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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
example/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.1.1
3 #
4 # Do not make changes to this file unless you know what you are doing - modify
5 # the SWIG interface file instead.
6 
7 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2023 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 import _IMP_example
17 
18 try:
19  import builtins as __builtin__
20 except ImportError:
21  import __builtin__
22 
23 def _swig_repr(self):
24  try:
25  strthis = "proxy of " + self.this.__repr__()
26  except __builtin__.Exception:
27  strthis = ""
28  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
29 
30 
31 def _swig_setattr_nondynamic_instance_variable(set):
32  def set_instance_attr(self, name, value):
33  if name == "this":
34  set(self, name, value)
35  elif name == "thisown":
36  self.this.own(value)
37  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
38  set(self, name, value)
39  else:
40  raise AttributeError("You cannot add instance attributes to %s" % self)
41  return set_instance_attr
42 
43 
44 def _swig_setattr_nondynamic_class_variable(set):
45  def set_class_attr(cls, name, value):
46  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
47  set(cls, name, value)
48  else:
49  raise AttributeError("You cannot add class attributes to %s" % cls)
50  return set_class_attr
51 
52 
53 def _swig_add_metaclass(metaclass):
54  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
55  def wrapper(cls):
56  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
57  return wrapper
58 
59 
60 class _SwigNonDynamicMeta(type):
61  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
63 
64 
65 import weakref
66 
67 class IMP_EXAMPLE_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_EXAMPLE_SwigPyIterator class."""
69 
70  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
71 
72  def __init__(self, *args, **kwargs):
73  raise AttributeError("No constructor defined - class is abstract")
74  __repr__ = _swig_repr
75  __swig_destroy__ = _IMP_example.delete_IMP_EXAMPLE_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
79  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_EXAMPLE_SwigPyIterator self, size_t n=1) -> IMP_EXAMPLE_SwigPyIterator"""
83  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_EXAMPLE_SwigPyIterator self, size_t n=1) -> IMP_EXAMPLE_SwigPyIterator"""
87  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_decr(self, n)
88 
89  def distance(self, x):
90  r"""distance(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> ptrdiff_t"""
91  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_distance(self, x)
92 
93  def equal(self, x):
94  r"""equal(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
95  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_EXAMPLE_SwigPyIterator self) -> IMP_EXAMPLE_SwigPyIterator"""
99  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
103  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
107  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
111  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_previous(self)
112 
113  def advance(self, n):
114  r"""advance(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
115  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_advance(self, n)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
119  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
123  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___ne__(self, x)
124 
125  def __iadd__(self, n):
126  r"""__iadd__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
127  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___iadd__(self, n)
128 
129  def __isub__(self, n):
130  r"""__isub__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
131  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___isub__(self, n)
132 
133  def __add__(self, n):
134  r"""__add__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
135  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___add__(self, n)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator
140  __sub__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_EXAMPLE_SwigPyIterator in _IMP_example:
147 _IMP_example.IMP_EXAMPLE_SwigPyIterator_swigregister(IMP_EXAMPLE_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_example.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_example.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_example.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_example.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_example.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_example.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_example.IMP_MEMORY
167 
168 IMP_NONE = _IMP_example.IMP_NONE
169 
170 IMP_USAGE = _IMP_example.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_example.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_example.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_example.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_example.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_example.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_example.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_example.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_example.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_example.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_example.IMPKERNEL_SHOW_WARNINGS
195 
196 
197 import sys
198 class _DirectorObjects(object):
199  """@internal Simple class to keep references to director objects
200  to prevent premature deletion."""
201  def __init__(self):
202  self._objects = []
203  def register(self, obj):
204  """Take a reference to a director object; will only work for
205  refcounted C++ classes"""
206  if hasattr(obj, 'get_ref_count'):
207  self._objects.append(obj)
208  def cleanup(self):
209  """Only drop our reference and allow cleanup by Python if no other
210  Python references exist (we hold 3 references: one in self._objects,
211  one in x, and one in the argument list for getrefcount) *and* no
212  other C++ references exist (the Python object always holds one)"""
213  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
214  or x.get_ref_count() > 1]
215 # Do in two steps so the references are kept until the end of the
216 # function (deleting references may trigger a fresh call to this method)
217  self._objects = objs
218  def get_object_count(self):
219  """Get number of director objects (useful for testing only)"""
220  return len(self._objects)
221 _director_objects = _DirectorObjects()
222 
223 class _ostream(object):
224  r"""Proxy of C++ std::ostream class."""
225 
226  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
227 
228  def __init__(self, *args, **kwargs):
229  raise AttributeError("No constructor defined")
230  __repr__ = _swig_repr
231 
232  def write(self, osa_buf):
233  r"""write(_ostream self, char const * osa_buf)"""
234  return _IMP_example._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_example:
237 _IMP_example._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_example.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_example.IMP_CGAL_HAS_BOOST_RANDOM
246 
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_SYSTEM
248 
249 IMP_CGAL_HAS_NUMPY = _IMP_example.IMP_CGAL_HAS_NUMPY
250 
251 IMPCGAL_SHOW_WARNINGS = _IMP_example.IMPCGAL_SHOW_WARNINGS
252 
253 import IMP.cgal
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_example.IMP_ALGEBRA_HAS_IMP_CGAL
255 
