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IMP Reference Guide  2.5.0
The Integrative Modeling Platform
example/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.5
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 # This wrapper is part of IMP,
8 # Copyright 2007-2015 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info
16 if version_info >= (2, 6, 0):
17  def swig_import_helper():
18  from os.path import dirname
19  import imp
20  fp = None
21  try:
22  fp, pathname, description = imp.find_module('_IMP_example', [dirname(__file__)])
23  except ImportError:
24  import _IMP_example
25  return _IMP_example
26  if fp is not None:
27  try:
28  _mod = imp.load_module('_IMP_example', fp, pathname, description)
29  finally:
30  fp.close()
31  return _mod
32  _IMP_example = swig_import_helper()
33  del swig_import_helper
34 else:
35  import _IMP_example
36 del version_info
37 try:
38  _swig_property = property
39 except NameError:
40  pass # Python < 2.2 doesn't have 'property'.
41 
42 
43 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
44  if (name == "thisown"):
45  return self.this.own(value)
46  if (name == "this"):
47  if type(value).__name__ == 'SwigPyObject':
48  self.__dict__[name] = value
49  return
50  method = class_type.__swig_setmethods__.get(name, None)
51  if method:
52  return method(self, value)
53  if (not static):
54  object.__setattr__(self, name, value)
55  else:
56  raise AttributeError("You cannot add attributes to %s" % self)
57 
58 
59 def _swig_setattr(self, class_type, name, value):
60  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
61 
62 
63 def _swig_getattr_nondynamic(self, class_type, name, static=1):
64  if (name == "thisown"):
65  return self.this.own()
66  method = class_type.__swig_getmethods__.get(name, None)
67  if method:
68  return method(self)
69  if (not static):
70  return object.__getattr__(self, name)
71  else:
72  raise AttributeError(name)
73 
74 def _swig_getattr(self, class_type, name):
75  return _swig_getattr_nondynamic(self, class_type, name, 0)
76 
77 
78 def _swig_repr(self):
79  try:
80  strthis = "proxy of " + self.this.__repr__()
81  except:
82  strthis = ""
83  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
84 
85 try:
86  _object = object
87  _newclass = 1
88 except AttributeError:
89  class _object:
90  pass
91  _newclass = 0
92 
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_EXAMPLE_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_EXAMPLE_SwigPyIterator class"""
115  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
116 
117  def __init__(self, *args, **kwargs):
118  raise AttributeError("No constructor defined - class is abstract")
119  __repr__ = _swig_repr
120  __swig_destroy__ = _IMP_example.delete_IMP_EXAMPLE_SwigPyIterator
121  __del__ = lambda self: None
122 
123  def value(self):
124  """value(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
125  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_value(self)
126 
127 
128  def incr(self, n=1):
129  """
130  incr(IMP_EXAMPLE_SwigPyIterator self, size_t n=1) -> IMP_EXAMPLE_SwigPyIterator
131  incr(IMP_EXAMPLE_SwigPyIterator self) -> IMP_EXAMPLE_SwigPyIterator
132  """
133  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_incr(self, n)
134 
135 
136  def decr(self, n=1):
137  """
138  decr(IMP_EXAMPLE_SwigPyIterator self, size_t n=1) -> IMP_EXAMPLE_SwigPyIterator
139  decr(IMP_EXAMPLE_SwigPyIterator self) -> IMP_EXAMPLE_SwigPyIterator
140  """
141  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_decr(self, n)
142 
143 
144  def distance(self, x):
145  """distance(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> ptrdiff_t"""
146  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_distance(self, x)
147 
148 
149  def equal(self, x):
150  """equal(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
151  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_equal(self, x)
152 
153 
154  def copy(self):
155  """copy(IMP_EXAMPLE_SwigPyIterator self) -> IMP_EXAMPLE_SwigPyIterator"""
156  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_copy(self)
157 
158 
159  def next(self):
160  """next(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
161  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_next(self)
162 
163 
164  def __next__(self):
165  """__next__(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
166  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___next__(self)
167 
168 
169  def previous(self):
170  """previous(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
171  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_previous(self)
172 
173 
174  def advance(self, n):
175  """advance(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
176  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_advance(self, n)
177 
178 
179  def __eq__(self, x):
180  """__eq__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
181  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___eq__(self, x)
182 
183 
184  def __ne__(self, x):
185  """__ne__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
186  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___ne__(self, x)
187 
188 
189  def __iadd__(self, n):
190  """__iadd__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
191  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___iadd__(self, n)
192 
193 
194  def __isub__(self, n):
195  """__isub__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
196  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___isub__(self, n)
197 
198 
199  def __add__(self, n):
200  """__add__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
201  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___add__(self, n)
202 
203 
204  def __sub__(self, *args):
205  """
206  __sub__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator
207  __sub__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> ptrdiff_t
208  """
209  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___sub__(self, *args)
210 
211  def __iter__(self):
212  return self
213 IMP_EXAMPLE_SwigPyIterator_swigregister = _IMP_example.IMP_EXAMPLE_SwigPyIterator_swigregister
214 IMP_EXAMPLE_SwigPyIterator_swigregister(IMP_EXAMPLE_SwigPyIterator)
215 
216 _value_types=[]
217 _object_types=[]
218 _raii_types=[]
219 _plural_types=[]
220 
221 
222 _IMP_example.IMP_DEBUG_swigconstant(_IMP_example)
223 IMP_DEBUG = _IMP_example.IMP_DEBUG
224 
225 _IMP_example.IMP_RELEASE_swigconstant(_IMP_example)
226 IMP_RELEASE = _IMP_example.IMP_RELEASE
227 
228 _IMP_example.IMP_SILENT_swigconstant(_IMP_example)
229 IMP_SILENT = _IMP_example.IMP_SILENT
230 
231 _IMP_example.IMP_PROGRESS_swigconstant(_IMP_example)
232 IMP_PROGRESS = _IMP_example.IMP_PROGRESS
233 
234 _IMP_example.IMP_TERSE_swigconstant(_IMP_example)
235 IMP_TERSE = _IMP_example.IMP_TERSE
236 
237 _IMP_example.IMP_VERBOSE_swigconstant(_IMP_example)
238 IMP_VERBOSE = _IMP_example.IMP_VERBOSE
239 
240 _IMP_example.IMP_MEMORY_swigconstant(_IMP_example)
241 IMP_MEMORY = _IMP_example.IMP_MEMORY
242 
243 _IMP_example.IMP_NONE_swigconstant(_IMP_example)
244 IMP_NONE = _IMP_example.IMP_NONE
245 
246 _IMP_example.IMP_USAGE_swigconstant(_IMP_example)
247 IMP_USAGE = _IMP_example.IMP_USAGE
248 
249 _IMP_example.IMP_INTERNAL_swigconstant(_IMP_example)
250 IMP_INTERNAL = _IMP_example.IMP_INTERNAL
251 
252 _IMP_example.IMP_KERNEL_HAS_LOG4CXX_swigconstant(_IMP_example)
253 IMP_KERNEL_HAS_LOG4CXX = _IMP_example.IMP_KERNEL_HAS_LOG4CXX
254 
255 _IMP_example.IMP_COMPILER_HAS_AUTO_swigconstant(_IMP_example)
256 IMP_COMPILER_HAS_AUTO = _IMP_example.IMP_COMPILER_HAS_AUTO
257 
258 _IMP_example.IMP_COMPILER_HAS_DEBUG_VECTOR_swigconstant(_IMP_example)
259 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_example.IMP_COMPILER_HAS_DEBUG_VECTOR
260 
261 _IMP_example.IMP_KERNEL_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
262 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_example.IMP_KERNEL_HAS_BOOST_RANDOM
263 
264 _IMP_example.IMP_KERNEL_HAS_GPERFTOOLS_swigconstant(_IMP_example)
265 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_example.IMP_KERNEL_HAS_GPERFTOOLS
266 
267 _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_example)
268 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
269 
270 _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_example)
271 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
272 
273 _IMP_example.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_example)
274 IMPKERNEL_SHOW_WARNINGS = _IMP_example.IMPKERNEL_SHOW_WARNINGS
275 import sys
276 class _DirectorObjects(object):
277  """@internal Simple class to keep references to director objects
278  to prevent premature deletion."""
