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IMP Reference Guide  2.6.1
The Integrative Modeling Platform
misc/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.7
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 2007-2016 IMP Inventors. All rights reserved.
9 
10 from __future__ import print_function, division, absolute_import
11 
12 
13 
14 
15 from sys import version_info
16 if version_info >= (2, 6, 0):
17  def swig_import_helper():
18  from os.path import dirname
19  import imp
20  fp = None
21  try:
22  fp, pathname, description = imp.find_module('_IMP_misc', [dirname(__file__)])
23  except ImportError:
24  import _IMP_misc
25  return _IMP_misc
26  if fp is not None:
27  try:
28  _mod = imp.load_module('_IMP_misc', fp, pathname, description)
29  finally:
30  fp.close()
31  return _mod
32  _IMP_misc = swig_import_helper()
33  del swig_import_helper
34 else:
35  import _IMP_misc
36 del version_info
37 try:
38  _swig_property = property
39 except NameError:
40  pass # Python < 2.2 doesn't have 'property'.
41 
42 
43 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
44  if (name == "thisown"):
45  return self.this.own(value)
46  if (name == "this"):
47  if type(value).__name__ == 'SwigPyObject':
48  self.__dict__[name] = value
49  return
50  method = class_type.__swig_setmethods__.get(name, None)
51  if method:
52  return method(self, value)
53  if (not static):
54  object.__setattr__(self, name, value)
55  else:
56  raise AttributeError("You cannot add attributes to %s" % self)
57 
58 
59 def _swig_setattr(self, class_type, name, value):
60  return _swig_setattr_nondynamic(self, class_type, name, value, 0)
61 
62 
63 def _swig_getattr_nondynamic(self, class_type, name, static=1):
64  if (name == "thisown"):
65  return self.this.own()
66  method = class_type.__swig_getmethods__.get(name, None)
67  if method:
68  return method(self)
69  if (not static):
70  return object.__getattr__(self, name)
71  else:
72  raise AttributeError(name)
73 
74 def _swig_getattr(self, class_type, name):
75  return _swig_getattr_nondynamic(self, class_type, name, 0)
76 
77 
78 def _swig_repr(self):
79  try:
80  strthis = "proxy of " + self.this.__repr__()
81  except:
82  strthis = ""
83  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
84 
85 try:
86  _object = object
87  _newclass = 1
88 except AttributeError:
89  class _object:
90  pass
91  _newclass = 0
92 
93 
94 
95 def _swig_setattr_nondynamic_method(set):
96  def set_attr(self, name, value):
97  if (name == "thisown"):
98  return self.this.own(value)
99  if hasattr(self, name) or (name == "this"):
100  set(self, name, value)
101  else:
102  raise AttributeError("You cannot add attributes to %s" % self)
103  return set_attr
104 
105 
106 try:
107  import weakref
108  weakref_proxy = weakref.proxy
109 except:
110  weakref_proxy = lambda x: x
111 
112 
113 class IMP_MISC_SwigPyIterator(object):
114  """Proxy of C++ swig::IMP_MISC_SwigPyIterator class"""
115  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
116 
117  def __init__(self, *args, **kwargs):
118  raise AttributeError("No constructor defined - class is abstract")
119  __repr__ = _swig_repr
120  __swig_destroy__ = _IMP_misc.delete_IMP_MISC_SwigPyIterator
121  __del__ = lambda self: None
122 
123  def value(self):
124  """value(IMP_MISC_SwigPyIterator self) -> PyObject *"""
125  return _IMP_misc.IMP_MISC_SwigPyIterator_value(self)
126 
127 
128  def incr(self, n=1):
129  """
130  incr(IMP_MISC_SwigPyIterator self, size_t n=1) -> IMP_MISC_SwigPyIterator
131  incr(IMP_MISC_SwigPyIterator self) -> IMP_MISC_SwigPyIterator
132  """
133  return _IMP_misc.IMP_MISC_SwigPyIterator_incr(self, n)
134 
135 
136  def decr(self, n=1):
137  """
138  decr(IMP_MISC_SwigPyIterator self, size_t n=1) -> IMP_MISC_SwigPyIterator
139  decr(IMP_MISC_SwigPyIterator self) -> IMP_MISC_SwigPyIterator
140  """
141  return _IMP_misc.IMP_MISC_SwigPyIterator_decr(self, n)
142 
143 
144  def distance(self, x):
145  """distance(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> ptrdiff_t"""
146  return _IMP_misc.IMP_MISC_SwigPyIterator_distance(self, x)
147 
148 
149  def equal(self, x):
150  """equal(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
151  return _IMP_misc.IMP_MISC_SwigPyIterator_equal(self, x)
152 
153 
154  def copy(self):
155  """copy(IMP_MISC_SwigPyIterator self) -> IMP_MISC_SwigPyIterator"""
156  return _IMP_misc.IMP_MISC_SwigPyIterator_copy(self)
157 
158 
159  def next(self):
160  """next(IMP_MISC_SwigPyIterator self) -> PyObject *"""
161  return _IMP_misc.IMP_MISC_SwigPyIterator_next(self)
162 
163 
164  def __next__(self):
165  """__next__(IMP_MISC_SwigPyIterator self) -> PyObject *"""
166  return _IMP_misc.IMP_MISC_SwigPyIterator___next__(self)
167 
168 
169  def previous(self):
170  """previous(IMP_MISC_SwigPyIterator self) -> PyObject *"""
171  return _IMP_misc.IMP_MISC_SwigPyIterator_previous(self)
172 
173 
174  def advance(self, n):
175  """advance(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
176  return _IMP_misc.IMP_MISC_SwigPyIterator_advance(self, n)
177 
178 
179  def __eq__(self, x):
180  """__eq__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
181  return _IMP_misc.IMP_MISC_SwigPyIterator___eq__(self, x)
182 
183 
184  def __ne__(self, x):
185  """__ne__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> bool"""
186  return _IMP_misc.IMP_MISC_SwigPyIterator___ne__(self, x)
187 
188 
189  def __iadd__(self, n):
190  """__iadd__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
191  return _IMP_misc.IMP_MISC_SwigPyIterator___iadd__(self, n)
192 
193 
194  def __isub__(self, n):
195  """__isub__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
196  return _IMP_misc.IMP_MISC_SwigPyIterator___isub__(self, n)
197 
198 
199  def __add__(self, n):
200  """__add__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator"""
201  return _IMP_misc.IMP_MISC_SwigPyIterator___add__(self, n)
202 
203 
204  def __sub__(self, *args):
205  """
206  __sub__(IMP_MISC_SwigPyIterator self, ptrdiff_t n) -> IMP_MISC_SwigPyIterator
207  __sub__(IMP_MISC_SwigPyIterator self, IMP_MISC_SwigPyIterator x) -> ptrdiff_t
208  """