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 
264 IMP_ALGEBRA_HAS_CGAL = _IMP_example.IMP_ALGEBRA_HAS_CGAL
265 
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_example.IMP_ALGEBRA_HAS_NUMPY
267 
268 IMP_ALGEBRA_HAS_ANN = _IMP_example.IMP_ALGEBRA_HAS_ANN
269 
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_example.IMPALGEBRA_SHOW_WARNINGS
271 
272 import IMP.algebra
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_example.IMP_DISPLAY_HAS_IMP_CGAL
274 
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_example.IMP_DISPLAY_HAS_BOOST_RANDOM
280 
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 
283 IMP_DISPLAY_HAS_CGAL = _IMP_example.IMP_DISPLAY_HAS_CGAL
284 
285 IMP_DISPLAY_HAS_NUMPY = _IMP_example.IMP_DISPLAY_HAS_NUMPY
286 
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_example.IMPDISPLAY_SHOW_WARNINGS
288 
289 import IMP.display
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
291 
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
293 
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
295 
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
297 
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
299 
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_CGAL
301 
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_example.IMP_SCORE_FUNCTOR_HAS_HDF5
303 
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_example.IMP_SCORE_FUNCTOR_HAS_NUMPY
305 
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_example.IMPSCOREFUNCTOR_SHOW_WARNINGS
307 
308 import IMP.score_functor
309 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_example.IMP_STATISTICS_HAS_IMP_CGAL
310 
311 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
312 
313 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
314 
315 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_example.IMP_STATISTICS_HAS_BOOST_RANDOM
316 
317 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_SYSTEM
318 
319 IMP_STATISTICS_HAS_CGAL = _IMP_example.IMP_STATISTICS_HAS_CGAL
320 
321 IMP_STATISTICS_HAS_NUMPY = _IMP_example.IMP_STATISTICS_HAS_NUMPY
322 
323 IMPSTATISTICS_SHOW_WARNINGS = _IMP_example.IMPSTATISTICS_SHOW_WARNINGS
324 
325 import IMP.statistics
326 IMP_CORE_HAS_IMP_CGAL = _IMP_example.IMP_CORE_HAS_IMP_CGAL
327 
328 IMP_CORE_HAS_IMP_KERNEL = _IMP_example.IMP_CORE_HAS_IMP_KERNEL
329 
330 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_FILESYSTEM
331 
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 
334 IMP_CORE_HAS_BOOST_RANDOM = _IMP_example.IMP_CORE_HAS_BOOST_RANDOM
335 
336 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_SYSTEM
337 
338 IMP_CORE_HAS_CGAL = _IMP_example.IMP_CORE_HAS_CGAL
339 
340 IMP_CORE_HAS_HDF5 = _IMP_example.IMP_CORE_HAS_HDF5
341 
342 IMP_CORE_HAS_NUMPY = _IMP_example.IMP_CORE_HAS_NUMPY
343 
344 IMPCORE_SHOW_WARNINGS = _IMP_example.IMPCORE_SHOW_WARNINGS
345 
346 import IMP.core
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_example.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 
349 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_example.IMP_CONTAINER_HAS_IMP_CGAL
350 
351 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_example.IMP_CONTAINER_HAS_IMP_DISPLAY
352 
353 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_example.IMP_CONTAINER_HAS_IMP_KERNEL
354 
355 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
356 
357 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
358 
359 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
360 
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_example.IMP_CONTAINER_HAS_BOOST_RANDOM
362 
363 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_SYSTEM
364 
365 IMP_CONTAINER_HAS_CGAL = _IMP_example.IMP_CONTAINER_HAS_CGAL
366 
367 IMP_CONTAINER_HAS_HDF5 = _IMP_example.IMP_CONTAINER_HAS_HDF5
368 
369 IMP_CONTAINER_HAS_NUMPY = _IMP_example.IMP_CONTAINER_HAS_NUMPY
370 
371 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_example.IMP_CONTAINER_HAS_PYTHON_IHM
372 
373 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_example.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
374 
375 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_example.IMP_CONTAINER_HAS_ROBIN_MAP
376 
377 IMPCONTAINER_SHOW_WARNINGS = _IMP_example.IMPCONTAINER_SHOW_WARNINGS
378 
379 import IMP.container
380 IMP_ATOM_HAS_IMP_CGAL = _IMP_example.IMP_ATOM_HAS_IMP_CGAL
381 
382 IMP_ATOM_HAS_IMP_KERNEL = _IMP_example.IMP_ATOM_HAS_IMP_KERNEL
383 
384 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
385 
386 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
387 
388 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_example.IMP_ATOM_HAS_BOOST_RANDOM
389 
390 IMP_ATOM_HAS_BOOST_REGEX = _IMP_example.IMP_ATOM_HAS_BOOST_REGEX
391 
392 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_example.IMP_ATOM_HAS_BOOST_SYSTEM
393 
394 IMP_ATOM_HAS_CGAL = _IMP_example.IMP_ATOM_HAS_CGAL
395 
396 IMP_ATOM_HAS_HDF5 = _IMP_example.IMP_ATOM_HAS_HDF5
397 
398 IMP_ATOM_HAS_NUMPY = _IMP_example.IMP_ATOM_HAS_NUMPY
399 
400 IMP_ATOM_HAS_PYTHON_IHM = _IMP_example.IMP_ATOM_HAS_PYTHON_IHM
401 
402 IMPATOM_SHOW_WARNINGS = _IMP_example.IMPATOM_SHOW_WARNINGS
403 
404 IMP_ATOM_TYPE_INDEX = _IMP_example.IMP_ATOM_TYPE_INDEX
405 
406 IMP_RESIDUE_TYPE_INDEX = _IMP_example.IMP_RESIDUE_TYPE_INDEX
407 
408 IMP_HIERARCHY_TYPE_INDEX = _IMP_example.IMP_HIERARCHY_TYPE_INDEX
409 
410 IMP_CHAIN_TYPE_INDEX = _IMP_example.IMP_CHAIN_TYPE_INDEX
411 
412 import IMP.atom
413 IMP_EM_HAS_IMP_CGAL = _IMP_example.IMP_EM_HAS_IMP_CGAL
414 
415 IMP_EM_HAS_IMP_CONTAINER = _IMP_example.IMP_EM_HAS_IMP_CONTAINER
416 
417 IMP_EM_HAS_IMP_DISPLAY = _IMP_example.IMP_EM_HAS_IMP_DISPLAY
418 
419 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EM_HAS_IMP_SCORE_FUNCTOR
420 
421 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EM_HAS_BOOST_FILESYSTEM
422 
423 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
424 
425 IMP_EM_HAS_BOOST_RANDOM = _IMP_example.IMP_EM_HAS_BOOST_RANDOM
426 
427 IMP_EM_HAS_BOOST_REGEX = _IMP_example.IMP_EM_HAS_BOOST_REGEX
428 
429 IMP_EM_HAS_BOOST_SYSTEM = _IMP_example.IMP_EM_HAS_BOOST_SYSTEM
430 
431 IMP_EM_HAS_CGAL = _IMP_example.IMP_EM_HAS_CGAL
432 
433 IMP_EM_HAS_HDF5 = _IMP_example.IMP_EM_HAS_HDF5
434 
435 IMP_EM_HAS_NUMPY = _IMP_example.IMP_EM_HAS_NUMPY
436 
437 IMP_EM_HAS_PYTHON_IHM = _IMP_example.IMP_EM_HAS_PYTHON_IHM
438 
439 IMPEM_SHOW_WARNINGS = _IMP_example.IMPEM_SHOW_WARNINGS
440 
441 import IMP.em
442 IMP_SAXS_HAS_IMP_CGAL = _IMP_example.IMP_SAXS_HAS_IMP_CGAL
443 
444 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_example.IMP_SAXS_HAS_IMP_CONTAINER
445 
446 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_example.IMP_SAXS_HAS_IMP_DISPLAY
447 
448 IMP_SAXS_HAS_IMP_KERNEL = _IMP_example.IMP_SAXS_HAS_IMP_KERNEL
449 
450 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
451 
452 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SAXS_HAS_BOOST_FILESYSTEM
453 
454 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
455 
456 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_example.IMP_SAXS_HAS_BOOST_RANDOM
457 
458 IMP_SAXS_HAS_BOOST_REGEX = _IMP_example.IMP_SAXS_HAS_BOOST_REGEX
459 
460 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_example.IMP_SAXS_HAS_BOOST_SYSTEM
461 
462 IMP_SAXS_HAS_CGAL = _IMP_example.IMP_SAXS_HAS_CGAL
463 
464 IMP_SAXS_HAS_HDF5 = _IMP_example.IMP_SAXS_HAS_HDF5
465 
466 IMP_SAXS_HAS_NUMPY = _IMP_example.IMP_SAXS_HAS_NUMPY
467 
468 IMP_SAXS_HAS_PYTHON_IHM = _IMP_example.IMP_SAXS_HAS_PYTHON_IHM
469 
470 IMPSAXS_SHOW_WARNINGS = _IMP_example.IMPSAXS_SHOW_WARNINGS
471 
472 import IMP.saxs
