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IMP Reference Guide  2.8.0
The Integrative Modeling Platform
example/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.10
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 2007-2017 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 as _swig_python_version_info
16 if _swig_python_version_info >= (2, 7, 0):
17  def swig_import_helper():
18  import importlib
19  pkg = __name__.rpartition('.')[0]
20  mname = '.'.join((pkg, '_IMP_example')).lstrip('.')
21  try:
22  return importlib.import_module(mname)
23  except ImportError:
24  return importlib.import_module('_IMP_example')
25  _IMP_example = swig_import_helper()
26  del swig_import_helper
27 elif _swig_python_version_info >= (2, 6, 0):
28  def swig_import_helper():
29  from os.path import dirname
30  import imp
31  fp = None
32  try:
33  fp, pathname, description = imp.find_module('_IMP_example', [dirname(__file__)])
34  except ImportError:
35  import _IMP_example
36  return _IMP_example
37  if fp is not None:
38  try:
39  _mod = imp.load_module('_IMP_example', fp, pathname, description)
40  finally:
41  fp.close()
42  return _mod
43  _IMP_example = swig_import_helper()
44  del swig_import_helper
45 else:
46  import _IMP_example
47 del _swig_python_version_info
48 try:
49  _swig_property = property
50 except NameError:
51  pass # Python < 2.2 doesn't have 'property'.
52 
53 try:
54  import builtins as __builtin__
55 except ImportError:
56  import __builtin__
57 
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59  if (name == "thisown"):
60  return self.this.own(value)
61  if (name == "this"):
62  if type(value).__name__ == 'SwigPyObject':
63  self.__dict__[name] = value
64  return
65  method = class_type.__swig_setmethods__.get(name, None)
66  if method:
67  return method(self, value)
68  if (not static):
69  object.__setattr__(self, name, value)
70  else:
71  raise AttributeError("You cannot add attributes to %s" % self)
72 
73 
74 def _swig_setattr(self, class_type, name, value):
75  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
76 
77 
78 def _swig_getattr(self, class_type, name):
79  if (name == "thisown"):
80  return self.this.own()
81  method = class_type.__swig_getmethods__.get(name, None)
82  if method:
83  return method(self)
84  raise AttributeError("'%s' object has no attribute '%s'" % (class_type.__name__, name))
85 
86 
87 def _swig_repr(self):
88  try:
89  strthis = "proxy of " + self.this.__repr__()
90  except __builtin__.Exception:
91  strthis = ""
92  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
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 __builtin__.Exception:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_EXAMPLE_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_EXAMPLE_SwigPyIterator class."""
115 
116  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
117 
118  def __init__(self, *args, **kwargs):
119  raise AttributeError("No constructor defined - class is abstract")
120  __repr__ = _swig_repr
121  __swig_destroy__ = _IMP_example.delete_IMP_EXAMPLE_SwigPyIterator
122  __del__ = lambda self: None
123 
124  def value(self):
125  """value(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
126  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_value(self)
127 
128 
129  def incr(self, n=1):
130  """
131  incr(IMP_EXAMPLE_SwigPyIterator self, size_t n=1) -> IMP_EXAMPLE_SwigPyIterator
132  incr(IMP_EXAMPLE_SwigPyIterator self) -> IMP_EXAMPLE_SwigPyIterator
133  """
134  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_incr(self, n)
135 
136 
137  def decr(self, n=1):
138  """
139  decr(IMP_EXAMPLE_SwigPyIterator self, size_t n=1) -> IMP_EXAMPLE_SwigPyIterator
140  decr(IMP_EXAMPLE_SwigPyIterator self) -> IMP_EXAMPLE_SwigPyIterator
141  """
142  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_decr(self, n)
143 
144 
145  def distance(self, x):
146  """distance(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> ptrdiff_t"""
147  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_distance(self, x)
148 
149 
150  def equal(self, x):
151  """equal(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
152  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_equal(self, x)
153 
154 
155  def copy(self):
156  """copy(IMP_EXAMPLE_SwigPyIterator self) -> IMP_EXAMPLE_SwigPyIterator"""
157  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_copy(self)
158 
159 
160  def next(self):
161  """next(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
162  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_next(self)
163 
164 
165  def __next__(self):
166  """__next__(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
167  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___next__(self)
168 
169 
170  def previous(self):
171  """previous(IMP_EXAMPLE_SwigPyIterator self) -> PyObject *"""
172  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_previous(self)
173 
174 
175  def advance(self, n):
176  """advance(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
177  return _IMP_example.IMP_EXAMPLE_SwigPyIterator_advance(self, n)
178 
179 
180  def __eq__(self, x):
181  """__eq__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
182  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___eq__(self, x)
183 
184 
185  def __ne__(self, x):
186  """__ne__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> bool"""
187  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___ne__(self, x)
188 
189 
190  def __iadd__(self, n):
191  """__iadd__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
192  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___iadd__(self, n)
193 
194 
195  def __isub__(self, n):
196  """__isub__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
197  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___isub__(self, n)
198 
199 
200  def __add__(self, n):
201  """__add__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator"""
202  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___add__(self, n)
203 
204 
205  def __sub__(self, *args):
206  """
207  __sub__(IMP_EXAMPLE_SwigPyIterator self, ptrdiff_t n) -> IMP_EXAMPLE_SwigPyIterator
208  __sub__(IMP_EXAMPLE_SwigPyIterator self, IMP_EXAMPLE_SwigPyIterator x) -> ptrdiff_t
209  """
210  return _IMP_example.IMP_EXAMPLE_SwigPyIterator___sub__(self, *args)
211 
212  def __iter__(self):
213  return self
214 IMP_EXAMPLE_SwigPyIterator_swigregister = _IMP_example.IMP_EXAMPLE_SwigPyIterator_swigregister
215 IMP_EXAMPLE_SwigPyIterator_swigregister(IMP_EXAMPLE_SwigPyIterator)
216 
217 
218 _value_types=[]
219 _object_types=[]
220 _raii_types=[]
221 _plural_types=[]
222 
223 IMP_DEBUG = _IMP_example.IMP_DEBUG
224 IMP_RELEASE = _IMP_example.IMP_RELEASE
225 IMP_SILENT = _IMP_example.IMP_SILENT
226 IMP_PROGRESS = _IMP_example.IMP_PROGRESS
227 IMP_TERSE = _IMP_example.IMP_TERSE
228 IMP_VERBOSE = _IMP_example.IMP_VERBOSE
229 IMP_MEMORY = _IMP_example.IMP_MEMORY
230 IMP_NONE = _IMP_example.IMP_NONE
231 IMP_USAGE = _IMP_example.IMP_USAGE
232 IMP_INTERNAL = _IMP_example.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_example.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_example.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_example.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_example.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_example.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_example.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_example.IMPKERNEL_SHOW_WARNINGS
242 
243 import sys
244 class _DirectorObjects(object):
245  """@internal Simple class to keep references to director objects
246  to prevent premature deletion."""