209  return _IMP_misc.IMP_MISC_SwigPyIterator___sub__(self, *args)
210 
211  def __iter__(self):
212  return self
213 IMP_MISC_SwigPyIterator_swigregister = _IMP_misc.IMP_MISC_SwigPyIterator_swigregister
214 IMP_MISC_SwigPyIterator_swigregister(IMP_MISC_SwigPyIterator)
215 
216 
217 _value_types=[]
218 _object_types=[]
219 _raii_types=[]
220 _plural_types=[]
221 
222 
223 _IMP_misc.IMP_DEBUG_swigconstant(_IMP_misc)
224 IMP_DEBUG = _IMP_misc.IMP_DEBUG
225 
226 _IMP_misc.IMP_RELEASE_swigconstant(_IMP_misc)
227 IMP_RELEASE = _IMP_misc.IMP_RELEASE
228 
229 _IMP_misc.IMP_SILENT_swigconstant(_IMP_misc)
230 IMP_SILENT = _IMP_misc.IMP_SILENT
231 
232 _IMP_misc.IMP_PROGRESS_swigconstant(_IMP_misc)
233 IMP_PROGRESS = _IMP_misc.IMP_PROGRESS
234 
235 _IMP_misc.IMP_TERSE_swigconstant(_IMP_misc)
236 IMP_TERSE = _IMP_misc.IMP_TERSE
237 
238 _IMP_misc.IMP_VERBOSE_swigconstant(_IMP_misc)
239 IMP_VERBOSE = _IMP_misc.IMP_VERBOSE
240 
241 _IMP_misc.IMP_MEMORY_swigconstant(_IMP_misc)
242 IMP_MEMORY = _IMP_misc.IMP_MEMORY
243 
244 _IMP_misc.IMP_NONE_swigconstant(_IMP_misc)
245 IMP_NONE = _IMP_misc.IMP_NONE
246 
247 _IMP_misc.IMP_USAGE_swigconstant(_IMP_misc)
248 IMP_USAGE = _IMP_misc.IMP_USAGE
249 
250 _IMP_misc.IMP_INTERNAL_swigconstant(_IMP_misc)
251 IMP_INTERNAL = _IMP_misc.IMP_INTERNAL
252 
253 _IMP_misc.IMP_KERNEL_HAS_LOG4CXX_swigconstant(_IMP_misc)
254 IMP_KERNEL_HAS_LOG4CXX = _IMP_misc.IMP_KERNEL_HAS_LOG4CXX
255 
256 _IMP_misc.IMP_COMPILER_HAS_AUTO_swigconstant(_IMP_misc)
257 IMP_COMPILER_HAS_AUTO = _IMP_misc.IMP_COMPILER_HAS_AUTO
258 
259 _IMP_misc.IMP_COMPILER_HAS_DEBUG_VECTOR_swigconstant(_IMP_misc)
260 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_misc.IMP_COMPILER_HAS_DEBUG_VECTOR
261 
262 _IMP_misc.IMP_COMPILER_HAS_UNIQUE_PTR_swigconstant(_IMP_misc)
263 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_misc.IMP_COMPILER_HAS_UNIQUE_PTR
264 
265 _IMP_misc.IMP_KERNEL_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
266 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_misc.IMP_KERNEL_HAS_BOOST_RANDOM
267 
268 _IMP_misc.IMP_KERNEL_HAS_GPERFTOOLS_swigconstant(_IMP_misc)
269 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_misc.IMP_KERNEL_HAS_GPERFTOOLS
270 
271 _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER_swigconstant(_IMP_misc)
272 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
273 
274 _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER_swigconstant(_IMP_misc)
275 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_misc.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
276 
277 _IMP_misc.IMPKERNEL_SHOW_WARNINGS_swigconstant(_IMP_misc)
278 IMPKERNEL_SHOW_WARNINGS = _IMP_misc.IMPKERNEL_SHOW_WARNINGS
279 
280 import sys
281 class _DirectorObjects(object):
282  """@internal Simple class to keep references to director objects
283  to prevent premature deletion."""
284  def __init__(self):
285  self._objects = []
286  def register(self, obj):
287  """Take a reference to a director object; will only work for
288  refcounted C++ classes"""
289  if hasattr(obj, 'get_ref_count'):
290  self._objects.append(obj)
291  def cleanup(self):
292  """Only drop our reference and allow cleanup by Python if no other
293  Python references exist (we hold 3 references: one in self._objects,
294  one in x, and one in the argument list for getrefcount) *and* no
295  other C++ references exist (the Python object always holds one)"""
296  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
297  or x.get_ref_count() > 1]
298 # Do in two steps so the references are kept until the end of the
299 # function (deleting references may trigger a fresh call to this method)
300  self._objects = objs
301  def get_object_count(self):
302  """Get number of director objects (useful for testing only)"""
303  return len(self._objects)
304 _director_objects = _DirectorObjects()
305 
306 class _ostream(object):
307  """Proxy of C++ std::ostream class"""
308  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
309 
310  def __init__(self, *args, **kwargs):
311  raise AttributeError("No constructor defined")
312  __repr__ = _swig_repr
313 
314  def write(self, osa_buf):
315  """write(_ostream self, char const * osa_buf)"""
316  return _IMP_misc._ostream_write(self, osa_buf)
317 
318 _ostream_swigregister = _IMP_misc._ostream_swigregister
319 _ostream_swigregister(_ostream)
320 
321 
322 _IMP_misc.IMP_COMPILER_HAS_OVERRIDE_swigconstant(_IMP_misc)
323 IMP_COMPILER_HAS_OVERRIDE = _IMP_misc.IMP_COMPILER_HAS_OVERRIDE
324 
325 _IMP_misc.IMP_COMPILER_HAS_FINAL_swigconstant(_IMP_misc)
326 IMP_COMPILER_HAS_FINAL = _IMP_misc.IMP_COMPILER_HAS_FINAL
327 
328 _IMP_misc.IMP_HAS_NOEXCEPT_swigconstant(_IMP_misc)
329 IMP_HAS_NOEXCEPT = _IMP_misc.IMP_HAS_NOEXCEPT
330 import IMP
331 
332 _IMP_misc.IMP_CGAL_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
333 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CGAL_HAS_BOOST_FILESYSTEM
334 
335 _IMP_misc.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
336 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
337 
338 _IMP_misc.IMP_CGAL_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
339 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_misc.IMP_CGAL_HAS_BOOST_RANDOM
340 
341 _IMP_misc.IMP_CGAL_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
342 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CGAL_HAS_BOOST_SYSTEM
343 
344 _IMP_misc.IMPCGAL_SHOW_WARNINGS_swigconstant(_IMP_misc)
345 IMPCGAL_SHOW_WARNINGS = _IMP_misc.IMPCGAL_SHOW_WARNINGS
346 import IMP.cgal
347 
348 _IMP_misc.IMP_ALGEBRA_HAS_IMP_CGAL_swigconstant(_IMP_misc)
349 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_misc.IMP_ALGEBRA_HAS_IMP_CGAL
350 
351 _IMP_misc.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
352 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
353 
354 _IMP_misc.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
355 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
356 
357 _IMP_misc.IMP_ALGEBRA_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
358 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_RANDOM
359 
360 _IMP_misc.IMP_ALGEBRA_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