473 IMP_ISD_HAS_IMP_CGAL = _IMP_example.IMP_ISD_HAS_IMP_CGAL
474 
475 IMP_ISD_HAS_IMP_DISPLAY = _IMP_example.IMP_ISD_HAS_IMP_DISPLAY
476 
477 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
478 
479 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ISD_HAS_BOOST_FILESYSTEM
480 
481 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
482 
483 IMP_ISD_HAS_BOOST_RANDOM = _IMP_example.IMP_ISD_HAS_BOOST_RANDOM
484 
485 IMP_ISD_HAS_BOOST_REGEX = _IMP_example.IMP_ISD_HAS_BOOST_REGEX
486 
487 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_example.IMP_ISD_HAS_BOOST_SYSTEM
488 
489 IMP_ISD_HAS_CGAL = _IMP_example.IMP_ISD_HAS_CGAL
490 
491 IMP_ISD_HAS_HDF5 = _IMP_example.IMP_ISD_HAS_HDF5
492 
493 IMP_ISD_HAS_NUMPY = _IMP_example.IMP_ISD_HAS_NUMPY
494 
495 IMP_ISD_HAS_PYTHON_IHM = _IMP_example.IMP_ISD_HAS_PYTHON_IHM
496 
497 IMPISD_SHOW_WARNINGS = _IMP_example.IMPISD_SHOW_WARNINGS
498 
499 import IMP.isd
500 IMP_RMF_HAS_IMP_CGAL = _IMP_example.IMP_RMF_HAS_IMP_CGAL
501 
502 IMP_RMF_HAS_IMP_EM = _IMP_example.IMP_RMF_HAS_IMP_EM
503 
504 IMP_RMF_HAS_IMP_SAXS = _IMP_example.IMP_RMF_HAS_IMP_SAXS
505 
506 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
507 
508 IMP_RMF_HAS_IMP_STATISTICS = _IMP_example.IMP_RMF_HAS_IMP_STATISTICS
509 
510 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_FILESYSTEM
511 
512 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
513 
514 IMP_RMF_HAS_BOOST_RANDOM = _IMP_example.IMP_RMF_HAS_BOOST_RANDOM
515 
516 IMP_RMF_HAS_BOOST_REGEX = _IMP_example.IMP_RMF_HAS_BOOST_REGEX
517 
518 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_SYSTEM
519 
520 IMP_RMF_HAS_CGAL = _IMP_example.IMP_RMF_HAS_CGAL
521 
522 IMP_RMF_HAS_HDF5 = _IMP_example.IMP_RMF_HAS_HDF5
523 
524 IMP_RMF_HAS_NUMPY = _IMP_example.IMP_RMF_HAS_NUMPY
525 
526 IMP_RMF_HAS_PYTHON_IHM = _IMP_example.IMP_RMF_HAS_PYTHON_IHM
527 
528 IMPRMF_SHOW_WARNINGS = _IMP_example.IMPRMF_SHOW_WARNINGS
529 
530 import IMP.rmf
531 import RMF
532 IMP_DOMINO_HAS_IMP_ATOM = _IMP_example.IMP_DOMINO_HAS_IMP_ATOM
533 
534 IMP_DOMINO_HAS_IMP_CGAL = _IMP_example.IMP_DOMINO_HAS_IMP_CGAL
535 
536 IMP_DOMINO_HAS_IMP_EM = _IMP_example.IMP_DOMINO_HAS_IMP_EM
537 
538 IMP_DOMINO_HAS_IMP_ISD = _IMP_example.IMP_DOMINO_HAS_IMP_ISD
539 
540 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_example.IMP_DOMINO_HAS_IMP_KERNEL
541 
542 IMP_DOMINO_HAS_IMP_RMF = _IMP_example.IMP_DOMINO_HAS_IMP_RMF
543 
544 IMP_DOMINO_HAS_IMP_SAXS = _IMP_example.IMP_DOMINO_HAS_IMP_SAXS
545 
546 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
547 
548 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_FILESYSTEM
549 
550 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
551 
552 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_example.IMP_DOMINO_HAS_BOOST_RANDOM
553 
554 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_example.IMP_DOMINO_HAS_BOOST_REGEX
555 
556 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_SYSTEM
557 
558 IMP_DOMINO_HAS_CGAL = _IMP_example.IMP_DOMINO_HAS_CGAL
559 
560 IMP_DOMINO_HAS_HDF5 = _IMP_example.IMP_DOMINO_HAS_HDF5
561 
562 IMP_DOMINO_HAS_NUMPY = _IMP_example.IMP_DOMINO_HAS_NUMPY
563 
564 IMP_DOMINO_HAS_RMF = _IMP_example.IMP_DOMINO_HAS_RMF
565 
566 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_example.IMP_DOMINO_HAS_PYTHON_IHM
567 
568 IMPDOMINO_SHOW_WARNINGS = _IMP_example.IMPDOMINO_SHOW_WARNINGS
569 
570 import RMF_HDF5
571 import IMP.domino
572 IMP_EXAMPLE_HAS_IMP_ALGEBRA = _IMP_example.IMP_EXAMPLE_HAS_IMP_ALGEBRA
573 
574 IMP_EXAMPLE_HAS_IMP_CGAL = _IMP_example.IMP_EXAMPLE_HAS_IMP_CGAL
575 
576 IMP_EXAMPLE_HAS_IMP_DISPLAY = _IMP_example.IMP_EXAMPLE_HAS_IMP_DISPLAY
577 
578 IMP_EXAMPLE_HAS_IMP_EM = _IMP_example.IMP_EXAMPLE_HAS_IMP_EM
579 
580 IMP_EXAMPLE_HAS_IMP_ISD = _IMP_example.IMP_EXAMPLE_HAS_IMP_ISD
581 
582 IMP_EXAMPLE_HAS_IMP_KERNEL = _IMP_example.IMP_EXAMPLE_HAS_IMP_KERNEL
583 
584 IMP_EXAMPLE_HAS_IMP_RMF = _IMP_example.IMP_EXAMPLE_HAS_IMP_RMF
585 
586 IMP_EXAMPLE_HAS_IMP_SAXS = _IMP_example.IMP_EXAMPLE_HAS_IMP_SAXS
587 
588 IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR
589 
590 IMP_EXAMPLE_HAS_IMP_STATISTICS = _IMP_example.IMP_EXAMPLE_HAS_IMP_STATISTICS
591 
592 IMP_EXAMPLE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_FILESYSTEM
593 
594 IMP_EXAMPLE_HAS_BOOST_GRAPH = _IMP_example.IMP_EXAMPLE_HAS_BOOST_GRAPH
595 
596 IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS
597 
598 IMP_EXAMPLE_HAS_BOOST_RANDOM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_RANDOM
599 
600 IMP_EXAMPLE_HAS_BOOST_REGEX = _IMP_example.IMP_EXAMPLE_HAS_BOOST_REGEX
601 
602 IMP_EXAMPLE_HAS_BOOST_SYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_SYSTEM
603 
604 IMP_EXAMPLE_HAS_CGAL = _IMP_example.IMP_EXAMPLE_HAS_CGAL
605 
606 IMP_EXAMPLE_HAS_HDF5 = _IMP_example.IMP_EXAMPLE_HAS_HDF5
607 
608 IMP_EXAMPLE_HAS_NUMPY = _IMP_example.IMP_EXAMPLE_HAS_NUMPY
609 
610 IMP_EXAMPLE_HAS_RMF = _IMP_example.IMP_EXAMPLE_HAS_RMF
611 
612 IMP_EXAMPLE_HAS_PYTHON_IHM = _IMP_example.IMP_EXAMPLE_HAS_PYTHON_IHM
613 
614 IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY = _IMP_example.IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY
615 
616 IMPEXAMPLE_SHOW_WARNINGS = _IMP_example.IMPEXAMPLE_SHOW_WARNINGS
617 
618 
619 _object_types.append("ExampleRestraint")
620 
621 
622 def _object_cast_to_ExampleRestraint(o):
623  r"""_object_cast_to_ExampleRestraint(Object o) -> ExampleRestraint"""
624  return _IMP_example._object_cast_to_ExampleRestraint(o)
625 
626 def ExampleDecorators(l=[]):
627  return [ExampleDecorator(x) for x in l]
628 _plural_types.append("ExampleDecorators")
629 
630 
631 _value_types.append("ExampleDecorator")
632 
633 
634 _object_types.append("ExampleUnaryFunction")
635 
636 
637 def _object_cast_to_ExampleUnaryFunction(o):
638  r"""_object_cast_to_ExampleUnaryFunction(Object o) -> ExampleUnaryFunction"""
639  return _IMP_example._object_cast_to_ExampleUnaryFunction(o)
640 
641 _object_types.append("ExampleSingletonModifier")
642 
643 
644 def _object_cast_to_ExampleSingletonModifier(o):
645  r"""_object_cast_to_ExampleSingletonModifier(Object o) -> ExampleSingletonModifier"""
646  return _IMP_example._object_cast_to_ExampleSingletonModifier(o)
647 
648 _object_types.append("ExamplePairScore")
649 
650 
651 def _object_cast_to_ExamplePairScore(o):
652  r"""_object_cast_to_ExamplePairScore(Object o) -> ExamplePairScore"""
653  return _IMP_example._object_cast_to_ExamplePairScore(o)
654 
655 _object_types.append("ExampleSubsetFilterTable")
656 
657 
658 def _object_cast_to_ExampleSubsetFilterTable(o):
659  r"""_object_cast_to_ExampleSubsetFilterTable(Object o) -> ExampleSubsetFilterTable"""
660  return _IMP_example._object_cast_to_ExampleSubsetFilterTable(o)
661 
662 _object_types.append("ExampleConstraint")
663 
664 
665 def _object_cast_to_ExampleConstraint(o):
666  r"""_object_cast_to_ExampleConstraint(Object o) -> ExampleConstraint"""
667  return _IMP_example._object_cast_to_ExampleConstraint(o)
668 
669 _object_types.append("ExampleObject")
670 
671 
672 def _object_cast_to_ExampleObject(o):
673  r"""_object_cast_to_ExampleObject(Object o) -> ExampleObject"""
674  return _IMP_example._object_cast_to_ExampleObject(o)
675 
676 ExampleTemplateClass3Ds=list
677 _plural_types.append("ExampleTemplateClass3Ds")
678 _value_types.append("ExampleTemplateClass3D")
679 
680 
681 def create_model_and_particles():
682  m = IMP.Model()
685  IMP.algebra.Vector3D(10,10,10))
686  for i in range(0,100):
687  p = m.add_particle("p")
688  sc.add(p)
691  d.set_coordinates_are_optimized(True)
692  return (m, sc)
693 
694 
695 
697  """An example restraint written in Python.
