IMP logo
IMP Reference Guide  2.14.0
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 2007-2020 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_NUMPY = _IMP_example.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_example.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_example.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_example.IMPKERNEL_SHOW_WARNINGS
243 
244 import sys
245 class _DirectorObjects(object):
246  """@internal Simple class to keep references to director objects
247  to prevent premature deletion."""
248  def __init__(self):
249  self._objects = []
250  def register(self, obj):
251  """Take a reference to a director object; will only work for
252  refcounted C++ classes"""
253  if hasattr(obj, 'get_ref_count'):
254  self._objects.append(obj)
255  def cleanup(self):
256  """Only drop our reference and allow cleanup by Python if no other
257  Python references exist (we hold 3 references: one in self._objects,
258  one in x, and one in the argument list for getrefcount) *and* no
259  other C++ references exist (the Python object always holds one)"""
260  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
261  or x.get_ref_count() > 1]
262 # Do in two steps so the references are kept until the end of the
263 # function (deleting references may trigger a fresh call to this method)
264  self._objects = objs
265  def get_object_count(self):
266  """Get number of director objects (useful for testing only)"""
267  return len(self._objects)
268 _director_objects = _DirectorObjects()
269 
270 class _ostream(object):
271  """Proxy of C++ std::ostream class."""
272 
273  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
274 
275  def __init__(self, *args, **kwargs):
276  raise AttributeError("No constructor defined")
277  __repr__ = _swig_repr
278 
279  def write(self, osa_buf):
280  """write(_ostream self, char const * osa_buf)"""
281  return _IMP_example._ostream_write(self, osa_buf)
282 
283 _ostream_swigregister = _IMP_example._ostream_swigregister
284 _ostream_swigregister(_ostream)
285 
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_example.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_example.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_example.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_example.IMP_C_OPEN_BINARY
290 import IMP
291 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_FILESYSTEM
292 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
293 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_example.IMP_CGAL_HAS_BOOST_RANDOM
294 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_example.IMP_CGAL_HAS_BOOST_SYSTEM
295 IMP_CGAL_HAS_NUMPY = _IMP_example.IMP_CGAL_HAS_NUMPY
296 IMPCGAL_SHOW_WARNINGS = _IMP_example.IMPCGAL_SHOW_WARNINGS
297 import IMP.cgal
298 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_example.IMP_ALGEBRA_HAS_IMP_CGAL
299 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
300 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
301 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_RANDOM
302 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_example.IMP_ALGEBRA_HAS_BOOST_SYSTEM
303 IMP_ALGEBRA_HAS_CGAL = _IMP_example.IMP_ALGEBRA_HAS_CGAL
304 IMP_ALGEBRA_HAS_NUMPY = _IMP_example.IMP_ALGEBRA_HAS_NUMPY
305 IMP_ALGEBRA_HAS_ANN = _IMP_example.IMP_ALGEBRA_HAS_ANN
306 IMPALGEBRA_SHOW_WARNINGS = _IMP_example.IMPALGEBRA_SHOW_WARNINGS
307 import IMP.algebra
308 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_example.IMP_DISPLAY_HAS_IMP_CGAL
309 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
310 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
311 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_example.IMP_DISPLAY_HAS_BOOST_RANDOM
312 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_example.IMP_DISPLAY_HAS_BOOST_SYSTEM
313 IMP_DISPLAY_HAS_CGAL = _IMP_example.IMP_DISPLAY_HAS_CGAL
314 IMP_DISPLAY_HAS_NUMPY = _IMP_example.IMP_DISPLAY_HAS_NUMPY
315 IMPDISPLAY_SHOW_WARNINGS = _IMP_example.IMPDISPLAY_SHOW_WARNINGS
316 import IMP.display
317 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
318 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
319 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
320 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
321 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_example.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
322 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_example.IMP_SCORE_FUNCTOR_HAS_CGAL
323 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_example.IMP_SCORE_FUNCTOR_HAS_HDF5
324 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_example.IMP_SCORE_FUNCTOR_HAS_NUMPY
325 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_example.IMPSCOREFUNCTOR_SHOW_WARNINGS
326 import IMP.score_functor
327 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_example.IMP_STATISTICS_HAS_IMP_CGAL
328 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
329 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
330 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_example.IMP_STATISTICS_HAS_BOOST_RANDOM
331 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_example.IMP_STATISTICS_HAS_BOOST_SYSTEM
332 IMP_STATISTICS_HAS_CGAL = _IMP_example.IMP_STATISTICS_HAS_CGAL
333 IMP_STATISTICS_HAS_NUMPY = _IMP_example.IMP_STATISTICS_HAS_NUMPY
334 IMPSTATISTICS_SHOW_WARNINGS = _IMP_example.IMPSTATISTICS_SHOW_WARNINGS
