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IMP Reference Guide  2.19.0
The Integrative Modeling Platform
scratch/__init__.py
1 # This file was automatically generated by SWIG (https://www.swig.org).
2 # Version 4.1.1
3 #
4 # Do not make changes to this file unless you know what you are doing - modify
5 # the SWIG interface file instead.
6 
7 
8 # This wrapper is part of IMP,
9 # Copyright 2007-2023 IMP Inventors. All rights reserved.
10 
11 from __future__ import print_function, division, absolute_import
12 
13 
14 
15 from sys import version_info as _swig_python_version_info
16 import _IMP_scratch
17 
18 try:
19  import builtins as __builtin__
20 except ImportError:
21  import __builtin__
22 
23 def _swig_repr(self):
24  try:
25  strthis = "proxy of " + self.this.__repr__()
26  except __builtin__.Exception:
27  strthis = ""
28  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
29 
30 
31 def _swig_setattr_nondynamic_instance_variable(set):
32  def set_instance_attr(self, name, value):
33  if name == "this":
34  set(self, name, value)
35  elif name == "thisown":
36  self.this.own(value)
37  elif hasattr(self, name) and isinstance(getattr(type(self), name), property):
38  set(self, name, value)
39  else:
40  raise AttributeError("You cannot add instance attributes to %s" % self)
41  return set_instance_attr
42 
43 
44 def _swig_setattr_nondynamic_class_variable(set):
45  def set_class_attr(cls, name, value):
46  if hasattr(cls, name) and not isinstance(getattr(cls, name), property):
47  set(cls, name, value)
48  else:
49  raise AttributeError("You cannot add class attributes to %s" % cls)
50  return set_class_attr
51 
52 
53 def _swig_add_metaclass(metaclass):
54  """Class decorator for adding a metaclass to a SWIG wrapped class - a slimmed down version of six.add_metaclass"""
55  def wrapper(cls):
56  return metaclass(cls.__name__, cls.__bases__, cls.__dict__.copy())
57  return wrapper
58 
59 
60 class _SwigNonDynamicMeta(type):
61  """Meta class to enforce nondynamic attributes (no new attributes) for a class"""
62  __setattr__ = _swig_setattr_nondynamic_class_variable(type.__setattr__)
63 
64 
65 import weakref
66 
67 class IMP_SCRATCH_SwigPyIterator(object):
68  r"""Proxy of C++ swig::IMP_SCRATCH_SwigPyIterator class."""
69 
70  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
71 
72  def __init__(self, *args, **kwargs):
73  raise AttributeError("No constructor defined - class is abstract")
74  __repr__ = _swig_repr
75  __swig_destroy__ = _IMP_scratch.delete_IMP_SCRATCH_SwigPyIterator
76 
77  def value(self):
78  r"""value(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
79  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_value(self)
80 
81  def incr(self, n=1):
82  r"""incr(IMP_SCRATCH_SwigPyIterator self, size_t n=1) -> IMP_SCRATCH_SwigPyIterator"""
83  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_incr(self, n)
84 
85  def decr(self, n=1):
86  r"""decr(IMP_SCRATCH_SwigPyIterator self, size_t n=1) -> IMP_SCRATCH_SwigPyIterator"""
87  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_decr(self, n)
88 
89  def distance(self, x):
90  r"""distance(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> ptrdiff_t"""
91  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_distance(self, x)
92 
93  def equal(self, x):
94  r"""equal(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> bool"""
95  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_equal(self, x)
96 
97  def copy(self):
98  r"""copy(IMP_SCRATCH_SwigPyIterator self) -> IMP_SCRATCH_SwigPyIterator"""
99  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_copy(self)
100 
101  def next(self):
102  r"""next(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
103  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_next(self)
104 
105  def __next__(self):
106  r"""__next__(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
107  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___next__(self)
108 
109  def previous(self):
110  r"""previous(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
111  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_previous(self)
112 
113  def advance(self, n):
114  r"""advance(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