698  This should be functionally equivalent to the C++ ExampleRestraint.
699  """
700  def __init__(self, m, p, k):
701  IMP.Restraint.__init__(self, m, "PythonExampleRestraint%1%")
702  self.p, self.k = p, k
703 
704  def do_add_score_and_derivatives(self, sa):
705  d = IMP.core.XYZ(self.get_model(), self.p)
706  score = .5 * self.k * d.get_z() * d.get_z()
707  if sa.get_derivative_accumulator():
708  deriv = self.k * d.get_z()
709  d.add_to_derivative(2, deriv, sa.get_derivative_accumulator())
710  sa.add_score(score)
711 
712  def do_get_inputs(self):
713  return [self.get_model().get_particle(self.p)]
714 
715 
716 
717 
719  """An example PairScore written in Python.
720  This should be functionally equivalent to the C++ ExamplePairScore.
721  """
722  def __init__(self, x0, k):
723  IMP.PairScore.__init__(self)
724  self.x0, self.k = x0, k
725 
726  def evaluate_index(self, m, pip, da):
727  d0 = IMP.core.XYZ(m, pip[0])
728  d1 = IMP.core.XYZ(m, pip[1])
729  diff = (d0.get_coordinates()
730  - d1.get_coordinates()).get_magnitude() - self.x0
731  score = .5 * self.k * diff * diff
732  if da:
733 # derivatives are requested
734  delta = d0.get_coordinates() - d1.get_coordinates()
735  udelta = delta.get_unit_vector()
736  dv = self.k * diff
737  d0.add_to_derivatives(udelta * dv, da)
738  d1.add_to_derivatives(-udelta * dv, da)
739  return score
740 
741  def do_get_inputs(self, m, pis):
742  return IMP.get_particles(m, pis)
743 
744 
745 
746 
748  """An example UnaryFunction written in Python.
749  This should be functionally equivalent to the C++ ExampleUnaryFunction.
750  """
751  def __init__(self, center, k):
752  IMP.UnaryFunction.__init__(self)
753  self.center, self.k = center, k
754 
755  def evaluate_with_derivative(self, feature):
756  return (self.evaluate(feature), self.k * (feature - self.center))
757 
758  def evaluate(self, feature):
759  return .5 * self.k * (feature - self.center) * (feature - self.center)
760 
761 
762 
763 
765  """An example Constraint written in Python.
766  This should be functionally equivalent to the C++ ExampleConstraint.
767  """
768 
769  k = None
770 
771  def __init__(self, p):
772  IMP.Constraint.__init__(self, p.get_model(), "ExampleConstraint%1%")
773  self.p = p
774  if self.k is None:
775  PythonExampleConstraint.k = IMP.IntKey("Constraint key")
776  if not p.has_attribute(self.k):
777  p.add_attribute(self.k, 0)
778 
779  def do_update_attributes(self):
780  self.p.set_value(self.k, self.p.get_value(self.k) + 1)
781 
782  def do_update_derivatives(self, da):
783  pass
784 
785  def do_get_inputs(self):
786  return [self.p]
787 
788  def do_get_outputs(self):
789  return [self.p]
790 
791 
792 
793 
795  """An example SingletonModifier written in Python.
796  This should be functionally equivalent to the C++
797  ExampleSingletonModifier.
798  """
799 
800  def __init__(self, bb):
801  IMP.SingletonModifier.__init__(self, "ExampleSingletonModifier%1%")
802  self.bb = bb
803 
804  def apply_index(self, m, pi):
805  d = IMP.core.XYZ(m, pi)
806  for i in range(3):
807 # shift the coordinate until it is in the box
808  while d.get_coordinate(i) < self.bb.get_corner(0)[i]:
809  d.set_coordinate(i,d.get_coordinate(i) + \
810  (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
811  while d.get_coordinate(i) > self.bb.get_corner(1)[i]:
812  d.set_coordinate(i,d.get_coordinate(i) - \
813  (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
814 
815  def do_get_inputs(self, m, pis):
816  return IMP.get_particles(m, pis)
817 
818  def do_get_outputs(self, m, pis):
819  return self.do_get_inputs(m, pis)
820 
821 
823  r"""Proxy of C++ IMP::example::ExampleRestraint class."""
824 
825  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
826 
827  def __init__(self, *args):
828  r"""
829  __init__(ExampleRestraint self, Model m, ParticleIndex p, double k) -> ExampleRestraint
830  __init__(ExampleRestraint self) -> ExampleRestraint
831  """
832  _IMP_example.ExampleRestraint_swiginit(self, _IMP_example.new_ExampleRestraint(*args))
833 
834  def do_add_score_and_derivatives(self, sa):
835  r"""do_add_score_and_derivatives(ExampleRestraint self, ScoreAccumulator sa)"""
836  return _IMP_example.ExampleRestraint_do_add_score_and_derivatives(self, sa)
837 
838  def do_get_inputs(self):
839  r"""do_get_inputs(ExampleRestraint self) -> IMP::ModelObjectsTemp"""
840  return _IMP_example.ExampleRestraint_do_get_inputs(self)
841 
842  def get_version_info(self):
843  r"""get_version_info(ExampleRestraint self) -> VersionInfo"""
844  return _IMP_example.ExampleRestraint_get_version_info(self)
845  __swig_destroy__ = _IMP_example.delete_ExampleRestraint
846 
847  def __str__(self):
848  r"""__str__(ExampleRestraint self) -> std::string"""
849  return _IMP_example.ExampleRestraint___str__(self)
850 
851  def __repr__(self):
852  r"""__repr__(ExampleRestraint self) -> std::string"""
853  return _IMP_example.ExampleRestraint___repr__(self)
854 
855  @staticmethod
856  def get_from(o):
857  return _object_cast_to_ExampleRestraint(o)
858 
859 
860  def _get_as_binary(self):
861  r"""_get_as_binary(ExampleRestraint self) -> PyObject *"""
862  return _IMP_example.ExampleRestraint__get_as_binary(self)
863 
864  def _set_from_binary(self, p):
865  r"""_set_from_binary(ExampleRestraint self, PyObject * p)"""
866  return _IMP_example.ExampleRestraint__set_from_binary(self, p)
867 
868  def __getstate__(self):
869  p = self._get_as_binary()
870  if len(self.__dict__) > 1:
871  d = self.__dict__.copy()
872  del d['this']
873  p = (d, p)
874  return p
875 
876  def __setstate__(self, p):
877  if not hasattr(self, 'this'):
878  self.__init__()
879  if isinstance(p, tuple):
880  d, p = p
881  self.__dict__.update(d)
882  return self._set_from_binary(p)
883 
884 
885 # Register ExampleRestraint in _IMP_example:
886 _IMP_example.ExampleRestraint_swigregister(ExampleRestraint)
888  r"""Proxy of C++ IMP::example::ExampleDecorator class."""