361 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_misc.IMP_ALGEBRA_HAS_BOOST_SYSTEM
362 
363 _IMP_misc.IMP_ALGEBRA_HAS_CGAL_swigconstant(_IMP_misc)
364 IMP_ALGEBRA_HAS_CGAL = _IMP_misc.IMP_ALGEBRA_HAS_CGAL
365 
366 _IMP_misc.IMP_ALGEBRA_HAS_ANN_swigconstant(_IMP_misc)
367 IMP_ALGEBRA_HAS_ANN = _IMP_misc.IMP_ALGEBRA_HAS_ANN
368 
369 _IMP_misc.IMPALGEBRA_SHOW_WARNINGS_swigconstant(_IMP_misc)
370 IMPALGEBRA_SHOW_WARNINGS = _IMP_misc.IMPALGEBRA_SHOW_WARNINGS
371 import IMP.algebra
372 
373 _IMP_misc.IMP_DISPLAY_HAS_IMP_CGAL_swigconstant(_IMP_misc)
374 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_misc.IMP_DISPLAY_HAS_IMP_CGAL
375 
376 _IMP_misc.IMP_DISPLAY_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
377 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
378 
379 _IMP_misc.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
380 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
381 
382 _IMP_misc.IMP_DISPLAY_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
383 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_RANDOM
384 
385 _IMP_misc.IMP_DISPLAY_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
386 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_misc.IMP_DISPLAY_HAS_BOOST_SYSTEM
387 
388 _IMP_misc.IMP_DISPLAY_HAS_CGAL_swigconstant(_IMP_misc)
389 IMP_DISPLAY_HAS_CGAL = _IMP_misc.IMP_DISPLAY_HAS_CGAL
390 
391 _IMP_misc.IMPDISPLAY_SHOW_WARNINGS_swigconstant(_IMP_misc)
392 IMPDISPLAY_SHOW_WARNINGS = _IMP_misc.IMPDISPLAY_SHOW_WARNINGS
393 import IMP.display
394 
395 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL_swigconstant(_IMP_misc)
396 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
397 
398 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
399 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
400 
401 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
402 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
403 
404 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
405 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
406 
407 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
408 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
409 
410 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_CGAL_swigconstant(_IMP_misc)
411 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_CGAL
412 
413 _IMP_misc.IMP_SCORE_FUNCTOR_HAS_HDF5_swigconstant(_IMP_misc)
414 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_misc.IMP_SCORE_FUNCTOR_HAS_HDF5
415 
416 _IMP_misc.IMPSCOREFUNCTOR_SHOW_WARNINGS_swigconstant(_IMP_misc)
417 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_misc.IMPSCOREFUNCTOR_SHOW_WARNINGS
418 import IMP.score_functor
419 
420 _IMP_misc.IMP_CORE_HAS_IMP_CGAL_swigconstant(_IMP_misc)
421 IMP_CORE_HAS_IMP_CGAL = _IMP_misc.IMP_CORE_HAS_IMP_CGAL
422 
423 _IMP_misc.IMP_CORE_HAS_IMP_KERNEL_swigconstant(_IMP_misc)
424 IMP_CORE_HAS_IMP_KERNEL = _IMP_misc.IMP_CORE_HAS_IMP_KERNEL
425 
426 _IMP_misc.IMP_CORE_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
427 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CORE_HAS_BOOST_FILESYSTEM
428 
429 _IMP_misc.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
430 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
431 
432 _IMP_misc.IMP_CORE_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
433 IMP_CORE_HAS_BOOST_RANDOM = _IMP_misc.IMP_CORE_HAS_BOOST_RANDOM
434 
435 _IMP_misc.IMP_CORE_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
436 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CORE_HAS_BOOST_SYSTEM
437 
438 _IMP_misc.IMP_CORE_HAS_CGAL_swigconstant(_IMP_misc)
439 IMP_CORE_HAS_CGAL = _IMP_misc.IMP_CORE_HAS_CGAL
440 
441 _IMP_misc.IMP_CORE_HAS_HDF5_swigconstant(_IMP_misc)
442 IMP_CORE_HAS_HDF5 = _IMP_misc.IMP_CORE_HAS_HDF5
443 
444 _IMP_misc.IMPCORE_SHOW_WARNINGS_swigconstant(_IMP_misc)
445 IMPCORE_SHOW_WARNINGS = _IMP_misc.IMPCORE_SHOW_WARNINGS
446 import IMP.core
447 
448 _IMP_misc.IMP_CONTAINER_HAS_IMP_ALGEBRA_swigconstant(_IMP_misc)
449 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_misc.IMP_CONTAINER_HAS_IMP_ALGEBRA
450 
451 _IMP_misc.IMP_CONTAINER_HAS_IMP_CGAL_swigconstant(_IMP_misc)
452 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_misc.IMP_CONTAINER_HAS_IMP_CGAL
453 
454 _IMP_misc.IMP_CONTAINER_HAS_IMP_DISPLAY_swigconstant(_IMP_misc)
455 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_misc.IMP_CONTAINER_HAS_IMP_DISPLAY
456 
457 _IMP_misc.IMP_CONTAINER_HAS_IMP_KERNEL_swigconstant(_IMP_misc)
458 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_misc.IMP_CONTAINER_HAS_IMP_KERNEL
459 
460 _IMP_misc.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_misc)
461 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
462 
463 _IMP_misc.IMP_CONTAINER_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
464 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
465 
466 _IMP_misc.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
467 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
468 
469 _IMP_misc.IMP_CONTAINER_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
470 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_RANDOM
471 
472 _IMP_misc.IMP_CONTAINER_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
473 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_misc.IMP_CONTAINER_HAS_BOOST_SYSTEM
474 
475 _IMP_misc.IMP_CONTAINER_HAS_CGAL_swigconstant(_IMP_misc)
476 IMP_CONTAINER_HAS_CGAL = _IMP_misc.IMP_CONTAINER_HAS_CGAL
477 
478 _IMP_misc.IMP_CONTAINER_HAS_HDF5_swigconstant(_IMP_misc)
479 IMP_CONTAINER_HAS_HDF5 = _IMP_misc.IMP_CONTAINER_HAS_HDF5
480 
481 _IMP_misc.IMPCONTAINER_SHOW_WARNINGS_swigconstant(_IMP_misc)
482 IMPCONTAINER_SHOW_WARNINGS = _IMP_misc.IMPCONTAINER_SHOW_WARNINGS
483 import IMP.container
484 
485 _IMP_misc.IMP_ATOM_HAS_IMP_CGAL_swigconstant(_IMP_misc)
486 IMP_ATOM_HAS_IMP_CGAL = _IMP_misc.IMP_ATOM_HAS_IMP_CGAL
487 
488 _IMP_misc.IMP_ATOM_HAS_IMP_KERNEL_swigconstant(_IMP_misc)
489 IMP_ATOM_HAS_IMP_KERNEL = _IMP_misc.IMP_ATOM_HAS_IMP_KERNEL
490 
491 _IMP_misc.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_misc)
492 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
493 
494 _IMP_misc.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
