecorator_get_check_level(self)
8676 def __eq__(self, *args):
8678 __eq__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8679 __eq__(_TrivialDerivedDecorator self, Particle d) -> bool
8681 return _IMP_kernel._TrivialDerivedDecorator___eq__(self, *args)
8683 def __ne__(self, *args):
8685 __ne__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8686 __ne__(_TrivialDerivedDecorator self, Particle d) -> bool
8688 return _IMP_kernel._TrivialDerivedDecorator___ne__(self, *args)
8690 def __le__(self, *args):
8692 __le__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8693 __le__(_TrivialDerivedDecorator self, Particle d) -> bool
8695 return _IMP_kernel._TrivialDerivedDecorator___le__(self, *args)
8697 def __lt__(self, *args):
8699 __lt__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8700 __lt__(_TrivialDerivedDecorator self, Particle d) -> bool
8702 return _IMP_kernel._TrivialDerivedDecorator___lt__(self, *args)
8704 def __ge__(self, *args):
8706 __ge__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8707 __ge__(_TrivialDerivedDecorator self, Particle d) -> bool
8709 return _IMP_kernel._TrivialDerivedDecorator___ge__(self, *args)
8711 def __gt__(self, *args):
8713 __gt__(_TrivialDerivedDecorator self, _TrivialDerivedDecorator o) -> bool
8714 __gt__(_TrivialDerivedDecorator self, Particle d) -> bool
8716 return _IMP_kernel._TrivialDerivedDecorator___gt__(self, *args)
8719 r"""__hash__(_TrivialDerivedDecorator self) -> std::size_t"""
8720 return _IMP_kernel._TrivialDerivedDecorator___hash__(self)
8723 r"""__str__(_TrivialDerivedDecorator self) -> std::string"""
8724 return _IMP_kernel._TrivialDerivedDecorator___str__(self)
8727 r"""__repr__(_TrivialDerivedDecorator self) -> std::string"""
8728 return _IMP_kernel._TrivialDerivedDecorator___repr__(self)
8730 def _get_as_binary(self):
8731 r"""_get_as_binary(_TrivialDerivedDecorator self) -> PyObject *"""
8732 return _IMP_kernel._TrivialDerivedDecorator__get_as_binary(self)
8734 def _set_from_binary(self, p):
8735 r"""_set_from_binary(_TrivialDerivedDecorator self, PyObject * p)"""
8736 return _IMP_kernel._TrivialDerivedDecorator__set_from_binary(self, p)
8738 def __getstate__(self):
8739 p = self._get_as_binary()
8740 if len(self.__dict__) > 1:
8741 d = self.__dict__.copy()
8746 def __setstate__(self, p):
8747 if not hasattr(self,
'this'):
8749 if isinstance(p, tuple):
8751 self.__dict__.update(d)
8752 return self._set_from_binary(p)
8754 __swig_destroy__ = _IMP_kernel.delete__TrivialDerivedDecorator
8757 _IMP_kernel._TrivialDerivedDecorator_swigregister(_TrivialDerivedDecorator)
8758 class _TrivialTraitsDecorator(
Decorator):
8759 r"""Proxy of C++ IMP::internal::_TrivialTraitsDecorator class."""
8761 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8763 def get_decorator_traits(self):
8764 r"""get_decorator_traits(_TrivialTraitsDecorator self) -> StringKey"""
8765 return _IMP_kernel._TrivialTraitsDecorator_get_decorator_traits(self)
8768 def get_default_decorator_traits():
8769 r"""get_default_decorator_traits() -> StringKey"""
8770 return _IMP_kernel._TrivialTraitsDecorator_get_default_decorator_traits()
8772 def __init__(self, *args):
8774 __init__(_TrivialTraitsDecorator self) -> _TrivialTraitsDecorator
8775 __init__(_TrivialTraitsDecorator self, Model m, ParticleIndex id, StringKey tr=get_default_key()) -> _TrivialTraitsDecorator
8776 __init__(_TrivialTraitsDecorator self, _ParticleAdaptor d, StringKey tr=get_default_key()) -> _TrivialTraitsDecorator
8778 _IMP_kernel._TrivialTraitsDecorator_swiginit(self, _IMP_kernel.new__TrivialTraitsDecorator(*args))
8780 def show(self, *args):
8781 r"""show(_TrivialTraitsDecorator self, _ostream out=std::cout)"""
8782 return _IMP_kernel._TrivialTraitsDecorator_show(self, *args)
8785 def setup_particle(*args):
8787 setup_particle(Model m, ParticleIndex pi, StringKey tr=IMP::internal::_TrivialTraitsDecorator::get_default_decorator_traits()) -> _TrivialTraitsDecorator
8788 setup_particle(_ParticleAdaptor d, StringKey tr=IMP::internal::_TrivialTraitsDecorator::get_default_decorator_traits()) -> _TrivialTraitsDecorator
8790 return _IMP_kernel._TrivialTraitsDecorator_setup_particle(*args)
8793 def get_is_setup(*args):
8795 get_is_setup(_ParticleAdaptor p, StringKey tr=get_default_key()) -> bool