889 
890  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
891 
892  def get_decorator_name(self):
893  r"""get_decorator_name(ExampleDecorator self) -> std::string"""
894  return _IMP_example.ExampleDecorator_get_decorator_name(self)
895 
896  def set_decorator_name(self, nm):
897  r"""set_decorator_name(ExampleDecorator self, std::string nm)"""
898  return _IMP_example.ExampleDecorator_set_decorator_name(self, nm)
899 
900  def __init__(self, *args):
901  r"""
902  __init__(ExampleDecorator self) -> ExampleDecorator
903  __init__(ExampleDecorator self, Model m, ParticleIndex id) -> ExampleDecorator
904  __init__(ExampleDecorator self, _ParticleAdaptor d) -> ExampleDecorator
905  """
906  _IMP_example.ExampleDecorator_swiginit(self, _IMP_example.new_ExampleDecorator(*args))
907 
908  @staticmethod
909  def get_is_setup(*args):
910  r"""
911  get_is_setup(Model m, ParticleIndex pi) -> bool
912  get_is_setup(_ParticleAdaptor p) -> bool
913  """
914  return _IMP_example.ExampleDecorator_get_is_setup(*args)
915 
916  def show(self, *args):
917  r"""show(ExampleDecorator self, _ostream out=std::cout)"""
918  return _IMP_example.ExampleDecorator_show(self, *args)
919 
920  @staticmethod
921  def setup_particle(*args):
922  r"""
923  setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
924  setup_particle(_ParticleAdaptor pa, std::string name) -> ExampleDecorator
925  """
926  return _IMP_example.ExampleDecorator_setup_particle(*args)
927 
928  def add_attribute(self, *args):
929  r"""
930  add_attribute(ExampleDecorator self, FloatKey k, IMP::Float v, bool opt)
931  add_attribute(ExampleDecorator self, FloatKey a0, IMP::Float a1)
932  add_attribute(ExampleDecorator self, IntKey a0, IMP::Int a1)
933  add_attribute(ExampleDecorator self, FloatsKey a0, IMP::Floats a1)
934  add_attribute(ExampleDecorator self, IntsKey a0, IMP::Ints a1)
935  add_attribute(ExampleDecorator self, StringKey a0, IMP::String a1)
936  add_attribute(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
937  add_attribute(ExampleDecorator self, ObjectKey a0, Object a1)
938  """
939  return _IMP_example.ExampleDecorator_add_attribute(self, *args)
940 
941  def get_value(self, *args):
942  r"""
943  get_value(ExampleDecorator self, FloatKey a0) -> IMP::Float
944  get_value(ExampleDecorator self, IntKey a0) -> IMP::Int
945  get_value(ExampleDecorator self, FloatsKey a0) -> IMP::Floats
946  get_value(ExampleDecorator self, IntsKey a0) -> IMP::Ints
947  get_value(ExampleDecorator self, StringKey a0) -> IMP::String
948  get_value(ExampleDecorator self, ParticleIndexKey a0) -> Particle
949  get_value(ExampleDecorator self, ObjectKey a0) -> Object
950  """
951  return _IMP_example.ExampleDecorator_get_value(self, *args)
952 
953  def set_value(self, *args):
954  r"""
955  set_value(ExampleDecorator self, FloatKey a0, IMP::Float a1)
956  set_value(ExampleDecorator self, IntKey a0, IMP::Int a1)
957  set_value(ExampleDecorator self, FloatsKey a0, IMP::Floats a1)
958  set_value(ExampleDecorator self, IntsKey a0, IMP::Ints a1)
959  set_value(ExampleDecorator self, StringKey a0, IMP::String a1)
960  set_value(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
961  set_value(ExampleDecorator self, ObjectKey a0, Object a1)
962  """
963  return _IMP_example.ExampleDecorator_set_value(self, *args)
964 
965  def remove_attribute(self, *args):
966  r"""
967  remove_attribute(ExampleDecorator self, FloatKey a0)
968  remove_attribute(ExampleDecorator self, IntKey a0)
969  remove_attribute(ExampleDecorator self, FloatsKey a0)
970  remove_attribute(ExampleDecorator self, IntsKey a0)
971  remove_attribute(ExampleDecorator self, StringKey a0)
972  remove_attribute(ExampleDecorator self, ParticleIndexKey a0)
973  remove_attribute(ExampleDecorator self, ObjectKey a0)
974  """
975  return _IMP_example.ExampleDecorator_remove_attribute(self, *args)
976 
977  def has_attribute(self, *args):
978  r"""
979  has_attribute(ExampleDecorator self, FloatKey a0) -> bool
980  has_attribute(ExampleDecorator self, IntKey a0) -> bool
981  has_attribute(ExampleDecorator self, FloatsKey a0) -> bool
982  has_attribute(ExampleDecorator self, IntsKey a0) -> bool
983  has_attribute(ExampleDecorator self, StringKey a0) -> bool
984  has_attribute(ExampleDecorator self, ParticleIndexKey a0) -> bool
985  has_attribute(ExampleDecorator self, ObjectKey a0) -> bool
986  """
987  return _IMP_example.ExampleDecorator_has_attribute(self, *args)
988 
989  def get_derivative(self, a0):
990  r"""get_derivative(ExampleDecorator self, FloatKey a0) -> double"""
991  return _IMP_example.ExampleDecorator_get_derivative(self, a0)
992 
993  def get_name(self):
994  r"""get_name(ExampleDecorator self) -> std::string"""
995  return _IMP_example.ExampleDecorator_get_name(self)
996 
997  def clear_caches(self):
998  r"""clear_caches(ExampleDecorator self)"""
999  return _IMP_example.ExampleDecorator_clear_caches(self)
1000 
1001  def set_name(self, a0):
1002  r"""set_name(ExampleDecorator self, std::string a0)"""
1003  return _IMP_example.ExampleDecorator_set_name(self, a0)
1004 
1005  def set_check_level(self, a0):
1006  r"""set_check_level(ExampleDecorator self, IMP::CheckLevel a0)"""
1007  return _IMP_example.ExampleDecorator_set_check_level(self, a0)
1008 
1009  def add_to_derivative(self, a0, a1, a2):
1010  r"""add_to_derivative(ExampleDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1011  return _IMP_example.ExampleDecorator_add_to_derivative(self, a0, a1, a2)
1012 
1013  def set_is_optimized(self, a0, a1):
1014  r"""set_is_optimized(ExampleDecorator self, FloatKey a0, bool a1)"""
1015  return _IMP_example.ExampleDecorator_set_is_optimized(self, a0, a1)
1016 
1017  def get_is_optimized(self, a0):
1018  r"""get_is_optimized(ExampleDecorator self, FloatKey a0) -> bool"""
1019  return _IMP_example.ExampleDecorator_get_is_optimized(self, a0)
1020 
1021  def get_check_level(self):
1022  r"""get_check_level(ExampleDecorator self) -> IMP::CheckLevel"""
1023  return _IMP_example.ExampleDecorator_get_check_level(self)
1024 
1025  def __eq__(self, *args):
1026  r"""
1027  __eq__(ExampleDecorator self, ExampleDecorator o) -> bool
1028  __eq__(ExampleDecorator self, Particle d) -> bool
1029  """
1030  return _IMP_example.ExampleDecorator___eq__(self, *args)
1031 
1032  def __ne__(self, *args):
1033  r"""
1034  __ne__(ExampleDecorator self, ExampleDecorator o) -> bool
1035  __ne__(ExampleDecorator self, Particle d) -> bool
1036  """
1037  return _IMP_example.ExampleDecorator___ne__(self, *args)
1038 
1039  def __le__(self, *args):
1040  r"""