335 import IMP.statistics
336 IMP_CORE_HAS_IMP_CGAL = _IMP_example.IMP_CORE_HAS_IMP_CGAL
337 IMP_CORE_HAS_IMP_KERNEL = _IMP_example.IMP_CORE_HAS_IMP_KERNEL
338 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_FILESYSTEM
339 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
340 IMP_CORE_HAS_BOOST_RANDOM = _IMP_example.IMP_CORE_HAS_BOOST_RANDOM
341 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_example.IMP_CORE_HAS_BOOST_SYSTEM
342 IMP_CORE_HAS_CGAL = _IMP_example.IMP_CORE_HAS_CGAL
343 IMP_CORE_HAS_HDF5 = _IMP_example.IMP_CORE_HAS_HDF5
344 IMP_CORE_HAS_NUMPY = _IMP_example.IMP_CORE_HAS_NUMPY
345 IMPCORE_SHOW_WARNINGS = _IMP_example.IMPCORE_SHOW_WARNINGS
346 import IMP.core
347 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_example.IMP_CONTAINER_HAS_IMP_ALGEBRA
348 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_example.IMP_CONTAINER_HAS_IMP_CGAL
349 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_example.IMP_CONTAINER_HAS_IMP_DISPLAY
350 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_example.IMP_CONTAINER_HAS_IMP_KERNEL
351 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
352 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
353 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
354 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_example.IMP_CONTAINER_HAS_BOOST_RANDOM
355 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_example.IMP_CONTAINER_HAS_BOOST_SYSTEM
356 IMP_CONTAINER_HAS_CGAL = _IMP_example.IMP_CONTAINER_HAS_CGAL
357 IMP_CONTAINER_HAS_HDF5 = _IMP_example.IMP_CONTAINER_HAS_HDF5
358 IMP_CONTAINER_HAS_NUMPY = _IMP_example.IMP_CONTAINER_HAS_NUMPY
359 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_example.IMP_CONTAINER_HAS_PYTHON_IHM
360 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_example.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
361 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_example.IMP_CONTAINER_HAS_ROBIN_MAP
362 IMPCONTAINER_SHOW_WARNINGS = _IMP_example.IMPCONTAINER_SHOW_WARNINGS
363 import IMP.container
364 IMP_ATOM_HAS_IMP_CGAL = _IMP_example.IMP_ATOM_HAS_IMP_CGAL
365 IMP_ATOM_HAS_IMP_KERNEL = _IMP_example.IMP_ATOM_HAS_IMP_KERNEL
366 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
367 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
368 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_example.IMP_ATOM_HAS_BOOST_RANDOM
369 IMP_ATOM_HAS_BOOST_REGEX = _IMP_example.IMP_ATOM_HAS_BOOST_REGEX
370 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_example.IMP_ATOM_HAS_BOOST_SYSTEM
371 IMP_ATOM_HAS_CGAL = _IMP_example.IMP_ATOM_HAS_CGAL
372 IMP_ATOM_HAS_HDF5 = _IMP_example.IMP_ATOM_HAS_HDF5
373 IMP_ATOM_HAS_NUMPY = _IMP_example.IMP_ATOM_HAS_NUMPY
374 IMP_ATOM_HAS_PYTHON_IHM = _IMP_example.IMP_ATOM_HAS_PYTHON_IHM
375 IMPATOM_SHOW_WARNINGS = _IMP_example.IMPATOM_SHOW_WARNINGS
376 IMP_ATOM_TYPE_INDEX = _IMP_example.IMP_ATOM_TYPE_INDEX
377 IMP_RESIDUE_TYPE_INDEX = _IMP_example.IMP_RESIDUE_TYPE_INDEX
378 IMP_HIERARCHY_TYPE_INDEX = _IMP_example.IMP_HIERARCHY_TYPE_INDEX
379 IMP_CHAIN_TYPE_INDEX = _IMP_example.IMP_CHAIN_TYPE_INDEX
380 import IMP.atom
381 IMP_EM_HAS_IMP_CGAL = _IMP_example.IMP_EM_HAS_IMP_CGAL
382 IMP_EM_HAS_IMP_CONTAINER = _IMP_example.IMP_EM_HAS_IMP_CONTAINER
383 IMP_EM_HAS_IMP_DISPLAY = _IMP_example.IMP_EM_HAS_IMP_DISPLAY
384 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EM_HAS_IMP_SCORE_FUNCTOR
385 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EM_HAS_BOOST_FILESYSTEM
386 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
387 IMP_EM_HAS_BOOST_RANDOM = _IMP_example.IMP_EM_HAS_BOOST_RANDOM
388 IMP_EM_HAS_BOOST_REGEX = _IMP_example.IMP_EM_HAS_BOOST_REGEX
389 IMP_EM_HAS_BOOST_SYSTEM = _IMP_example.IMP_EM_HAS_BOOST_SYSTEM
390 IMP_EM_HAS_CGAL = _IMP_example.IMP_EM_HAS_CGAL
391 IMP_EM_HAS_HDF5 = _IMP_example.IMP_EM_HAS_HDF5
392 IMP_EM_HAS_NUMPY = _IMP_example.IMP_EM_HAS_NUMPY
393 IMP_EM_HAS_PYTHON_IHM = _IMP_example.IMP_EM_HAS_PYTHON_IHM
394 IMPEM_SHOW_WARNINGS = _IMP_example.IMPEM_SHOW_WARNINGS
395 import IMP.em
396 IMP_SAXS_HAS_IMP_CGAL = _IMP_example.IMP_SAXS_HAS_IMP_CGAL
397 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_example.IMP_SAXS_HAS_IMP_CONTAINER
398 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_example.IMP_SAXS_HAS_IMP_DISPLAY
399 IMP_SAXS_HAS_IMP_KERNEL = _IMP_example.IMP_SAXS_HAS_IMP_KERNEL
400 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
401 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_SAXS_HAS_BOOST_FILESYSTEM
402 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
403 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_example.IMP_SAXS_HAS_BOOST_RANDOM
404 IMP_SAXS_HAS_BOOST_REGEX = _IMP_example.IMP_SAXS_HAS_BOOST_REGEX
405 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_example.IMP_SAXS_HAS_BOOST_SYSTEM
406 IMP_SAXS_HAS_CGAL = _IMP_example.IMP_SAXS_HAS_CGAL
407 IMP_SAXS_HAS_HDF5 = _IMP_example.IMP_SAXS_HAS_HDF5
408 IMP_SAXS_HAS_NUMPY = _IMP_example.IMP_SAXS_HAS_NUMPY
409 IMP_SAXS_HAS_PYTHON_IHM = _IMP_example.IMP_SAXS_HAS_PYTHON_IHM
410 IMPSAXS_SHOW_WARNINGS = _IMP_example.IMPSAXS_SHOW_WARNINGS
411 import IMP.saxs
412 IMP_ISD_HAS_IMP_CGAL = _IMP_example.IMP_ISD_HAS_IMP_CGAL
413 IMP_ISD_HAS_IMP_DISPLAY = _IMP_example.IMP_ISD_HAS_IMP_DISPLAY
414 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
415 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_ISD_HAS_BOOST_FILESYSTEM