247  def __init__(self):
248  self._objects = []
249  def register(self, obj):
250  """Take a reference to a director object; will only work for
251  refcounted C++ classes"""
252  if hasattr(obj, 'get_ref_count'):
253  self._objects.append(obj)
254  def cleanup(self):
255  """Only drop our reference and allow cleanup by Python if no other
256  Python references exist (we hold 3 references: one in self._objects,
257  one in x, and one in the argument list for getrefcount) *and* no
258  other C++ references exist (the Python object always holds one)"""
259  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
260  or x.get_ref_count() > 1]
261 # Do in two steps so the references are kept until the end of the
262 # function (deleting references may trigger a fresh call to this method)
263  self._objects = objs
264  def get_object_count(self):
265  """Get number of director objects (useful for testing only)"""
266  return len(self._objects)
267 _director_objects = _DirectorObjects()
268 
269 class _ostream(object):
270  """Proxy of C++ std::ostream class."""
271 
272  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
273 
274  def __init__(self, *args, **kwargs):
275  raise AttributeError("No constructor defined")
276  __repr__ = _swig_repr
277 
278  def write(self, osa_buf):
279  """write(_ostream self, char const * osa_buf)"""
280  return _IMP_example._ostream_write(self, osa_buf)
281 
282 _ostream_swigregister = _IMP_example._ostream_swigregister
283 _ostream_swigregister(_ostream)
284 
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_example.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_example.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_example.IMP_HAS_NOEXCEPT
288 import IMP
289 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_FILESYSTEM
290 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
291 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_example.IMP_CGAL_HAS_BOOST_RANDOM
292 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_SYSTEM
293 IMPCGAL_SHOW_WARNINGS = _IMP_example.IMPCGAL_SHOW_WARNINGS
294 import IMP.cgal
295 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_example.IMP_ALGEBRA_HAS_IMP_CGAL
296 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
297 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
298 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_RANDOM
299 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_SYSTEM
300 IMP_ALGEBRA_HAS_CGAL = _IMP_example.IMP_ALGEBRA_HAS_CGAL
301 IMP_ALGEBRA_HAS_ANN = _IMP_example.IMP_ALGEBRA_HAS_ANN
302 IMPALGEBRA_SHOW_WARNINGS = _IMP_example.IMPALGEBRA_SHOW_WARNINGS
303 import IMP.algebra
304 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_example.IMP_DISPLAY_HAS_IMP_CGAL
305 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
306 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
307 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_example.IMP_DISPLAY_HAS_BOOST_RANDOM
308 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_SYSTEM
309 IMP_DISPLAY_HAS_CGAL = _IMP_example.IMP_DISPLAY_HAS_CGAL
310 IMPDISPLAY_SHOW_WARNINGS = _IMP_example.IMPDISPLAY_SHOW_WARNINGS
311 import IMP.display
312 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
313 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
314 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
315 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
316 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
317 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_CGAL
318 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_example.IMP_SCORE_FUNCTOR_HAS_HDF5
319 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_example.IMPSCOREFUNCTOR_SHOW_WARNINGS
320 import IMP.score_functor
321 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_example.IMP_STATISTICS_HAS_IMP_CGAL
322 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
323 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
324 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_example.IMP_STATISTICS_HAS_BOOST_RANDOM
325 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_SYSTEM
326 IMP_STATISTICS_HAS_CGAL = _IMP_example.IMP_STATISTICS_HAS_CGAL
327 IMPSTATISTICS_SHOW_WARNINGS = _IMP_example.IMPSTATISTICS_SHOW_WARNINGS
328 import IMP.statistics
329 IMP_CORE_HAS_IMP_CGAL = _IMP_example.IMP_CORE_HAS_IMP_CGAL
330 IMP_CORE_HAS_IMP_KERNEL = _IMP_example.IMP_CORE_HAS_IMP_KERNEL
331 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_FILESYSTEM
332 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
333 IMP_CORE_HAS_BOOST_RANDOM = _IMP_example.IMP_CORE_HAS_BOOST_RANDOM
334 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_SYSTEM
335 IMP_CORE_HAS_CGAL = _IMP_example.IMP_CORE_HAS_CGAL
336 IMP_CORE_HAS_HDF5 = _IMP_example.IMP_CORE_HAS_HDF5
337 IMPCORE_SHOW_WARNINGS = _IMP_example.IMPCORE_SHOW_WARNINGS
338 import IMP.core
339 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_example.IMP_CONTAINER_HAS_IMP_ALGEBRA
340 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_example.IMP_CONTAINER_HAS_IMP_CGAL
341 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_example.IMP_CONTAINER_HAS_IMP_DISPLAY
342 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_example.IMP_CONTAINER_HAS_IMP_KERNEL
343 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
344 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
345 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
346 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_example.IMP_CONTAINER_HAS_BOOST_RANDOM
347 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_SYSTEM
348 IMP_CONTAINER_HAS_CGAL = _IMP_example.IMP_CONTAINER_HAS_CGAL
349 IMP_CONTAINER_HAS_HDF5 = _IMP_example.IMP_CONTAINER_HAS_HDF5
350 IMPCONTAINER_SHOW_WARNINGS = _IMP_example.IMPCONTAINER_SHOW_WARNINGS
351 import IMP.container
352 IMP_ATOM_HAS_IMP_CGAL = _IMP_example.IMP_ATOM_HAS_IMP_CGAL
353 IMP_ATOM_HAS_IMP_KERNEL = _IMP_example.IMP_ATOM_HAS_IMP_KERNEL
354 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
355 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