8796 get_is_setup(Model m, ParticleIndex pi, StringKey k=get_default_key()) -> bool
8798 return _IMP_kernel._TrivialTraitsDecorator_get_is_setup(*args)
8801 def get_default_key():
8802 r"""get_default_key() -> StringKey"""
8803 return _IMP_kernel._TrivialTraitsDecorator_get_default_key()
8807 add_attribute(_TrivialTraitsDecorator self, FloatKey k, IMP::Float v, bool opt)
8808 add_attribute(_TrivialTraitsDecorator self, FloatKey a0, IMP::Float a1)
8809 add_attribute(_TrivialTraitsDecorator self, IntKey a0, IMP::Int a1)
8810 add_attribute(_TrivialTraitsDecorator self, FloatsKey a0, IMP::Floats a1)
8811 add_attribute(_TrivialTraitsDecorator self, IntsKey a0, IMP::Ints a1)
8812 add_attribute(_TrivialTraitsDecorator self, StringKey a0, IMP::String a1)
8813 add_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0, Particle a1)
8814 add_attribute(_TrivialTraitsDecorator self, ObjectKey a0, Object a1)
8815 add_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0, IMP::Float a1)
8816 add_attribute(_TrivialTraitsDecorator self, SparseIntKey a0, IMP::Int a1)
8817 add_attribute(_TrivialTraitsDecorator self, SparseStringKey a0, IMP::String a1)
8818 add_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8820 return _IMP_kernel._TrivialTraitsDecorator_add_attribute(self, *args)
8822 def get_value(self, *args):
8824 get_value(_TrivialTraitsDecorator self, FloatKey a0) -> IMP::Float
8825 get_value(_TrivialTraitsDecorator self, IntKey a0) -> IMP::Int
8826 get_value(_TrivialTraitsDecorator self, FloatsKey a0) -> IMP::Floats
8827 get_value(_TrivialTraitsDecorator self, IntsKey a0) -> IMP::Ints
8828 get_value(_TrivialTraitsDecorator self, StringKey a0) -> IMP::String
8829 get_value(_TrivialTraitsDecorator self, ParticleIndexKey a0) -> Particle
8830 get_value(_TrivialTraitsDecorator self, ObjectKey a0) -> Object
8831 get_value(_TrivialTraitsDecorator self, SparseFloatKey a0) -> IMP::Float
8832 get_value(_TrivialTraitsDecorator self, SparseIntKey a0) -> IMP::Int
8833 get_value(_TrivialTraitsDecorator self, SparseStringKey a0) -> IMP::String
8834 get_value(_TrivialTraitsDecorator self, SparseParticleIndexKey a0) -> ParticleIndex
8836 return _IMP_kernel._TrivialTraitsDecorator_get_value(self, *args)
8838 def set_value(self, *args):
8840 set_value(_TrivialTraitsDecorator self, FloatKey a0, IMP::Float a1)
8841 set_value(_TrivialTraitsDecorator self, IntKey a0, IMP::Int a1)
8842 set_value(_TrivialTraitsDecorator self, FloatsKey a0, IMP::Floats a1)
8843 set_value(_TrivialTraitsDecorator self, IntsKey a0, IMP::Ints a1)
8844 set_value(_TrivialTraitsDecorator self, StringKey a0, IMP::String a1)
8845 set_value(_TrivialTraitsDecorator self, ParticleIndexKey a0, Particle a1)
8846 set_value(_TrivialTraitsDecorator self, ObjectKey a0, Object a1)
8847 set_value(_TrivialTraitsDecorator self, SparseFloatKey a0, IMP::Float a1)
8848 set_value(_TrivialTraitsDecorator self, SparseIntKey a0, IMP::Int a1)
8849 set_value(_TrivialTraitsDecorator self, SparseStringKey a0, IMP::String a1)
8850 set_value(_TrivialTraitsDecorator self, SparseParticleIndexKey a0, ParticleIndex a1)
8852 return _IMP_kernel._TrivialTraitsDecorator_set_value(self, *args)
8856 remove_attribute(_TrivialTraitsDecorator self, FloatKey a0)
8857 remove_attribute(_TrivialTraitsDecorator self, IntKey a0)
8858 remove_attribute(_TrivialTraitsDecorator self, FloatsKey a0)
8859 remove_attribute(_TrivialTraitsDecorator self, IntsKey a0)
8860 remove_attribute(_TrivialTraitsDecorator self, StringKey a0)
8861 remove_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0)
8862 remove_attribute(_TrivialTraitsDecorator self, ObjectKey a0)
8863 remove_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0)
8864 remove_attribute(_TrivialTraitsDecorator self, SparseIntKey a0)
8865 remove_attribute(_TrivialTraitsDecorator self, SparseStringKey a0)
8866 remove_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0)
8868 return _IMP_kernel._TrivialTraitsDecorator_remove_attribute(self, *args)
8870 def has_attribute(self, *args):
8872 has_attribute(_TrivialTraitsDecorator self, FloatKey a0) -> bool
8873 has_attribute(_TrivialTraitsDecorator self, IntKey a0) -> bool
8874 has_attribute(_TrivialTraitsDecorator self, FloatsKey a0) -> bool
8875 has_attribute(_TrivialTraitsDecorator self, IntsKey a0) -> bool
8876 has_attribute(_TrivialTraitsDecorator self, StringKey a0) -> bool