279  def __init__(self):
280  self._objects = []
281  def register(self, obj):
282  """Take a reference to a director object; will only work for
283  refcounted C++ classes"""
284  if hasattr(obj, 'get_ref_count'):
285  self._objects.append(obj)
286  def cleanup(self):
287  """Only drop our reference and allow cleanup by Python if no other
288  Python references exist (we hold 3 references: one in self._objects,
289  one in x, and one in the argument list for getrefcount) *and* no
290  other C++ references exist (the Python object always holds one)"""
291  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
292  or x.get_ref_count() > 1]
293  # Do in two steps so the references are kept until the end of the
294  # function (deleting references may trigger a fresh call to this method)
295  self._objects = objs
296  def get_object_count(self):
297  """Get number of director objects (useful for testing only)"""
298  return len(self._objects)
299 _director_objects = _DirectorObjects()
300 
301 class _ostream(object):
302  """Proxy of C++ std::ostream class"""
303  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
304 
305  def __init__(self, *args, **kwargs):
306  raise AttributeError("No constructor defined")
307  __repr__ = _swig_repr
308 
309  def write(self, osa_buf):
310  """write(_ostream self, char const * osa_buf)"""
311  return _IMP_example._ostream_write(self, osa_buf)
312 
313 _ostream_swigregister = _IMP_example._ostream_swigregister
314 _ostream_swigregister(_ostream)
315 
316 
317 _IMP_example.IMP_COMPILER_HAS_OVERRIDE_swigconstant(_IMP_example)
318 IMP_COMPILER_HAS_OVERRIDE = _IMP_example.IMP_COMPILER_HAS_OVERRIDE
319 
320 _IMP_example.IMP_COMPILER_HAS_FINAL_swigconstant(_IMP_example)
321 IMP_COMPILER_HAS_FINAL = _IMP_example.IMP_COMPILER_HAS_FINAL
322 
323 _IMP_example.IMP_HAS_NOEXCEPT_swigconstant(_IMP_example)
324 IMP_HAS_NOEXCEPT = _IMP_example.IMP_HAS_NOEXCEPT
325 import IMP
326 
327 _IMP_example.IMP_CGAL_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_example)
328 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_FILESYSTEM
329 
330 _IMP_example.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_example)
331 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
332 
333 _IMP_example.IMP_CGAL_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
334 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_example.IMP_CGAL_HAS_BOOST_RANDOM
335 
336 _IMP_example.IMP_CGAL_HAS_BOOST_SYSTEM_swigconstant(_IMP_example)
337 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_SYSTEM
338 
339 _IMP_example.IMPCGAL_SHOW_WARNINGS_swigconstant(_IMP_example)
340 IMPCGAL_SHOW_WARNINGS = _IMP_example.IMPCGAL_SHOW_WARNINGS
341 import IMP.cgal
342 
343 _IMP_example.IMP_ALGEBRA_HAS_IMP_CGAL_swigconstant(_IMP_example)
344 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_example.IMP_ALGEBRA_HAS_IMP_CGAL
345 
346 _IMP_example.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_example)
347 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
348 
349 _IMP_example.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_example)
350 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
351 
352 _IMP_example.IMP_ALGEBRA_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
353 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_RANDOM
354 
355 _IMP_example.IMP_ALGEBRA_HAS_BOOST_SYSTEM_swigconstant(_IMP_example)
356 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_SYSTEM
357 
358 _IMP_example.IMP_ALGEBRA_HAS_CGAL_swigconstant(_IMP_example)
359 IMP_ALGEBRA_HAS_CGAL = _IMP_example.IMP_ALGEBRA_HAS_CGAL
360 
361 _IMP_example.IMP_ALGEBRA_HAS_ANN_swigconstant(_IMP_example)
362 IMP_ALGEBRA_HAS_ANN = _IMP_example.IMP_ALGEBRA_HAS_ANN
363 
364 _IMP_example.IMPALGEBRA_SHOW_WARNINGS_swigconstant(_IMP_example)
365 IMPALGEBRA_SHOW_WARNINGS = _IMP_example.IMPALGEBRA_SHOW_WARNINGS
366 import IMP.algebra
367 
368 _IMP_example.IMP_DISPLAY_HAS_IMP_CGAL_swigconstant(_IMP_example)
369 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_example.IMP_DISPLAY_HAS_IMP_CGAL
370 
371 _IMP_example.IMP_DISPLAY_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_example)
372 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
373 
374 _IMP_example.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_example)
375 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
376 
377 _IMP_example.IMP_DISPLAY_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
378 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_example.IMP_DISPLAY_HAS_BOOST_RANDOM
379 
380 _IMP_example.IMP_DISPLAY_HAS_BOOST_SYSTEM_swigconstant(_IMP_example)
381 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_SYSTEM
382 
383 _IMP_example.IMP_DISPLAY_HAS_CGAL_swigconstant(_IMP_example)
384 IMP_DISPLAY_HAS_CGAL = _IMP_example.IMP_DISPLAY_HAS_CGAL
385 
386 _IMP_example.IMPDISPLAY_SHOW_WARNINGS_swigconstant(_IMP_example)
387 IMPDISPLAY_SHOW_WARNINGS = _IMP_example.IMPDISPLAY_SHOW_WARNINGS
388 import IMP.display
389 
390 _IMP_example.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL_swigconstant(_IMP_example)
391 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
392 
393 _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_example)
394 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
395 
396 _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_example)
397 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
398 
399 _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
400 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
401 
402 _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM_swigconstant(_IMP_example)
403 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
404 
405 _IMP_example.IMP_SCORE_FUNCTOR_HAS_CGAL_swigconstant(_IMP_example)
406 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_CGAL
407 
408 _IMP_example.IMP_SCORE_FUNCTOR_HAS_HDF5_swigconstant(_IMP_example)
409 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_example.IMP_SCORE_FUNCTOR_HAS_HDF5
410 
411 _IMP_example.IMPSCOREFUNCTOR_SHOW_WARNINGS_swigconstant(_IMP_example)
412 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_example.IMPSCOREFUNCTOR_SHOW_WARNINGS
413 import IMP.score_functor
414 
415 _IMP_example.IMP_STATISTICS_HAS_IMP_CGAL_swigconstant(_IMP_example)
416 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_example.IMP_STATISTICS_HAS_IMP_CGAL
417 
418 _IMP_example.IMP_STATISTICS_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_example)
419 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
420 
421 _IMP_example.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_example)
422 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
423 
424 _IMP_example.IMP_STATISTICS_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
425 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_example.IMP_STATISTICS_HAS_BOOST_RANDOM
426 
427 _IMP_example.IMP_STATISTICS_HAS_BOOST_SYSTEM_swigconstant(_IMP_example)
428 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_SYSTEM
429 
430 _IMP_example.IMP_STATISTICS_HAS_CGAL_swigconstant(_IMP_example)
431 IMP_STATISTICS_HAS_CGAL = _IMP_example.IMP_STATISTICS_HAS_CGAL
432 
433 _IMP_example.IMPSTATISTICS_SHOW_WARNINGS_swigconstant(_IMP_example)
434 IMPSTATISTICS_SHOW_WARNINGS = _IMP_example.IMPSTATISTICS_SHOW_WARNINGS
435 import IMP.statistics
436 
437 _IMP_example.IMP_CORE_HAS_IMP_CGAL_swigconstant(_IMP_example)
438 IMP_CORE_HAS_IMP_CGAL = _IMP_example.IMP_CORE_HAS_IMP_CGAL
439 
440 _IMP_example.IMP_CORE_HAS_IMP_KERNEL_swigconstant(_IMP_example)
441 IMP_CORE_HAS_IMP_KERNEL = _IMP_example.IMP_CORE_HAS_IMP_KERNEL
442 