1041  __le__(ExampleDecorator self, ExampleDecorator o) -> bool
1042  __le__(ExampleDecorator self, Particle d) -> bool
1043  """
1044  return _IMP_example.ExampleDecorator___le__(self, *args)
1045 
1046  def __lt__(self, *args):
1047  r"""
1048  __lt__(ExampleDecorator self, ExampleDecorator o) -> bool
1049  __lt__(ExampleDecorator self, Particle d) -> bool
1050  """
1051  return _IMP_example.ExampleDecorator___lt__(self, *args)
1052 
1053  def __ge__(self, *args):
1054  r"""
1055  __ge__(ExampleDecorator self, ExampleDecorator o) -> bool
1056  __ge__(ExampleDecorator self, Particle d) -> bool
1057  """
1058  return _IMP_example.ExampleDecorator___ge__(self, *args)
1059 
1060  def __gt__(self, *args):
1061  r"""
1062  __gt__(ExampleDecorator self, ExampleDecorator o) -> bool
1063  __gt__(ExampleDecorator self, Particle d) -> bool
1064  """
1065  return _IMP_example.ExampleDecorator___gt__(self, *args)
1066 
1067  def __hash__(self):
1068  r"""__hash__(ExampleDecorator self) -> std::size_t"""
1069  return _IMP_example.ExampleDecorator___hash__(self)
1070 
1071  def __str__(self):
1072  r"""__str__(ExampleDecorator self) -> std::string"""
1073  return _IMP_example.ExampleDecorator___str__(self)
1074 
1075  def __repr__(self):
1076  r"""__repr__(ExampleDecorator self) -> std::string"""
1077  return _IMP_example.ExampleDecorator___repr__(self)
1078 
1079  def _get_as_binary(self):
1080  r"""_get_as_binary(ExampleDecorator self) -> PyObject *"""
1081  return _IMP_example.ExampleDecorator__get_as_binary(self)
1082 
1083  def _set_from_binary(self, p):
1084  r"""_set_from_binary(ExampleDecorator self, PyObject * p)"""
1085  return _IMP_example.ExampleDecorator__set_from_binary(self, p)
1086 
1087  def __getstate__(self):
1088  p = self._get_as_binary()
1089  if len(self.__dict__) > 1:
1090  d = self.__dict__.copy()
1091  del d['this']
1092  p = (d, p)
1093  return p
1094 
1095  def __setstate__(self, p):
1096  if not hasattr(self, 'this'):
1097  self.__init__()
1098  if isinstance(p, tuple):
1099  d, p = p
1100  self.__dict__.update(d)
1101  return self._set_from_binary(p)
1102 
1103  __swig_destroy__ = _IMP_example.delete_ExampleDecorator
1104 
1105 # Register ExampleDecorator in _IMP_example:
1106 _IMP_example.ExampleDecorator_swigregister(ExampleDecorator)
1107 
1108 def __lshift__(out, n):
1109  r"""__lshift__(_ostream out, ExampleDecorator n) -> _ostream"""
1110  return _IMP_example.__lshift__(out, n)
1112  r"""Proxy of C++ IMP::example::ExampleUnaryFunction class."""
1113 
1114  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1115 
1116  def __init__(self, *args):
1117  r"""
1118  __init__(ExampleUnaryFunction self, IMP::Float center, IMP::Float k) -> ExampleUnaryFunction
1119  __init__(ExampleUnaryFunction self) -> ExampleUnaryFunction
1120  """
1121  _IMP_example.ExampleUnaryFunction_swiginit(self, _IMP_example.new_ExampleUnaryFunction(*args))
1122 
1123  def get_version_info(self):
1124  r"""get_version_info(ExampleUnaryFunction self) -> VersionInfo"""
1125  return _IMP_example.ExampleUnaryFunction_get_version_info(self)
1126  __swig_destroy__ = _IMP_example.delete_ExampleUnaryFunction
1127 
1128  def __str__(self):
1129  r"""__str__(ExampleUnaryFunction self) -> std::string"""
1130  return _IMP_example.ExampleUnaryFunction___str__(self)
1131 
1132  def __repr__(self):
1133  r"""__repr__(ExampleUnaryFunction self) -> std::string"""
1134  return _IMP_example.ExampleUnaryFunction___repr__(self)
1135 
1136  @staticmethod
1137  def get_from(o):
1138  return _object_cast_to_ExampleUnaryFunction(o)
1139 
1140 
1141  def _get_as_binary(self):
1142  r"""_get_as_binary(ExampleUnaryFunction self) -> PyObject *"""
1143  return _IMP_example.ExampleUnaryFunction__get_as_binary(self)
1144 
1145  def _set_from_binary(self, p):
1146  r"""_set_from_binary(ExampleUnaryFunction self, PyObject * p)"""
1147  return _IMP_example.ExampleUnaryFunction__set_from_binary(self, p)
1148 
1149  def __getstate__(self):
1150  p = self._get_as_binary()
1151  if len(self.__dict__) > 1:
1152  d = self.__dict__.copy()
1153  del d['this']
1154  p = (d, p)
1155  return p
1156 
1157  def __setstate__(self, p):
1158  if not hasattr(self, 'this'):
1159  self.__init__()
1160  if isinstance(p, tuple):
1161  d, p = p
1162  self.__dict__.update(d)
1163  return self._set_from_binary(p)
1164 
1165 
1166 # Register ExampleUnaryFunction in _IMP_example:
1167 _IMP_example.ExampleUnaryFunction_swigregister(ExampleUnaryFunction)
1168 class ExampleObject(IMP.Object):
1169  r"""Proxy of C++ IMP::example::ExampleObject class."""
1170 
1171  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1172 
1173  def __init__(self, *args):
1174  r"""
1175  __init__(ExampleObject self, IMP::Floats const & data) -> ExampleObject
1176  __init__(ExampleObject self) -> ExampleObject
1177  """
1178  _IMP_example.ExampleObject_swiginit(self, _IMP_example.new_ExampleObject(*args))
1179 
1180  def get_data(self, i):
1181  r"""get_data(ExampleObject self, unsigned int i) -> double"""
1182  return _IMP_example.ExampleObject_get_data(self, i)
1183 
1184  def get_version_info(self):
1185  r"""get_version_info(ExampleObject self) -> VersionInfo"""
1186  return _IMP_example.ExampleObject_get_version_info(self)
1187  __swig_destroy__ = _IMP_example.delete_ExampleObject
1188 
1189  def __str__(self):
1190  r"""__str__(ExampleObject self) -> std::string"""
1191  return _IMP_example.ExampleObject___str__(self)
1192 
1193  def __repr__(self):
1194  r"""__repr__(ExampleObject self) -> std::string"""
1195  return _IMP_example.ExampleObject___repr__(self)
1196 
1197  @staticmethod
1198  def get_from(o):
1199  return _object_cast_to_ExampleObject(o)
1200 
1201 
1202  def _get_as_binary(self):
1203  r"""_get_as_binary(ExampleObject self) -> PyObject *"""
1204  return _IMP_example.ExampleObject__get_as_binary(self)
1205 
1206  def _set_from_binary(self, p):
1207  r"""_set_from_binary(ExampleObject self, PyObject * p)"""
1208  return _IMP_example.ExampleObject__set_from_binary(self, p)
1209 
1210  def __getstate__(self):
1211  p = self._get_as_binary()
1212  if len(self.__dict__) > 1:
1213  d = self.__dict__.copy()
1214  del d['this']
1215  p = (d, p)
1216  return p
1217 
1218  def __setstate__(self, p):
1219  if not hasattr(self, 'this'):
1220  self.__init__()
1221  if isinstance(p, tuple):
1222  d, p = p
1223  self.__dict__.update(d)
1224  return self._set_from_binary(p)
1225 
1226 
1227 # Register ExampleObject in _IMP_example:
1228 _IMP_example.ExampleObject_swigregister(ExampleObject)
1230  r"""Proxy of C++ IMP::example::ExampleSingletonModifier class."""