8877 has_attribute(_TrivialTraitsDecorator self, ParticleIndexKey a0) -> bool
8878 has_attribute(_TrivialTraitsDecorator self, ObjectKey a0) -> bool
8879 has_attribute(_TrivialTraitsDecorator self, SparseFloatKey a0) -> bool
8880 has_attribute(_TrivialTraitsDecorator self, SparseIntKey a0) -> bool
8881 has_attribute(_TrivialTraitsDecorator self, SparseStringKey a0) -> bool
8882 has_attribute(_TrivialTraitsDecorator self, SparseParticleIndexKey a0) -> bool
8884 return _IMP_kernel._TrivialTraitsDecorator_has_attribute(self, *args)
8886 def get_derivative(self, a0):
8887 r"""get_derivative(_TrivialTraitsDecorator self, FloatKey a0) -> double"""
8888 return _IMP_kernel._TrivialTraitsDecorator_get_derivative(self, a0)
8891 r"""get_name(_TrivialTraitsDecorator self) -> std::string"""
8892 return _IMP_kernel._TrivialTraitsDecorator_get_name(self)
8895 r"""clear_caches(_TrivialTraitsDecorator self)"""
8896 return _IMP_kernel._TrivialTraitsDecorator_clear_caches(self)
8898 def set_name(self, a0):
8899 r"""set_name(_TrivialTraitsDecorator self, std::string a0)"""
8900 return _IMP_kernel._TrivialTraitsDecorator_set_name(self, a0)
8903 r"""set_check_level(_TrivialTraitsDecorator self, IMP::CheckLevel a0)"""
8904 return _IMP_kernel._TrivialTraitsDecorator_set_check_level(self, a0)
8906 def add_to_derivative(self, a0, a1, a2):
8907 r"""add_to_derivative(_TrivialTraitsDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
8908 return _IMP_kernel._TrivialTraitsDecorator_add_to_derivative(self, a0, a1, a2)
8911 r"""set_is_optimized(_TrivialTraitsDecorator self, FloatKey a0, bool a1)"""
8912 return _IMP_kernel._TrivialTraitsDecorator_set_is_optimized(self, a0, a1)
8914 def get_is_optimized(self, a0):
8915 r"""get_is_optimized(_TrivialTraitsDecorator self, FloatKey a0) -> bool"""
8916 return _IMP_kernel._TrivialTraitsDecorator_get_is_optimized(self, a0)
8918 def get_check_level(self):
8919 r"""get_check_level(_TrivialTraitsDecorator self) -> IMP::CheckLevel"""
8920 return _IMP_kernel._TrivialTraitsDecorator_get_check_level(self)
8922 def __eq__(self, *args):
8924 __eq__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
8925 __eq__(_TrivialTraitsDecorator self, Particle d) -> bool
8927 return _IMP_kernel._TrivialTraitsDecorator___eq__(self, *args)
8929 def __ne__(self, *args):
8931 __ne__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
8932 __ne__(_TrivialTraitsDecorator self, Particle d) -> bool
8934 return _IMP_kernel._TrivialTraitsDecorator___ne__(self, *args)
8936 def __le__(self, *args):
8938 __le__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
8939 __le__(_TrivialTraitsDecorator self, Particle d) -> bool
8941 return _IMP_kernel._TrivialTraitsDecorator___le__(self, *args)
8943 def __lt__(self, *args):
8945 __lt__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
8946 __lt__(_TrivialTraitsDecorator self, Particle d) -> bool
8948 return _IMP_kernel._TrivialTraitsDecorator___lt__(self, *args)
8950 def __ge__(self, *args):
8952 __ge__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
8953 __ge__(_TrivialTraitsDecorator self, Particle d) -> bool
8955 return _IMP_kernel._TrivialTraitsDecorator___ge__(self, *args)
8957 def __gt__(self, *args):
8959 __gt__(_TrivialTraitsDecorator self, _TrivialTraitsDecorator o) -> bool
8960 __gt__(_TrivialTraitsDecorator self, Particle d) -> bool
8962 return _IMP_kernel._TrivialTraitsDecorator___gt__(self, *args)
8965 r"""__hash__(_TrivialTraitsDecorator self) -> std::size_t"""
8966 return _IMP_kernel._TrivialTraitsDecorator___hash__(self)
8969 r"""__str__(_TrivialTraitsDecorator self) -> std::string"""
8970 return _IMP_kernel._TrivialTraitsDecorator___str__(self)
8973 r"""__repr__(_TrivialTraitsDecorator self) -> std::string"""
8974 return _IMP_kernel._TrivialTraitsDecorator___repr__(self)
8975 __swig_destroy__ = _IMP_kernel.delete__TrivialTraitsDecorator
8978 _IMP_kernel._TrivialTraitsDecorator_swigregister(_TrivialTraitsDecorator)
8980 def __lshift__(*args):
8982 __lshift__(_ostream out, _TrivialDecorator n) -> _ostream
8983 __lshift__(_ostream out, _TrivialDerivedDecorator n) -> _ostream
8984 __lshift__(_ostream out, _TrivialTraitsDecorator n) -> _ostream
8986 return _IMP_kernel.__lshift__(*args)
8988 r"""Proxy of C++ IMP::internal::_ConstOptimizer class."""