416 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
417 IMP_ISD_HAS_BOOST_RANDOM = _IMP_example.IMP_ISD_HAS_BOOST_RANDOM
418 IMP_ISD_HAS_BOOST_REGEX = _IMP_example.IMP_ISD_HAS_BOOST_REGEX
419 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_example.IMP_ISD_HAS_BOOST_SYSTEM
420 IMP_ISD_HAS_CGAL = _IMP_example.IMP_ISD_HAS_CGAL
421 IMP_ISD_HAS_HDF5 = _IMP_example.IMP_ISD_HAS_HDF5
422 IMP_ISD_HAS_NUMPY = _IMP_example.IMP_ISD_HAS_NUMPY
423 IMP_ISD_HAS_PYTHON_IHM = _IMP_example.IMP_ISD_HAS_PYTHON_IHM
424 IMPISD_SHOW_WARNINGS = _IMP_example.IMPISD_SHOW_WARNINGS
425 import IMP.isd
426 IMP_RMF_HAS_IMP_CGAL = _IMP_example.IMP_RMF_HAS_IMP_CGAL
427 IMP_RMF_HAS_IMP_EM = _IMP_example.IMP_RMF_HAS_IMP_EM
428 IMP_RMF_HAS_IMP_SAXS = _IMP_example.IMP_RMF_HAS_IMP_SAXS
429 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
430 IMP_RMF_HAS_IMP_STATISTICS = _IMP_example.IMP_RMF_HAS_IMP_STATISTICS
431 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_FILESYSTEM
432 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
433 IMP_RMF_HAS_BOOST_RANDOM = _IMP_example.IMP_RMF_HAS_BOOST_RANDOM
434 IMP_RMF_HAS_BOOST_REGEX = _IMP_example.IMP_RMF_HAS_BOOST_REGEX
435 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_example.IMP_RMF_HAS_BOOST_SYSTEM
436 IMP_RMF_HAS_CGAL = _IMP_example.IMP_RMF_HAS_CGAL
437 IMP_RMF_HAS_HDF5 = _IMP_example.IMP_RMF_HAS_HDF5
438 IMP_RMF_HAS_NUMPY = _IMP_example.IMP_RMF_HAS_NUMPY
439 IMP_RMF_HAS_PYTHON_IHM = _IMP_example.IMP_RMF_HAS_PYTHON_IHM
440 IMPRMF_SHOW_WARNINGS = _IMP_example.IMPRMF_SHOW_WARNINGS
441 import IMP.rmf
442 import RMF
443 IMP_DOMINO_HAS_IMP_ATOM = _IMP_example.IMP_DOMINO_HAS_IMP_ATOM
444 IMP_DOMINO_HAS_IMP_CGAL = _IMP_example.IMP_DOMINO_HAS_IMP_CGAL
445 IMP_DOMINO_HAS_IMP_EM = _IMP_example.IMP_DOMINO_HAS_IMP_EM
446 IMP_DOMINO_HAS_IMP_ISD = _IMP_example.IMP_DOMINO_HAS_IMP_ISD
447 IMP_DOMINO_HAS_IMP_KERNEL = _IMP_example.IMP_DOMINO_HAS_IMP_KERNEL
448 IMP_DOMINO_HAS_IMP_RMF = _IMP_example.IMP_DOMINO_HAS_IMP_RMF
449 IMP_DOMINO_HAS_IMP_SAXS = _IMP_example.IMP_DOMINO_HAS_IMP_SAXS
450 IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_DOMINO_HAS_IMP_SCORE_FUNCTOR
451 IMP_DOMINO_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_FILESYSTEM
452 IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_DOMINO_HAS_BOOST_PROGRAMOPTIONS
453 IMP_DOMINO_HAS_BOOST_RANDOM = _IMP_example.IMP_DOMINO_HAS_BOOST_RANDOM
454 IMP_DOMINO_HAS_BOOST_REGEX = _IMP_example.IMP_DOMINO_HAS_BOOST_REGEX
455 IMP_DOMINO_HAS_BOOST_SYSTEM = _IMP_example.IMP_DOMINO_HAS_BOOST_SYSTEM
456 IMP_DOMINO_HAS_CGAL = _IMP_example.IMP_DOMINO_HAS_CGAL
457 IMP_DOMINO_HAS_HDF5 = _IMP_example.IMP_DOMINO_HAS_HDF5
458 IMP_DOMINO_HAS_NUMPY = _IMP_example.IMP_DOMINO_HAS_NUMPY
459 IMP_DOMINO_HAS_RMF = _IMP_example.IMP_DOMINO_HAS_RMF
460 IMP_DOMINO_HAS_PYTHON_IHM = _IMP_example.IMP_DOMINO_HAS_PYTHON_IHM
461 IMPDOMINO_SHOW_WARNINGS = _IMP_example.IMPDOMINO_SHOW_WARNINGS
462 import RMF_HDF5
463 import IMP.domino
464 IMP_EXAMPLE_HAS_IMP_ALGEBRA = _IMP_example.IMP_EXAMPLE_HAS_IMP_ALGEBRA
465 IMP_EXAMPLE_HAS_IMP_CGAL = _IMP_example.IMP_EXAMPLE_HAS_IMP_CGAL
466 IMP_EXAMPLE_HAS_IMP_DISPLAY = _IMP_example.IMP_EXAMPLE_HAS_IMP_DISPLAY
467 IMP_EXAMPLE_HAS_IMP_EM = _IMP_example.IMP_EXAMPLE_HAS_IMP_EM
468 IMP_EXAMPLE_HAS_IMP_ISD = _IMP_example.IMP_EXAMPLE_HAS_IMP_ISD
469 IMP_EXAMPLE_HAS_IMP_KERNEL = _IMP_example.IMP_EXAMPLE_HAS_IMP_KERNEL
470 IMP_EXAMPLE_HAS_IMP_RMF = _IMP_example.IMP_EXAMPLE_HAS_IMP_RMF
471 IMP_EXAMPLE_HAS_IMP_SAXS = _IMP_example.IMP_EXAMPLE_HAS_IMP_SAXS
472 IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR = _IMP_example.IMP_EXAMPLE_HAS_IMP_SCORE_FUNCTOR
473 IMP_EXAMPLE_HAS_IMP_STATISTICS = _IMP_example.IMP_EXAMPLE_HAS_IMP_STATISTICS
474 IMP_EXAMPLE_HAS_BOOST_FILESYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_FILESYSTEM
475 IMP_EXAMPLE_HAS_BOOST_GRAPH = _IMP_example.IMP_EXAMPLE_HAS_BOOST_GRAPH
476 IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS = _IMP_example.IMP_EXAMPLE_HAS_BOOST_PROGRAMOPTIONS
477 IMP_EXAMPLE_HAS_BOOST_RANDOM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_RANDOM
478 IMP_EXAMPLE_HAS_BOOST_REGEX = _IMP_example.IMP_EXAMPLE_HAS_BOOST_REGEX
479 IMP_EXAMPLE_HAS_BOOST_SYSTEM = _IMP_example.IMP_EXAMPLE_HAS_BOOST_SYSTEM
480 IMP_EXAMPLE_HAS_CGAL = _IMP_example.IMP_EXAMPLE_HAS_CGAL
481 IMP_EXAMPLE_HAS_HDF5 = _IMP_example.IMP_EXAMPLE_HAS_HDF5
482 IMP_EXAMPLE_HAS_NUMPY = _IMP_example.IMP_EXAMPLE_HAS_NUMPY
483 IMP_EXAMPLE_HAS_RMF = _IMP_example.IMP_EXAMPLE_HAS_RMF
484 IMP_EXAMPLE_HAS_PYTHON_IHM = _IMP_example.IMP_EXAMPLE_HAS_PYTHON_IHM
485 IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY = _IMP_example.IMP_EXAMPLE_HAS_EXAMPLEDEPENDENCY
486 IMPEXAMPLE_SHOW_WARNINGS = _IMP_example.IMPEXAMPLE_SHOW_WARNINGS
487 
488 _object_types.append("ExampleRestraint")
489 
490 
491 def _object_cast_to_ExampleRestraint(o):
492  """_object_cast_to_ExampleRestraint(Object o) -> ExampleRestraint"""
493  return _IMP_example._object_cast_to_ExampleRestraint(o)
494 
495 def ExampleDecorators(l=[]):
496  return [ExampleDecorator(x) for x in l]
497 _plural_types.append("ExampleDecorators")
498 
499 
500 _value_types.append("ExampleDecorator")
501 
502 
503 _object_types.append("ExampleUnaryFunction")
504 
505 
506 def _object_cast_to_ExampleUnaryFunction(o):
507  """_object_cast_to_ExampleUnaryFunction(Object o) -> ExampleUnaryFunction"""
508  return _IMP_example._object_cast_to_ExampleUnaryFunction(o)
509 