495 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
496 
497 _IMP_misc.IMP_ATOM_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
498 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_misc.IMP_ATOM_HAS_BOOST_RANDOM
499 
500 _IMP_misc.IMP_ATOM_HAS_BOOST_REGEX_swigconstant(_IMP_misc)
501 IMP_ATOM_HAS_BOOST_REGEX = _IMP_misc.IMP_ATOM_HAS_BOOST_REGEX
502 
503 _IMP_misc.IMP_ATOM_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
504 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_misc.IMP_ATOM_HAS_BOOST_SYSTEM
505 
506 _IMP_misc.IMP_ATOM_HAS_CGAL_swigconstant(_IMP_misc)
507 IMP_ATOM_HAS_CGAL = _IMP_misc.IMP_ATOM_HAS_CGAL
508 
509 _IMP_misc.IMP_ATOM_HAS_HDF5_swigconstant(_IMP_misc)
510 IMP_ATOM_HAS_HDF5 = _IMP_misc.IMP_ATOM_HAS_HDF5
511 
512 _IMP_misc.IMPATOM_SHOW_WARNINGS_swigconstant(_IMP_misc)
513 IMPATOM_SHOW_WARNINGS = _IMP_misc.IMPATOM_SHOW_WARNINGS
514 
515 _IMP_misc.IMP_ATOM_TYPE_INDEX_swigconstant(_IMP_misc)
516 IMP_ATOM_TYPE_INDEX = _IMP_misc.IMP_ATOM_TYPE_INDEX
517 
518 _IMP_misc.IMP_RESIDUE_TYPE_INDEX_swigconstant(_IMP_misc)
519 IMP_RESIDUE_TYPE_INDEX = _IMP_misc.IMP_RESIDUE_TYPE_INDEX
520 
521 _IMP_misc.IMP_HIERARCHY_TYPE_INDEX_swigconstant(_IMP_misc)
522 IMP_HIERARCHY_TYPE_INDEX = _IMP_misc.IMP_HIERARCHY_TYPE_INDEX
523 import IMP.atom
524 
525 _IMP_misc.IMP_MISC_HAS_IMP_ALGEBRA_swigconstant(_IMP_misc)
526 IMP_MISC_HAS_IMP_ALGEBRA = _IMP_misc.IMP_MISC_HAS_IMP_ALGEBRA
527 
528 _IMP_misc.IMP_MISC_HAS_IMP_CGAL_swigconstant(_IMP_misc)
529 IMP_MISC_HAS_IMP_CGAL = _IMP_misc.IMP_MISC_HAS_IMP_CGAL
530 
531 _IMP_misc.IMP_MISC_HAS_IMP_CONTAINER_swigconstant(_IMP_misc)
532 IMP_MISC_HAS_IMP_CONTAINER = _IMP_misc.IMP_MISC_HAS_IMP_CONTAINER
533 
534 _IMP_misc.IMP_MISC_HAS_IMP_DISPLAY_swigconstant(_IMP_misc)
535 IMP_MISC_HAS_IMP_DISPLAY = _IMP_misc.IMP_MISC_HAS_IMP_DISPLAY
536 
537 _IMP_misc.IMP_MISC_HAS_IMP_KERNEL_swigconstant(_IMP_misc)
538 IMP_MISC_HAS_IMP_KERNEL = _IMP_misc.IMP_MISC_HAS_IMP_KERNEL
539 
540 _IMP_misc.IMP_MISC_HAS_IMP_SCORE_FUNCTOR_swigconstant(_IMP_misc)
541 IMP_MISC_HAS_IMP_SCORE_FUNCTOR = _IMP_misc.IMP_MISC_HAS_IMP_SCORE_FUNCTOR
542 
543 _IMP_misc.IMP_MISC_HAS_BOOST_FILESYSTEM_swigconstant(_IMP_misc)
544 IMP_MISC_HAS_BOOST_FILESYSTEM = _IMP_misc.IMP_MISC_HAS_BOOST_FILESYSTEM
545 
546 _IMP_misc.IMP_MISC_HAS_BOOST_PROGRAMOPTIONS_swigconstant(_IMP_misc)
547 IMP_MISC_HAS_BOOST_PROGRAMOPTIONS = _IMP_misc.IMP_MISC_HAS_BOOST_PROGRAMOPTIONS
548 
549 _IMP_misc.IMP_MISC_HAS_BOOST_RANDOM_swigconstant(_IMP_misc)
550 IMP_MISC_HAS_BOOST_RANDOM = _IMP_misc.IMP_MISC_HAS_BOOST_RANDOM
551 
552 _IMP_misc.IMP_MISC_HAS_BOOST_REGEX_swigconstant(_IMP_misc)
553 IMP_MISC_HAS_BOOST_REGEX = _IMP_misc.IMP_MISC_HAS_BOOST_REGEX
554 
555 _IMP_misc.IMP_MISC_HAS_BOOST_SYSTEM_swigconstant(_IMP_misc)
556 IMP_MISC_HAS_BOOST_SYSTEM = _IMP_misc.IMP_MISC_HAS_BOOST_SYSTEM
557 
558 _IMP_misc.IMP_MISC_HAS_CGAL_swigconstant(_IMP_misc)
559 IMP_MISC_HAS_CGAL = _IMP_misc.IMP_MISC_HAS_CGAL
560 
561 _IMP_misc.IMP_MISC_HAS_HDF5_swigconstant(_IMP_misc)
562 IMP_MISC_HAS_HDF5 = _IMP_misc.IMP_MISC_HAS_HDF5
563 
564 _IMP_misc.IMPMISC_SHOW_WARNINGS_swigconstant(_IMP_misc)
565 IMPMISC_SHOW_WARNINGS = _IMP_misc.IMPMISC_SHOW_WARNINGS
566 
567 _object_types.append("WormLikeChain")
568 
569 
570 def _object_cast_to_WormLikeChain(o):
571  """_object_cast_to_WormLikeChain(Object o) -> WormLikeChain"""
572  return _IMP_misc._object_cast_to_WormLikeChain(o)
573 
574 _object_types.append("StateAdaptor")
575 
576 
577 def _object_cast_to_StateAdaptor(o):
578  """_object_cast_to_StateAdaptor(Object o) -> StateAdaptor"""
579  return _IMP_misc._object_cast_to_StateAdaptor(o)
580 
581 _object_types.append("CommonEndpointPairFilter")
582 
583 
584 def _object_cast_to_CommonEndpointPairFilter(o):
585  """_object_cast_to_CommonEndpointPairFilter(Object o) -> CommonEndpointPairFilter"""
586  return _IMP_misc._object_cast_to_CommonEndpointPairFilter(o)
587 
588 _object_types.append("LogPairScore")
589 
590 
591 def _object_cast_to_LogPairScore(o):
592  """_object_cast_to_LogPairScore(Object o) -> LogPairScore"""
593  return _IMP_misc._object_cast_to_LogPairScore(o)
594 
595 _object_types.append("LowestRefinedPairScore")
596 
597 
598 def _object_cast_to_LowestRefinedPairScore(o):
599  """_object_cast_to_LowestRefinedPairScore(Object o) -> LowestRefinedPairScore"""
600  return _IMP_misc._object_cast_to_LowestRefinedPairScore(o)
601 
602 _object_types.append("SoftCylinderPairScore")
603 
604 
605 def _object_cast_to_SoftCylinderPairScore(o):
606  """_object_cast_to_SoftCylinderPairScore(Object o) -> SoftCylinderPairScore"""
607  return _IMP_misc._object_cast_to_SoftCylinderPairScore(o)
608 
609 _object_types.append("DecayPairContainerOptimizerState")
610 
611 
612 def _object_cast_to_DecayPairContainerOptimizerState(o):
613  """_object_cast_to_DecayPairContainerOptimizerState(Object o) -> DecayPairContainerOptimizerState"""
614  return _IMP_misc._object_cast_to_DecayPairContainerOptimizerState(o)
615 
616 def CustomXYZRs(l=[]):
617  return [CustomXYZR(x) for x in l]
618 _plural_types.append("CustomXYZRs")
619 
620 
621 _value_types.append("CustomXYZR")
622 
623 class WormLikeChain(IMP.UnaryFunction):
624  """Proxy of C++ IMP::misc::WormLikeChain class"""
625  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
626 
627  def __init__(self, l_max, lp):
628  """__init__(IMP::misc::WormLikeChain self, IMP::Float l_max, IMP::Float lp) -> WormLikeChain"""
629  this = _IMP_misc.new_WormLikeChain(l_max, lp)
630  try:
631  self.this.append(this)
632  except:
633  self.this = this
634 
635  def get_version_info(self):
636  """get_version_info(WormLikeChain self) -> VersionInfo"""
637  return _IMP_misc.WormLikeChain_get_version_info(self)
638 
639 
640  def do_show(self, out):
641  """do_show(WormLikeChain self, _ostream out)"""
642  return _IMP_misc.WormLikeChain_do_show(self, out)
643 
644 
645  def __str__(self):
646  """__str__(WormLikeChain self) -> std::string"""
647  return _IMP_misc.WormLikeChain___str__(self)
648 
649 
650  def __repr__(self):
651  """__repr__(WormLikeChain self) -> std::string"""
652  return _IMP_misc.WormLikeChain___repr__(self)
653 
654 
655  @staticmethod