443 _IMP_example.IMP_CORE_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_example)
444 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_FILESYSTEM
445 
446 _IMP_example.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_example)
447 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
448 
449 _IMP_example.IMP_CORE_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
450 IMP_CORE_HAS_BOOST_RANDOM = _IMP_example.IMP_CORE_HAS_BOOST_RANDOM
451 
452 _IMP_example.IMP_CORE_HAS_BOOST_SYSTEM_swigconstant(_IMP_example)
453 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_SYSTEM
454 
455 _IMP_example.IMP_CORE_HAS_CGAL_swigconstant(_IMP_example)
456 IMP_CORE_HAS_CGAL = _IMP_example.IMP_CORE_HAS_CGAL
457 
458 _IMP_example.IMP_CORE_HAS_HDF5_swigconstant(_IMP_example)
459 IMP_CORE_HAS_HDF5 = _IMP_example.IMP_CORE_HAS_HDF5
460 
461 _IMP_example.IMPCORE_SHOW_WARNINGS_swigconstant(_IMP_example)
462 IMPCORE_SHOW_WARNINGS = _IMP_example.IMPCORE_SHOW_WARNINGS
463 import IMP.core
464 
465 _IMP_example.IMP_CONTAINER_HAS_IMP_ALGEBRA_swigconstant(_IMP_example)
466 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_example.IMP_CONTAINER_HAS_IMP_ALGEBRA
467 
468 _IMP_example.IMP_CONTAINER_HAS_IMP_CGAL_swigconstant(_IMP_example)
469 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_example.IMP_CONTAINER_HAS_IMP_CGAL
470 
471 _IMP_example.IMP_CONTAINER_HAS_IMP_DISPLAY_swigconstant(_IMP_example)
472 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_example.IMP_CONTAINER_HAS_IMP_DISPLAY
473 
474 _IMP_example.IMP_CONTAINER_HAS_IMP_KERNEL_swigconstant(_IMP_example)
475 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_example.IMP_CONTAINER_HAS_IMP_KERNEL
476 
477 _IMP_example.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_example)
478 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
479 
480 _IMP_example.IMP_CONTAINER_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_example)
481 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
482 
483 _IMP_example.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_example)
484 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
485 
486 _IMP_example.IMP_CONTAINER_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
487 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_example.IMP_CONTAINER_HAS_BOOST_RANDOM
488 
489 _IMP_example.IMP_CONTAINER_HAS_BOOST_SYSTEM_swigconstant(_IMP_example)
490 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_SYSTEM
491 
492 _IMP_example.IMP_CONTAINER_HAS_CGAL_swigconstant(_IMP_example)
493 IMP_CONTAINER_HAS_CGAL = _IMP_example.IMP_CONTAINER_HAS_CGAL
494 
495 _IMP_example.IMP_CONTAINER_HAS_HDF5_swigconstant(_IMP_example)
496 IMP_CONTAINER_HAS_HDF5 = _IMP_example.IMP_CONTAINER_HAS_HDF5
497 
498 _IMP_example.IMPCONTAINER_SHOW_WARNINGS_swigconstant(_IMP_example)
499 IMPCONTAINER_SHOW_WARNINGS = _IMP_example.IMPCONTAINER_SHOW_WARNINGS
500 import IMP.container
501 
502 _IMP_example.IMP_ATOM_HAS_IMP_CGAL_swigconstant(_IMP_example)
503 IMP_ATOM_HAS_IMP_CGAL = _IMP_example.IMP_ATOM_HAS_IMP_CGAL
504 
505 _IMP_example.IMP_ATOM_HAS_IMP_KERNEL_swigconstant(_IMP_example)
506 IMP_ATOM_HAS_IMP_KERNEL = _IMP_example.IMP_ATOM_HAS_IMP_KERNEL
507 
508 _IMP_example.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_example)
509 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
510 
511 _IMP_example.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_example)
512 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
513 
514 _IMP_example.IMP_ATOM_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
515 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_example.IMP_ATOM_HAS_BOOST_RANDOM
516 
517 _IMP_example.IMP_ATOM_HAS_BOOST_REGEX_swigconstant(_IMP_example)
518 IMP_ATOM_HAS_BOOST_REGEX = _IMP_example.IMP_ATOM_HAS_BOOST_REGEX
519 
520 _IMP_example.IMP_ATOM_HAS_BOOST_SYSTEM_swigconstant(_IMP_example)
521 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_example.IMP_ATOM_HAS_BOOST_SYSTEM
522 
523 _IMP_example.IMP_ATOM_HAS_CGAL_swigconstant(_IMP_example)
524 IMP_ATOM_HAS_CGAL = _IMP_example.IMP_ATOM_HAS_CGAL
525 
526 _IMP_example.IMP_ATOM_HAS_HDF5_swigconstant(_IMP_example)
527 IMP_ATOM_HAS_HDF5 = _IMP_example.IMP_ATOM_HAS_HDF5
528 
529 _IMP_example.IMPATOM_SHOW_WARNINGS_swigconstant(_IMP_example)
530 IMPATOM_SHOW_WARNINGS = _IMP_example.IMPATOM_SHOW_WARNINGS
531 
532 _IMP_example.IMP_ATOM_TYPE_INDEX_swigconstant(_IMP_example)
533 IMP_ATOM_TYPE_INDEX = _IMP_example.IMP_ATOM_TYPE_INDEX
534 
535 _IMP_example.IMP_RESIDUE_TYPE_INDEX_swigconstant(_IMP_example)
536 IMP_RESIDUE_TYPE_INDEX = _IMP_example.IMP_RESIDUE_TYPE_INDEX
537 
538 _IMP_example.IMP_HIERARCHY_TYPE_INDEX_swigconstant(_IMP_example)
539 IMP_HIERARCHY_TYPE_INDEX = _IMP_example.IMP_HIERARCHY_TYPE_INDEX
540 import IMP.atom
541 
542 _IMP_example.IMP_RMF_HAS_IMP_CGAL_swigconstant(_IMP_example)
543 IMP_RMF_HAS_IMP_CGAL = _IMP_example.IMP_RMF_HAS_IMP_CGAL
544 
545 _IMP_example.IMP_RMF_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_example)
546 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
547 
548 _IMP_example.IMP_RMF_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_example)
549 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_FILESYSTEM
550 
551 _IMP_example.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_example)
552 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
553 
554 _IMP_example.IMP_RMF_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
555 IMP_RMF_HAS_BOOST_RANDOM = _IMP_example.IMP_RMF_HAS_BOOST_RANDOM
556 
557 _IMP_example.IMP_RMF_HAS_BOOST_REGEX_swigconstant(_IMP_example)
558 IMP_RMF_HAS_BOOST_REGEX = _IMP_example.IMP_RMF_HAS_BOOST_REGEX
559 
560 _IMP_example.IMP_RMF_HAS_BOOST_SYSTEM_swigconstant(_IMP_example)
561 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_SYSTEM
562 
563 _IMP_example.IMP_RMF_HAS_CGAL_swigconstant(_IMP_example)
564 IMP_RMF_HAS_CGAL = _IMP_example.IMP_RMF_HAS_CGAL
565 
566 _IMP_example.IMP_RMF_HAS_HDF5_swigconstant(_IMP_example)
567 IMP_RMF_HAS_HDF5 = _IMP_example.IMP_RMF_HAS_HDF5
568 
569 _IMP_example.IMPRMF_SHOW_WARNINGS_swigconstant(_IMP_example)
570 IMPRMF_SHOW_WARNINGS = _IMP_example.IMPRMF_SHOW_WARNINGS
571 import IMP.rmf
572 import RMF
573 
574 _IMP_example.IMP_DOMINO_HAS_IMP_ATOM_swigconstant(_IMP_example)
575 IMP_DOMINO_HAS_IMP_ATOM = _IMP_example.IMP_DOMINO_HAS_IMP_ATOM
576 
577 _IMP_example.IMP_DOMINO_HAS_IMP_CGAL_swigconstant(_IMP_example)
578 IMP_DOMINO_HAS_IMP_CGAL = _IMP_example.IMP_DOMINO_HAS_IMP_CGAL
579 
580 _IMP_example.IMP_DOMINO_HAS_IMP_KERNEL_swigconstant(_IMP_example)
581 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_example.IMP_DOMINO_HAS_IMP_KERNEL
582 
583 _IMP_example.IMP_DOMINO_HAS_IMP_RMF_swigconstant(_IMP_example)
584 IMP_DOMINO_HAS_IMP_RMF = _IMP_example.IMP_DOMINO_HAS_IMP_RMF
585 
586 _IMP_example.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_example)
587 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
588 
589 _IMP_example.IMP_DOMINO_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_example)
590 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_FILESYSTEM
591 
592 _IMP_example.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_example)
593 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
594 
595 _IMP_example.IMP_DOMINO_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
596 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_example.IMP_DOMINO_HAS_BOOST_RANDOM
597 
598 _IMP_example.IMP_DOMINO_HAS_BOOST_REGEX_swigconstant(_IMP_example)
599 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_example.IMP_DOMINO_HAS_BOOST_REGEX
600 
601 _IMP_example.IMP_DOMINO_HAS_BOOST_SYSTEM_swigconstant(_IMP_example)