510 _object_types.append("ExampleSingletonModifier")
511 
512 
513 def _object_cast_to_ExampleSingletonModifier(o):
514  """_object_cast_to_ExampleSingletonModifier(Object o) -> ExampleSingletonModifier"""
515  return _IMP_example._object_cast_to_ExampleSingletonModifier(o)
516 
517 _object_types.append("ExamplePairScore")
518 
519 
520 def _object_cast_to_ExamplePairScore(o):
521  """_object_cast_to_ExamplePairScore(Object o) -> ExamplePairScore"""
522  return _IMP_example._object_cast_to_ExamplePairScore(o)
523 
524 _object_types.append("ExampleSubsetFilterTable")
525 
526 
527 def _object_cast_to_ExampleSubsetFilterTable(o):
528  """_object_cast_to_ExampleSubsetFilterTable(Object o) -> ExampleSubsetFilterTable"""
529  return _IMP_example._object_cast_to_ExampleSubsetFilterTable(o)
530 
531 _object_types.append("ExampleConstraint")
532 
533 
534 def _object_cast_to_ExampleConstraint(o):
535  """_object_cast_to_ExampleConstraint(Object o) -> ExampleConstraint"""
536  return _IMP_example._object_cast_to_ExampleConstraint(o)
537 
538 _object_types.append("ExampleObject")
539 
540 
541 def _object_cast_to_ExampleObject(o):
542  """_object_cast_to_ExampleObject(Object o) -> ExampleObject"""
543  return _IMP_example._object_cast_to_ExampleObject(o)
544 
545 ExampleTemplateClass3Ds=list
546 _plural_types.append("ExampleTemplateClass3Ds")
547 _value_types.append("ExampleTemplateClass3D")
548 
549 
550 def create_model_and_particles():
551  m = IMP.Model()
554  IMP.algebra.Vector3D(10,10,10))
555  for i in range(0,100):
556  p = m.add_particle("p")
557  sc.add(p)
560  d.set_coordinates_are_optimized(True)
561  return (m, sc)
562 
563 
564 
566  """An example restraint written in Python.
567  This should be functionally equivalent to the C++ ExampleRestraint.
568  """
569  def __init__(self, m, p, k):
570  IMP.Restraint.__init__(self, m, "PythonExampleRestraint%1%")
571  self.p, self.k = p, k
572 
573  def do_add_score_and_derivatives(self, sa):
574  d = IMP.core.XYZ(self.get_model(), self.p)
575  score = .5 * self.k * d.get_z() * d.get_z()
576  if sa.get_derivative_accumulator():
577  deriv = self.k * d.get_z()
578  d.add_to_derivative(2, deriv, sa.get_derivative_accumulator())
579  sa.add_score(score)
580 
581  def do_get_inputs(self):
582  return [self.get_model().get_particle(self.p)]
583 
584 
585 
586 
588  """An example PairScore written in Python.
589  This should be functionally equivalent to the C++ ExamplePairScore.
590  """
591  def __init__(self, x0, k):
592  IMP.PairScore.__init__(self)
593  self.x0, self.k = x0, k
594 
595  def evaluate_index(self, m, pip, da):
596  d0 = IMP.core.XYZ(m, pip[0])
597  d1 = IMP.core.XYZ(m, pip[1])
598  diff = (d0.get_coordinates()
599  - d1.get_coordinates()).get_magnitude() - self.x0
600  score = .5 * self.k * diff * diff
601  if da:
602 # derivatives are requested
603  delta = d0.get_coordinates() - d1.get_coordinates()
604  udelta = delta.get_unit_vector()
605  dv = self.k * diff
606  d0.add_to_derivatives(udelta * dv, da)
607  d1.add_to_derivatives(-udelta * dv, da)
608  return score
609 
610  def do_get_inputs(self, m, pis):
611  return IMP.get_particles(m, pis)
612 
613 
614 
615 
617  """An example UnaryFunction written in Python.
618  This should be functionally equivalent to the C++ ExampleUnaryFunction.
619  """
620  def __init__(self, center, k):
621  IMP.UnaryFunction.__init__(self)
622  self.center, self.k = center, k
623 
624  def evaluate_with_derivative(self, feature):
625  return (self.evaluate(feature), self.k * (feature - self.center))
626 
627  def evaluate(self, feature):
628  return .5 * self.k * (feature - self.center) * (feature - self.center)
629 
630 
631 
632 
634  """An example Constraint written in Python.
635  This should be functionally equivalent to the C++ ExampleConstraint.
636  """
637 
638  k = None
639 
640  def __init__(self, p):
641  IMP.Constraint.__init__(self, p.get_model(), "ExampleConstraint%1%")
642  self.p = p
643  if self.k is None:
644  PythonExampleConstraint.k = IMP.IntKey("Constraint key")
645  if not p.has_attribute(self.k):
646  p.add_attribute(self.k, 0)
647 
648  def do_update_attributes(self):
649  self.p.set_value(self.k, self.p.get_value(self.k) + 1)
650 
651  def do_update_derivatives(self, da):
652  pass
653 
654  def do_get_inputs(self):
655  return [self.p]
656 
657  def do_get_outputs(self):
658  return [self.p]
659 
660 
661 
662 
664  """An example SingletonModifier written in Python.
665  This should be functionally equivalent to the C++
666  ExampleSingletonModifier.
667  """
668 
669  def __init__(self, bb):
670  IMP.SingletonModifier.__init__(self, "ExampleSingletonModifier%1%")
671  self.bb = bb
672 
673  def apply_index(self, m, pi):
674  d = IMP.core.XYZ(m, pi)
675  for i in range(3):
676 # shift the coordinate until it is in the box
677  while d.get_coordinate(i) < self.bb.get_corner(0)[i]:
678  d.set_coordinate(i,d.get_coordinate(i) + \
679  (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
680  while d.get_coordinate(i) > self.bb.get_corner(1)[i]:
681  d.set_coordinate(i,d.get_coordinate(i) - \
682  (self.bb.get_corner(1)[i] - self.bb.get_corner(0)[i]))
683 
684  def do_get_inputs(self, m, pis):
685  return IMP.get_particles(m, pis)
686 
687  def do_get_outputs(self, m, pis):
688  return self.do_get_inputs(m, pis)
689 
690 
692  """Proxy of C++ IMP::example::ExampleRestraint class."""
