IMP  2.4.0
The Integrative Modeling Platform
scratch/__init__.py
1 # This file was automatically generated by SWIG (http://www.swig.org).
2 # Version 3.0.2
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 
9 
10 
11 from sys import version_info
12 if version_info >= (2,6,0):
13  def swig_import_helper():
14  from os.path import dirname
15  import imp
16  fp = None
17  try:
18  fp, pathname, description = imp.find_module('_IMP_scratch', [dirname(__file__)])
19  except ImportError:
20  import _IMP_scratch
21  return _IMP_scratch
22  if fp is not None:
23  try:
24  _mod = imp.load_module('_IMP_scratch', fp, pathname, description)
25  finally:
26  fp.close()
27  return _mod
28  _IMP_scratch = swig_import_helper()
29  del swig_import_helper
30 else:
31  import _IMP_scratch
32 del version_info
33 try:
34  _swig_property = property
35 except NameError:
36  pass # Python < 2.2 doesn't have 'property'.
37 def _swig_setattr_nondynamic(self,class_type,name,value,static=1):
38  if (name == "thisown"): return self.this.own(value)
39  if (name == "this"):
40  if type(value).__name__ == 'SwigPyObject':
41  self.__dict__[name] = value
42  return
43  method = class_type.__swig_setmethods__.get(name,None)
44  if method: return method(self,value)
45  if (not static):
46  self.__dict__[name] = value
47  else:
48  raise AttributeError("You cannot add attributes to %s" % self)
49 
50 def _swig_setattr(self,class_type,name,value):
51  return _swig_setattr_nondynamic(self,class_type,name,value,0)
52 
53 def _swig_getattr(self,class_type,name):
54  if (name == "thisown"): return self.this.own()
55  method = class_type.__swig_getmethods__.get(name,None)
56  if method: return method(self)
57  raise AttributeError(name)
58 
59 def _swig_repr(self):
60  try: strthis = "proxy of " + self.this.__repr__()
61  except: strthis = ""
62  return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
63 
64 try:
65  _object = object
66  _newclass = 1
67 except AttributeError:
68  class _object : pass
69  _newclass = 0
70 
71 
72 def _swig_setattr_nondynamic_method(set):
73  def set_attr(self,name,value):
74  if (name == "thisown"): return self.this.own(value)
75  if hasattr(self,name) or (name == "this"):
76  set(self,name,value)
77  else:
78  raise AttributeError("You cannot add attributes to %s" % self)
79  return set_attr
80 
81 
82 try:
83  import weakref
84  weakref_proxy = weakref.proxy
85 except:
86  weakref_proxy = lambda x: x
87 
88 
89 class IMP_SCRATCH_SwigPyIterator(object):
90  """Proxy of C++ swig::IMP_SCRATCH_SwigPyIterator class"""
91  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
92  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined - class is abstract")
93  __repr__ = _swig_repr
94  __swig_destroy__ = _IMP_scratch.delete_IMP_SCRATCH_SwigPyIterator
95  __del__ = lambda self : None;
96  def value(self):
97  """value(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
98  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_value(self)
99 
100  def incr(self, n=1):
101  """
102  incr(IMP_SCRATCH_SwigPyIterator self, size_t n=1) -> IMP_SCRATCH_SwigPyIterator
103  incr(IMP_SCRATCH_SwigPyIterator self) -> IMP_SCRATCH_SwigPyIterator
104  """
105  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_incr(self, n)
106 
107  def decr(self, n=1):
108  """
109  decr(IMP_SCRATCH_SwigPyIterator self, size_t n=1) -> IMP_SCRATCH_SwigPyIterator
110  decr(IMP_SCRATCH_SwigPyIterator self) -> IMP_SCRATCH_SwigPyIterator
111  """
112  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_decr(self, n)
113 
114  def distance(self, *args):
115  """distance(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> ptrdiff_t"""
116  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_distance(self, *args)
117 
118  def equal(self, *args):