115  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_advance(self, n)
116 
117  def __eq__(self, x):
118  r"""__eq__(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> bool"""
119  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___eq__(self, x)
120 
121  def __ne__(self, x):
122  r"""__ne__(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> bool"""
123  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___ne__(self, x)
124 
125  def __iadd__(self, n):
126  r"""__iadd__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
127  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___iadd__(self, n)
128 
129  def __isub__(self, n):
130  r"""__isub__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
131  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___isub__(self, n)
132 
133  def __add__(self, n):
134  r"""__add__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
135  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___add__(self, n)
136 
137  def __sub__(self, *args):
138  r"""
139  __sub__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator
140  __sub__(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> ptrdiff_t
141  """
142  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___sub__(self, *args)
143  def __iter__(self):
144  return self
145 
146 # Register IMP_SCRATCH_SwigPyIterator in _IMP_scratch:
147 _IMP_scratch.IMP_SCRATCH_SwigPyIterator_swigregister(IMP_SCRATCH_SwigPyIterator)
148 
149 _value_types=[]
150 _object_types=[]
151 _raii_types=[]
152 _plural_types=[]
153 
154 IMP_DEBUG = _IMP_scratch.IMP_DEBUG
155 
156 IMP_RELEASE = _IMP_scratch.IMP_RELEASE
157 
158 IMP_SILENT = _IMP_scratch.IMP_SILENT
159 
160 IMP_PROGRESS = _IMP_scratch.IMP_PROGRESS
161 
162 IMP_TERSE = _IMP_scratch.IMP_TERSE
163 
164 IMP_VERBOSE = _IMP_scratch.IMP_VERBOSE
165 
166 IMP_MEMORY = _IMP_scratch.IMP_MEMORY
167 
168 IMP_NONE = _IMP_scratch.IMP_NONE
169 
170 IMP_USAGE = _IMP_scratch.IMP_USAGE
171 
172 IMP_INTERNAL = _IMP_scratch.IMP_INTERNAL
173 
174 IMP_KERNEL_HAS_LOG4CXX = _IMP_scratch.IMP_KERNEL_HAS_LOG4CXX
175 
176 IMP_COMPILER_HAS_CEREAL_RAW_POINTER = _IMP_scratch.IMP_COMPILER_HAS_CEREAL_RAW_POINTER
177 
178 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_scratch.IMP_COMPILER_HAS_DEBUG_VECTOR
179 
180 IMP_COMPILER_HAS_RANDOM_SHUFFLE = _IMP_scratch.IMP_COMPILER_HAS_RANDOM_SHUFFLE
181 
182 IMP_COMPILER_HAS_THREE_WAY = _IMP_scratch.IMP_COMPILER_HAS_THREE_WAY
183 
184 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_scratch.IMP_KERNEL_HAS_BOOST_RANDOM
185 
186 IMP_KERNEL_HAS_NUMPY = _IMP_scratch.IMP_KERNEL_HAS_NUMPY
187 
188 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_scratch.IMP_KERNEL_HAS_GPERFTOOLS
189 
190 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_scratch.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
191 
192 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_scratch.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
193 
194 IMPKERNEL_SHOW_WARNINGS = _IMP_scratch.IMPKERNEL_SHOW_WARNINGS
195 
196 
197 import sys
198 class _DirectorObjects(object):
199  """@internal Simple class to keep references to director objects
200  to prevent premature deletion."""
201  def __init__(self):
202  self._objects = []
203  def register(self, obj):
204  """Take a reference to a director object; will only work for
205  refcounted C++ classes"""
206  if hasattr(obj, 'get_ref_count'):
207  self._objects.append(obj)
208  def cleanup(self):
209  """Only drop our reference and allow cleanup by Python if no other
210  Python references exist (we hold 3 references: one in self._objects,
211  one in x, and one in the argument list for getrefcount) *and* no
212  other C++ references exist (the Python object always holds one)"""
213  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
214  or x.get_ref_count() > 1]
215 # Do in two steps so the references are kept until the end of the
216 # function (deleting references may trigger a fresh call to this method)
217  self._objects = objs
218  def get_object_count(self):
219  """Get number of director objects (useful for testing only)"""
220  return len(self._objects)
221 _director_objects = _DirectorObjects()
222 
223 class _ostream(object):
224  r"""Proxy of C++ std::ostream class."""