1231 
1232  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1233 
1234  def __init__(self, *args):
1235  r"""
1236  __init__(ExampleSingletonModifier self, BoundingBox3D bb) -> ExampleSingletonModifier
1237  __init__(ExampleSingletonModifier self) -> ExampleSingletonModifier
1238  """
1239  _IMP_example.ExampleSingletonModifier_swiginit(self, _IMP_example.new_ExampleSingletonModifier(*args))
1240 
1241  def do_get_inputs(self, m, pis):
1242  r"""do_get_inputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1243  return _IMP_example.ExampleSingletonModifier_do_get_inputs(self, m, pis)
1244 
1245  def do_get_outputs(self, m, pis):
1246  r"""do_get_outputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1247  return _IMP_example.ExampleSingletonModifier_do_get_outputs(self, m, pis)
1248 
1249  def get_version_info(self):
1250  r"""get_version_info(ExampleSingletonModifier self) -> VersionInfo"""
1251  return _IMP_example.ExampleSingletonModifier_get_version_info(self)
1252  __swig_destroy__ = _IMP_example.delete_ExampleSingletonModifier
1253 
1254  def __str__(self):
1255  r"""__str__(ExampleSingletonModifier self) -> std::string"""
1256  return _IMP_example.ExampleSingletonModifier___str__(self)
1257 
1258  def __repr__(self):
1259  r"""__repr__(ExampleSingletonModifier self) -> std::string"""
1260  return _IMP_example.ExampleSingletonModifier___repr__(self)
1261 
1262  @staticmethod
1263  def get_from(o):
1264  return _object_cast_to_ExampleSingletonModifier(o)
1265 
1266 
1267  def _get_as_binary(self):
1268  r"""_get_as_binary(ExampleSingletonModifier self) -> PyObject *"""
1269  return _IMP_example.ExampleSingletonModifier__get_as_binary(self)
1270 
1271  def _set_from_binary(self, p):
1272  r"""_set_from_binary(ExampleSingletonModifier self, PyObject * p)"""
1273  return _IMP_example.ExampleSingletonModifier__set_from_binary(self, p)
1274 
1275  def __getstate__(self):
1276  p = self._get_as_binary()
1277  if len(self.__dict__) > 1:
1278  d = self.__dict__.copy()
1279  del d['this']
1280  p = (d, p)
1281  return p
1282 
1283  def __setstate__(self, p):
1284  if not hasattr(self, 'this'):
1285  self.__init__()
1286  if isinstance(p, tuple):
1287  d, p = p
1288  self.__dict__.update(d)
1289  return self._set_from_binary(p)
1290 
1291 
1292 # Register ExampleSingletonModifier in _IMP_example:
1293 _IMP_example.ExampleSingletonModifier_swigregister(ExampleSingletonModifier)
1295  r"""Proxy of C++ IMP::example::ExamplePairScore class."""
1296 
1297  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1298 
1299  def __init__(self, *args):
1300  r"""
1301  __init__(ExamplePairScore self, double x0, double k) -> ExamplePairScore
1302  __init__(ExamplePairScore self) -> ExamplePairScore
1303  """
1304  _IMP_example.ExamplePairScore_swiginit(self, _IMP_example.new_ExamplePairScore(*args))
1305 
1306  def do_get_inputs(self, m, pis):
1307  r"""do_get_inputs(ExamplePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1308  return _IMP_example.ExamplePairScore_do_get_inputs(self, m, pis)
1309 
1310  def get_version_info(self):
1311  r"""get_version_info(ExamplePairScore self) -> VersionInfo"""
1312  return _IMP_example.ExamplePairScore_get_version_info(self)
1313  __swig_destroy__ = _IMP_example.delete_ExamplePairScore
1314 
1315  def __str__(self):
1316  r"""__str__(ExamplePairScore self) -> std::string"""
1317  return _IMP_example.ExamplePairScore___str__(self)
1318 
1319  def __repr__(self):
1320  r"""__repr__(ExamplePairScore self) -> std::string"""
1321  return _IMP_example.ExamplePairScore___repr__(self)
1322 
1323  @staticmethod
1324  def get_from(o):
1325  return _object_cast_to_ExamplePairScore(o)
1326 
1327 
1328  def _get_as_binary(self):
1329  r"""_get_as_binary(ExamplePairScore self) -> PyObject *"""
1330  return _IMP_example.ExamplePairScore__get_as_binary(self)
1331 
1332  def _set_from_binary(self, p):
1333  r"""_set_from_binary(ExamplePairScore self, PyObject * p)"""
1334  return _IMP_example.ExamplePairScore__set_from_binary(self, p)
1335 
1336  def __getstate__(self):
1337  p = self._get_as_binary()
1338  if len(self.__dict__) > 1:
1339  d = self.__dict__.copy()
1340  del d['this']
1341  p = (d, p)
1342  return p
1343 
1344  def __setstate__(self, p):
1345  if not hasattr(self, 'this'):
1346  self.__init__()
1347  if isinstance(p, tuple):
1348  d, p = p
1349  self.__dict__.update(d)
1350  return self._set_from_binary(p)
1351 
1352 
1353 # Register ExamplePairScore in _IMP_example:
1354 _IMP_example.ExamplePairScore_swigregister(ExamplePairScore)
1356  r"""Proxy of C++ IMP::example::ExampleSubsetFilterTable class."""
1357 
1358  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1359 
1360  def __init__(self, max_diff, pt):
1361  r"""__init__(ExampleSubsetFilterTable self, unsigned int max_diff, IMP::ParticlesTemp const & pt) -> ExampleSubsetFilterTable"""
1362  _IMP_example.ExampleSubsetFilterTable_swiginit(self, _IMP_example.new_ExampleSubsetFilterTable(max_diff, pt))
1363 
1364  def get_version_info(self):
1365  r"""get_version_info(ExampleSubsetFilterTable self) -> VersionInfo"""
1366  return _IMP_example.ExampleSubsetFilterTable_get_version_info(self)
1367  __swig_destroy__ = _IMP_example.delete_ExampleSubsetFilterTable
1368 
1369  def __str__(self):
1370  r"""__str__(ExampleSubsetFilterTable self) -> std::string"""
1371  return _IMP_example.ExampleSubsetFilterTable___str__(self)
1372 
1373  def __repr__(self):
1374  r"""__repr__(ExampleSubsetFilterTable self) -> std::string"""
1375  return _IMP_example.ExampleSubsetFilterTable___repr__(self)
1376 
1377  @staticmethod
1378  def get_from(o):
1379  return _object_cast_to_ExampleSubsetFilterTable(o)
1380 
1381 
1382 # Register ExampleSubsetFilterTable in _IMP_example:
1383 _IMP_example.ExampleSubsetFilterTable_swigregister(ExampleSubsetFilterTable)
1385  r"""Proxy of C++ IMP::example::ExampleConstraint class."""