8990 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
8992 def __init__(self, *args):
8994 __init__(_ConstOptimizer self, Model m) -> _ConstOptimizer
8995 __init__(_ConstOptimizer self) -> _ConstOptimizer
8997 _IMP_kernel._ConstOptimizer_swiginit(self, _IMP_kernel.new__ConstOptimizer(*args))
8999 def do_optimize(self, max_steps):
9000 r"""do_optimize(_ConstOptimizer self, unsigned int max_steps) -> IMP::Float"""
9001 return _IMP_kernel._ConstOptimizer_do_optimize(self, max_steps)
9004 r"""get_version_info(_ConstOptimizer self) -> VersionInfo"""
9005 return _IMP_kernel._ConstOptimizer_get_version_info(self)
9006 __swig_destroy__ = _IMP_kernel.delete__ConstOptimizer
9009 r"""__str__(_ConstOptimizer self) -> std::string"""
9010 return _IMP_kernel._ConstOptimizer___str__(self)
9013 r"""__repr__(_ConstOptimizer self) -> std::string"""
9014 return _IMP_kernel._ConstOptimizer___repr__(self)
9018 return _object_cast_to__ConstOptimizer(o)
9021 def _get_as_binary(self):
9022 r"""_get_as_binary(_ConstOptimizer self) -> PyObject *"""
9023 return _IMP_kernel._ConstOptimizer__get_as_binary(self)
9025 def _set_from_binary(self, p):
9026 r"""_set_from_binary(_ConstOptimizer self, PyObject * p)"""
9027 return _IMP_kernel._ConstOptimizer__set_from_binary(self, p)
9029 def __getstate__(self):
9030 p = self._get_as_binary()
9031 if len(self.__dict__) > 1:
9032 d = self.__dict__.copy()
9037 def __setstate__(self, p):
9038 if not hasattr(self,
'this'):
9040 if isinstance(p, tuple):
9042 self.__dict__.update(d)
9043 return self._set_from_binary(p)
9047 _IMP_kernel._ConstOptimizer_swigregister(_ConstOptimizer)
9050 r"""get_particle(Particle p) -> Particle"""
9051 return _IMP_kernel.get_particle(p)
9053 def _decorator_test(p):
9054 r"""_decorator_test(Particle p)"""
9055 return _IMP_kernel._decorator_test(p)
9057 def _overloaded_decorator(*args):
9059 _overloaded_decorator(_TrivialDecorator a) -> int
9060 _overloaded_decorator(_TrivialDerivedDecorator a) -> int
9062 return _IMP_kernel._overloaded_decorator(*args)
9064 def _take_particles(*args):
9066 _take_particles(IMP::Particles const & ps) -> unsigned int
9067 _take_particles(Model m, IMP::Particles const & ps) -> unsigned int
9068 _take_particles(Model m, IMP::Particles const & ps, TextOutput out) -> unsigned int
9070 return _IMP_kernel._take_particles(*args)
9072 def _give_particles(m):
9073 r"""_give_particles(Model m) -> IMP::Particles const &"""
9074 return _IMP_kernel._give_particles(m)
9076 def _pass_particles(ps):
9077 r"""_pass_particles(IMP::Particles const & ps) -> IMP::Particles const &"""
9078 return _IMP_kernel._pass_particles(ps)
9080 def _pass_particle(ps):
9081 r"""_pass_particle(Particle ps) -> Particle"""
9082 return _IMP_kernel._pass_particle(ps)
9084 def _pass_particle_pair(pp):
9085 r"""_pass_particle_pair(IMP::ParticlePair const & pp) -> IMP::ParticlePair const &"""
9086 return _IMP_kernel._pass_particle_pair(pp)
9088 def _give_particles_copy(m):
9089 r"""_give_particles_copy(Model m) -> IMP::Particles"""
9090 return _IMP_kernel._give_particles_copy(m)
9092 def _pass_float_keys(input):
9093 r"""_pass_float_keys(IMP::FloatKeys const & input) -> IMP::FloatKeys"""
9094 return _IMP_kernel._pass_float_keys(input)
9098 _pass(IMP::Particles const & p) -> IMP::Particles const
9099 _pass(IMP::Restraints const & p) -> IMP::Restraints const &
9101 return _IMP_kernel._pass(*args)
9103 def _pass_decorators(p):
9104 r"""_pass_decorators(IMP::internal::_TrivialDecorators const & p) -> IMP::internal::_TrivialDecorators const &"""
9105 return _IMP_kernel._pass_decorators(p)
9107 def _pass_decorator_traits(p):
9108 r"""_pass_decorator_traits(IMP::internal::_TrivialTraitsDecorators const & p) -> IMP::internal::_TrivialTraitsDecorators const &"""
9109 return _IMP_kernel._pass_decorator_traits(p)
9111 def _pass_particle_pairs(p):
9112 r"""_pass_particle_pairs(IMP::ParticlePairsTemp const & p) -> IMP::ParticlePairsTemp"""
9113 return _IMP_kernel._pass_particle_pairs(p)
9115 def _pass_particle_index_pairs(p):
9116 r"""_pass_particle_index_pairs(IMP::ParticleIndexPairs const & p) -> IMP::ParticleIndexPairs"""
9117 return _IMP_kernel._pass_particle_index_pairs(p)
9119 def _pass_model_objects(p):
9120 r"""_pass_model_objects(IMP::ModelObjectsTemp const & p) -> IMP::ModelObjectsTemp"""
9121 return _IMP_kernel._pass_model_objects(p)
9123 def _pass_particles_temps(ps):
9124 r"""_pass_particles_temps(IMP::ParticlesTemps const & ps) -> IMP::ParticlesTemps"""
9125 return _IMP_kernel._pass_particles_temps(ps)
9127 def _test_overload(*args):
9129 _test_overload(IMP::Particles const & ps) -> int
9130 _test_overload(IMP::Restraints const & ps) -> int
9132 return _IMP_kernel._test_overload(*args)
9134 def _get_range(m, k):
9135 r"""_get_range(Model m, FloatKey k) -> IMP::FloatRange"""
9136 return _IMP_kernel._get_range(m, k)
9138 def _create_particles_from_pdb(name, m):
9139 r"""_create_particles_from_pdb(std::string name, Model m) -> IMP::ParticleIndexes"""
9140 return _IMP_kernel._create_particles_from_pdb(name, m)
9142 r"""Proxy of C++ IMP::internal::_LogPairScore class."""