119  """equal(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> bool"""
120  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_equal(self, *args)
121 
122  def copy(self):
123  """copy(IMP_SCRATCH_SwigPyIterator self) -> IMP_SCRATCH_SwigPyIterator"""
124  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_copy(self)
125 
126  def next(self):
127  """next(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
128  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_next(self)
129 
130  def __next__(self):
131  """__next__(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
132  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___next__(self)
133 
134  def previous(self):
135  """previous(IMP_SCRATCH_SwigPyIterator self) -> PyObject *"""
136  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_previous(self)
137 
138  def advance(self, *args):
139  """advance(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
140  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator_advance(self, *args)
141 
142  def __eq__(self, *args):
143  """__eq__(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> bool"""
144  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___eq__(self, *args)
145 
146  def __ne__(self, *args):
147  """__ne__(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> bool"""
148  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___ne__(self, *args)
149 
150  def __iadd__(self, *args):
151  """__iadd__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
152  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___iadd__(self, *args)
153 
154  def __isub__(self, *args):
155  """__isub__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
156  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___isub__(self, *args)
157 
158  def __add__(self, *args):
159  """__add__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator"""
160  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___add__(self, *args)
161 
162  def __sub__(self, *args):
163  """
164  __sub__(IMP_SCRATCH_SwigPyIterator self, ptrdiff_t n) -> IMP_SCRATCH_SwigPyIterator
165  __sub__(IMP_SCRATCH_SwigPyIterator self, IMP_SCRATCH_SwigPyIterator x) -> ptrdiff_t
166  """
167  return _IMP_scratch.IMP_SCRATCH_SwigPyIterator___sub__(self, *args)
168 
169  def __iter__(self): return self
170 IMP_SCRATCH_SwigPyIterator_swigregister = _IMP_scratch.IMP_SCRATCH_SwigPyIterator_swigregister
171 IMP_SCRATCH_SwigPyIterator_swigregister(IMP_SCRATCH_SwigPyIterator)
172 
173 _value_types=[]
174 _object_types=[]
175 _raii_types=[]
176 _plural_types=[]
177 
178 IMP_DEBUG = _IMP_scratch.IMP_DEBUG
179 IMP_RELEASE = _IMP_scratch.IMP_RELEASE
180 IMP_SILENT = _IMP_scratch.IMP_SILENT
181 IMP_PROGRESS = _IMP_scratch.IMP_PROGRESS
182 IMP_TERSE = _IMP_scratch.IMP_TERSE
183 IMP_VERBOSE = _IMP_scratch.IMP_VERBOSE
184 IMP_MEMORY = _IMP_scratch.IMP_MEMORY
185 IMP_NONE = _IMP_scratch.IMP_NONE
186 IMP_USAGE = _IMP_scratch.IMP_USAGE
187 IMP_INTERNAL = _IMP_scratch.IMP_INTERNAL
188 IMP_BASE_HAS_LOG4CXX = _IMP_scratch.IMP_BASE_HAS_LOG4CXX
189 IMP_COMPILER_HAS_AUTO = _IMP_scratch.IMP_COMPILER_HAS_AUTO
190 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_scratch.IMP_COMPILER_HAS_DEBUG_VECTOR
191 IMP_BASE_HAS_BOOST_RANDOM = _IMP_scratch.IMP_BASE_HAS_BOOST_RANDOM
192 IMP_BASE_HAS_GPERFTOOLS = _IMP_scratch.IMP_BASE_HAS_GPERFTOOLS
193 IMP_BASE_HAS_TCMALLOC_HEAPCHECKER = _IMP_scratch.IMP_BASE_HAS_TCMALLOC_HEAPCHECKER
194 IMP_BASE_HAS_TCMALLOC_HEAPPROFILER = _IMP_scratch.IMP_BASE_HAS_TCMALLOC_HEAPPROFILER
195 IMPBASE_SHOW_WARNINGS = _IMP_scratch.IMPBASE_SHOW_WARNINGS
196 import sys
197 class _DirectorObjects(object):
198  """@internal Simple class to keep references to director objects
199  to prevent premature deletion."""