656  def get_from(o):
657  return _object_cast_to_WormLikeChain(o)
658 
659 WormLikeChain_swigregister = _IMP_misc.WormLikeChain_swigregister
660 WormLikeChain_swigregister(WormLikeChain)
661 
662 class LowestRefinedPairScore(IMP.PairScore):
663  """Proxy of C++ IMP::misc::LowestRefinedPairScore class"""
664  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
665 
666  def __init__(self, r, f):
667  """__init__(IMP::misc::LowestRefinedPairScore self, Refiner r, PairScore f) -> LowestRefinedPairScore"""
668  this = _IMP_misc.new_LowestRefinedPairScore(r, f)
669  try:
670  self.this.append(this)
671  except:
672  self.this = this
673 
674  def do_get_inputs(self, m, pis):
675  """do_get_inputs(LowestRefinedPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
676  return _IMP_misc.LowestRefinedPairScore_do_get_inputs(self, m, pis)
677 
678 
679  def get_version_info(self):
680  """get_version_info(LowestRefinedPairScore self) -> VersionInfo"""
681  return _IMP_misc.LowestRefinedPairScore_get_version_info(self)
682 
683 
684  def __str__(self):
685  """__str__(LowestRefinedPairScore self) -> std::string"""
686  return _IMP_misc.LowestRefinedPairScore___str__(self)
687 
688 
689  def __repr__(self):
690  """__repr__(LowestRefinedPairScore self) -> std::string"""
691  return _IMP_misc.LowestRefinedPairScore___repr__(self)
692 
693 
694  @staticmethod
695  def get_from(o):
696  return _object_cast_to_LowestRefinedPairScore(o)
697 
698 LowestRefinedPairScore_swigregister = _IMP_misc.LowestRefinedPairScore_swigregister
699 LowestRefinedPairScore_swigregister(LowestRefinedPairScore)
700 
701 class LogPairScore(IMP.PairScore):
702  """Proxy of C++ IMP::misc::LogPairScore class"""
703  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
704 
705  def __init__(self):
706  """__init__(IMP::misc::LogPairScore self) -> LogPairScore"""
707  this = _IMP_misc.new_LogPairScore()
708  try:
709  self.this.append(this)
710  except:
711  self.this = this
712 
713  def do_get_inputs(self, arg2, arg3):
714  """do_get_inputs(LogPairScore self, Model arg2, IMP::ParticleIndexes const & arg3) -> IMP::ModelObjectsTemp"""
715  return _IMP_misc.LogPairScore_do_get_inputs(self, arg2, arg3)
716 
717 
718  def get_version_info(self):
719  """get_version_info(LogPairScore self) -> VersionInfo"""
720  return _IMP_misc.LogPairScore_get_version_info(self)
721 
722 
723  def get_particle_pairs(self):
724  """get_particle_pairs(LogPairScore self) -> IMP::ParticlePairsTemp"""
725  return _IMP_misc.LogPairScore_get_particle_pairs(self)
726 
727 
728  def clear(self):
729  """clear(LogPairScore self)"""
730  return _IMP_misc.LogPairScore_clear(self)
731 
732 
733  def get_contains(self, pp):
734  """get_contains(LogPairScore self, IMP::ParticlePair const & pp) -> bool"""
735  return _IMP_misc.LogPairScore_get_contains(self, pp)
736 
737 
738  def __str__(self):
739  """__str__(LogPairScore self) -> std::string"""
740  return _IMP_misc.LogPairScore___str__(self)
741 
742 
743  def __repr__(self):
744  """__repr__(LogPairScore self) -> std::string"""
745  return _IMP_misc.LogPairScore___repr__(self)
746 
747 
748  @staticmethod
749  def get_from(o):
750  return _object_cast_to_LogPairScore(o)
751 
752 LogPairScore_swigregister = _IMP_misc.LogPairScore_swigregister
753 LogPairScore_swigregister(LogPairScore)
754 
755 class StateAdaptor(IMP.ScoreState):
756  """Proxy of C++ IMP::misc::StateAdaptor class"""
757  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
758 
759  def __init__(self, m, before, after):
760  """__init__(IMP::misc::StateAdaptor self, Model m, OptimizerState before, OptimizerState after) -> StateAdaptor"""
761  this = _IMP_misc.new_StateAdaptor(m, before, after)
762  try:
763  self.this.append(this)
764  except:
765  self.this = this
766 
767  def do_before_evaluate(self):
768  """do_before_evaluate(StateAdaptor self)"""
769  return _IMP_misc.StateAdaptor_do_before_evaluate(self)
770 
771 
772  def do_after_evaluate(self, da):
773  """do_after_evaluate(StateAdaptor self, DerivativeAccumulator da)"""
774  return _IMP_misc.StateAdaptor_do_after_evaluate(self, da)
775 
776 
777  def do_get_inputs(self):
778  """do_get_inputs(StateAdaptor self) -> IMP::ModelObjectsTemp"""
779  return _IMP_misc.StateAdaptor_do_get_inputs(self)
780 
781 
782  def do_get_outputs(self):
783  """do_get_outputs(StateAdaptor self) -> IMP::ModelObjectsTemp"""
784  return _IMP_misc.StateAdaptor_do_get_outputs(self)
785 
786 
787  def get_version_info(self):
788  """get_version_info(StateAdaptor self) -> VersionInfo"""
789  return _IMP_misc.StateAdaptor_get_version_info(self)
790 
791 
792  def __str__(self):
793  """__str__(StateAdaptor self) -> std::string"""
794  return _IMP_misc.StateAdaptor___str__(self)
795 
796 
797  def __repr__(self):
798  """__repr__(StateAdaptor self) -> std::string"""
799  return _IMP_misc.StateAdaptor___repr__(self)
800 
801 
802  @staticmethod
803  def get_from(o):
804  return _object_cast_to_StateAdaptor(o)
805 
806 StateAdaptor_swigregister = _IMP_misc.StateAdaptor_swigregister
807 StateAdaptor_swigregister(StateAdaptor)
808 
809 class CommonEndpointPairFilter(IMP.PairPredicate):
810  """Proxy of C++ IMP::misc::CommonEndpointPairFilter class"""
811  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
812 
813  def __init__(self):
814  """__init__(IMP::misc::CommonEndpointPairFilter self) -> CommonEndpointPairFilter"""
815  this = _IMP_misc.new_CommonEndpointPairFilter()
816  try:
817  self.this.append(this)
818  except:
819  self.this = this
820 
821  def do_get_inputs(self, m, pis):
822  """do_get_inputs(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
823  return _IMP_misc.CommonEndpointPairFilter_do_get_inputs(self, m, pis)
824 
825 
826  def get_value(self, *args):
827  """
828  get_value(CommonEndpointPairFilter self, IMP::ParticlePair const & a) -> int
829  get_value(CommonEndpointPairFilter self, IMP::ParticlePairsTemp const & o) -> IMP::Ints
830  """
831  return _IMP_misc.CommonEndpointPairFilter_get_value(self, *args)
832 
833 
834  def get_value_index(self, *args):
835  """
836  get_value_index(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexPair const & p) -> int