356 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_example.IMP_ATOM_HAS_BOOST_RANDOM
357 IMP_ATOM_HAS_BOOST_REGEX = _IMP_example.IMP_ATOM_HAS_BOOST_REGEX
358 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_example.IMP_ATOM_HAS_BOOST_SYSTEM
359 IMP_ATOM_HAS_CGAL = _IMP_example.IMP_ATOM_HAS_CGAL
360 IMP_ATOM_HAS_HDF5 = _IMP_example.IMP_ATOM_HAS_HDF5
361 IMPATOM_SHOW_WARNINGS = _IMP_example.IMPATOM_SHOW_WARNINGS
362 IMP_ATOM_TYPE_INDEX = _IMP_example.IMP_ATOM_TYPE_INDEX
363 IMP_RESIDUE_TYPE_INDEX = _IMP_example.IMP_RESIDUE_TYPE_INDEX
364 IMP_HIERARCHY_TYPE_INDEX = _IMP_example.IMP_HIERARCHY_TYPE_INDEX
365 import IMP.atom
366 IMP_RMF_HAS_IMP_CGAL = _IMP_example.IMP_RMF_HAS_IMP_CGAL
367 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
368 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_FILESYSTEM
369 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
370 IMP_RMF_HAS_BOOST_RANDOM = _IMP_example.IMP_RMF_HAS_BOOST_RANDOM
371 IMP_RMF_HAS_BOOST_REGEX = _IMP_example.IMP_RMF_HAS_BOOST_REGEX
372 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_SYSTEM
373 IMP_RMF_HAS_CGAL = _IMP_example.IMP_RMF_HAS_CGAL
374 IMP_RMF_HAS_HDF5 = _IMP_example.IMP_RMF_HAS_HDF5
375 IMPRMF_SHOW_WARNINGS = _IMP_example.IMPRMF_SHOW_WARNINGS
376 import IMP.rmf
377 import RMF
378 IMP_DOMINO_HAS_IMP_ATOM = _IMP_example.IMP_DOMINO_HAS_IMP_ATOM
379 IMP_DOMINO_HAS_IMP_CGAL = _IMP_example.IMP_DOMINO_HAS_IMP_CGAL
380 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_example.IMP_DOMINO_HAS_IMP_KERNEL
381 IMP_DOMINO_HAS_IMP_RMF = _IMP_example.IMP_DOMINO_HAS_IMP_RMF
382 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
383 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_FILESYSTEM
384 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
385 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_example.IMP_DOMINO_HAS_BOOST_RANDOM
386 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_example.IMP_DOMINO_HAS_BOOST_REGEX
387 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_SYSTEM
388 IMP_DOMINO_HAS_CGAL = _IMP_example.IMP_DOMINO_HAS_CGAL
389 IMP_DOMINO_HAS_HDF5 = _IMP_example.IMP_DOMINO_HAS_HDF5
390 IMP_DOMINO_HAS_RMF = _IMP_example.IMP_DOMINO_HAS_RMF
391 IMPDOMINO_SHOW_WARNINGS = _IMP_example.IMPDOMINO_SHOW_WARNINGS
392 import RMF_HDF5
393 import IMP.domino
394 IMP_EXAMPLE_HAS_IMP_ALGEBRA = _IMP_example.IMP_EXAMPLE_HAS_IMP_ALGEBRA
395 IMP_EXAMPLE_HAS_IMP_CGAL = _IMP_example.IMP_EXAMPLE_HAS_IMP_CGAL
396 IMP_EXAMPLE_HAS_IMP_DISPLAY = _IMP_example.IMP_EXAMPLE_HAS_IMP_DISPLAY
397 IMP_EXAMPLE_HAS_IMP_KERNEL = _IMP_example.IMP_EXAMPLE_HAS_IMP_KERNEL
398 IMP_EXAMPLE_HAS_IMP_RMF = _IMP_example.IMP_EXAMPLE_HAS_IMP_RMF
399 IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR
400 IMP_EXAMPLE_HAS_IMP_STATISTICS = _IMP_example.IMP_EXAMPLE_HAS_IMP_STATISTICS
401 IMP_EXAMPLE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_FILESYSTEM
402 IMP_EXAMPLE_HAS_BOOST_GRAPH = _IMP_example.IMP_EXAMPLE_HAS_BOOST_GRAPH
403 IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS
404 IMP_EXAMPLE_HAS_BOOST_RANDOM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_RANDOM
405 IMP_EXAMPLE_HAS_BOOST_REGEX = _IMP_example.IMP_EXAMPLE_HAS_BOOST_REGEX
406 IMP_EXAMPLE_HAS_BOOST_SYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_SYSTEM
407 IMP_EXAMPLE_HAS_CGAL = _IMP_example.IMP_EXAMPLE_HAS_CGAL
408 IMP_EXAMPLE_HAS_HDF5 = _IMP_example.IMP_EXAMPLE_HAS_HDF5
409 IMP_EXAMPLE_HAS_RMF = _IMP_example.IMP_EXAMPLE_HAS_RMF
410 IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY = _IMP_example.IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY
411 IMPEXAMPLE_SHOW_WARNINGS = _IMP_example.IMPEXAMPLE_SHOW_WARNINGS
412 
413 _object_types.append("ExampleRestraint")
414 
415 
416 def _object_cast_to_ExampleRestraint(o):
417  """_object_cast_to_ExampleRestraint(Object o) -> ExampleRestraint"""
418  return _IMP_example._object_cast_to_ExampleRestraint(o)
419 
420 def ExampleDecorators(l=[]):
421  return [ExampleDecorator(x) for x in l]
422 _plural_types.append("ExampleDecorators")
423 
424 
425 _value_types.append("ExampleDecorator")
426 
427 
428 _object_types.append("ExampleUnaryFunction")
429 
430 
431 def _object_cast_to_ExampleUnaryFunction(o):
432  """_object_cast_to_ExampleUnaryFunction(Object o) -> ExampleUnaryFunction"""
433  return _IMP_example._object_cast_to_ExampleUnaryFunction(o)
434 
435 _object_types.append("ExampleSingletonModifier")
436 
437 
438 def _object_cast_to_ExampleSingletonModifier(o):
439  """_object_cast_to_ExampleSingletonModifier(Object o) -> ExampleSingletonModifier"""
440  return _IMP_example._object_cast_to_ExampleSingletonModifier(o)
441 
442 _object_types.append("ExamplePairScore")
443 
444 
445 def _object_cast_to_ExamplePairScore(o):
446  """_object_cast_to_ExamplePairScore(Object o) -> ExamplePairScore"""
447  return _IMP_example._object_cast_to_ExamplePairScore(o)
448 
449 _object_types.append("ExampleSubsetFilterTable")
450 
451 
452 def _object_cast_to_ExampleSubsetFilterTable(o):
453  """_object_cast_to_ExampleSubsetFilterTable(Object o) -> ExampleSubsetFilterTable"""
454  return _IMP_example._object_cast_to_ExampleSubsetFilterTable(o)
455 
456 _object_types.append("ExampleConstraint")
457 
458 
459 def _object_cast_to_ExampleConstraint(o):
460  """_object_cast_to_ExampleConstraint(Object o) -> ExampleConstraint"""
461  return _IMP_example._object_cast_to_ExampleConstraint(o)
462 
463 _object_types.append("ExampleObject")
464 
465 
466 def _object_cast_to_ExampleObject(o):
467  """_object_cast_to_ExampleObject(Object o) -> ExampleObject"""
468  return _IMP_example._object_cast_to_ExampleObject(o)
469 
470 ExampleTemplateClass3Ds=list
471 _plural_types.append("ExampleTemplateClass3Ds")
472 _value_types.append("ExampleTemplateClass3D")
473 
474 
475 def create_model_and_particles():
476  m = IMP.Model()
479  IMP.algebra.Vector3D(10,10,10))
480  for i in range(0,100):
481  p = m.add_particle("p")
482  sc.add(p)
485  d.set_coordinates_are_optimized(True)
486  return (m, sc)
487 
488 
489 
491  """An example restraint written in Python.