200  def __init__(self):
201  self._objects = []
202  def register(self, obj):
203  """Take a reference to a director object; will only work for
204  refcounted C++ classes"""
205  if hasattr(obj, 'get_ref_count'):
206  self._objects.append(obj)
207  def cleanup(self):
208  """Only drop our reference and allow cleanup by Python if no other
209  Python references exist (we hold 3 references: one in self._objects,
210  one in x, and one in the argument list for getrefcount) *and* no
211  other C++ references exist (the Python object always holds one)"""
212  objs = [x for x in self._objects if sys.getrefcount(x) > 3 \
213  or x.get_ref_count() > 1]
214  # Do in two steps so the references are kept until the end of the
215  # function (deleting references may trigger a fresh call to this method)
216  self._objects = objs
217  def get_object_count(self):
218  """Get number of director objects (useful for testing only)"""
219  return len(self._objects)
220 _director_objects = _DirectorObjects()
221 
222 class _ostream(object):
223  """Proxy of C++ std::ostream class"""
224  thisown = _swig_property(lambda x: x.this.own(), lambda x, v: x.this.own(v), doc='The membership flag')
225  def __init__(self, *args, **kwargs): raise AttributeError("No constructor defined")
226  __repr__ = _swig_repr
227  def write(self, *args):
228  """write(_ostream self, char const * osa_buf)"""
229  return _IMP_scratch._ostream_write(self, *args)
230 
231 _ostream_swigregister = _IMP_scratch._ostream_swigregister
232 _ostream_swigregister(_ostream)
233 
234 IMP_COMPILER_HAS_OVERRIDE = _IMP_scratch.IMP_COMPILER_HAS_OVERRIDE
235 IMP_COMPILER_HAS_FINAL = _IMP_scratch.IMP_COMPILER_HAS_FINAL
236 IMP_HAS_NOEXCEPT = _IMP_scratch.IMP_HAS_NOEXCEPT
237 import IMP.base
238 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_CGAL_HAS_BOOST_FILESYSTEM
239 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
240 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_scratch.IMP_CGAL_HAS_BOOST_RANDOM
241 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_CGAL_HAS_BOOST_SYSTEM
242 IMPCGAL_SHOW_WARNINGS = _IMP_scratch.IMPCGAL_SHOW_WARNINGS
243 import IMP.cgal
244 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_scratch.IMP_ALGEBRA_HAS_IMP_CGAL
245 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
246 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
247 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_RANDOM
248 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_ALGEBRA_HAS_BOOST_SYSTEM
249 IMP_ALGEBRA_HAS_CGAL = _IMP_scratch.IMP_ALGEBRA_HAS_CGAL
250 IMP_ALGEBRA_HAS_ANN = _IMP_scratch.IMP_ALGEBRA_HAS_ANN
251 IMPALGEBRA_SHOW_WARNINGS = _IMP_scratch.IMPALGEBRA_SHOW_WARNINGS
252 import IMP.algebra
253 IMP_KERNEL_HAS_IMP_CGAL = _IMP_scratch.IMP_KERNEL_HAS_IMP_CGAL
254 IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_KERNEL_HAS_BOOST_PROGRAMOPTIONS
255 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_scratch.IMP_KERNEL_HAS_BOOST_RANDOM
256 IMP_KERNEL_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_KERNEL_HAS_BOOST_SYSTEM
257 IMP_KERNEL_HAS_CGAL = _IMP_scratch.IMP_KERNEL_HAS_CGAL
258 IMPKERNEL_SHOW_WARNINGS = _IMP_scratch.IMPKERNEL_SHOW_WARNINGS
259 import IMP.kernel
260 IMP_DISPLAY_HAS_IMP_BASE = _IMP_scratch.IMP_DISPLAY_HAS_IMP_BASE