837  get_value_index(CommonEndpointPairFilter self, Model m, IMP::ParticleIndexPairs const & o) -> IMP::Ints
838  """
839  return _IMP_misc.CommonEndpointPairFilter_get_value_index(self, *args)
840 
841 
842  def get_version_info(self):
843  """get_version_info(CommonEndpointPairFilter self) -> VersionInfo"""
844  return _IMP_misc.CommonEndpointPairFilter_get_version_info(self)
845 
846 
847  def __str__(self):
848  """__str__(CommonEndpointPairFilter self) -> std::string"""
849  return _IMP_misc.CommonEndpointPairFilter___str__(self)
850 
851 
852  def __repr__(self):
853  """__repr__(CommonEndpointPairFilter self) -> std::string"""
854  return _IMP_misc.CommonEndpointPairFilter___repr__(self)
855 
856 
857  @staticmethod
858  def get_from(o):
859  return _object_cast_to_CommonEndpointPairFilter(o)
860 
861 CommonEndpointPairFilter_swigregister = _IMP_misc.CommonEndpointPairFilter_swigregister
862 CommonEndpointPairFilter_swigregister(CommonEndpointPairFilter)
863 
864 class CustomXYZR(IMP.core.XYZ):
865  """Proxy of C++ IMP::misc::CustomXYZR class"""
866  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
867 
868  def get_decorator_traits(self):
869  """get_decorator_traits(CustomXYZR self) -> FloatKey"""
870  return _IMP_misc.CustomXYZR_get_decorator_traits(self)
871 
872 
873  def get_default_decorator_traits():
874  """get_default_decorator_traits() -> FloatKey"""
875  return _IMP_misc.CustomXYZR_get_default_decorator_traits()
876 
877  get_default_decorator_traits = staticmethod(get_default_decorator_traits)
878 
879  def __init__(self, *args):
880  """
881  __init__(IMP::misc::CustomXYZR self) -> CustomXYZR
882  __init__(IMP::misc::CustomXYZR self, Model m, ParticleIndex id, FloatKey tr) -> CustomXYZR
883  __init__(IMP::misc::CustomXYZR self, Model m, ParticleIndex id) -> CustomXYZR
884  __init__(IMP::misc::CustomXYZR self, _ParticleAdaptor d, FloatKey tr) -> CustomXYZR
885  __init__(IMP::misc::CustomXYZR self, _ParticleAdaptor d) -> CustomXYZR
886  """
887  this = _IMP_misc.new_CustomXYZR(*args)
888  try:
889  self.this.append(this)
890  except:
891  self.this = this
892 
893  def show(self, *args):
894  """
895  show(CustomXYZR self, _ostream out)
896  show(CustomXYZR self)
897  """
898  return _IMP_misc.CustomXYZR_show(self, *args)
899 
900 
901  def setup_particle(*args):
902  """
903  setup_particle(Model m, ParticleIndex pi, FloatKey tr) -> CustomXYZR
904  setup_particle(Model m, ParticleIndex pi) -> CustomXYZR
905  setup_particle(_ParticleAdaptor d, FloatKey tr) -> CustomXYZR
906  setup_particle(_ParticleAdaptor d) -> CustomXYZR
907  setup_particle(Model m, ParticleIndex pi, double radius, FloatKey tr) -> CustomXYZR
908  setup_particle(Model m, ParticleIndex pi, double radius) -> CustomXYZR
909  setup_particle(_ParticleAdaptor d, double radius, FloatKey tr) -> CustomXYZR
910  setup_particle(_ParticleAdaptor d, double radius) -> CustomXYZR
911  setup_particle(Model m, ParticleIndex pi, Sphere3D ball, FloatKey tr) -> CustomXYZR
912  setup_particle(Model m, ParticleIndex pi, Sphere3D ball) -> CustomXYZR
913  setup_particle(_ParticleAdaptor d, Sphere3D ball, FloatKey tr) -> CustomXYZR
914  setup_particle(_ParticleAdaptor d, Sphere3D ball) -> CustomXYZR
915  """
916  return _IMP_misc.CustomXYZR_setup_particle(*args)
917 
918  setup_particle = staticmethod(setup_particle)
919 
920  def get_is_setup(*args):
921  """
922  get_is_setup(_ParticleAdaptor p, FloatKey tr) -> bool
923  get_is_setup(_ParticleAdaptor p) -> bool
924  get_is_setup(Model m, ParticleIndex pi, FloatKey radius_key) -> bool
925  get_is_setup(Model m, ParticleIndex pi) -> bool
926  """
927  return _IMP_misc.CustomXYZR_get_is_setup(*args)
928 
929  get_is_setup = staticmethod(get_is_setup)
930 
931  def get_radius(self):
932  """get_radius(CustomXYZR self) -> IMP::Float"""
933  return _IMP_misc.CustomXYZR_get_radius(self)
934 
935 
936  def set_radius(self, t):
937  """set_radius(CustomXYZR self, IMP::Float t)"""
938  return _IMP_misc.CustomXYZR_set_radius(self, t)
939 
940 
941  def get_sphere(self):
942  """get_sphere(CustomXYZR self) -> Sphere3D"""
943  return _IMP_misc.CustomXYZR_get_sphere(self)
944 
945 
946  def set_sphere(self, s):
947  """set_sphere(CustomXYZR self, Sphere3D s)"""
948  return _IMP_misc.CustomXYZR_set_sphere(self, s)
949 
950 
951  def get_default_radius_key():
952  """get_default_radius_key() -> FloatKey"""
953  return _IMP_misc.CustomXYZR_get_default_radius_key()
954 
955  get_default_radius_key = staticmethod(get_default_radius_key)
956 
957  def add_to_radius_derivative(self, v, d):
958  """add_to_radius_derivative(CustomXYZR self, double v, DerivativeAccumulator d)"""
959  return _IMP_misc.CustomXYZR_add_to_radius_derivative(self, v, d)
960 
961 
962  def get_traits(self):
963  """get_traits(CustomXYZR self) -> FloatKey"""
964  return _IMP_misc.CustomXYZR_get_traits(self)
965 
966 
967  def add_attribute(self, *args):
968  """
969  add_attribute(CustomXYZR self, FloatKey k, IMP::Float v, bool opt)
970  add_attribute(CustomXYZR self, FloatKey a0, IMP::Float a1)
971  add_attribute(CustomXYZR self, IntKey a0, IMP::Int a1)
972  add_attribute(CustomXYZR self, StringKey a0, IMP::String a1)
973  add_attribute(CustomXYZR self, ParticleIndexKey a0, Particle a1)
974  add_attribute(CustomXYZR self, ObjectKey a0, Object a1)
975  """
976  return _IMP_misc.CustomXYZR_add_attribute(self, *args)
977 
978 
979  def get_value(self, *args):
980  """
981  get_value(CustomXYZR self, FloatKey a0) -> IMP::Float
982  get_value(CustomXYZR self, IntKey a0) -> IMP::Int
983  get_value(CustomXYZR self, StringKey a0) -> IMP::String
984  get_value(CustomXYZR self, ParticleIndexKey a0) -> Particle
985  get_value(CustomXYZR self, ObjectKey a0) -> Object
986  """
987  return _IMP_misc.CustomXYZR_get_value(self, *args)
988 
989 
990  def set_value(self, *args):
991  """
992  set_value(CustomXYZR self, FloatKey a0, IMP::Float a1)
993  set_value(CustomXYZR self, IntKey a0, IMP::Int a1)
994  set_value(CustomXYZR self, StringKey a0, IMP::String a1)
995  set_value(CustomXYZR self, ParticleIndexKey a0, Particle a1)
996  set_value(CustomXYZR self, ObjectKey a0, Object a1)