492  This should be functionally equivalent to the C++ ExampleRestraint.
493  """
494  def __init__(self, m, p, k):
495  IMP.Restraint.__init__(self, m, "PythonExampleRestraint%1%")
496  self.p, self.k = p, k
497 
498  def do_add_score_and_derivatives(self, sa):
499  d = IMP.core.XYZ(self.get_model(), self.p)
500  score = .5 * self.k * d.get_z() * d.get_z()
501  if sa.get_derivative_accumulator():
502  deriv = self.k * d.get_z()
503  d.add_to_derivative(2, deriv, sa.get_derivative_accumulator())
504  sa.add_score(score)
505 
506  def do_get_inputs(self):
507  return [self.get_model().get_particle(self.p)]
508 
509 
510 
511 
513  """An example PairScore written in Python.
514  This should be functionally equivalent to the C++ ExamplePairScore.
515  """
516  def __init__(self, x0, k):
517  IMP.PairScore.__init__(self)
518  self.x0, self.k = x0, k
519 
520  def evaluate_index(self, m, pip, da):
521  d0 = IMP.core.XYZ(m, pip[0])
522  d1 = IMP.core.XYZ(m, pip[1])
523  diff = (d0.get_coordinates()
524  - d1.get_coordinates()).get_magnitude() - self.x0
525  score = .5 * self.k * diff * diff
526  if da:
527 # derivatives are requested
528  delta = d0.get_coordinates() - d1.get_coordinates()
529  udelta = delta.get_unit_vector()
530  dv = self.k * diff
531  d0.add_to_derivatives(udelta * dv, da)
532  d1.add_to_derivatives(-udelta * dv, da)
533  return score
534 
535  def do_get_inputs(self, m, pis):
536  return IMP.get_particles(m, pis)
537 
538 
539 
540 
542  """An example UnaryFunction written in Python.
543  This should be functionally equivalent to the C++ ExampleUnaryFunction.
544  """
545  def __init__(self, center, k):
546  IMP.UnaryFunction.__init__(self)
547  self.center, self.k = center, k
548 
549  def evaluate_with_derivative(self, feature):
550  return (self.evaluate(feature), self.k * (feature - self.center))
551 
552  def evaluate(self, feature):
553  return .5 * self.k * (feature - self.center) * (feature - self.center)
554 
555 
556 
557 
559  """An example Constraint written in Python.
560  This should be functionally equivalent to the C++ ExampleConstraint.
561  """
562 
563  k = None
564 
565  def __init__(self, p):
566  IMP.Constraint.__init__(self, p.get_model(), "ExampleConstraint%1%")
567  self.p = p
568  if self.k is None:
569  PythonExampleConstraint.k = IMP.IntKey("Constraint key")
570  if not p.has_attribute(self.k):
571  p.add_attribute(self.k, 0)
572 
573  def do_update_attributes(self):
574  self.p.set_value(self.k, self.p.get_value(self.k) + 1)
575 
576  def do_update_derivatives(self, da):
577  pass
578 
579  def do_get_inputs(self):
580  return [self.p]
581 
582  def do_get_outputs(self):
583  return [self.p]
584 
585 
586 
587 
589  """An example SingletonModifier written in Python.
590  This should be functionally equivalent to the C++
591  ExampleSingletonModifier.
592  """
593 
594  def __init__(self, bb):
595  IMP.SingletonModifier.__init__(self, "ExampleSingletonModifier%1%")
596  self.bb = bb
597 
598  def apply_index(self, m, pi):
599  d = IMP.core.XYZ(m, pi)
600  for i in range(3):
601 # shift the coordinate until it is in the box
602  while d.get_coordinate(i) < self.bb.get_corner(0)[i]:
603  d.set_coordinate(i,d.get_coordinate(i) + \
604  (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
605  while d.get_coordinate(i) > self.bb.get_corner(1)[i]:
606  d.set_coordinate(i,d.get_coordinate(i) - \
607  (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
608 
609  def do_get_inputs(self, m, pis):
610  return IMP.get_particles(m, pis)
611 
612  def do_get_outputs(self, m, pis):
613  return self.do_get_inputs(m, pis)
614 
615 
617  """Proxy of C++ IMP::example::ExampleRestraint class."""
618 
619  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
620 
621  def __init__(self, m, p, k):
622  """__init__(IMP::example::ExampleRestraint self, Model m, ParticleIndex p, double k) -> ExampleRestraint"""
623  this = _IMP_example.new_ExampleRestraint(m, p, k)
624  try:
625  self.this.append(this)
626  except __builtin__.Exception:
627  self.this = this
628 
629  def do_add_score_and_derivatives(self, sa):
630  """do_add_score_and_derivatives(ExampleRestraint self, ScoreAccumulator sa)"""
631  return _IMP_example.ExampleRestraint_do_add_score_and_derivatives(self, sa)
632 
633 
634  def do_get_inputs(self):
635  """do_get_inputs(ExampleRestraint self) -> IMP::ModelObjectsTemp"""
636  return _IMP_example.ExampleRestraint_do_get_inputs(self)
637 
638 
639  def get_version_info(self):
640  """get_version_info(ExampleRestraint self) -> VersionInfo"""
641  return _IMP_example.ExampleRestraint_get_version_info(self)
642 
643 
644  def __str__(self):
645  """__str__(ExampleRestraint self) -> std::string"""
646  return _IMP_example.ExampleRestraint___str__(self)
647 
648 
649  def __repr__(self):
650  """__repr__(ExampleRestraint self) -> std::string"""
651  return _IMP_example.ExampleRestraint___repr__(self)
652 
653 
654  @staticmethod
655  def get_from(o):
656  return _object_cast_to_ExampleRestraint(o)
657 
658 ExampleRestraint_swigregister = _IMP_example.ExampleRestraint_swigregister
659 ExampleRestraint_swigregister(ExampleRestraint)
660 
662  """Proxy of C++ IMP::example::ExampleDecorator class."""