693 
694  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
695 
696  def __init__(self, m, p, k):
697  """__init__(IMP::example::ExampleRestraint self, Model m, ParticleIndex p, double k) -> ExampleRestraint"""
698  this = _IMP_example.new_ExampleRestraint(m, p, k)
699  try:
700  self.this.append(this)
701  except __builtin__.Exception:
702  self.this = this
703 
704  def do_add_score_and_derivatives(self, sa):
705  """do_add_score_and_derivatives(ExampleRestraint self, ScoreAccumulator sa)"""
706  return _IMP_example.ExampleRestraint_do_add_score_and_derivatives(self, sa)
707 
708 
709  def do_get_inputs(self):
710  """do_get_inputs(ExampleRestraint self) -> IMP::ModelObjectsTemp"""
711  return _IMP_example.ExampleRestraint_do_get_inputs(self)
712 
713 
714  def get_version_info(self):
715  """get_version_info(ExampleRestraint self) -> VersionInfo"""
716  return _IMP_example.ExampleRestraint_get_version_info(self)
717 
718 
719  def __str__(self):
720  """__str__(ExampleRestraint self) -> std::string"""
721  return _IMP_example.ExampleRestraint___str__(self)
722 
723 
724  def __repr__(self):
725  """__repr__(ExampleRestraint self) -> std::string"""
726  return _IMP_example.ExampleRestraint___repr__(self)
727 
728 
729  @staticmethod
730  def get_from(o):
731  return _object_cast_to_ExampleRestraint(o)
732 
733 ExampleRestraint_swigregister = _IMP_example.ExampleRestraint_swigregister
734 ExampleRestraint_swigregister(ExampleRestraint)
735 
737  """Proxy of C++ IMP::example::ExampleDecorator class."""
738 
739  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
740 
741  def get_decorator_name(self):
742  """get_decorator_name(ExampleDecorator self) -> std::string"""
743  return _IMP_example.ExampleDecorator_get_decorator_name(self)
744 
745 
746  def set_decorator_name(self, nm):
747  """set_decorator_name(ExampleDecorator self, std::string nm)"""
748  return _IMP_example.ExampleDecorator_set_decorator_name(self, nm)
749 
750 
751  def __init__(self, *args):
752  """
753  __init__(IMP::example::ExampleDecorator self) -> ExampleDecorator
754  __init__(IMP::example::ExampleDecorator self, Model m, ParticleIndex id) -> ExampleDecorator
755  __init__(IMP::example::ExampleDecorator self, _ParticleAdaptor d) -> ExampleDecorator
756  """
757  this = _IMP_example.new_ExampleDecorator(*args)
758  try:
759  self.this.append(this)
760  except __builtin__.Exception:
761  self.this = this
762 
763  def get_is_setup(*args):
764  """
765  get_is_setup(Model m, ParticleIndex pi) -> bool
766  get_is_setup(_ParticleAdaptor p) -> bool
767  """
768  return _IMP_example.ExampleDecorator_get_is_setup(*args)
769 
770  get_is_setup = staticmethod(get_is_setup)
771 
772  def show(self, *args):
773  """
774  show(ExampleDecorator self, _ostream out)
775  show(ExampleDecorator self)
776  """
777  return _IMP_example.ExampleDecorator_show(self, *args)
778 
779 
780  def setup_particle(*args):
781  """
782  setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
783  setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
784  """
785  return _IMP_example.ExampleDecorator_setup_particle(*args)
786 
787  setup_particle = staticmethod(setup_particle)
788 
789  def add_attribute(self, *args):
790  """
791  add_attribute(ExampleDecorator self, FloatKey k, IMP::Float v, bool opt)
792  add_attribute(ExampleDecorator self, FloatKey a0, IMP::Float a1)
793  add_attribute(ExampleDecorator self, IntKey a0, IMP::Int a1)
794  add_attribute(ExampleDecorator self, FloatsKey a0, IMP::Floats a1)
795  add_attribute(ExampleDecorator self, IntsKey a0, IMP::Ints a1)
796  add_attribute(ExampleDecorator self, StringKey a0, IMP::String a1)
797  add_attribute(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
798  add_attribute(ExampleDecorator self, ObjectKey a0, Object a1)
799  """
800  return _IMP_example.ExampleDecorator_add_attribute(self, *args)
801 
802 
803  def get_value(self, *args):
804  """
805  get_value(ExampleDecorator self, FloatKey a0) -> IMP::Float
806  get_value(ExampleDecorator self, IntKey a0) -> IMP::Int
807  get_value(ExampleDecorator self, FloatsKey a0) -> IMP::Floats
808  get_value(ExampleDecorator self, IntsKey a0) -> IMP::Ints
809  get_value(ExampleDecorator self, StringKey a0) -> IMP::String
810  get_value(ExampleDecorator self, ParticleIndexKey a0) -> Particle
811  get_value(ExampleDecorator self, ObjectKey a0) -> Object
812  """
813  return _IMP_example.ExampleDecorator_get_value(self, *args)
814 
815 
816  def set_value(self, *args):
817  """
818  set_value(ExampleDecorator self, FloatKey a0, IMP::Float a1)
819  set_value(ExampleDecorator self, IntKey a0, IMP::Int a1)
820  set_value(ExampleDecorator self, FloatsKey a0, IMP::Floats a1)
821  set_value(ExampleDecorator self, IntsKey a0, IMP::Ints a1)
822  set_value(ExampleDecorator self, StringKey a0, IMP::String a1)
823  set_value(ExampleDecorator self, ParticleIndexKey a0, Particle a1)
824  set_value(ExampleDecorator self, ObjectKey a0, Object a1)
825  """
826  return _IMP_example.ExampleDecorator_set_value(self, *args)
827 
828 
829  def remove_attribute(self, *args):
830  """
831  remove_attribute(ExampleDecorator self, FloatKey a0)
832  remove_attribute(ExampleDecorator self, IntKey a0)
833  remove_attribute(ExampleDecorator self, FloatsKey a0)
834  remove_attribute(ExampleDecorator self, IntsKey a0)