997  """
998  return _IMP_misc.CustomXYZR_set_value(self, *args)
999 
1000 
1001  def remove_attribute(self, *args):
1002  """
1003  remove_attribute(CustomXYZR self, FloatKey a0)
1004  remove_attribute(CustomXYZR self, IntKey a0)
1005  remove_attribute(CustomXYZR self, StringKey a0)
1006  remove_attribute(CustomXYZR self, ParticleIndexKey a0)
1007  remove_attribute(CustomXYZR self, ObjectKey a0)
1008  """
1009  return _IMP_misc.CustomXYZR_remove_attribute(self, *args)
1010 
1011 
1012  def has_attribute(self, *args):
1013  """
1014  has_attribute(CustomXYZR self, FloatKey a0) -> bool
1015  has_attribute(CustomXYZR self, IntKey a0) -> bool
1016  has_attribute(CustomXYZR self, StringKey a0) -> bool
1017  has_attribute(CustomXYZR self, ParticleIndexKey a0) -> bool
1018  has_attribute(CustomXYZR self, ObjectKey a0) -> bool
1019  """
1020  return _IMP_misc.CustomXYZR_has_attribute(self, *args)
1021 
1022 
1023  def get_derivative(self, a0):
1024  """get_derivative(CustomXYZR self, FloatKey a0) -> double"""
1025  return _IMP_misc.CustomXYZR_get_derivative(self, a0)
1026 
1027 
1028  def get_name(self):
1029  """get_name(CustomXYZR self) -> std::string"""
1030  return _IMP_misc.CustomXYZR_get_name(self)
1031 
1032 
1033  def clear_caches(self):
1034  """clear_caches(CustomXYZR self)"""
1035  return _IMP_misc.CustomXYZR_clear_caches(self)
1036 
1037 
1038  def set_name(self, a0):
1039  """set_name(CustomXYZR self, std::string a0)"""
1040  return _IMP_misc.CustomXYZR_set_name(self, a0)
1041 
1042 
1043  def set_check_level(self, a0):
1044  """set_check_level(CustomXYZR self, IMP::CheckLevel a0)"""
1045  return _IMP_misc.CustomXYZR_set_check_level(self, a0)
1046 
1047 
1048  def add_to_derivative(self, a0, a1, a2):
1049  """add_to_derivative(CustomXYZR self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1050  return _IMP_misc.CustomXYZR_add_to_derivative(self, a0, a1, a2)
1051 
1052 
1053  def set_is_optimized(self, a0, a1):
1054  """set_is_optimized(CustomXYZR self, FloatKey a0, bool a1)"""
1055  return _IMP_misc.CustomXYZR_set_is_optimized(self, a0, a1)
1056 
1057 
1058  def get_is_optimized(self, a0):
1059  """get_is_optimized(CustomXYZR self, FloatKey a0) -> bool"""
1060  return _IMP_misc.CustomXYZR_get_is_optimized(self, a0)
1061 
1062 
1063  def get_check_level(self):
1064  """get_check_level(CustomXYZR self) -> IMP::CheckLevel"""
1065  return _IMP_misc.CustomXYZR_get_check_level(self)
1066 
1067 
1068  def __eq__(self, *args):
1069  """
1070  __eq__(CustomXYZR self, CustomXYZR o) -> bool
1071  __eq__(CustomXYZR self, Particle d) -> bool
1072  """
1073  return _IMP_misc.CustomXYZR___eq__(self, *args)
1074 
1075 
1076  def __ne__(self, *args):
1077  """
1078  __ne__(CustomXYZR self, CustomXYZR o) -> bool
1079  __ne__(CustomXYZR self, Particle d) -> bool
1080  """
1081  return _IMP_misc.CustomXYZR___ne__(self, *args)
1082 
1083 
1084  def __le__(self, *args):
1085  """
1086  __le__(CustomXYZR self, CustomXYZR o) -> bool
1087  __le__(CustomXYZR self, Particle d) -> bool
1088  """
1089  return _IMP_misc.CustomXYZR___le__(self, *args)
1090 
1091 
1092  def __lt__(self, *args):
1093  """
1094  __lt__(CustomXYZR self, CustomXYZR o) -> bool
1095  __lt__(CustomXYZR self, Particle d) -> bool
1096  """
1097  return _IMP_misc.CustomXYZR___lt__(self, *args)
1098 
1099 
1100  def __ge__(self, *args):
1101  """
1102  __ge__(CustomXYZR self, CustomXYZR o) -> bool
1103  __ge__(CustomXYZR self, Particle d) -> bool
1104  """
1105  return _IMP_misc.CustomXYZR___ge__(self, *args)
1106 
1107 
1108  def __gt__(self, *args):
1109  """
1110  __gt__(CustomXYZR self, CustomXYZR o) -> bool
1111  __gt__(CustomXYZR self, Particle d) -> bool
1112  """
1113  return _IMP_misc.CustomXYZR___gt__(self, *args)
1114 
1115 
1116  def __hash__(self):
1117  """__hash__(CustomXYZR self) -> std::size_t"""
1118  return _IMP_misc.CustomXYZR___hash__(self)
1119 
1120 
1121  def __str__(self):
1122  """__str__(CustomXYZR self) -> std::string"""
1123  return _IMP_misc.CustomXYZR___str__(self)
1124 
1125 
1126  def __repr__(self):
1127  """__repr__(CustomXYZR self) -> std::string"""
1128  return _IMP_misc.CustomXYZR___repr__(self)
1129 
1130  __swig_destroy__ = _IMP_misc.delete_CustomXYZR
1131  __del__ = lambda self: None
1132 CustomXYZR_swigregister = _IMP_misc.CustomXYZR_swigregister
1133 CustomXYZR_swigregister(CustomXYZR)
1134 
1135 def CustomXYZR_get_default_decorator_traits():
1136  """CustomXYZR_get_default_decorator_traits() -> FloatKey"""
1137  return _IMP_misc.CustomXYZR_get_default_decorator_traits()
1138 
1139 def CustomXYZR_setup_particle(*args):
1140  """
1141  setup_particle(Model m, ParticleIndex pi, FloatKey tr) -> CustomXYZR
1142  setup_particle(Model m, ParticleIndex pi) -> CustomXYZR
1143  setup_particle(_ParticleAdaptor d, FloatKey tr) -> CustomXYZR
1144  setup_particle(_ParticleAdaptor d) -> CustomXYZR
1145  setup_particle(Model m, ParticleIndex pi, double radius, FloatKey tr) -> CustomXYZR
1146  setup_particle(Model m, ParticleIndex pi, double radius) -> CustomXYZR
1147  setup_particle(_ParticleAdaptor d, double radius, FloatKey tr) -> CustomXYZR
1148  setup_particle(_ParticleAdaptor d, double radius) -> CustomXYZR
1149  setup_particle(Model m, ParticleIndex pi, Sphere3D ball, FloatKey tr) -> CustomXYZR
1150  setup_particle(Model m, ParticleIndex pi, Sphere3D ball) -> CustomXYZR
1151  setup_particle(_ParticleAdaptor d, Sphere3D ball, FloatKey tr) -> CustomXYZR
1152  CustomXYZR_setup_particle(_ParticleAdaptor d, Sphere3D ball) -> CustomXYZR
1153  """
1154  return _IMP_misc.CustomXYZR_setup_particle(*args)
1155 
1156 def CustomXYZR_get_is_setup(*args):
1157  """
1158  get_is_setup(_ParticleAdaptor p, FloatKey tr) -> bool
1159  get_is_setup(_ParticleAdaptor p) -> bool
1160  get_is_setup(Model m, ParticleIndex pi, FloatKey radius_key) -> bool
1161  CustomXYZR_get_is_setup(Model m, ParticleIndex pi) -> bool
1162  """
1163  return _IMP_misc.CustomXYZR_get_is_setup(*args)
1164 
1165 def CustomXYZR_get_default_radius_key():
1166  """CustomXYZR_get_default_radius_key() -> FloatKey"""
1167  return _IMP_misc.CustomXYZR_get_default_radius_key()
1168 
1169 
1170 def __lshift__(out, n):