225 
226  thisown = property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc="The membership flag")
227 
228  def __init__(self, *args, **kwargs):
229  raise AttributeError("No constructor defined")
230  __repr__ = _swig_repr
231 
232  def write(self, osa_buf):
233  r"""write(_ostream self, char const * osa_buf)"""
234  return _IMP_scratch._ostream_write(self, osa_buf)
235 
236 # Register _ostream in _IMP_scratch:
237 _IMP_scratch._ostream_swigregister(_ostream)
238 IMP_C_OPEN_BINARY = _IMP_scratch.IMP_C_OPEN_BINARY
239 
240 import IMP
241 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_CGAL_HAS_BOOST_FILESYSTEM
242 
243 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
244 
245 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_scratch.IMP_CGAL_HAS_BOOST_RANDOM
246 
247 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_CGAL_HAS_BOOST_SYSTEM
248 
249 IMP_CGAL_HAS_NUMPY = _IMP_scratch.IMP_CGAL_HAS_NUMPY
250 
251 IMPCGAL_SHOW_WARNINGS = _IMP_scratch.IMPCGAL_SHOW_WARNINGS
252 
253 import IMP.cgal
254 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_scratch.IMP_ALGEBRA_HAS_IMP_CGAL
255 
256 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
257 
258 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
259 
260 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_RANDOM
261 
262 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_SYSTEM
263 
264 IMP_ALGEBRA_HAS_CGAL = _IMP_scratch.IMP_ALGEBRA_HAS_CGAL
265 
266 IMP_ALGEBRA_HAS_NUMPY = _IMP_scratch.IMP_ALGEBRA_HAS_NUMPY
267 
268 IMP_ALGEBRA_HAS_ANN = _IMP_scratch.IMP_ALGEBRA_HAS_ANN
269 
270 IMPALGEBRA_SHOW_WARNINGS = _IMP_scratch.IMPALGEBRA_SHOW_WARNINGS
271 
272 import IMP.algebra
273 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_scratch.IMP_DISPLAY_HAS_IMP_CGAL
274 
275 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
276 
277 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
278 
279 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_RANDOM
280 
281 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_SYSTEM
282 
283 IMP_DISPLAY_HAS_CGAL = _IMP_scratch.IMP_DISPLAY_HAS_CGAL
284 
285 IMP_DISPLAY_HAS_NUMPY = _IMP_scratch.IMP_DISPLAY_HAS_NUMPY
286 
287 IMPDISPLAY_SHOW_WARNINGS = _IMP_scratch.IMPDISPLAY_SHOW_WARNINGS
288 
289 import IMP.display
290 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
291 
292 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
293 
294 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
295 
296 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
297 
298 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
299 
300 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_CGAL
301 
302 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_HDF5
303 
304 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_NUMPY
305 
306 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_scratch.IMPSCOREFUNCTOR_SHOW_WARNINGS
307 
308 import IMP.score_functor
309 IMP_CORE_HAS_IMP_CGAL = _IMP_scratch.IMP_CORE_HAS_IMP_CGAL
310 
311 IMP_CORE_HAS_IMP_KERNEL = _IMP_scratch.IMP_CORE_HAS_IMP_KERNEL
312 
313 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_CORE_HAS_BOOST_FILESYSTEM
314 
315 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
316 
317 IMP_CORE_HAS_BOOST_RANDOM = _IMP_scratch.IMP_CORE_HAS_BOOST_RANDOM
318 
319 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_CORE_HAS_BOOST_SYSTEM
320 
321 IMP_CORE_HAS_CGAL = _IMP_scratch.IMP_CORE_HAS_CGAL
322 
323 IMP_CORE_HAS_HDF5 = _IMP_scratch.IMP_CORE_HAS_HDF5
324 
325 IMP_CORE_HAS_NUMPY = _IMP_scratch.IMP_CORE_HAS_NUMPY
326 
327 IMPCORE_SHOW_WARNINGS = _IMP_scratch.IMPCORE_SHOW_WARNINGS