663 
664  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
665 
666  def get_decorator_name(self):
667  """get_decorator_name(ExampleDecorator self) -> std::string"""
668  return _IMP_example.ExampleDecorator_get_decorator_name(self)
669 
670 
671  def set_decorator_name(self, nm):
672  """set_decorator_name(ExampleDecorator self, std::string nm)"""
673  return _IMP_example.ExampleDecorator_set_decorator_name(self, nm)
674 
675 
676  def __init__(self, *args):
677  """
678  __init__(IMP::example::ExampleDecorator self) -> ExampleDecorator
679  __init__(IMP::example::ExampleDecorator self, Model m, ParticleIndex id) -> ExampleDecorator
680  __init__(IMP::example::ExampleDecorator self, _ParticleAdaptor d) -> ExampleDecorator
681  """
682  this = _IMP_example.new_ExampleDecorator(*args)
683  try:
684  self.this.append(this)
685  except __builtin__.Exception:
686  self.this = this
687 
688  def get_is_setup(*args):
689  """
690  get_is_setup(Model m, ParticleIndex pi) -> bool
691  get_is_setup(_ParticleAdaptor p) -> bool
692  """
693  return _IMP_example.ExampleDecorator_get_is_setup(*args)
694 
695  get_is_setup = staticmethod(get_is_setup)
696 
697  def show(self, *args):
698  """
699  show(ExampleDecorator self, _ostream out)
700  show(ExampleDecorator self)
701  """
702  return _IMP_example.ExampleDecorator_show(self, *args)
703 
704 
705  def setup_particle(*args):
706  """
707  setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
708  setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
709  """
710  return _IMP_example.ExampleDecorator_setup_particle(*args)
711 
712  setup_particle = staticmethod(setup_particle)
713 
714  def add_attribute(self, *args):
715  """
716  add_attribute(ExampleDecorator self, FloatKey k, IMP::Float v, bool opt)
717  add_attribute(ExampleDecorator self, FloatKey a0, IMP::Float a1)
718  add_attribute(ExampleDecorator self, IntKey a0, IMP::Int a1)
719  add_attribute(ExampleDecorator self, StringKey a0, IMP::String a1)
720  add_attribute(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
721  add_attribute(ExampleDecorator self, ObjectKey a0, Object a1)
722  """
723  return _IMP_example.ExampleDecorator_add_attribute(self, *args)
724 
725 
726  def get_value(self, *args):
727  """
728  get_value(ExampleDecorator self, FloatKey a0) -> IMP::Float
729  get_value(ExampleDecorator self, IntKey a0) -> IMP::Int
730  get_value(ExampleDecorator self, StringKey a0) -> IMP::String
731  get_value(ExampleDecorator self, ParticleIndexKey a0) -> Particle
732  get_value(ExampleDecorator self, ObjectKey a0) -> Object
733  """
734  return _IMP_example.ExampleDecorator_get_value(self, *args)
735 
736 
737  def set_value(self, *args):
738  """
739  set_value(ExampleDecorator self, FloatKey a0, IMP::Float a1)
740  set_value(ExampleDecorator self, IntKey a0, IMP::Int a1)
741  set_value(ExampleDecorator self, StringKey a0, IMP::String a1)
742  set_value(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
743  set_value(ExampleDecorator self, ObjectKey a0, Object a1)
744  """
745  return _IMP_example.ExampleDecorator_set_value(self, *args)
746 
747 
748  def remove_attribute(self, *args):
749  """
750  remove_attribute(ExampleDecorator self, FloatKey a0)
751  remove_attribute(ExampleDecorator self, IntKey a0)
752  remove_attribute(ExampleDecorator self, StringKey a0)
753  remove_attribute(ExampleDecorator self, ParticleIndexKey a0)
754  remove_attribute(ExampleDecorator self, ObjectKey a0)
755  """
756  return _IMP_example.ExampleDecorator_remove_attribute(self, *args)
757 
758 
759  def has_attribute(self, *args):
760  """
761  has_attribute(ExampleDecorator self, FloatKey a0) -> bool
762  has_attribute(ExampleDecorator self, IntKey a0) -> bool
763  has_attribute(ExampleDecorator self, StringKey a0) -> bool
764  has_attribute(ExampleDecorator self, ParticleIndexKey a0) -> bool
765  has_attribute(ExampleDecorator self, ObjectKey a0) -> bool
766  """
767  return _IMP_example.ExampleDecorator_has_attribute(self, *args)
768 
769 
770  def get_derivative(self, a0):
771  """get_derivative(ExampleDecorator self, FloatKey a0) -> double"""
772  return _IMP_example.ExampleDecorator_get_derivative(self, a0)
773 
774 
775  def get_name(self):
776  """get_name(ExampleDecorator self) -> std::string"""
777  return _IMP_example.ExampleDecorator_get_name(self)
778 
779 
780  def clear_caches(self):
781  """clear_caches(ExampleDecorator self)"""
782  return _IMP_example.ExampleDecorator_clear_caches(self)
783 
784 
785  def set_name(self, a0):
786  """set_name(ExampleDecorator self, std::string a0)"""
787  return _IMP_example.ExampleDecorator_set_name(self, a0)
788 
789 
790  def set_check_level(self, a0):
791  """set_check_level(ExampleDecorator self, IMP::CheckLevel a0)"""
792  return _IMP_example.ExampleDecorator_set_check_level(self, a0)
793 
794 
795  def add_to_derivative(self, a0, a1, a2):
796  """add_to_derivative(ExampleDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
797  return _IMP_example.ExampleDecorator_add_to_derivative(self, a0, a1, a2)
798 
799 
800  def set_is_optimized(self, a0, a1):
801  """set_is_optimized(ExampleDecorator self, FloatKey a0, bool a1)"""
802  return _IMP_example.ExampleDecorator_set_is_optimized(self, a0, a1)
803 
804 
805  def get_is_optimized(self, a0):
806  """get_is_optimized(ExampleDecorator self, FloatKey a0) -> bool"""
807  return _IMP_example.ExampleDecorator_get_is_optimized(self, a0)
808 