9144 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9145 __repr__ = _swig_repr
9148 r"""__init__(_LogPairScore self) -> _LogPairScore"""
9149 _IMP_kernel._LogPairScore_swiginit(self, _IMP_kernel.new__LogPairScore())
9151 def do_get_inputs(self, arg2, arg3):
9152 r"""do_get_inputs(_LogPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
9153 return _IMP_kernel._LogPairScore_do_get_inputs(self, arg2, arg3)
9155 def evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked=False):
9156 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"""
9157 return _IMP_kernel._LogPairScore_evaluate_indexes(self, m, p, da, lower_bound, upper_bound, all_indexes_checked)
9159 def evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked=False):
9160 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"""
9161 return _IMP_kernel._LogPairScore_evaluate_indexes_scores(self, m, p, da, lower_bound, upper_bound, score, all_indexes_checked)
9163 def evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked=False):
9164 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"""
9165 return _IMP_kernel._LogPairScore_evaluate_indexes_delta(self, m, p, da, indexes, score, all_indexes_checked)
9167 def evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked=False):
9168 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"""
9169 return _IMP_kernel._LogPairScore_evaluate_if_good_indexes(self, m, p, da, max, lower_bound, upper_bound, all_indexes_checked)
9172 r"""get_version_info(_LogPairScore self) -> VersionInfo"""
9173 return _IMP_kernel._LogPairScore_get_version_info(self)
9174 __swig_destroy__ = _IMP_kernel.delete__LogPairScore
9176 def get_particle_pairs(self):
9177 r"""get_particle_pairs(_LogPairScore self) -> IMP::ParticlePairsTemp"""
9178 return _IMP_kernel._LogPairScore_get_particle_pairs(self)
9181 r"""clear(_LogPairScore self)"""
9182 return _IMP_kernel._LogPairScore_clear(self)
9184 def get_contains(self, pp):
9185 r"""get_contains(_LogPairScore self, IMP::ParticlePair const & pp) -> bool"""
9186 return _IMP_kernel._LogPairScore_get_contains(self, pp)
9189 _IMP_kernel._LogPairScore_swigregister(_LogPairScore)
9191 def _overloaded_particles(*args):
9193 _overloaded_particles(Particle arg1)
9194 _overloaded_particles(IMP::Particles const & arg1)
9195 _overloaded_particles(IMP::ParticlesTemp const & arg1)
9196 _overloaded_particles(Model arg1, IMP::ParticleIndexes const & arg2)
9197 _overloaded_particles(IMP::internal::_TrivialDecorators const & arg1)
9198 _overloaded_particles(_TrivialDecorator arg1)
9200 return _IMP_kernel._overloaded_particles(*args)
9201 class _ImplicitParticles(object):
9202 r"""Proxy of C++ IMP::internal::_ImplicitParticles class."""
9204 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9205 __repr__ = _swig_repr
9207 def __init__(self, *args):
9209 __init__(_ImplicitParticles self, Particle arg2) -> _ImplicitParticles
9210 __init__(_ImplicitParticles self, IMP::Particles const & arg2) -> _ImplicitParticles
9211 __init__(_ImplicitParticles self, IMP::ParticlesTemp const & arg2) -> _ImplicitParticles
9212 __init__(_ImplicitParticles self, Model arg2, IMP::ParticleIndexes const & arg3) -> _ImplicitParticles
9213 __init__(_ImplicitParticles self, IMP::internal::_TrivialDecorators const & arg2) -> _ImplicitParticles
9214 __init__(_ImplicitParticles self, _TrivialDecorator arg2) -> _ImplicitParticles
9216 _IMP_kernel._ImplicitParticles_swiginit(self, _IMP_kernel.new__ImplicitParticles(*args))
9217 __swig_destroy__ = _IMP_kernel.delete__ImplicitParticles
9220 _IMP_kernel._ImplicitParticles_swigregister(_ImplicitParticles)
9222 def _implicit_particles(arg1):
9223 r"""_implicit_particles(_ImplicitParticles arg1)"""
9224 return _IMP_kernel._implicit_particles(arg1)
9226 def _take_particle_adaptor(pa):
9227 r"""_take_particle_adaptor(_ParticleAdaptor pa) -> ParticleIndex"""
9228 return _IMP_kernel._take_particle_adaptor(pa)
9230 def _take_particle_indexes_adaptor(pa):
9231 r"""_take_particle_indexes_adaptor(_ParticleIndexesAdaptor pa) -> IMP::ParticleIndexes"""
9232 return _IMP_kernel._take_particle_indexes_adaptor(pa)
9234 r"""Proxy of C++ IMP::ScopedSetAttribute< IMP::FloatKey,IMP::Float > class."""