328 
329 import IMP.core
330 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_scratch.IMP_CONTAINER_HAS_IMP_ALGEBRA
331 
332 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_scratch.IMP_CONTAINER_HAS_IMP_CGAL
333 
334 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_scratch.IMP_CONTAINER_HAS_IMP_DISPLAY
335 
336 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_scratch.IMP_CONTAINER_HAS_IMP_KERNEL
337 
338 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_scratch.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
339 
340 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
341 
342 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
343 
344 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_RANDOM
345 
346 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_SYSTEM
347 
348 IMP_CONTAINER_HAS_CGAL = _IMP_scratch.IMP_CONTAINER_HAS_CGAL
349 
350 IMP_CONTAINER_HAS_HDF5 = _IMP_scratch.IMP_CONTAINER_HAS_HDF5
351 
352 IMP_CONTAINER_HAS_NUMPY = _IMP_scratch.IMP_CONTAINER_HAS_NUMPY
353 
354 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_scratch.IMP_CONTAINER_HAS_PYTHON_IHM
355 
356 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_scratch.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
357 
358 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_scratch.IMP_CONTAINER_HAS_ROBIN_MAP
359 
360 IMPCONTAINER_SHOW_WARNINGS = _IMP_scratch.IMPCONTAINER_SHOW_WARNINGS
361 
362 import IMP.container
363 IMP_SCRATCH_HAS_IMP_ALGEBRA = _IMP_scratch.IMP_SCRATCH_HAS_IMP_ALGEBRA
364 
365 IMP_SCRATCH_HAS_IMP_CGAL = _IMP_scratch.IMP_SCRATCH_HAS_IMP_CGAL
366 
367 IMP_SCRATCH_HAS_IMP_DISPLAY = _IMP_scratch.IMP_SCRATCH_HAS_IMP_DISPLAY
368 
369 IMP_SCRATCH_HAS_IMP_KERNEL = _IMP_scratch.IMP_SCRATCH_HAS_IMP_KERNEL
370 
371 IMP_SCRATCH_HAS_IMP_SCORE_FUNCTOR = _IMP_scratch.IMP_SCRATCH_HAS_IMP_SCORE_FUNCTOR
372 
373 IMP_SCRATCH_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_FILESYSTEM
374 
375 IMP_SCRATCH_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_PROGRAMOPTIONS
376 
377 IMP_SCRATCH_HAS_BOOST_RANDOM = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_RANDOM
378 
379 IMP_SCRATCH_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_SYSTEM
380 
381 IMP_SCRATCH_HAS_CGAL = _IMP_scratch.IMP_SCRATCH_HAS_CGAL
382 
383 IMP_SCRATCH_HAS_HDF5 = _IMP_scratch.IMP_SCRATCH_HAS_HDF5
384 
385 IMP_SCRATCH_HAS_NUMPY = _IMP_scratch.IMP_SCRATCH_HAS_NUMPY
386 
387 IMP_SCRATCH_HAS_PYTHON_IHM = _IMP_scratch.IMP_SCRATCH_HAS_PYTHON_IHM
388 
389 IMPSCRATCH_SHOW_WARNINGS = _IMP_scratch.IMPSCRATCH_SHOW_WARNINGS
390 
391 
392 def get_module_version():
393  r"""get_module_version() -> std::string const"""
394  return _IMP_scratch.get_module_version()
395 
396 def get_example_path(fname):
397  r"""get_example_path(std::string fname) -> std::string"""
398  return _IMP_scratch.get_example_path(fname)
399 
400 def get_data_path(fname):
401  r"""get_data_path(std::string fname) -> std::string"""
402  return _IMP_scratch.get_data_path(fname)
403 
404 from . import _version_check
405 _version_check.check_version(get_module_version())
406 __version__ = get_module_version()
407 
408 
def get_data_path
Return the full path to one of this module's data files.
def get_module_version
Return the version of this module, as a string.
def get_example_path
Return the full path to one of this module's example files.
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
Composable functors to implement scores via compile-time composition.
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...
Output IMP model data in various file formats.