809 
810  def get_check_level(self):
811  """get_check_level(ExampleDecorator self) -> IMP::CheckLevel"""
812  return _IMP_example.ExampleDecorator_get_check_level(self)
813 
814 
815  def __eq__(self, *args):
816  """
817  __eq__(ExampleDecorator self, ExampleDecorator o) -> bool
818  __eq__(ExampleDecorator self, Particle d) -> bool
819  """
820  return _IMP_example.ExampleDecorator___eq__(self, *args)
821 
822 
823  def __ne__(self, *args):
824  """
825  __ne__(ExampleDecorator self, ExampleDecorator o) -> bool
826  __ne__(ExampleDecorator self, Particle d) -> bool
827  """
828  return _IMP_example.ExampleDecorator___ne__(self, *args)
829 
830 
831  def __le__(self, *args):
832  """
833  __le__(ExampleDecorator self, ExampleDecorator o) -> bool
834  __le__(ExampleDecorator self, Particle d) -> bool
835  """
836  return _IMP_example.ExampleDecorator___le__(self, *args)
837 
838 
839  def __lt__(self, *args):
840  """
841  __lt__(ExampleDecorator self, ExampleDecorator o) -> bool
842  __lt__(ExampleDecorator self, Particle d) -> bool
843  """
844  return _IMP_example.ExampleDecorator___lt__(self, *args)
845 
846 
847  def __ge__(self, *args):
848  """
849  __ge__(ExampleDecorator self, ExampleDecorator o) -> bool
850  __ge__(ExampleDecorator self, Particle d) -> bool
851  """
852  return _IMP_example.ExampleDecorator___ge__(self, *args)
853 
854 
855  def __gt__(self, *args):
856  """
857  __gt__(ExampleDecorator self, ExampleDecorator o) -> bool
858  __gt__(ExampleDecorator self, Particle d) -> bool
859  """
860  return _IMP_example.ExampleDecorator___gt__(self, *args)
861 
862 
863  def __hash__(self):
864  """__hash__(ExampleDecorator self) -> std::size_t"""
865  return _IMP_example.ExampleDecorator___hash__(self)
866 
867 
868  def __str__(self):
869  """__str__(ExampleDecorator self) -> std::string"""
870  return _IMP_example.ExampleDecorator___str__(self)
871 
872 
873  def __repr__(self):
874  """__repr__(ExampleDecorator self) -> std::string"""
875  return _IMP_example.ExampleDecorator___repr__(self)
876 
877  __swig_destroy__ = _IMP_example.delete_ExampleDecorator
878  __del__ = lambda self: None
879 ExampleDecorator_swigregister = _IMP_example.ExampleDecorator_swigregister
880 ExampleDecorator_swigregister(ExampleDecorator)
881 
882 def ExampleDecorator_get_is_setup(*args):
883  """
884  get_is_setup(Model m, ParticleIndex pi) -> bool
885  ExampleDecorator_get_is_setup(_ParticleAdaptor p) -> bool
886  """
887  return _IMP_example.ExampleDecorator_get_is_setup(*args)
888 
889 def ExampleDecorator_setup_particle(*args):
890  """
891  setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
892  ExampleDecorator_setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
893  """
894  return _IMP_example.ExampleDecorator_setup_particle(*args)
895 
896 
897 def __lshift__(out, n):
898  """__lshift__(_ostream out, ExampleDecorator n) -> _ostream"""
899  return _IMP_example.__lshift__(out, n)
901  """Proxy of C++ IMP::example::ExampleUnaryFunction class."""
902 
903  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
904 
905  def __init__(self, center, k):
906  """__init__(IMP::example::ExampleUnaryFunction self, IMP::Float center, IMP::Float k) -> ExampleUnaryFunction"""
907  this = _IMP_example.new_ExampleUnaryFunction(center, k)
908  try:
909  self.this.append(this)
910  except __builtin__.Exception:
911  self.this = this
912 
913  def get_version_info(self):
914  """get_version_info(ExampleUnaryFunction self) -> VersionInfo"""
915  return _IMP_example.ExampleUnaryFunction_get_version_info(self)
916 
917 
918  def __str__(self):
919  """__str__(ExampleUnaryFunction self) -> std::string"""
920  return _IMP_example.ExampleUnaryFunction___str__(self)
921 
922 
923  def __repr__(self):
924  """__repr__(ExampleUnaryFunction self) -> std::string"""
925  return _IMP_example.ExampleUnaryFunction___repr__(self)
926 
927 
928  @staticmethod
929  def get_from(o):
930  return _object_cast_to_ExampleUnaryFunction(o)
931 
932 ExampleUnaryFunction_swigregister = _IMP_example.ExampleUnaryFunction_swigregister
933 ExampleUnaryFunction_swigregister(ExampleUnaryFunction)
934 
936  """Proxy of C++ IMP::example::ExampleObject class."""
937 
938  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
939 
940  def __init__(self, data):
941  """__init__(IMP::example::ExampleObject self, IMP::Floats const & data) -> ExampleObject"""
942  this = _IMP_example.new_ExampleObject(data)
943  try:
944  self.this.append(this)
945  except __builtin__.Exception:
946  self.this = this
947 
948  def get_data(self, i):
949  """get_data(ExampleObject self, unsigned int i) -> double"""
950  return _IMP_example.ExampleObject_get_data(self, i)
951 
952 
953  def get_version_info(self):
954  """get_version_info(ExampleObject self) -> VersionInfo"""
955  return _IMP_example.ExampleObject_get_version_info(self)
956 
957 
958  def __str__(self):
959  """__str__(ExampleObject self) -> std::string"""
960  return _IMP_example.ExampleObject___str__(self)
961 
962 
963  def __repr__(self):
964  """__repr__(ExampleObject self) -> std::string"""
965  return _IMP_example.ExampleObject___repr__(self)
966 
967 
968  @staticmethod
969  def get_from(o):
970  return _object_cast_to_ExampleObject(o)
971 
972 ExampleObject_swigregister = _IMP_example.ExampleObject_swigregister
973 ExampleObject_swigregister(ExampleObject)
974 
976  """Proxy of C++ IMP::example::ExampleSingletonModifier class."""