9236 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9238 def __init__(self, *args):
9240 __init__(ScopedSetFloatAttribute self) -> ScopedSetFloatAttribute
9241 __init__(ScopedSetFloatAttribute self, Particle p, FloatKey key, double const & value) -> ScopedSetFloatAttribute
9243 _IMP_kernel.ScopedSetFloatAttribute_swiginit(self, _IMP_kernel.new_ScopedSetFloatAttribute(*args))
9245 def set(self, p, key, value):
9246 r"""set(ScopedSetFloatAttribute self, Particle p, FloatKey key, double const & value)"""
9247 return _IMP_kernel.ScopedSetFloatAttribute_set(self, p, key, value)
9250 r"""reset(ScopedSetFloatAttribute self)"""
9251 return _IMP_kernel.ScopedSetFloatAttribute_reset(self)
9252 __swig_destroy__ = _IMP_kernel.delete_ScopedSetFloatAttribute
9254 def show(self, *args):
9255 r"""show(ScopedSetFloatAttribute self, _ostream out=std::cout)"""
9256 return _IMP_kernel.ScopedSetFloatAttribute_show(self, *args)
9259 r"""__str__(ScopedSetFloatAttribute self) -> std::string"""
9260 return _IMP_kernel.ScopedSetFloatAttribute___str__(self)
9263 r"""__repr__(ScopedSetFloatAttribute self) -> std::string"""
9264 return _IMP_kernel.ScopedSetFloatAttribute___repr__(self)
9267 _IMP_kernel.ScopedSetFloatAttribute_swigregister(ScopedSetFloatAttribute)
9269 def _get_module_data_path(module, file_name):
9270 r"""_get_module_data_path(std::string module, std::string file_name) -> std::string"""
9271 return _IMP_kernel._get_module_data_path(module, file_name)
9273 def _get_module_example_path(module, file_name):
9274 r"""_get_module_example_path(std::string module, std::string file_name) -> std::string"""
9275 return _IMP_kernel._get_module_example_path(module, file_name)
9284 if sys.platform ==
'win32' and 'IMP_LD_PATH' in os.environ:
9285 dirs = os.environ[
'IMP_LD_PATH'].split(
":")
9286 pathcomps = os.environ[
'PATH'].split(
";")
9288 if d
not in pathcomps:
9289 os.environ[
'PATH'] = d +
';' + os.environ[
'PATH']
9297 """Allow command line tools to easily implement multiple commands.
9298 Typically, an IMP command line tool will use an instance of this class
9299 to provide a consistent interface to multiple distinct commands
9300 from a single binary, rather than providing a potentially large
9301 number of binaries. This is similar to the way a number of common
9302 command line tools outside of IMP function (e.g. Git provides a single
9303 `git` tool which implements multiple commands - `git add`, `git commit`,
9304 `git push` and so on).
9306 Each command is implemented with a Python module of the same name
9307 that can be imported from the module (for example, if `module_name`
9308 is `IMP.foo`, the `bar` command is provided by the `IMP.foo.bar` Python
9309 module, which would usually be found as `modules/foo/pyext/src/bar.py`).
9310 Each such module should have a docstring and a `%main()` method
9311 that takes no arguments (the module should also call its `%main()` method
9312 if it is run directly, i.e. with something like
9313 `if __name__=="__main__": %main()`). The encompassing module
9314 (`IMP.foo` in the example) should define `_all_commands` as a Python
9315 list of all valid commands.
9317 See the `multifit` and `cnmultifit` command line tools for example
9321 def __init__(self, short_help, long_help, module_name):
9323 @param short_help A few words that describe the command line tool.
9324 @param long_help Longer text, used in the `help` command.
9325 @param module_name Name of the module (e.g. `IMP.foo`) that
9326 implements the commands.
9328 self.short_help = short_help
9329 self.long_help = long_help
9330 self.module_name = module_name
9331 self._all_commands = self.import_module()._all_commands
9332 self._progname = os.path.basename(sys.argv[0])
9335 """Call this method to act upon the user-provided command line"""
9336 if len(sys.argv) <= 1:
9337 print(self.short_help +
" Use '%s help' for help." % self._progname)
9339 command = sys.argv[1]
9340 if command
in (
'help',
'--help',
'-h'):
9341 if len(sys.argv) == 3:
9342 self.show_command_help(sys.argv[2])
9345 elif command ==
'--version':
9347 elif command
in self._all_commands:
9348 self.do_command(command)
9350 self.unknown_command(command)
9352 def import_module(self, mod=None):
9353 modname = self.module_name
9355 modname +=
"." + mod
9356 return __import__(modname, {}, {}, [
''])
9358 def unknown_command(self, command):
9359 print(
"Unknown command: '%s'" % command)
9360 print(
"Use '%s help' for help." % self._progname)
9363 def _get_version(self):
9366 def show_version(self):
9367 print(self._progname +
' ' + self._get_version())
9369 def show_help(self):
9370 ver = self._get_version()
9371 print(
"%s, version %s." % (self._progname, ver))
9372 print(self.long_help +
"""