602 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_SYSTEM
603 
604 _IMP_example.IMP_DOMINO_HAS_CGAL_swigconstant(_IMP_example)
605 IMP_DOMINO_HAS_CGAL = _IMP_example.IMP_DOMINO_HAS_CGAL
606 
607 _IMP_example.IMP_DOMINO_HAS_HDF5_swigconstant(_IMP_example)
608 IMP_DOMINO_HAS_HDF5 = _IMP_example.IMP_DOMINO_HAS_HDF5
609 
610 _IMP_example.IMP_DOMINO_HAS_RMF_swigconstant(_IMP_example)
611 IMP_DOMINO_HAS_RMF = _IMP_example.IMP_DOMINO_HAS_RMF
612 
613 _IMP_example.IMPDOMINO_SHOW_WARNINGS_swigconstant(_IMP_example)
614 IMPDOMINO_SHOW_WARNINGS = _IMP_example.IMPDOMINO_SHOW_WARNINGS
615 import RMF_HDF5
616 import IMP.domino
617 
618 _IMP_example.IMP_EXAMPLE_HAS_IMP_ALGEBRA_swigconstant(_IMP_example)
619 IMP_EXAMPLE_HAS_IMP_ALGEBRA = _IMP_example.IMP_EXAMPLE_HAS_IMP_ALGEBRA
620 
621 _IMP_example.IMP_EXAMPLE_HAS_IMP_CGAL_swigconstant(_IMP_example)
622 IMP_EXAMPLE_HAS_IMP_CGAL = _IMP_example.IMP_EXAMPLE_HAS_IMP_CGAL
623 
624 _IMP_example.IMP_EXAMPLE_HAS_IMP_DISPLAY_swigconstant(_IMP_example)
625 IMP_EXAMPLE_HAS_IMP_DISPLAY = _IMP_example.IMP_EXAMPLE_HAS_IMP_DISPLAY
626 
627 _IMP_example.IMP_EXAMPLE_HAS_IMP_KERNEL_swigconstant(_IMP_example)
628 IMP_EXAMPLE_HAS_IMP_KERNEL = _IMP_example.IMP_EXAMPLE_HAS_IMP_KERNEL
629 
630 _IMP_example.IMP_EXAMPLE_HAS_IMP_RMF_swigconstant(_IMP_example)
631 IMP_EXAMPLE_HAS_IMP_RMF = _IMP_example.IMP_EXAMPLE_HAS_IMP_RMF
632 
633 _IMP_example.IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_example)
634 IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR
635 
636 _IMP_example.IMP_EXAMPLE_HAS_IMP_STATISTICS_swigconstant(_IMP_example)
637 IMP_EXAMPLE_HAS_IMP_STATISTICS = _IMP_example.IMP_EXAMPLE_HAS_IMP_STATISTICS
638 
639 _IMP_example.IMP_EXAMPLE_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_example)
640 IMP_EXAMPLE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_FILESYSTEM
641 
642 _IMP_example.IMP_EXAMPLE_HAS_BOOST_GRAPH_swigconstant(_IMP_example)
643 IMP_EXAMPLE_HAS_BOOST_GRAPH = _IMP_example.IMP_EXAMPLE_HAS_BOOST_GRAPH
644 
645 _IMP_example.IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_example)
646 IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS
647 
648 _IMP_example.IMP_EXAMPLE_HAS_BOOST_RANDOM_swigconstant(_IMP_example)
649 IMP_EXAMPLE_HAS_BOOST_RANDOM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_RANDOM
650 
651 _IMP_example.IMP_EXAMPLE_HAS_BOOST_REGEX_swigconstant(_IMP_example)
652 IMP_EXAMPLE_HAS_BOOST_REGEX = _IMP_example.IMP_EXAMPLE_HAS_BOOST_REGEX
653 
654 _IMP_example.IMP_EXAMPLE_HAS_BOOST_SYSTEM_swigconstant(_IMP_example)
655 IMP_EXAMPLE_HAS_BOOST_SYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_SYSTEM
656 
657 _IMP_example.IMP_EXAMPLE_HAS_CGAL_swigconstant(_IMP_example)
658 IMP_EXAMPLE_HAS_CGAL = _IMP_example.IMP_EXAMPLE_HAS_CGAL
659 
660 _IMP_example.IMP_EXAMPLE_HAS_HDF5_swigconstant(_IMP_example)
661 IMP_EXAMPLE_HAS_HDF5 = _IMP_example.IMP_EXAMPLE_HAS_HDF5
662 
663 _IMP_example.IMP_EXAMPLE_HAS_RMF_swigconstant(_IMP_example)
664 IMP_EXAMPLE_HAS_RMF = _IMP_example.IMP_EXAMPLE_HAS_RMF
665 
666 _IMP_example.IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY_swigconstant(_IMP_example)
667 IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY = _IMP_example.IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY
668 
669 _IMP_example.IMPEXAMPLE_SHOW_WARNINGS_swigconstant(_IMP_example)
670 IMPEXAMPLE_SHOW_WARNINGS = _IMP_example.IMPEXAMPLE_SHOW_WARNINGS
671 _object_types.append("ExampleRestraint")
672 
673 
674 def _object_cast_to_ExampleRestraint(o):
675  """_object_cast_to_ExampleRestraint(Object o) -> ExampleRestraint"""
676  return _IMP_example._object_cast_to_ExampleRestraint(o)
677 def ExampleDecorators(l=[]):
678  return [ExampleDecorator(x) for x in l]
679 _plural_types.append("ExampleDecorators")
680 
681 _value_types.append("ExampleDecorator")
682 
683 _object_types.append("ExampleUnaryFunction")
684 
685 
686 def _object_cast_to_ExampleUnaryFunction(o):
687  """_object_cast_to_ExampleUnaryFunction(Object o) -> ExampleUnaryFunction"""
688  return _IMP_example._object_cast_to_ExampleUnaryFunction(o)
689 _object_types.append("ExampleSingletonModifier")
690 
691 
692 def _object_cast_to_ExampleSingletonModifier(o):
693  """_object_cast_to_ExampleSingletonModifier(Object o) -> ExampleSingletonModifier"""
694  return _IMP_example._object_cast_to_ExampleSingletonModifier(o)
695 _object_types.append("ExamplePairScore")
696 
697 
698 def _object_cast_to_ExamplePairScore(o):
699  """_object_cast_to_ExamplePairScore(Object o) -> ExamplePairScore"""
700  return _IMP_example._object_cast_to_ExamplePairScore(o)
701 _object_types.append("ExampleSubsetFilterTable")
702 
703 
704 def _object_cast_to_ExampleSubsetFilterTable(o):
705  """_object_cast_to_ExampleSubsetFilterTable(Object o) -> ExampleSubsetFilterTable"""
706  return _IMP_example._object_cast_to_ExampleSubsetFilterTable(o)
707 _object_types.append("ExampleConstraint")
708 
709 
710 def _object_cast_to_ExampleConstraint(o):
711  """_object_cast_to_ExampleConstraint(Object o) -> ExampleConstraint"""
712  return _IMP_example._object_cast_to_ExampleConstraint(o)
713 _object_types.append("ExampleObject")
714 
715 
716 def _object_cast_to_ExampleObject(o):
717  """_object_cast_to_ExampleObject(Object o) -> ExampleObject"""
718  return _IMP_example._object_cast_to_ExampleObject(o)
719 ExampleTemplateClass3Ds=list
720 _plural_types.append("ExampleTemplateClass3Ds")
721 _value_types.append("ExampleTemplateClass3D")
722 
723 def create_model_and_particles():
724  m = IMP.Model()
725  sc = IMP.container.ListSingletonContainer(m)
726  b = IMP.algebra.BoundingBox3D(IMP.algebra.Vector3D(0,0,0),
727  IMP.algebra.Vector3D(10,10,10))
728  for i in range(0,100):
729  p = m.add_particle("p")
730  sc.add(p)
731  d = IMP.core.XYZR.setup_particle(m, p,
732  IMP.algebra.Sphere3D(IMP.algebra.get_random_vector_in(b), 1))
733  d.set_coordinates_are_optimized(True)
734  return (m, sc)
735 
736 class PythonExampleRestraint(IMP.Restraint):
737  """An example restraint written in Python.
738  This should be functionally equivalent to the C++ ExampleRestraint.
739  """
740  def __init__(self, m, p, k):
741  IMP.Restraint.__init__(self, m, "PythonExampleRestraint%1%")
742  self.p, self.k = p, k
743 
744  def do_add_score_and_derivatives(self, sa):
745  d = IMP.core.XYZ(self.get_model(), self.p)
746  score = .5 * self.k * d.get_z() * d.get_z()
747  if sa.get_derivative_accumulator():
748  deriv = self.k * d.get_z()
749  d.add_to_derivative(2, deriv, sa.get_derivative_accumulator())
750  sa.add_score(score)
751 
752  def do_get_inputs(self):
753  return [self.get_model().get_particle(self.p)]
754 
755 
756 class PythonExamplePairScore(IMP.PairScore):
757  """An example PairScore written in Python.
758  This should be functionally equivalent to the C++ ExamplePairScore.
759  """
760  def __init__(self, x0, k):
761  IMP.PairScore.__init__(self)
762  self.x0, self.k = x0, k
763 
764  def evaluate_index(self, m, pip, da):
765  d0 = IMP.core.XYZ(m, pip[0])
766  d1 = IMP.core.XYZ(m, pip[1])
767  diff = (d0.get_coordinates()
768  - d1.get_coordinates()).get_magnitude() - self.x0
769  score = .5 * self.k * diff * diff
770  if da:
771  # derivatives are requested
772  delta = d0.get_coordinates() - d1.get_coordinates()
773  udelta = delta.get_unit_vector()
774  dv = self.k * diff
775  d0.add_to_derivatives(udelta * dv, da)
776  d1.add_to_derivatives(-udelta * dv, da)
777  return score
778 
779  def do_get_inputs(self, m, pis):
780  return IMP.get_particles(m, pis)
781 
782 
783 class PythonExampleUnaryFunction(IMP.UnaryFunction):
784  """An example UnaryFunction written in Python.