977 
978  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
979 
980  def __init__(self, bb):
981  """__init__(IMP::example::ExampleSingletonModifier self, BoundingBox3D bb) -> ExampleSingletonModifier"""
982  this = _IMP_example.new_ExampleSingletonModifier(bb)
983  try:
984  self.this.append(this)
985  except __builtin__.Exception:
986  self.this = this
987 
988  def do_get_inputs(self, m, pis):
989  """do_get_inputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
990  return _IMP_example.ExampleSingletonModifier_do_get_inputs(self, m, pis)
991 
992 
993  def do_get_outputs(self, m, pis):
994  """do_get_outputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
995  return _IMP_example.ExampleSingletonModifier_do_get_outputs(self, m, pis)
996 
997 
998  def get_version_info(self):
999  """get_version_info(ExampleSingletonModifier self) -> VersionInfo"""
1000  return _IMP_example.ExampleSingletonModifier_get_version_info(self)
1001 
1002 
1003  def __str__(self):
1004  """__str__(ExampleSingletonModifier self) -> std::string"""
1005  return _IMP_example.ExampleSingletonModifier___str__(self)
1006 
1007 
1008  def __repr__(self):
1009  """__repr__(ExampleSingletonModifier self) -> std::string"""
1010  return _IMP_example.ExampleSingletonModifier___repr__(self)
1011 
1012 
1013  @staticmethod
1014  def get_from(o):
1015  return _object_cast_to_ExampleSingletonModifier(o)
1016 
1017 ExampleSingletonModifier_swigregister = _IMP_example.ExampleSingletonModifier_swigregister
1018 ExampleSingletonModifier_swigregister(ExampleSingletonModifier)
1019 
1021  """Proxy of C++ IMP::example::ExamplePairScore class."""
1022 
1023  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1024 
1025  def __init__(self, x0, k):
1026  """__init__(IMP::example::ExamplePairScore self, double x0, double k) -> ExamplePairScore"""
1027  this = _IMP_example.new_ExamplePairScore(x0, k)
1028  try:
1029  self.this.append(this)
1030  except __builtin__.Exception:
1031  self.this = this
1032 
1033  def do_get_inputs(self, m, pis):
1034  """do_get_inputs(ExamplePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1035  return _IMP_example.ExamplePairScore_do_get_inputs(self, m, pis)
1036 
1037 
1038  def get_version_info(self):
1039  """get_version_info(ExamplePairScore self) -> VersionInfo"""
1040  return _IMP_example.ExamplePairScore_get_version_info(self)
1041 
1042 
1043  def __str__(self):
1044  """__str__(ExamplePairScore self) -> std::string"""
1045  return _IMP_example.ExamplePairScore___str__(self)
1046 
1047 
1048  def __repr__(self):
1049  """__repr__(ExamplePairScore self) -> std::string"""
1050  return _IMP_example.ExamplePairScore___repr__(self)
1051 
1052 
1053  @staticmethod
1054  def get_from(o):
1055  return _object_cast_to_ExamplePairScore(o)
1056 
1057 ExamplePairScore_swigregister = _IMP_example.ExamplePairScore_swigregister
1058 ExamplePairScore_swigregister(ExamplePairScore)
1059 
1061  """Proxy of C++ IMP::example::ExampleSubsetFilterTable class."""
1062 
1063  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1064 
1065  def __init__(self, max_diff, pt):
1066  """__init__(IMP::example::ExampleSubsetFilterTable self, unsigned int max_diff, IMP::ParticlesTemp const & pt) -> ExampleSubsetFilterTable"""
1067  this = _IMP_example.new_ExampleSubsetFilterTable(max_diff, pt)
1068  try:
1069  self.this.append(this)
1070  except __builtin__.Exception:
1071  self.this = this
1072 
1073  def get_version_info(self):
1074  """get_version_info(ExampleSubsetFilterTable self) -> VersionInfo"""
1075  return _IMP_example.ExampleSubsetFilterTable_get_version_info(self)
1076 
1077 
1078  def __str__(self):
1079  """__str__(ExampleSubsetFilterTable self) -> std::string"""
1080  return _IMP_example.ExampleSubsetFilterTable___str__(self)
1081 
1082 
1083  def __repr__(self):
1084  """__repr__(ExampleSubsetFilterTable self) -> std::string"""
1085  return _IMP_example.ExampleSubsetFilterTable___repr__(self)
1086 
1087 
1088  @staticmethod
1089  def get_from(o):
1090  return _object_cast_to_ExampleSubsetFilterTable(o)
1091 
1092 ExampleSubsetFilterTable_swigregister = _IMP_example.ExampleSubsetFilterTable_swigregister
1093 ExampleSubsetFilterTable_swigregister(ExampleSubsetFilterTable)
1094 
1096  """Proxy of C++ IMP::example::ExampleConstraint class."""