9374 This program is part of IMP, the Integrative Modeling Platform,
9376 For additional information about IMP, see <https://integrativemodeling.org>.
9378 Usage: %s <command> [options] [args]
9381 commands = self._all_commands[:] + [
'help']
9383 cmdlen = max([len(c)
for c
in commands])
9386 doc =
'Get help on using %s.' % self._progname
9388 doc = self.import_module(c).__doc__
or "<no help>"
9389 c +=
' ' * (cmdlen - len(c))
9390 print(
' ' + c +
' ' + doc)
9392 Use "%s help <command>" for detailed help on any command
9393 or "%s --version" to see the version number.""" % (self._progname,
9396 def do_command(self, command):
9397 mod = self.import_module(command)
9398 sys.argv[0] = self._progname +
' ' + command
9402 def show_command_help(self, command):
9403 if command ==
'help':
9405 elif command
in self._all_commands
or command ==
'help':
9406 mod = self.import_module(command)
9407 sys.argv = [self._progname +
' ' + command,
'--help']
9410 self.unknown_command(command)
9417 g = networkx.DiGraph()
9418 if len(ig.get_vertices()) == 0:
9427 return self.p.get_name()
9429 def __call__(self, name):
9430 return self.p.__call__(name)
9432 for vi
in ig.get_vertices():
9433 n = ig.get_vertex_name(vi)
9434 g.add_node(NodeWrapper(n))
9435 for vi
in ig.get_vertices():
9436 n = ig.get_vertex_name(vi)
9437 for ni
in ig.get_out_neighbors(vi):
9438 nn = ig.get_vertex_name(ni)
9439 g.add_edge(NodeWrapper(n), NodeWrapper(nn))
9446 n0 = name.get_name()
9449 n1 = str(n0).replace(
'"',
'')
9450 n2 = n1.replace(
"\n",
'')
9453 from altgraph
import Graph, Dot
9454 graph = Graph.Graph()
9455 for i, v
in enumerate(g.get_vertices()):
9457 for i, v
in enumerate(g.get_vertices()):
9458 for n
in g.get_out_neighbors(v):
9459 graph.add_edge(v, n)
9460 dot = Dot.Dot(graph)
9461 for i, v
in enumerate(g.get_vertices()):
9462 dot.node_style(i, label=clean(g.get_vertex_name(v)))
9470 st = g.get_graphviz_string()
9471 with open(tfn,
"w")
as fh:
9474 print(
"running dot")
9475 sp = subprocess.Popen([
"dot",
"-Tpdf", tfn,
"-o" + tfon])
9479 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")
9482 if platform.system() ==
"Darwin":
9485 cmd = [
"gv",
"acroread",
"xpdf"]
9488 print(
"launching viewer " + c)
9490 subprocess.check_call([c, tfon])
9496 print(
"Could not display file. It is saved at " + tfon)
9506 """Mark a Python module as deprecated.
9507 @note The `module` argument would normally be `__name__`.
9508 @see [deprecation support](@ref deprecation)."""
9510 "Module %s is deprecated. %s\n" % (module, help_message))
9513 """Python decorator to mark a class as deprecated.
9514 @see [deprecation support](@ref deprecation)."""
9516 orig_init = obj.__init__
9519 @functools.wraps(orig_init, (
'__name__',
'__doc__'))
9520 def __init__(obj, *args, **keys):
9522 % (type(obj), help_message))
9523 orig_init(obj, *args, **keys)
9524 obj.__init__ = __init__
9529 """Python decorator to mark a method as deprecated.
9530 @see [deprecation support](@ref deprecation)."""
9531 def out_wrapper(obj):
9532 @functools.wraps(obj)
9533 def wrapper(cls, *args, **keys):
9535 % (obj.__name__, type(cls), help_message))
9536 return obj(cls, *args, **keys)
9541 """Python decorator to mark a function as deprecated.
9542 @see [deprecation support](@ref deprecation)."""
9543 def out_wrapper(obj):
9544 @functools.wraps(obj)
9545 def wrapper(*args, **keys):
9547 % (obj.__name__, help_message))
9548 return obj(*args, **keys)
9552 @contextlib.contextmanager
9554 """Context manager to temporarily allow (or disallow) deprecated code.
9555 @see [deprecation support](@ref deprecation)."""
9562 def _get_all_flags(ntokens):
9563 r"""_get_all_flags(unsigned int ntokens) -> IMP::Strings"""
9564 return _IMP_kernel._get_all_flags(ntokens)
9566 def _print_internal_help(out, description):
9567 r"""_print_internal_help(_ostream out, std::string description)"""
9568 return _IMP_kernel._print_internal_help(out, description)
9574 class _PassThroughAction(argparse.Action):
9575 """Pass an argument through to the IMP Boost parser"""
9576 def __call__(self, parser, namespace, values, option_string=None):
9577 parser._boost_command_line.append(option_string)
9579 parser._boost_command_line.append(values)
9582 if option_string
in (
'-h',
'--help',
'--help_advanced',
'--version'):
9583 parser._handle_boost()
9587 """IMP-specific subclass of argparse.ArgumentParser.
9588 This adds options common to all IMP applications
9589 (see IMP::setup_from_argv()).
9592 def __init__(self, *args, **kwargs):
9594 kwargs[
'add_help'] =
False
9595 super().__init__(*args, **kwargs)
9596 for ntoken
in (0, 1):
9597 flags = _get_all_flags(ntoken)
9599 arg = [
'-h',
'--help']
if f ==
'help' else [
'--' + f]
9600 self.add_argument(*arg, help=argparse.SUPPRESS,
9601 nargs=
None if ntoken
else 0,
9602 action=_PassThroughAction,
9603 default=argparse.SUPPRESS)
9606 """Parse the command line and return optional and positional arguments.