835  remove_attribute(ExampleDecorator self, StringKey a0)
836  remove_attribute(ExampleDecorator self, ParticleIndexKey a0)
837  remove_attribute(ExampleDecorator self, ObjectKey a0)
838  """
839  return _IMP_example.ExampleDecorator_remove_attribute(self, *args)
840 
841 
842  def has_attribute(self, *args):
843  """
844  has_attribute(ExampleDecorator self, FloatKey a0) -> bool
845  has_attribute(ExampleDecorator self, IntKey a0) -> bool
846  has_attribute(ExampleDecorator self, FloatsKey a0) -> bool
847  has_attribute(ExampleDecorator self, IntsKey a0) -> bool
848  has_attribute(ExampleDecorator self, StringKey a0) -> bool
849  has_attribute(ExampleDecorator self, ParticleIndexKey a0) -> bool
850  has_attribute(ExampleDecorator self, ObjectKey a0) -> bool
851  """
852  return _IMP_example.ExampleDecorator_has_attribute(self, *args)
853 
854 
855  def get_derivative(self, a0):
856  """get_derivative(ExampleDecorator self, FloatKey a0) -> double"""
857  return _IMP_example.ExampleDecorator_get_derivative(self, a0)
858 
859 
860  def get_name(self):
861  """get_name(ExampleDecorator self) -> std::string"""
862  return _IMP_example.ExampleDecorator_get_name(self)
863 
864 
865  def clear_caches(self):
866  """clear_caches(ExampleDecorator self)"""
867  return _IMP_example.ExampleDecorator_clear_caches(self)
868 
869 
870  def set_name(self, a0):
871  """set_name(ExampleDecorator self, std::string a0)"""
872  return _IMP_example.ExampleDecorator_set_name(self, a0)
873 
874 
875  def set_check_level(self, a0):
876  """set_check_level(ExampleDecorator self, IMP::CheckLevel a0)"""
877  return _IMP_example.ExampleDecorator_set_check_level(self, a0)
878 
879 
880  def add_to_derivative(self, a0, a1, a2):
881  """add_to_derivative(ExampleDecorator self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
882  return _IMP_example.ExampleDecorator_add_to_derivative(self, a0, a1, a2)
883 
884 
885  def set_is_optimized(self, a0, a1):
886  """set_is_optimized(ExampleDecorator self, FloatKey a0, bool a1)"""
887  return _IMP_example.ExampleDecorator_set_is_optimized(self, a0, a1)
888 
889 
890  def get_is_optimized(self, a0):
891  """get_is_optimized(ExampleDecorator self, FloatKey a0) -> bool"""
892  return _IMP_example.ExampleDecorator_get_is_optimized(self, a0)
893 
894 
895  def get_check_level(self):
896  """get_check_level(ExampleDecorator self) -> IMP::CheckLevel"""
897  return _IMP_example.ExampleDecorator_get_check_level(self)
898 
899 
900  def __eq__(self, *args):
901  """
902  __eq__(ExampleDecorator self, ExampleDecorator o) -> bool
903  __eq__(ExampleDecorator self, Particle d) -> bool
904  """
905  return _IMP_example.ExampleDecorator___eq__(self, *args)
906 
907 
908  def __ne__(self, *args):
909  """
910  __ne__(ExampleDecorator self, ExampleDecorator o) -> bool
911  __ne__(ExampleDecorator self, Particle d) -> bool
912  """
913  return _IMP_example.ExampleDecorator___ne__(self, *args)
914 
915 
916  def __le__(self, *args):
917  """
918  __le__(ExampleDecorator self, ExampleDecorator o) -> bool
919  __le__(ExampleDecorator self, Particle d) -> bool
920  """
921  return _IMP_example.ExampleDecorator___le__(self, *args)
922 
923 
924  def __lt__(self, *args):
925  """
926  __lt__(ExampleDecorator self, ExampleDecorator o) -> bool
927  __lt__(ExampleDecorator self, Particle d) -> bool
928  """
929  return _IMP_example.ExampleDecorator___lt__(self, *args)
930 
931 
932  def __ge__(self, *args):
933  """
934  __ge__(ExampleDecorator self, ExampleDecorator o) -> bool
935  __ge__(ExampleDecorator self, Particle d) -> bool
936  """
937  return _IMP_example.ExampleDecorator___ge__(self, *args)
938 
939 
940  def __gt__(self, *args):
941  """
942  __gt__(ExampleDecorator self, ExampleDecorator o) -> bool
943  __gt__(ExampleDecorator self, Particle d) -> bool
944  """
945  return _IMP_example.ExampleDecorator___gt__(self, *args)
946 
947 
948  def __hash__(self):
949  """__hash__(ExampleDecorator self) -> std::size_t"""
950  return _IMP_example.ExampleDecorator___hash__(self)
951 
952 
953  def __str__(self):
954  """__str__(ExampleDecorator self) -> std::string"""
955  return _IMP_example.ExampleDecorator___str__(self)
956 
957 
958  def __repr__(self):
959  """__repr__(ExampleDecorator self) -> std::string"""
960  return _IMP_example.ExampleDecorator___repr__(self)
961 
962  __swig_destroy__ = _IMP_example.delete_ExampleDecorator
963  __del__ = lambda self: None
964 ExampleDecorator_swigregister = _IMP_example.ExampleDecorator_swigregister
965 ExampleDecorator_swigregister(ExampleDecorator)
966 
967 def ExampleDecorator_get_is_setup(*args):
968  """
969  get_is_setup(Model m, ParticleIndex pi) -> bool
970  ExampleDecorator_get_is_setup(_ParticleAdaptor p) -> bool
971  """
972  return _IMP_example.ExampleDecorator_get_is_setup(*args)
973 
974 def ExampleDecorator_setup_particle(*args):
975  """
976  setup_particle(Model m, ParticleIndex pi, std::string name) -> ExampleDecorator
977  ExampleDecorator_setup_particle(_ParticleAdaptor decorator, std::string name) -> ExampleDecorator
978  """
979  return _IMP_example.ExampleDecorator_setup_particle(*args)
980 
981 
982 def __lshift__(out, n):
983  """__lshift__(_ostream out, ExampleDecorator n) -> _ostream"""
984  return _IMP_example.__lshift__(out, n)
986  """Proxy of C++ IMP::example::ExampleUnaryFunction class."""