1097 
1098  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1099 
1100  def __init__(self, p):
1101  """__init__(IMP::example::ExampleConstraint self, Particle p) -> ExampleConstraint"""
1102  this = _IMP_example.new_ExampleConstraint(p)
1103  try:
1104  self.this.append(this)
1105  except __builtin__.Exception:
1106  self.this = this
1107 
1108  def do_get_inputs(self):
1109  """do_get_inputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1110  return _IMP_example.ExampleConstraint_do_get_inputs(self)
1111 
1112 
1113  def do_get_outputs(self):
1114  """do_get_outputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1115  return _IMP_example.ExampleConstraint_do_get_outputs(self)
1116 
1117 
1118  def get_key():
1119  """get_key() -> IntKey"""
1120  return _IMP_example.ExampleConstraint_get_key()
1121 
1122  get_key = staticmethod(get_key)
1123 
1124  def get_version_info(self):
1125  """get_version_info(ExampleConstraint self) -> VersionInfo"""
1126  return _IMP_example.ExampleConstraint_get_version_info(self)
1127 
1128 
1129  def __str__(self):
1130  """__str__(ExampleConstraint self) -> std::string"""
1131  return _IMP_example.ExampleConstraint___str__(self)
1132 
1133 
1134  def __repr__(self):
1135  """__repr__(ExampleConstraint self) -> std::string"""
1136  return _IMP_example.ExampleConstraint___repr__(self)
1137 
1138 
1139  @staticmethod
1140  def get_from(o):
1141  return _object_cast_to_ExampleConstraint(o)
1142 
1143 ExampleConstraint_swigregister = _IMP_example.ExampleConstraint_swigregister
1144 ExampleConstraint_swigregister(ExampleConstraint)
1145 
1146 def ExampleConstraint_get_key():
1147  """ExampleConstraint_get_key() -> IntKey"""
1148  return _IMP_example.ExampleConstraint_get_key()
1149 
1150 
1151 def create_serial_mover(m, pis):
1152  """create_serial_mover(Model m, IMP::ParticleIndexes const & pis) -> MonteCarloMover"""
1153  return _IMP_example.create_serial_mover(m, pis)
1154 
1155 def optimize_balls(*args):
1156  """
1157  optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states, IMP::LogLevel ll)
1158  optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states)
1159  optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded)
1160  optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs)
1161  optimize_balls(Model m, IMP::ParticleIndexes const & pis)
1162  """
1163  return _IMP_example.optimize_balls(*args)
1164 
1165 def optimize_assembly(*args):
1166  """
1167  optimize_assembly(Model m, IMP::ParticleIndexes const & components, IMP::RestraintsTemp const & interactions, IMP::RestraintsTemp const & other_restraints, BoundingBox3D bb, PairScore ev, double cutoff, IMP::PairPredicates const & excluded)
1168  optimize_assembly(Model m, IMP::ParticleIndexes const & components, IMP::RestraintsTemp const & interactions, IMP::RestraintsTemp const & other_restraints, BoundingBox3D bb, PairScore ev, double cutoff)
1169  """
1170  return _IMP_example.optimize_assembly(*args)
1171 
1172 def get_number_of_incidences(psa, psb, point_distance):
1173  """get_number_of_incidences(IMP::ParticlesTemp const & psa, IMP::ParticlesTemp const & psb, double point_distance) -> unsigned int"""
1174  return _IMP_example.get_number_of_incidences(psa, psb, point_distance)
1175 
1176 def create_chain_restraint(m, ps, length_factor, k, name):
1177  """create_chain_restraint(Model m, IMP::ParticleIndexes const & ps, double length_factor, double k, std::string name) -> Restraint"""
1178  return _IMP_example.create_chain_restraint(m, ps, length_factor, k, name)
1179 
1180 def create_excluded_volume(ps, k, name):
1181  """create_excluded_volume(IMP::ParticlesTemp const & ps, double k, std::string name) -> Restraint"""
1182  return _IMP_example.create_excluded_volume(ps, k, name)
1183 class ExampleTemplateClass3D(object):
1184  """Proxy of C++ IMP::example::ExampleTemplateClassD<(3)> class."""
1185 
1186  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1187 
1188  def __init__(self, *args):
1189  """
1190  __init__(IMP::example::ExampleTemplateClassD<(3)> self) -> ExampleTemplateClass3D
1191  __init__(IMP::example::ExampleTemplateClassD<(3)> self, Vector3D a, Vector3D b) -> ExampleTemplateClass3D
1192  """
1193  this = _IMP_example.new_ExampleTemplateClass3D(*args)
1194  try:
1195  self.this.append(this)
1196  except __builtin__.Exception:
1197  self.this = this
1198 
1199  def get_point(self, i):
1200  """get_point(ExampleTemplateClass3D self, unsigned int i) -> Vector3D"""
1201  return _IMP_example.ExampleTemplateClass3D_get_point(self, i)
1202 
1203 
1204  def show(self, *args):
1205  """
1206  show(ExampleTemplateClass3D self, _ostream out)
1207  show(ExampleTemplateClass3D self)
1208  """
1209  return _IMP_example.ExampleTemplateClass3D_show(self, *args)
1210 
1211 
1212  def __str__(self):
1213  """__str__(ExampleTemplateClass3D self) -> std::string"""
1214  return _IMP_example.ExampleTemplateClass3D___str__(self)
1215 
1216 
1217  def __repr__(self):
1218  """__repr__(ExampleTemplateClass3D self) -> std::string"""
1219  return _IMP_example.ExampleTemplateClass3D___repr__(self)
1220 
1221  __swig_destroy__ = _IMP_example.delete_ExampleTemplateClass3D
1222  __del__ = lambda self: None
1223 ExampleTemplateClass3D_swigregister = _IMP_example.ExampleTemplateClass3D_swigregister
1224 ExampleTemplateClass3D_swigregister(ExampleTemplateClass3D)
1225 
1226 
1227 def get_module_version():
1228  """get_module_version() -> std::string const"""
1229  return _IMP_example.get_module_version()
1230 
1231 def get_example_path(fname):
1232  """get_example_path(std::string fname) -> std::string"""
1233  return _IMP_example.get_example_path(fname)
1234 
1235 def get_data_path(fname):
1236  """get_data_path(std::string fname) -> std::string"""
1237  return _IMP_example.get_data_path(fname)
1238 
1239 from . import _version_check
1240 _version_check.check_version(get_module_version())
1241 __version__ = get_module_version()
1242 
1243 
1244 
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:37
virtual double evaluate(double feature) const
Calculate score with respect to the given feature.
Definition: UnaryFunction.h:33
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.
virtual void do_add_score_and_derivatives(ScoreAccumulator sa) const
A restraint should override this to compute the score and derivatives.
Make CGAL functionality available to IMP.
A line segment templated on the dimension.
ParticlesTemp get_particles(Model *m, const ParticleIndexes &ps)
virtual void clear_caches()
Definition: Object.h:227
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.
Vector3D get_random_vector_in(const Cylinder3D &c)
Generate a random vector in a cylinder with uniform density.
core::MonteCarloMover * create_serial_mover(Model *m, const ParticleIndexes &pis)
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:72
An example simple object which is reference counted.
Definition: ExampleObject.h:29
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:106
Store a list of ParticleIndexes.
An example restraint written in Python.
Restraint * create_excluded_volume(const ParticlesTemp &ps, double k, std::string name)
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const =0
Overload this method to specify the inputs.
void optimize_balls(Model *m, const ParticleIndexes &pis, const RestraintsTemp &rs=RestraintsTemp(), const PairPredicates &excluded=PairPredicates(), const OptimizerStates &opt_states=OptimizerStates(), LogLevel ll=DEFAULT)
Restrain a particle to be in the x,y plane.
void optimize_assembly(Model *m, const ParticleIndexes &components, const RestraintsTemp &interactions, const RestraintsTemp &other_restraints, const algebra::BoundingBox3D &bb, PairScore *ev, double cutoff, const PairPredicates &excluded=PairPredicates())
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:118
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
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Definition: Object.h:173
virtual DerivativePair evaluate_with_derivative(double feature) const
Calculate score and derivative with respect to the given feature.
Definition: UnaryFunction.h:48
VectorD< 3 > Vector3D
Definition: VectorD.h:395
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:40
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:25
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.
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:52