785  This should be functionally equivalent to the C++ ExampleUnaryFunction.
786  """
787  def __init__(self, center, k):
788  IMP.UnaryFunction.__init__(self)
789  self.center, self.k = center, k
790 
791  def evaluate_with_derivative(self, feature):
792  return (self.evaluate(feature), self.k * (feature - self.center))
793 
794  def evaluate(self, feature):
795  return .5 * self.k * (feature - self.center) * (feature - self.center)
796 
797 
798 class PythonExampleConstraint(IMP.Constraint):
799  """An example Constraint written in Python.
800  This should be functionally equivalent to the C++ ExampleConstraint.
801  """
802 
803  k = None
804 
805  def __init__(self, p):
806  IMP.Constraint.__init__(self, p.get_model(), "ExampleConstraint%1%")
807  self.p = p
808  if self.k is None:
809  PythonExampleConstraint.k = IMP.IntKey("Constraint key")
810  if not p.has_attribute(self.k):
811  p.add_attribute(self.k, 0)
812 
813  def do_update_attributes(self):
814  self.p.set_value(self.k, self.p.get_value(self.k) + 1)
815 
816  def do_update_derivatives(self, da):
817  pass
818 
819  def do_get_inputs(self):
820  return [self.p]
821 
822  def do_get_outputs(self):
823  return [self.p]
824 
825 
826 class PythonExampleSingletonModifier(IMP.SingletonModifier):
827  """An example SingletonModifier written in Python.
828  This should be functionally equivalent to the C++
829  ExampleSingletonModifier.
830  """
831 
832  def __init__(self, bb):
833  IMP.SingletonModifier.__init__(self, "ExampleSingletonModifier%1%")
834  self.bb = bb
835 
836  def apply_index(self, m, pi):
837  d = IMP.core.XYZ(m, pi)
838  for i in range(3):
839  # shift the coordinate until it is in the box
840  while d.get_coordinate(i) < self.bb.get_corner(0)[i]:
841  d.set_coordinate(i,d.get_coordinate(i) + \
842  (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
843  while d.get_coordinate(i) > self.bb.get_corner(1)[i]:
844  d.set_coordinate(i,d.get_coordinate(i) - \
845  (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
846 
847  def do_get_inputs(self, m, pis):
848  return IMP.get_particles(m, pis)
849 
850  def do_get_outputs(self, m, pis):
851  return self.do_get_inputs(m, pis)
852 
853 
854 class ExampleRestraint(IMP.Restraint):
855  """Proxy of C++ IMP::example::ExampleRestraint class"""
856  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
857 
858  def __init__(self, m, p, k):
859  """__init__(IMP::example::ExampleRestraint self, Model m, ParticleIndex p, double k) -> ExampleRestraint"""
860  this = _IMP_example.new_ExampleRestraint(m, p, k)
861  try:
862  self.this.append(this)
863  except:
864  self.this = this
865 
866  def do_add_score_and_derivatives(self, sa):
867  """do_add_score_and_derivatives(ExampleRestraint self, ScoreAccumulator sa)"""
868  return _IMP_example.ExampleRestraint_do_add_score_and_derivatives(self, sa)
869 
870 
871  def do_get_inputs(self):
872  """do_get_inputs(ExampleRestraint self) -> IMP::ModelObjectsTemp"""
873  return _IMP_example.ExampleRestraint_do_get_inputs(self)
874 
875 
876  def get_version_info(self):
877  """get_version_info(ExampleRestraint self) -> VersionInfo"""
878  return _IMP_example.ExampleRestraint_get_version_info(self)
879 
880 
881  def __str__(self):
882  """__str__(ExampleRestraint self) -> std::string"""
883  return _IMP_example.ExampleRestraint___str__(self)
884 
885 
886  def __repr__(self):
887  """__repr__(ExampleRestraint self) -> std::string"""
888  return _IMP_example.ExampleRestraint___repr__(self)
889 
890  def get_from(o):
891  return _object_cast_to_ExampleRestraint(o)
892  get_from = staticmethod(get_from)
893 
894 ExampleRestraint_swigregister = _IMP_example.ExampleRestraint_swigregister
895 ExampleRestraint_swigregister(ExampleRestraint)
896 
897 class ExampleDecorator(IMP.Decorator):
898  """Proxy of C++ IMP::example::ExampleDecorator class"""
899  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
900 
901  def get_decorator_name(self):
902  """get_decorator_name(ExampleDecorator self) -> std::string"""
903  return _IMP_example.ExampleDecorator_get_decorator_name(self)
904 
905 
906  def set_decorator_name(self, nm):
907  """set_decorator_name(ExampleDecorator self, std::string nm)"""
908  return _IMP_example.ExampleDecorator_set_decorator_name(self, nm)
909 
910 
911  def __init__(self, *args):
912  """
913  __init__(IMP::example::ExampleDecorator self) -> ExampleDecorator
914  __init__(IMP::example::ExampleDecorator self, Model m, ParticleIndex id) -> ExampleDecorator
915  __init__(IMP::example::ExampleDecorator self, _ParticleAdaptor d) -> ExampleDecorator
916  """
917  this = _IMP_example.new_ExampleDecorator(*args)
918  try:
919  self.this.append(this)
920  except:
921  self.this = this
922 
923  def get_is_setup(*args):
924  """
925  get_is_setup(Model m, ParticleIndex pi) -> bool
926  get_is_setup(_ParticleAdaptor p) -> bool
927  """
928  return _IMP_example.ExampleDecorator_get_is_setup(*args)
929 
930  get_is_setup = staticmethod(get_is_setup)
931 
932  def show(self, *args):
933  """
934  show(ExampleDecorator self, _ostream out)
935  show(ExampleDecorator self)
936  """
937  return _IMP_example.ExampleDecorator_show(self, *args)
938 
939 
940  def setup_particle(*args):
941  """
942  setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
943  setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
944  """
945  return _IMP_example.ExampleDecorator_setup_particle(*args)
946 
947  setup_particle = staticmethod(setup_particle)
948 
949  def add_attribute(self, *args):
950  """
951  add_attribute(ExampleDecorator self, FloatKey k, IMP::Float v, bool opt)
952  add_attribute(ExampleDecorator self, FloatKey a0, IMP::Float a1)
953  add_attribute(ExampleDecorator self, IntKey a0, IMP::Int a1)
954  add_attribute(ExampleDecorator self, StringKey a0, IMP::String a1)
955  add_attribute(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
956  add_attribute(ExampleDecorator self, ObjectKey a0, Object a1)
957  """
958  return _IMP_example.ExampleDecorator_add_attribute(self, *args)
959 
960 
961  def get_value(self, *args):
962  """
963  get_value(ExampleDecorator self, FloatKey a0) -> IMP::Float
964  get_value(ExampleDecorator self, IntKey a0) -> IMP::Int
965  get_value(ExampleDecorator self, StringKey a0) -> IMP::String
966  get_value(ExampleDecorator self, ParticleIndexKey a0) -> Particle
967  get_value(ExampleDecorator self, ObjectKey a0) -> Object
968  """
969  return _IMP_example.ExampleDecorator_get_value(self, *args)
970 
971 
972  def set_value(self, *args):
973  """
974  set_value(ExampleDecorator self, FloatKey a0, IMP::Float a1)
975  set_value(ExampleDecorator self, IntKey a0, IMP::Int a1)
976  set_value(ExampleDecorator self, StringKey a0, IMP::String a1)
977  set_value(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
978  set_value(ExampleDecorator self, ObjectKey a0, Object a1)
979  """
980  return _IMP_example.ExampleDecorator_set_value(self, *args)
981 
982 
983  def remove_attribute(self, *args):
984  """
985  remove_attribute(ExampleDecorator self, FloatKey a0)
986  remove_attribute(ExampleDecorator self, IntKey a0)
987  remove_attribute(ExampleDecorator self, StringKey a0)
988  remove_attribute(ExampleDecorator self, ParticleIndexKey a0)
989  remove_attribute(ExampleDecorator self, ObjectKey a0)
990  """
991  return _IMP_example.ExampleDecorator_remove_attribute(self, *args)
992 
993 
994  def has_attribute(self, *args):
995  """
996  has_attribute(ExampleDecorator self, FloatKey a0) -> bool
997  has_attribute(ExampleDecorator self, IntKey a0) -> bool
998  has_attribute(ExampleDecorator self, StringKey a0) -> bool
999  has_attribute(ExampleDecorator self, ParticleIndexKey a0) -> bool
1000  has_attribute(ExampleDecorator self, ObjectKey a0) -> bool
1001  """
1002  return _IMP_example.ExampleDecorator_has_attribute(self, *args)
1003 
1004 
1005  def get_derivative(self, a0):