9607 This functions in the same way as the method in the base class
9608 argparse.ArgumentParser, except that it also processes optional
9609 arguments common to all IMP applications (these are not returned
9610 in `args`, but can be obtained in the usual way, e.g. by calling
9611 IMP::get_string_flag()).
9614 self._boost_command_line = [sys.argv[0]]
9616 if len(self._boost_command_line) > 1:
9617 self._handle_boost()
9620 def _get_description(self):
9621 return self.format_help() +
"\nOptions common to all IMP applications:"
9623 def print_help(self, file=None):
9624 _print_internal_help(file
if file
else sys.stdout,
9625 self._get_description())
9627 def _handle_boost(self):
9629 self._get_description(),
9632 class RandomNumberGenerator(object):
9633 r"""Proxy of C++ IMP::RandomNumberGenerator class."""
9635 thisown = property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
"The membership flag")
9636 __repr__ = _swig_repr
9639 r"""seed(RandomNumberGenerator self, int x)"""
9640 return _IMP_kernel.RandomNumberGenerator_seed(self, x)
9643 r"""__call__(RandomNumberGenerator self) -> int"""
9644 return _IMP_kernel.RandomNumberGenerator___call__(self)
9647 r"""__init__(RandomNumberGenerator self) -> RandomNumberGenerator"""
9648 _IMP_kernel.RandomNumberGenerator_swiginit(self, _IMP_kernel.new_RandomNumberGenerator())
9649 __swig_destroy__ = _IMP_kernel.delete_RandomNumberGenerator
9652 _IMP_kernel.RandomNumberGenerator_swigregister(RandomNumberGenerator)
9656 get_random_float_uniform() -> float
9657 get_random_float_uniform(float min, float max) -> float
9659 return _IMP_kernel.get_random_float_uniform(*args)
9663 get_random_double_uniform() -> double
9664 get_random_double_uniform(double min, double max) -> double
9666 return _IMP_kernel.get_random_double_uniform(*args)
9668 def get_random_floats_normal(n, mean=0.0, stddev=1.0):
9669 r"""get_random_floats_normal(unsigned int n, float mean=0.0, float stddev=1.0) -> IMP::Vector< float,std::allocator< float > >"""
9670 return _IMP_kernel.get_random_floats_normal(n, mean, stddev)
9672 def get_random_doubles_normal(n, mean=0.0, stddev=1.0):
9673 r"""get_random_doubles_normal(unsigned int n, double mean=0.0, double stddev=1.0) -> IMP::Vector< double,std::allocator< double > >"""
9674 return _IMP_kernel.get_random_doubles_normal(n, mean, stddev)
9676 def get_random_floats_uniform(n):
9677 r"""get_random_floats_uniform(unsigned int n) -> IMP::Vector< float,std::allocator< float > >"""
9678 return _IMP_kernel.get_random_floats_uniform(n)
9680 def get_random_doubles_uniform(n):
9681 r"""get_random_doubles_uniform(unsigned int n) -> IMP::Vector< double,std::allocator< double > >"""
9682 return _IMP_kernel.get_random_doubles_uniform(n)
9685 r"""get_random_seed() -> boost::uint64_t"""
9686 return _IMP_kernel.get_random_seed()
9688 def _get_derivatives_numpy(m, k, m_pyobj, read_only):
9689 r"""_get_derivatives_numpy(Model m, FloatKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9690 return _IMP_kernel._get_derivatives_numpy(m, k, m_pyobj, read_only)
9692 def _get_floats_numpy(m, k, m_pyobj, read_only):
9693 r"""_get_floats_numpy(Model m, FloatKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9694 return _IMP_kernel._get_floats_numpy(m, k, m_pyobj, read_only)
9696 def _get_ints_numpy(m, k, m_pyobj, read_only):
9697 r"""_get_ints_numpy(Model m, IntKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9698 return _IMP_kernel._get_ints_numpy(m, k, m_pyobj, read_only)
9700 def _get_vector3ds_numpy(m, k, m_pyobj, read_only):
9701 r"""_get_vector3ds_numpy(Model m, Vector3DKey k, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9702 return _IMP_kernel._get_vector3ds_numpy(m, k, m_pyobj, read_only)
9704 def _get_spheres_numpy(m, m_pyobj, read_only):
9705 r"""_get_spheres_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9706 return _IMP_kernel._get_spheres_numpy(m, m_pyobj, read_only)
9708 def _get_sphere_derivatives_numpy(m, m_pyobj, read_only):
9709 r"""_get_sphere_derivatives_numpy(Model m, PyObject * m_pyobj, bool read_only) -> PyObject *"""
9710 return _IMP_kernel._get_sphere_derivatives_numpy(m, m_pyobj, read_only)
9714 ParticleIndex = numpy.intc
9719 def get_module_name():
9720 r"""get_module_name() -> std::string const"""
9721 return _IMP_kernel.get_module_name()
9724 r"""get_module_version() -> std::string const"""
9725 return _IMP_kernel.get_module_version()
9728 r"""get_example_path(std::string fname) -> std::string"""
9729 return _IMP_kernel.get_example_path(fname)
9732 r"""get_data_path(std::string fname) -> std::string"""
9733 return _IMP_kernel.get_data_path(fname)
9735 from .
import _version_check
9740 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.
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.