987 
988  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
989 
990  def __init__(self, center, k):
991  """__init__(IMP::example::ExampleUnaryFunction self, IMP::Float center, IMP::Float k) -> ExampleUnaryFunction"""
992  this = _IMP_example.new_ExampleUnaryFunction(center, k)
993  try:
994  self.this.append(this)
995  except __builtin__.Exception:
996  self.this = this
997 
998  def get_version_info(self):
999  """get_version_info(ExampleUnaryFunction self) -> VersionInfo"""
1000  return _IMP_example.ExampleUnaryFunction_get_version_info(self)
1001 
1002 
1003  def __str__(self):
1004  """__str__(ExampleUnaryFunction self) -> std::string"""
1005  return _IMP_example.ExampleUnaryFunction___str__(self)
1006 
1007 
1008  def __repr__(self):
1009  """__repr__(ExampleUnaryFunction self) -> std::string"""
1010  return _IMP_example.ExampleUnaryFunction___repr__(self)
1011 
1012 
1013  @staticmethod
1014  def get_from(o):
1015  return _object_cast_to_ExampleUnaryFunction(o)
1016 
1017 ExampleUnaryFunction_swigregister = _IMP_example.ExampleUnaryFunction_swigregister
1018 ExampleUnaryFunction_swigregister(ExampleUnaryFunction)
1019 
1020 class ExampleObject(IMP.Object):
1021  """Proxy of C++ IMP::example::ExampleObject 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, data):
1026  """__init__(IMP::example::ExampleObject self, IMP::Floats const & data) -> ExampleObject"""
1027  this = _IMP_example.new_ExampleObject(data)
1028  try:
1029  self.this.append(this)
1030  except __builtin__.Exception:
1031  self.this = this
1032 
1033  def get_data(self, i):
1034  """get_data(ExampleObject self, unsigned int i) -> double"""
1035  return _IMP_example.ExampleObject_get_data(self, i)
1036 
1037 
1038  def get_version_info(self):
1039  """get_version_info(ExampleObject self) -> VersionInfo"""
1040  return _IMP_example.ExampleObject_get_version_info(self)
1041 
1042 
1043  def __str__(self):
1044  """__str__(ExampleObject self) -> std::string"""
1045  return _IMP_example.ExampleObject___str__(self)
1046 
1047 
1048  def __repr__(self):
1049  """__repr__(ExampleObject self) -> std::string"""
1050  return _IMP_example.ExampleObject___repr__(self)
1051 
1052 
1053  @staticmethod
1054  def get_from(o):
1055  return _object_cast_to_ExampleObject(o)
1056 
1057 ExampleObject_swigregister = _IMP_example.ExampleObject_swigregister
1058 ExampleObject_swigregister(ExampleObject)
1059 
1061  """Proxy of C++ IMP::example::ExampleSingletonModifier 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, bb):
1066  """__init__(IMP::example::ExampleSingletonModifier self, BoundingBox3D bb) -> ExampleSingletonModifier"""
1067  this = _IMP_example.new_ExampleSingletonModifier(bb)
1068  try:
1069  self.this.append(this)
1070  except __builtin__.Exception:
1071  self.this = this
1072 
1073  def do_get_inputs(self, m, pis):
1074  """do_get_inputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1075  return _IMP_example.ExampleSingletonModifier_do_get_inputs(self, m, pis)
1076 
1077 
1078  def do_get_outputs(self, m, pis):
1079  """do_get_outputs(ExampleSingletonModifier self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1080  return _IMP_example.ExampleSingletonModifier_do_get_outputs(self, m, pis)
1081 
1082 
1083  def get_version_info(self):
1084  """get_version_info(ExampleSingletonModifier self) -> VersionInfo"""
1085  return _IMP_example.ExampleSingletonModifier_get_version_info(self)
1086 
1087 
1088  def __str__(self):
1089  """__str__(ExampleSingletonModifier self) -> std::string"""
1090  return _IMP_example.ExampleSingletonModifier___str__(self)
1091 
1092 
1093  def __repr__(self):
1094  """__repr__(ExampleSingletonModifier self) -> std::string"""
1095  return _IMP_example.ExampleSingletonModifier___repr__(self)
1096 
1097 
1098  @staticmethod
1099  def get_from(o):
1100  return _object_cast_to_ExampleSingletonModifier(o)
1101 
1102 ExampleSingletonModifier_swigregister = _IMP_example.ExampleSingletonModifier_swigregister
1103 ExampleSingletonModifier_swigregister(ExampleSingletonModifier)
1104 
1106  """Proxy of C++ IMP::example::ExamplePairScore class."""
1107 
1108  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1109 
1110  def __init__(self, x0, k):
1111  """__init__(IMP::example::ExamplePairScore self, double x0, double k) -> ExamplePairScore"""
1112  this = _IMP_example.new_ExamplePairScore(x0, k)
1113  try:
1114  self.this.append(this)
1115  except __builtin__.Exception:
1116  self.this = this
1117 
1118  def do_get_inputs(self, m, pis):
1119  """do_get_inputs(ExamplePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1120  return _IMP_example.ExamplePairScore_do_get_inputs(self, m, pis)
1121 
1122 
1123  def get_version_info(self):
1124  """get_version_info(ExamplePairScore self) -> VersionInfo"""
1125  return _IMP_example.ExamplePairScore_get_version_info(self)
1126 
1127 
1128  def __str__(self):
1129  """__str__(ExamplePairScore self) -> std::string"""
1130  return _IMP_example.ExamplePairScore___str__(self)
1131 
1132 
1133  def __repr__(self):
1134  """__repr__(ExamplePairScore self) -> std::string"""
1135  return _IMP_example.ExamplePairScore___repr__(self)
1136 
1137 
1138  @staticmethod
1139  def get_from(o):
1140  return _object_cast_to_ExamplePairScore(o)
1141 
1142 ExamplePairScore_swigregister = _IMP_example.ExamplePairScore_swigregister
1143 ExamplePairScore_swigregister(ExamplePairScore)
1144 
1146  """Proxy of C++ IMP::example::ExampleSubsetFilterTable class."""
1147 
1148  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1149 
1150  def __init__(self, max_diff, pt):
1151  """__init__(IMP::example::ExampleSubsetFilterTable self, unsigned int max_diff, IMP::ParticlesTemp const & pt) -> ExampleSubsetFilterTable"""
1152  this = _IMP_example.new_ExampleSubsetFilterTable(max_diff, pt)
1153  try:
1154  self.this.append(this)
1155  except __builtin__.Exception:
1156  self.this = this
1157 
1158  def get_version_info(self):
1159  """get_version_info(ExampleSubsetFilterTable self) -> VersionInfo"""
1160  return _IMP_example.ExampleSubsetFilterTable_get_version_info(self)
1161 
1162 
1163  def __str__(self):
1164  """__str__(ExampleSubsetFilterTable self) -> std::string"""
1165  return _IMP_example.ExampleSubsetFilterTable___str__(self)
1166 
1167 
1168  def __repr__(self):
1169  """__repr__(ExampleSubsetFilterTable self) -> std::string"""
1170  return _IMP_example.ExampleSubsetFilterTable___repr__(self)
1171 
1172 
1173  @staticmethod
1174  def get_from(o):
1175  return _object_cast_to_ExampleSubsetFilterTable(o)
1176 
1177 ExampleSubsetFilterTable_swigregister = _IMP_example.ExampleSubsetFilterTable_swigregister
1178 ExampleSubsetFilterTable_swigregister(ExampleSubsetFilterTable)
1179 
1181  """Proxy of C++ IMP::example::ExampleConstraint class."""