1006  """get_derivative(ExampleDecorator self, FloatKey a0) -> double"""
1007  return _IMP_example.ExampleDecorator_get_derivative(self, a0)
1008 
1009 
1010  def get_name(self):
1011  """get_name(ExampleDecorator self) -> std::string"""
1012  return _IMP_example.ExampleDecorator_get_name(self)
1013 
1014 
1015  def clear_caches(self):
1016  """clear_caches(ExampleDecorator self)"""
1017  return _IMP_example.ExampleDecorator_clear_caches(self)
1018 
1019 
1020  def set_name(self, a0):
1021  """set_name(ExampleDecorator self, std::string a0)"""
1022  return _IMP_example.ExampleDecorator_set_name(self, a0)
1023 
1024 
1025  def set_check_level(self, a0):
1026  """set_check_level(ExampleDecorator self, IMP::CheckLevel a0)"""
1027  return _IMP_example.ExampleDecorator_set_check_level(self, a0)
1028 
1029 
1030  def add_to_derivative(self, a0, a1, a2):
1031  """add_to_derivative(ExampleDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1032  return _IMP_example.ExampleDecorator_add_to_derivative(self, a0, a1, a2)
1033 
1034 
1035  def set_is_optimized(self, a0, a1):
1036  """set_is_optimized(ExampleDecorator self, FloatKey a0, bool a1)"""
1037  return _IMP_example.ExampleDecorator_set_is_optimized(self, a0, a1)
1038 
1039 
1040  def get_is_optimized(self, a0):
1041  """get_is_optimized(ExampleDecorator self, FloatKey a0) -> bool"""
1042  return _IMP_example.ExampleDecorator_get_is_optimized(self, a0)
1043 
1044 
1045  def get_check_level(self):
1046  """get_check_level(ExampleDecorator self) -> IMP::CheckLevel"""
1047  return _IMP_example.ExampleDecorator_get_check_level(self)
1048 
1049 
1050  def __eq__(self, *args):
1051  """
1052  __eq__(ExampleDecorator self, ExampleDecorator o) -> bool
1053  __eq__(ExampleDecorator self, Particle d) -> bool
1054  """
1055  return _IMP_example.ExampleDecorator___eq__(self, *args)
1056 
1057 
1058  def __ne__(self, *args):
1059  """
1060  __ne__(ExampleDecorator self, ExampleDecorator o) -> bool
1061  __ne__(ExampleDecorator self, Particle d) -> bool
1062  """
1063  return _IMP_example.ExampleDecorator___ne__(self, *args)
1064 
1065 
1066  def __le__(self, *args):
1067  """
1068  __le__(ExampleDecorator self, ExampleDecorator o) -> bool
1069  __le__(ExampleDecorator self, Particle d) -> bool
1070  """
1071  return _IMP_example.ExampleDecorator___le__(self, *args)
1072 
1073 
1074  def __lt__(self, *args):
1075  """
1076  __lt__(ExampleDecorator self, ExampleDecorator o) -> bool
1077  __lt__(ExampleDecorator self, Particle d) -> bool
1078  """
1079  return _IMP_example.ExampleDecorator___lt__(self, *args)
1080 
1081 
1082  def __ge__(self, *args):
1083  """
1084  __ge__(ExampleDecorator self, ExampleDecorator o) -> bool
1085  __ge__(ExampleDecorator self, Particle d) -> bool
1086  """
1087  return _IMP_example.ExampleDecorator___ge__(self, *args)
1088 
1089 
1090  def __gt__(self, *args):
1091  """
1092  __gt__(ExampleDecorator self, ExampleDecorator o) -> bool
1093  __gt__(ExampleDecorator self, Particle d) -> bool
1094  """
1095  return _IMP_example.ExampleDecorator___gt__(self, *args)
1096 
1097 
1098  def __hash__(self):
1099  """__hash__(ExampleDecorator self) -> std::size_t"""
1100  return _IMP_example.ExampleDecorator___hash__(self)
1101 
1102 
1103  def __str__(self):
1104  """__str__(ExampleDecorator self) -> std::string"""
1105  return _IMP_example.ExampleDecorator___str__(self)
1106 
1107 
1108  def __repr__(self):
1109  """__repr__(ExampleDecorator self) -> std::string"""
1110  return _IMP_example.ExampleDecorator___repr__(self)
1111 
1112  __swig_destroy__ = _IMP_example.delete_ExampleDecorator
1113  __del__ = lambda self: None
1114 ExampleDecorator_swigregister = _IMP_example.ExampleDecorator_swigregister
1115 ExampleDecorator_swigregister(ExampleDecorator)
1116 
1117 def ExampleDecorator_get_is_setup(*args):
1118  """
1119  get_is_setup(Model m, ParticleIndex pi) -> bool
1120  ExampleDecorator_get_is_setup(_ParticleAdaptor p) -> bool
1121  """
1122  return _IMP_example.ExampleDecorator_get_is_setup(*args)
1123 
1124 def ExampleDecorator_setup_particle(*args):
1125  """
1126  setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
1127  ExampleDecorator_setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
1128  """
1129  return _IMP_example.ExampleDecorator_setup_particle(*args)
1130 
1131 
1132 def __lshift__(out, n):
1133  """__lshift__(_ostream out, ExampleDecorator n) -> _ostream"""
1134  return _IMP_example.__lshift__(out, n)
1135 class ExampleUnaryFunction(IMP.UnaryFunction):
1136  """Proxy of C++ IMP::example::ExampleUnaryFunction class"""
1137  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1138 
1139  def __init__(self, center, k):
1140  """__init__(IMP::example::ExampleUnaryFunction self, IMP::Float center, IMP::Float k) -> ExampleUnaryFunction"""
1141  this = _IMP_example.new_ExampleUnaryFunction(center, k)
1142  try:
1143  self.this.append(this)
1144  except:
1145  self.this = this
1146 
1147  def get_version_info(self):
1148  """get_version_info(ExampleUnaryFunction self) -> VersionInfo"""
1149  return _IMP_example.ExampleUnaryFunction_get_version_info(self)
1150 
1151 
1152  def __str__(self):
1153  """__str__(ExampleUnaryFunction self) -> std::string"""
1154  return _IMP_example.ExampleUnaryFunction___str__(self)
1155 
1156 
1157  def __repr__(self):
1158  """__repr__(ExampleUnaryFunction self) -> std::string"""
1159  return _IMP_example.ExampleUnaryFunction___repr__(self)
1160 
1161  def get_from(o):
1162  return _object_cast_to_ExampleUnaryFunction(o)
1163  get_from = staticmethod(get_from)
1164 
1165 ExampleUnaryFunction_swigregister = _IMP_example.ExampleUnaryFunction_swigregister
1166 ExampleUnaryFunction_swigregister(ExampleUnaryFunction)
1167 
1168 class ExampleObject(IMP.Object):
1169  """Proxy of C++ IMP::example::ExampleObject class"""
1170  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1171 
1172  def __init__(self, data):
1173  """__init__(IMP::example::ExampleObject self, IMP::Floats const & data) -> ExampleObject"""
1174  this = _IMP_example.new_ExampleObject(data)
1175  try:
1176  self.this.append(this)
1177  except:
1178  self.this = this
1179 
1180  def get_data(self, i):
1181  """get_data(ExampleObject self, unsigned int i) -> double"""
1182  return _IMP_example.ExampleObject_get_data(self, i)
1183 
1184 
1185  def get_version_info(self):
1186  """get_version_info(ExampleObject self) -> VersionInfo"""
1187  return _IMP_example.ExampleObject_get_version_info(self)
1188 
1189 
1190  def __str__(self):
1191  """__str__(ExampleObject self) -> std::string"""
1192  return _IMP_example.ExampleObject___str__(self)
1193 
1194 
1195  def __repr__(self):
1196  """__repr__(ExampleObject self) -> std::string"""
1197  return _IMP_example.ExampleObject___repr__(self)
1198 
1199  def get_from(o):
1200  return _object_cast_to_ExampleObject(o)
1201  get_from = staticmethod(get_from)
1202 
1203 ExampleObject_swigregister = _IMP_example.ExampleObject_swigregister
1204 ExampleObject_swigregister(ExampleObject)
1205 
1206 class ExampleSingletonModifier(IMP.SingletonModifier):
1207  """Proxy of C++ IMP::example::ExampleSingletonModifier class"""
1208  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1209 
1210  def __init__(self, bb):
1211  """__init__(IMP::example::ExampleSingletonModifier self, BoundingBox3D bb) -> ExampleSingletonModifier"""
1212  this = _IMP_example.new_ExampleSingletonModifier(bb)
1213  try:
1214  self.this.append(this)
1215  except:
1216  self.this = this
1217 
1218  def do_get_inputs(self, m, pis):
1219  """do_get_inputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1220  return _IMP_example.ExampleSingletonModifier_do_get_inputs(self, m, pis)
1221 
1222 
1223  def do_get_outputs(self, m, pis):
1224  """do_get_outputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1225  return _IMP_example.ExampleSingletonModifier_do_get_outputs(self, m, pis)