1386 
1387  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1388 
1389  def __init__(self, *args):
1390  r"""
1391  __init__(ExampleConstraint self, Particle p) -> ExampleConstraint
1392  __init__(ExampleConstraint self) -> ExampleConstraint
1393  """
1394  _IMP_example.ExampleConstraint_swiginit(self, _IMP_example.new_ExampleConstraint(*args))
1395 
1396  def do_get_inputs(self):
1397  r"""do_get_inputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1398  return _IMP_example.ExampleConstraint_do_get_inputs(self)
1399 
1400  def do_get_outputs(self):
1401  r"""do_get_outputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1402  return _IMP_example.ExampleConstraint_do_get_outputs(self)
1403 
1404  @staticmethod
1405  def get_key():
1406  r"""get_key() -> IntKey"""
1407  return _IMP_example.ExampleConstraint_get_key()
1408 
1409  def get_version_info(self):
1410  r"""get_version_info(ExampleConstraint self) -> VersionInfo"""
1411  return _IMP_example.ExampleConstraint_get_version_info(self)
1412  __swig_destroy__ = _IMP_example.delete_ExampleConstraint
1413 
1414  def __str__(self):
1415  r"""__str__(ExampleConstraint self) -> std::string"""
1416  return _IMP_example.ExampleConstraint___str__(self)
1417 
1418  def __repr__(self):
1419  r"""__repr__(ExampleConstraint self) -> std::string"""
1420  return _IMP_example.ExampleConstraint___repr__(self)
1421 
1422  @staticmethod
1423  def get_from(o):
1424  return _object_cast_to_ExampleConstraint(o)
1425 
1426 
1427  def _get_as_binary(self):
1428  r"""_get_as_binary(ExampleConstraint self) -> PyObject *"""
1429  return _IMP_example.ExampleConstraint__get_as_binary(self)
1430 
1431  def _set_from_binary(self, p):
1432  r"""_set_from_binary(ExampleConstraint self, PyObject * p)"""
1433  return _IMP_example.ExampleConstraint__set_from_binary(self, p)
1434 
1435  def __getstate__(self):
1436  p = self._get_as_binary()
1437  if len(self.__dict__) > 1:
1438  d = self.__dict__.copy()
1439  del d['this']
1440  p = (d, p)
1441  return p
1442 
1443  def __setstate__(self, p):
1444  if not hasattr(self, 'this'):
1445  self.__init__()
1446  if isinstance(p, tuple):
1447  d, p = p
1448  self.__dict__.update(d)
1449  return self._set_from_binary(p)
1450 
1451 
1452 # Register ExampleConstraint in _IMP_example:
1453 _IMP_example.ExampleConstraint_swigregister(ExampleConstraint)
1454 
1455 def get_number_of_incidences(psa, psb, point_distance):
1456  r"""get_number_of_incidences(IMP::ParticlesTemp const & psa, IMP::ParticlesTemp const & psb, double point_distance) -> unsigned int"""
1457  return _IMP_example.get_number_of_incidences(psa, psb, point_distance)
1458 
1459 def create_chain_restraint(m, ps, length_factor, k, name):
1460  r"""create_chain_restraint(Model m, IMP::ParticleIndexes const & ps, double length_factor, double k, std::string name) -> Restraint"""
1461  return _IMP_example.create_chain_restraint(m, ps, length_factor, k, name)
1462 
1463 def create_excluded_volume(m, ps, k, name):
1464  r"""create_excluded_volume(Model m, IMP::ParticleIndexes const & ps, double k, std::string name) -> Restraint"""
1465  return _IMP_example.create_excluded_volume(m, ps, k, name)
1466 class ExampleTemplateClass3D(object):
1467  r"""Proxy of C++ IMP::example::ExampleTemplateClassD< 3 > class."""
1468 
1469  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
1470 
1471  def __init__(self, *args):
1472  r"""
1473  __init__(ExampleTemplateClass3D self) -> ExampleTemplateClass3D
1474  __init__(ExampleTemplateClass3D self, Vector3D a, Vector3D b) -> ExampleTemplateClass3D
1475  """
1476  _IMP_example.ExampleTemplateClass3D_swiginit(self, _IMP_example.new_ExampleTemplateClass3D(*args))
1477 
1478  def get_point(self, i):
1479  r"""get_point(ExampleTemplateClass3D self, unsigned int i) -> Vector3D"""
1480  return _IMP_example.ExampleTemplateClass3D_get_point(self, i)
1481 
1482  def show(self, *args):
1483  r"""show(ExampleTemplateClass3D self, _ostream out=std::cout)"""
1484  return _IMP_example.ExampleTemplateClass3D_show(self, *args)
1485 
1486  def __str__(self):
1487  r"""__str__(ExampleTemplateClass3D self) -> std::string"""
1488  return _IMP_example.ExampleTemplateClass3D___str__(self)
1489 
1490  def __repr__(self):
1491  r"""__repr__(ExampleTemplateClass3D self) -> std::string"""
1492  return _IMP_example.ExampleTemplateClass3D___repr__(self)
1493  __swig_destroy__ = _IMP_example.delete_ExampleTemplateClass3D
1494 
1495 # Register ExampleTemplateClass3D in _IMP_example:
1496 _IMP_example.ExampleTemplateClass3D_swigregister(ExampleTemplateClass3D)
1497 
1498 def get_module_version():
1499  r"""get_module_version() -> std::string const"""
1500  return _IMP_example.get_module_version()
1501 
1502 def get_example_path(fname):
1503  r"""get_example_path(std::string fname) -> std::string"""
1504  return _IMP_example.get_example_path(fname)
1505 
1506 def get_data_path(fname):
1507  r"""get_data_path(std::string fname) -> std::string"""
1508  return _IMP_example.get_data_path(fname)
1509 
1510 from . import _version_check
1511 _version_check.check_version(get_module_version())
1512 __version__ = get_module_version()
1513 
1514 
unsigned int get_number_of_incidences(const ParticlesTemp &psa, const ParticlesTemp &psb, double point_distance)
Definition: counting.h:23
A base class for modifiers of ParticlesTemp.
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:44
virtual double evaluate(double feature) const
Calculate score with respect to the given feature.
Definition: UnaryFunction.h:35
An example PairScore written in Python.
An example SingletonModifier written in Python.
Various classes to hold sets of particles.
static XYZR setup_particle(Model *m, ParticleIndex pi)
Definition: XYZR.h:48
An example UnaryFunction written in Python.
Make CGAL functionality available to IMP.
A line segment templated on the dimension.
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
Get the particles from a list of indexes.
virtual void clear_caches()
Definition: Object.h:270
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the outputs.
Composable functors to implement scores via compile-time composition.
Restraint * create_excluded_volume(Model *m, const ParticleIndexes &ps, double k, std::string name)
Vector3D get_random_vector_in(const Cylinder3D &c)
Generate a random vector in a cylinder with uniform density.
Code to compute statistical measures.
Implement a constraint on the Model.
Definition: Constraint.h:49
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:86
An example simple object which is reference counted.
Definition: ExampleObject.h:31
A simple decorator which adds a name to a particle.
An example Constraint written in Python.
Common base class for heavy weight IMP objects.
Definition: Object.h:111
Store a list of ParticleIndexes.
An example restraint written in Python.
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the inputs.
Restrain a particle to be in the x,y plane.
Basic utilities for handling cryo-electron microscopy 3D density maps.
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h:119
virtual ModelObjectsTemp do_get_outputs() const =0
Basic functionality that is expected to be used by a wide variety of IMP users.
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
virtual void apply_index(Model *m, ParticleIndex v) const =0
std::string get_module_version()
Return the version of this module, as a string.
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Definition: Object.h:206
virtual DerivativePair evaluate_with_derivative(double feature) const
Calculate score and derivative with respect to the given feature.
Definition: UnaryFunction.h:50
VectorD< 3 > Vector3D
Definition: VectorD.h:425
void set_check_level(CheckLevel l)
Apply a harmonic to the distance between two particles.
Restraint * create_chain_restraint(Model *m, const ParticleIndexes &ps, double length_factor, double k, std::string name)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
Model * get_model() const
Definition: ModelObject.h:64
A trivial constraint that just increments a counter.
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Support for the RMF file format for storing hierarchical molecular data and markup.
Abstract single variable functor class for score functions.
Definition: UnaryFunction.h:27
virtual ModelObjectsTemp do_get_inputs() const =0
Divide-and-conquer inferential optimization in discrete space.
virtual double evaluate_index(Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da) const =0
Compute the score and the derivative if needed.
Support for small angle X-ray scattering (SAXS) data.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:56