1171  """__lshift__(_ostream out, CustomXYZR n) -> _ostream"""
1172  return _IMP_misc.__lshift__(out, n)
1173 
1174 def get_distance(a, b):
1175  """get_distance(CustomXYZR a, CustomXYZR b) -> double"""
1176  return _IMP_misc.get_distance(a, b)
1177 
1178 def get_sphere_d_geometry(d):
1179  """get_sphere_d_geometry(CustomXYZR d) -> Sphere3D"""
1180  return _IMP_misc.get_sphere_d_geometry(d)
1181 
1182 def set_sphere_d_geometry(d, v):
1183  """set_sphere_d_geometry(CustomXYZR d, Sphere3D v)"""
1184  return _IMP_misc.set_sphere_d_geometry(d, v)
1185 class SoftCylinderPairScore(IMP.PairScore):
1186  """Proxy of C++ IMP::misc::SoftCylinderPairScore class"""
1187  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1188 
1189  def __init__(self, k):
1190  """__init__(IMP::misc::SoftCylinderPairScore self, double k) -> SoftCylinderPairScore"""
1191  this = _IMP_misc.new_SoftCylinderPairScore(k)
1192  try:
1193  self.this.append(this)
1194  except:
1195  self.this = this
1196 
1197  def do_get_inputs(self, m, pis):
1198  """do_get_inputs(SoftCylinderPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1199  return _IMP_misc.SoftCylinderPairScore_do_get_inputs(self, m, pis)
1200 
1201 
1202  def get_version_info(self):
1203  """get_version_info(SoftCylinderPairScore self) -> VersionInfo"""
1204  return _IMP_misc.SoftCylinderPairScore_get_version_info(self)
1205 
1206 
1207  def __str__(self):
1208  """__str__(SoftCylinderPairScore self) -> std::string"""
1209  return _IMP_misc.SoftCylinderPairScore___str__(self)
1210 
1211 
1212  def __repr__(self):
1213  """__repr__(SoftCylinderPairScore self) -> std::string"""
1214  return _IMP_misc.SoftCylinderPairScore___repr__(self)
1215 
1216 
1217  @staticmethod
1218  def get_from(o):
1219  return _object_cast_to_SoftCylinderPairScore(o)
1220 
1221 SoftCylinderPairScore_swigregister = _IMP_misc.SoftCylinderPairScore_swigregister
1222 SoftCylinderPairScore_swigregister(SoftCylinderPairScore)
1223 
1224 class DecayPairContainerOptimizerState(IMP.OptimizerState):
1225  """Proxy of C++ IMP::misc::DecayPairContainerOptimizerState class"""
1226  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
1227 
1228  def __init__(self, *args):
1229  """
1230  __init__(IMP::misc::DecayPairContainerOptimizerState self, Model m, PairPredicate pred, IMP::ParticleIndexPairs const & initial_list, std::string name) -> DecayPairContainerOptimizerState
1231  __init__(IMP::misc::DecayPairContainerOptimizerState self, Model m, PairPredicate pred, IMP::ParticleIndexPairs const & initial_list) -> DecayPairContainerOptimizerState
1232  """
1233  this = _IMP_misc.new_DecayPairContainerOptimizerState(*args)
1234  try:
1235  self.this.append(this)
1236  except:
1237  self.this = this
1238 
1239  def get_output_container(self):
1240  """get_output_container(DecayPairContainerOptimizerState self) -> PairContainer"""
1241  return _IMP_misc.DecayPairContainerOptimizerState_get_output_container(self)
1242 
1243 
1244  def do_update(self, call_num):
1245  """do_update(DecayPairContainerOptimizerState self, unsigned int call_num)"""
1246  return _IMP_misc.DecayPairContainerOptimizerState_do_update(self, call_num)
1247 
1248 
1249  def get_version_info(self):
1250  """get_version_info(DecayPairContainerOptimizerState self) -> VersionInfo"""
1251  return _IMP_misc.DecayPairContainerOptimizerState_get_version_info(self)
1252 
1253 
1254  def __str__(self):
1255  """__str__(DecayPairContainerOptimizerState self) -> std::string"""
1256  return _IMP_misc.DecayPairContainerOptimizerState___str__(self)
1257 
1258 
1259  def __repr__(self):
1260  """__repr__(DecayPairContainerOptimizerState self) -> std::string"""
1261  return _IMP_misc.DecayPairContainerOptimizerState___repr__(self)
1262 
1263 
1264  @staticmethod
1265  def get_from(o):
1266  return _object_cast_to_DecayPairContainerOptimizerState(o)
1267 
1268 DecayPairContainerOptimizerState_swigregister = _IMP_misc.DecayPairContainerOptimizerState_swigregister
1269 DecayPairContainerOptimizerState_swigregister(DecayPairContainerOptimizerState)
1270 
1271 
1272 def get_module_version():
1273  """get_module_version() -> std::string const"""
1274  return _IMP_misc.get_module_version()
1275 
1276 def get_example_path(fname):
1277  """get_example_path(std::string fname) -> std::string"""
1278  return _IMP_misc.get_example_path(fname)
1279 
1280 def get_data_path(fname):
1281  """get_data_path(std::string fname) -> std::string"""
1282  return _IMP_misc.get_data_path(fname)
1283 
1284 from . import _version_check
1285 _version_check.check_version(get_module_version())
1286 __version__ = get_module_version()
1287 
1288 
1289 
Abstract class for scoring object(s) of type ParticleIndexPair.
Definition: PairScore.h:37
Various classes to hold sets of particles.
const algebra::Sphere3D get_sphere_d_geometry(CustomXYZR d)
Definition: CustomXYZR.h:90
Make CGAL functionality available to IMP.
virtual void clear_caches()
Definition: Object.h:227
virtual ModelObjectsTemp do_get_outputs(Model *m, const ParticleIndexes &pis) const =0
Composable functors to implement scores via compile-time composition.
double get_distance(const Plane3D &pln, const Vector3D &p)
Return the distance between a plane and a point in 3D.
Definition: Plane3D.h:63
ScoreStates maintain invariants in the Model.
Definition: ScoreState.h:53
virtual ModelObjectsTemp do_get_inputs(Model *m, const ParticleIndexes &pis) const =0
A decorator for a particle with x,y,z coordinates.
Definition: XYZ.h:30
void set_sphere_d_geometry(CustomXYZR d, const algebra::Sphere3D &v)
Definition: CustomXYZR.h:95
Basic functionality that is expected to be used by a wide variety of IMP users.
Abstract predicate function.
Definition: PairPredicate.h:31
General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP...
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
Definition: Object.h:173
Shared optimizer state that is invoked upon commitment of new coordinates.
void set_check_level(CheckLevel l)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
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.
Abstract single variable functor class for score functions.
Definition: UnaryFunction.h:25