1226 
1227 
1228  def get_version_info(self):
1229  """get_version_info(ExampleSingletonModifier self) -> VersionInfo"""
1230  return _IMP_example.ExampleSingletonModifier_get_version_info(self)
1231 
1232 
1233  def __str__(self):
1234  """__str__(ExampleSingletonModifier self) -> std::string"""
1235  return _IMP_example.ExampleSingletonModifier___str__(self)
1236 
1237 
1238  def __repr__(self):
1239  """__repr__(ExampleSingletonModifier self) -> std::string"""
1240  return _IMP_example.ExampleSingletonModifier___repr__(self)
1241 
1242  def get_from(o):
1243  return _object_cast_to_ExampleSingletonModifier(o)
1244  get_from = staticmethod(get_from)
1245 
1246 ExampleSingletonModifier_swigregister = _IMP_example.ExampleSingletonModifier_swigregister
1247 ExampleSingletonModifier_swigregister(ExampleSingletonModifier)
1248 
1249 class ExamplePairScore(IMP.PairScore):
1250  """Proxy of C++ IMP::example::ExamplePairScore class"""
1251  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1252 
1253  def __init__(self, x0, k):
1254  """__init__(IMP::example::ExamplePairScore self, double x0, double k) -> ExamplePairScore"""
1255  this = _IMP_example.new_ExamplePairScore(x0, k)
1256  try:
1257  self.this.append(this)
1258  except:
1259  self.this = this
1260 
1261  def do_get_inputs(self, m, pis):
1262  """do_get_inputs(ExamplePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1263  return _IMP_example.ExamplePairScore_do_get_inputs(self, m, pis)
1264 
1265 
1266  def get_version_info(self):
1267  """get_version_info(ExamplePairScore self) -> VersionInfo"""
1268  return _IMP_example.ExamplePairScore_get_version_info(self)
1269 
1270 
1271  def __str__(self):
1272  """__str__(ExamplePairScore self) -> std::string"""
1273  return _IMP_example.ExamplePairScore___str__(self)
1274 
1275 
1276  def __repr__(self):
1277  """__repr__(ExamplePairScore self) -> std::string"""
1278  return _IMP_example.ExamplePairScore___repr__(self)
1279 
1280  def get_from(o):
1281  return _object_cast_to_ExamplePairScore(o)
1282  get_from = staticmethod(get_from)
1283 
1284 ExamplePairScore_swigregister = _IMP_example.ExamplePairScore_swigregister
1285 ExamplePairScore_swigregister(ExamplePairScore)
1286 
1287 class ExampleSubsetFilterTable(IMP.domino.SubsetFilterTable):
1288  """Proxy of C++ IMP::example::ExampleSubsetFilterTable class"""
1289  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1290 
1291  def __init__(self, max_diff, pt):
1292  """__init__(IMP::example::ExampleSubsetFilterTable self, unsigned int max_diff, IMP::ParticlesTemp const & pt) -> ExampleSubsetFilterTable"""
1293  this = _IMP_example.new_ExampleSubsetFilterTable(max_diff, pt)
1294  try:
1295  self.this.append(this)
1296  except:
1297  self.this = this
1298 
1299  def get_version_info(self):
1300  """get_version_info(ExampleSubsetFilterTable self) -> VersionInfo"""
1301  return _IMP_example.ExampleSubsetFilterTable_get_version_info(self)
1302 
1303 
1304  def __str__(self):
1305  """__str__(ExampleSubsetFilterTable self) -> std::string"""
1306  return _IMP_example.ExampleSubsetFilterTable___str__(self)
1307 
1308 
1309  def __repr__(self):
1310  """__repr__(ExampleSubsetFilterTable self) -> std::string"""
1311  return _IMP_example.ExampleSubsetFilterTable___repr__(self)
1312 
1313  def get_from(o):
1314  return _object_cast_to_ExampleSubsetFilterTable(o)
1315  get_from = staticmethod(get_from)
1316 
1317 ExampleSubsetFilterTable_swigregister = _IMP_example.ExampleSubsetFilterTable_swigregister
1318 ExampleSubsetFilterTable_swigregister(ExampleSubsetFilterTable)
1319 
1320 class ExampleConstraint(IMP.Constraint):
1321  """Proxy of C++ IMP::example::ExampleConstraint class"""
1322  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1323 
1324  def __init__(self, p):
1325  """__init__(IMP::example::ExampleConstraint self, Particle p) -> ExampleConstraint"""
1326  this = _IMP_example.new_ExampleConstraint(p)
1327  try:
1328  self.this.append(this)
1329  except:
1330  self.this = this
1331 
1332  def do_get_inputs(self):
1333  """do_get_inputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1334  return _IMP_example.ExampleConstraint_do_get_inputs(self)
1335 
1336 
1337  def do_get_outputs(self):
1338  """do_get_outputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1339  return _IMP_example.ExampleConstraint_do_get_outputs(self)
1340 
1341 
1342  def get_key():
1343  """get_key() -> IntKey"""
1344  return _IMP_example.ExampleConstraint_get_key()
1345 
1346  get_key = staticmethod(get_key)
1347 
1348  def get_version_info(self):
1349  """get_version_info(ExampleConstraint self) -> VersionInfo"""
1350  return _IMP_example.ExampleConstraint_get_version_info(self)
1351 
1352 
1353  def __str__(self):
1354  """__str__(ExampleConstraint self) -> std::string"""
1355  return _IMP_example.ExampleConstraint___str__(self)
1356 
1357 
1358  def __repr__(self):
1359  """__repr__(ExampleConstraint self) -> std::string"""
1360  return _IMP_example.ExampleConstraint___repr__(self)
1361 
1362  def get_from(o):
1363  return _object_cast_to_ExampleConstraint(o)
1364  get_from = staticmethod(get_from)
1365 
1366 ExampleConstraint_swigregister = _IMP_example.ExampleConstraint_swigregister
1367 ExampleConstraint_swigregister(ExampleConstraint)
1368 
1369 def ExampleConstraint_get_key():
1370  """ExampleConstraint_get_key() -> IntKey"""
1371  return _IMP_example.ExampleConstraint_get_key()
1372 
1373 
1374 def create_serial_mover(ps):
1375  """create_serial_mover(IMP::ParticlesTemp const & ps) -> MonteCarloMover"""
1376  return _IMP_example.create_serial_mover(ps)
1377 
1378 def optimize_balls(*args):
1379  """
1380  optimize_balls(IMP::ParticlesTemp const & ps, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states, IMP::LogLevel ll)
1381  optimize_balls(IMP::ParticlesTemp const & ps, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states)
1382  optimize_balls(IMP::ParticlesTemp const & ps, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded)
1383  optimize_balls(IMP::ParticlesTemp const & ps, IMP::RestraintsTemp const & rs)
1384  optimize_balls(IMP::ParticlesTemp const & ps)
1385  """
1386  return _IMP_example.optimize_balls(*args)
1387 
1388 def optimize_assembly(*args):
1389  """
1390  optimize_assembly(Model m, IMP::ParticlesTemp const & components, IMP::RestraintsTemp const & interactions, IMP::RestraintsTemp const & other_restraints, BoundingBox3D bb, PairScore ev, double cutoff, IMP::PairPredicates const & excluded)
1391  optimize_assembly(Model m, IMP::ParticlesTemp const & components, IMP::RestraintsTemp const & interactions, IMP::RestraintsTemp const & other_restraints, BoundingBox3D bb, PairScore ev, double cutoff)
1392  """
1393  return _IMP_example.optimize_assembly(*args)
1394 
1395 def get_number_of_incidences(psa, psb, point_distance):
1396  """get_number_of_incidences(IMP::ParticlesTemp const & psa, IMP::ParticlesTemp const & psb, double point_distance) -> unsigned int"""
1397  return _IMP_example.get_number_of_incidences(psa, psb, point_distance)
1398 
1399 def create_chain_restraint(ps, length_factor, k, name):
1400  """create_chain_restraint(IMP::ParticlesTemp const & ps, double length_factor, double k, std::string name) -> Restraint"""
1401  return _IMP_example.create_chain_restraint(ps, length_factor, k, name)
1402 
1403 def create_excluded_volume(ps, k, name):
1404  """create_excluded_volume(IMP::ParticlesTemp const & ps, double k, std::string name) -> Restraint"""
1405  return _IMP_example.create_excluded_volume(ps, k, name)
1406 class ExampleTemplateClass3D(object):
1407  """Proxy of C++ IMP::example::ExampleTemplateClassD<(3)> class"""
1408  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1409 
1410  def __init__(self, *args):
1411  """
1412  __init__(IMP::example::ExampleTemplateClassD<(3)> self) -> ExampleTemplateClass3D