1182 
1183  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1184 
1185  def __init__(self, p):
1186  """__init__(IMP::example::ExampleConstraint self, Particle p) -> ExampleConstraint"""
1187  this = _IMP_example.new_ExampleConstraint(p)
1188  try:
1189  self.this.append(this)
1190  except __builtin__.Exception:
1191  self.this = this
1192 
1193  def do_get_inputs(self):
1194  """do_get_inputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1195  return _IMP_example.ExampleConstraint_do_get_inputs(self)
1196 
1197 
1198  def do_get_outputs(self):
1199  """do_get_outputs(ExampleConstraint self) -> IMP::ModelObjectsTemp"""
1200  return _IMP_example.ExampleConstraint_do_get_outputs(self)
1201 
1202 
1203  def get_key():
1204  """get_key() -> IntKey"""
1205  return _IMP_example.ExampleConstraint_get_key()
1206 
1207  get_key = staticmethod(get_key)
1208 
1209  def get_version_info(self):
1210  """get_version_info(ExampleConstraint self) -> VersionInfo"""
1211  return _IMP_example.ExampleConstraint_get_version_info(self)
1212 
1213 
1214  def __str__(self):
1215  """__str__(ExampleConstraint self) -> std::string"""
1216  return _IMP_example.ExampleConstraint___str__(self)
1217 
1218 
1219  def __repr__(self):
1220  """__repr__(ExampleConstraint self) -> std::string"""
1221  return _IMP_example.ExampleConstraint___repr__(self)
1222 
1223 
1224  @staticmethod
1225  def get_from(o):
1226  return _object_cast_to_ExampleConstraint(o)
1227 
1228 ExampleConstraint_swigregister = _IMP_example.ExampleConstraint_swigregister
1229 ExampleConstraint_swigregister(ExampleConstraint)
1230 
1231 def ExampleConstraint_get_key():
1232  """ExampleConstraint_get_key() -> IntKey"""
1233  return _IMP_example.ExampleConstraint_get_key()
1234 
1235 
1236 def create_serial_mover(m, pis):
1237  """create_serial_mover(Model m, IMP::ParticleIndexes const & pis) -> MonteCarloMover"""
1238  return _IMP_example.create_serial_mover(m, pis)
1239 
1240 def optimize_balls(*args):
1241  """
1242  optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states, IMP::LogLevel ll)
1243  optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded, IMP::OptimizerStates const & opt_states)
1244  optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs, IMP::PairPredicates const & excluded)
1245  optimize_balls(Model m, IMP::ParticleIndexes const & pis, IMP::RestraintsTemp const & rs)
1246  optimize_balls(Model m, IMP::ParticleIndexes const & pis)
1247  """
1248  return _IMP_example.optimize_balls(*args)
1249 
1250 def optimize_assembly(*args):
1251  """
1252  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)
1253  optimize_assembly(Model m, IMP::ParticleIndexes const & components, IMP::RestraintsTemp const & interactions, IMP::RestraintsTemp const & other_restraints, BoundingBox3D bb, PairScore ev, double cutoff)
1254  """
1255  return _IMP_example.optimize_assembly(*args)
1256 
1257 def get_number_of_incidences(psa, psb, point_distance):
1258  """get_number_of_incidences(IMP::ParticlesTemp const & psa, IMP::ParticlesTemp const & psb, double point_distance) -> unsigned int"""
1259  return _IMP_example.get_number_of_incidences(psa, psb, point_distance)
1260 
1261 def create_chain_restraint(m, ps, length_factor, k, name):
1262  """create_chain_restraint(Model m, IMP::ParticleIndexes const & ps, double length_factor, double k, std::string name) -> Restraint"""
1263  return _IMP_example.create_chain_restraint(m, ps, length_factor, k, name)
1264 
1265 def create_excluded_volume(m, ps, k, name):
1266  """create_excluded_volume(Model m, IMP::ParticleIndexes const & ps, double k, std::string name) -> Restraint"""
1267  return _IMP_example.create_excluded_volume(m, ps, k, name)
1268 class ExampleTemplateClass3D(object):
1269  """Proxy of C++ IMP::example::ExampleTemplateClassD<(3)> class."""
1270 
1271  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1272 
1273  def __init__(self, *args):
1274  """
1275  __init__(IMP::example::ExampleTemplateClassD<(3)> self) -> ExampleTemplateClass3D
1276  __init__(IMP::example::ExampleTemplateClassD<(3)> self, Vector3D a, Vector3D b) -> ExampleTemplateClass3D
1277  """
1278  this = _IMP_example.new_ExampleTemplateClass3D(*args)
1279  try:
1280  self.this.append(this)
1281  except __builtin__.Exception:
1282  self.this = this
1283 
1284  def get_point(self, i):
1285  """get_point(ExampleTemplateClass3D self, unsigned int i) -> Vector3D"""
1286  return _IMP_example.ExampleTemplateClass3D_get_point(self, i)
1287 
1288 
1289  def show(self, *args):
1290  """
1291  show(ExampleTemplateClass3D self, _ostream out)
1292  show(ExampleTemplateClass3D self)
1293  """
1294  return _IMP_example.ExampleTemplateClass3D_show(self, *args)
1295 
1296 
1297  def __str__(self):
1298  """__str__(ExampleTemplateClass3D self) -> std::string"""
1299  return _IMP_example.ExampleTemplateClass3D___str__(self)
1300 
1301 
1302  def __repr__(self):
1303  """__repr__(ExampleTemplateClass3D self) -> std::string"""
1304  return _IMP_example.ExampleTemplateClass3D___repr__(self)
1305 
1306  __swig_destroy__ = _IMP_example.delete_ExampleTemplateClass3D
1307  __del__ = lambda self: None
1308 ExampleTemplateClass3D_swigregister = _IMP_example.ExampleTemplateClass3D_swigregister
1309 ExampleTemplateClass3D_swigregister(ExampleTemplateClass3D)
1310 
1311 
1312 def get_module_version():
1313  """get_module_version() -> std::string const"""
1314  return _IMP_example.get_module_version()
1315 
1316 def get_example_path(fname):
1317  """get_example_path(std::string fname) -> std::string"""
1318  return _IMP_example.get_example_path(fname)
1319 
1320 def get_data_path(fname):
1321  """get_data_path(std::string fname) -> std::string"""
1322  return _IMP_example.get_data_path(fname)
1323 
1324 from . import _version_check
1325 _version_check.check_version(get_module_version())
1326 __version__ = get_module_version()
1327 
1328 
1329 
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.
Restraint * create_excluded_volume(Model *m, const ParticleIndexes &ps, double k, std::string name)
Vector3D get_random_vector_in(const Cylinder3D &c)
Generate a random vector in a cylinder with uniform density.
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.
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())
Basic utilities for handling cryo-electron microscopy 3D density maps.
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
Interface to specialized Particle types (e.g. atoms)
Definition: Decorator.h: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
std::string get_module_version()
Return the version of this module, as a string.
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Definition: Object.h: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:421
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.
Support for small angle X-ray scattering (SAXS) data.
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
A restraint is a term in an IMP ScoringFunction.
Definition: Restraint.h:54