1413  __init__(IMP::example::ExampleTemplateClassD<(3)> self, Vector3D a, Vector3D b) -> ExampleTemplateClass3D
1414  """
1415  this = _IMP_example.new_ExampleTemplateClass3D(*args)
1416  try:
1417  self.this.append(this)
1418  except:
1419  self.this = this
1420 
1421  def get_point(self, i):
1422  """get_point(ExampleTemplateClass3D self, unsigned int i) -> Vector3D"""
1423  return _IMP_example.ExampleTemplateClass3D_get_point(self, i)
1424 
1425 
1426  def show(self, *args):
1427  """
1428  show(ExampleTemplateClass3D self, _ostream out)
1429  show(ExampleTemplateClass3D self)
1430  """
1431  return _IMP_example.ExampleTemplateClass3D_show(self, *args)
1432 
1433 
1434  def __str__(self):
1435  """__str__(ExampleTemplateClass3D self) -> std::string"""
1436  return _IMP_example.ExampleTemplateClass3D___str__(self)
1437 
1438 
1439  def __repr__(self):
1440  """__repr__(ExampleTemplateClass3D self) -> std::string"""
1441  return _IMP_example.ExampleTemplateClass3D___repr__(self)
1442 
1443  __swig_destroy__ = _IMP_example.delete_ExampleTemplateClass3D
1444  __del__ = lambda self: None
1445 ExampleTemplateClass3D_swigregister = _IMP_example.ExampleTemplateClass3D_swigregister
1446 ExampleTemplateClass3D_swigregister(ExampleTemplateClass3D)
1447 
1448 
1449 def get_module_version():
1450  """get_module_version() -> std::string const"""
1451  return _IMP_example.get_module_version()
1452 
1453 def get_example_path(fname):
1454  """get_example_path(std::string fname) -> std::string"""
1455  return _IMP_example.get_example_path(fname)
1456 
1457 def get_data_path(fname):
1458  """get_data_path(std::string fname) -> std::string"""
1459  return _IMP_example.get_data_path(fname)
1460 from . import _version_check
1461 _version_check.check_version(get_module_version())
1462 __version__ = get_module_version()
1463 
1464 
1465 
IMP::example::get_number_of_incidences
unsigned int get_number_of_incidences(const ParticlesTemp &psa, const ParticlesTemp &psb, double point_distance)
Definition: counting.h:23
IMP::SingletonModifier
A base class for modifiers of ParticlesTemp.
Definition: SingletonModifier.h:33
IMP::PairScore
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:38
IMP::SingletonModifier::apply_index
virtual void apply_index(Model *m, ParticleIndex v) const
IMP::UnaryFunction::evaluate
virtual double evaluate(double feature) const
Calculate score with respect to the given feature.
Definition: UnaryFunction.h:33
IMP::example::create_serial_mover
core::MonteCarloMover * create_serial_mover(const ParticlesTemp &ps)
IMP::example.PythonExamplePairScore
An example PairScore written in Python.
Definition: example/__init__.py:756
IMP::example.PythonExampleSingletonModifier
An example SingletonModifier written in Python.
Definition: example/__init__.py:826
IMP::container
Various classes to hold sets of particles.
IMP::core::XYZR::setup_particle
static XYZR setup_particle(Model *m, ParticleIndex pi)
Definition: XYZR.h:48
IMP::example.PythonExampleUnaryFunction
An example UnaryFunction written in Python.
Definition: example/__init__.py:783
IMP::Restraint::do_add_score_and_derivatives
virtual void do_add_score_and_derivatives(ScoreAccumulator sa) const
A restraint should override this to compute the score and derivatives.
IMP::cgal
Make CGAL functionality available to IMP.
IMP::example::optimize_assembly
void optimize_assembly(Model *m, const ParticlesTemp &components, const RestraintsTemp &interactions, const RestraintsTemp &other_restraints, const algebra::BoundingBox3D &bb, PairScore *ev, double cutoff, const PairPredicates &excluded=PairPredicates())
IMP::example::ExampleTemplateClassD
A line segment templated on the dimension.
Definition: ExampleTemplateClass.h:32
IMP::get_particles
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
IMP::Object::clear_caches
virtual void clear_caches()
Definition: Object.h:227
IMP::ParticleOutputs::do_get_outputs
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const =0
IMP::score_functor
Composable functors to implement scores via compile-time composition.
IMP::example::create_chain_restraint
Restraint * create_chain_restraint(const ParticlesTemp &ps, double length_factor, double k, std::string name)
Definition: creating_restraints.h:31
IMP::algebra::get_random_vector_in
Vector3D get_random_vector_in(const Cylinder3D &c)
Generate a random vector in a cylinder with uniform density.
IMP::example::optimize_balls
void optimize_balls(const ParticlesTemp &ps, const RestraintsTemp &rs=RestraintsTemp(), const PairPredicates &excluded=PairPredicates(), const OptimizerStates &opt_states=OptimizerStates(), LogLevel ll=DEFAULT)
IMP::statistics
Code to compute statistical measures.
IMP::Constraint
Implement a constraint on the Model.
Definition: Constraint.h:49
IMP::Model
Class for storing model, its restraints, constraints, and particles.
Definition: Model.h:72
IMP::example::ExampleObject
An example simple object which is reference counted.
Definition: ExampleObject.h:29
IMP::example::ExampleDecorator
A simple decorator which adds a name to a particle.
Definition: ExampleDecorator.h:32
IMP::example.PythonExampleConstraint
An example Constraint written in Python.
Definition: example/__init__.py:798
IMP::Object
Common base class for heavy weight IMP objects.
Definition: Object.h:106
IMP::container::ListSingletonContainer
Store a list of ParticleIndexes.
Definition: ListSingletonContainer.h:33
IMP::example.PythonExampleRestraint
An example restraint written in Python.
Definition: example/__init__.py:736
IMP::example::create_excluded_volume
Restraint * create_excluded_volume(const ParticlesTemp &ps, double k, std::string name)
Definition: creating_restraints.h:50
IMP::ParticleInputs::do_get_inputs
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const =0
IMP::example::ExampleRestraint
Restrain a particle to be in the x,y plane.
Definition: ExampleRestraint.h:25
IMP::core::XYZ
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
IMP::ModelObject::do_get_outputs
virtual ModelObjectsTemp do_get_outputs() const =0
IMP::core
Basic functionality that is expected to be used by a wide variety of IMP users.
IMP::algebra
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
IMP::Object::get_version_info
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Definition: Object.h:173
IMP::UnaryFunction::evaluate_with_derivative
virtual DerivativePair evaluate_with_derivative(double feature) const
Calculate score and derivative with respect to the given feature.
Definition: UnaryFunction.h:48
IMP::algebra::Vector3D
VectorD< 3 > Vector3D
Definition: VectorD.h:395
IMP::Object::set_check_level
void set_check_level(CheckLevel l)
IMP::example::ExamplePairScore
Apply a harmonic to the distance between two particles.
Definition: ExamplePairScore.h:25
IMP::example::get_example_path
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
IMP::ModelObject::get_model
Model * get_model() const
Definition: ModelObject.h:40
IMP::example::ExampleConstraint
A trivial constraint that just increments a counter.
Definition: ExampleConstraint.h:23
IMP::display
Output IMP model data in various file formats.
IMP::atom
Functionality for loading, creating, manipulating and scoring atomic structures.
IMP::example::get_data_path
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
IMP::rmf
Support for the RMF file format for storing hierarchical molecular data and markup.
IMP::UnaryFunction
Abstract single variable functor class for score functions.
Definition: UnaryFunction.h:25
IMP::ModelObject::do_get_inputs
virtual ModelObjectsTemp do_get_inputs() const =0
IMP::domino
Divide-and-conquer inferential optimization in discrete space.
IMP::PairScore::evaluate_index
virtual double evaluate_index(Model *m, const ParticleIndexPair &vt, DerivativeAccumulator *da) const =0
Compute the score and the derivative if needed.
IMP::Restraint
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:52