261 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_scratch.IMP_DISPLAY_HAS_IMP_CGAL
262 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
263 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
264 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_RANDOM
265 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_DISPLAY_HAS_BOOST_SYSTEM
266 IMP_DISPLAY_HAS_CGAL = _IMP_scratch.IMP_DISPLAY_HAS_CGAL
267 IMPDISPLAY_SHOW_WARNINGS = _IMP_scratch.IMPDISPLAY_SHOW_WARNINGS
268 import IMP.display
269 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
270 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
271 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
272 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
273 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
274 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_CGAL
275 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_scratch.IMP_SCORE_FUNCTOR_HAS_HDF5
276 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_scratch.IMPSCOREFUNCTOR_SHOW_WARNINGS
277 import IMP.score_functor
278 IMP_CORE_HAS_IMP_BASE = _IMP_scratch.IMP_CORE_HAS_IMP_BASE
279 IMP_CORE_HAS_IMP_CGAL = _IMP_scratch.IMP_CORE_HAS_IMP_CGAL
280 IMP_CORE_HAS_IMP_KERNEL = _IMP_scratch.IMP_CORE_HAS_IMP_KERNEL
281 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_CORE_HAS_BOOST_FILESYSTEM
282 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
283 IMP_CORE_HAS_BOOST_RANDOM = _IMP_scratch.IMP_CORE_HAS_BOOST_RANDOM
284 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_CORE_HAS_BOOST_SYSTEM
285 IMP_CORE_HAS_CGAL = _IMP_scratch.IMP_CORE_HAS_CGAL
286 IMP_CORE_HAS_HDF5 = _IMP_scratch.IMP_CORE_HAS_HDF5
287 IMPCORE_SHOW_WARNINGS = _IMP_scratch.IMPCORE_SHOW_WARNINGS
288 import IMP.core
289 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_scratch.IMP_CONTAINER_HAS_IMP_ALGEBRA
290 IMP_CONTAINER_HAS_IMP_BASE = _IMP_scratch.IMP_CONTAINER_HAS_IMP_BASE
291 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_scratch.IMP_CONTAINER_HAS_IMP_CGAL
292 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_scratch.IMP_CONTAINER_HAS_IMP_DISPLAY
293 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_scratch.IMP_CONTAINER_HAS_IMP_KERNEL
294 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_scratch.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
295 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
296 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
297 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_RANDOM
298 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_CONTAINER_HAS_BOOST_SYSTEM
299 IMP_CONTAINER_HAS_CGAL = _IMP_scratch.IMP_CONTAINER_HAS_CGAL
300 IMP_CONTAINER_HAS_HDF5 = _IMP_scratch.IMP_CONTAINER_HAS_HDF5
301 IMPCONTAINER_SHOW_WARNINGS = _IMP_scratch.IMPCONTAINER_SHOW_WARNINGS
302 import IMP.container
303 IMP_SCRATCH_HAS_IMP_ALGEBRA = _IMP_scratch.IMP_SCRATCH_HAS_IMP_ALGEBRA
304 IMP_SCRATCH_HAS_IMP_BASE = _IMP_scratch.IMP_SCRATCH_HAS_IMP_BASE
305 IMP_SCRATCH_HAS_IMP_CGAL = _IMP_scratch.IMP_SCRATCH_HAS_IMP_CGAL
306 IMP_SCRATCH_HAS_IMP_DISPLAY = _IMP_scratch.IMP_SCRATCH_HAS_IMP_DISPLAY
307 IMP_SCRATCH_HAS_IMP_KERNEL = _IMP_scratch.IMP_SCRATCH_HAS_IMP_KERNEL
308 IMP_SCRATCH_HAS_IMP_SCORE_FUNCTOR = _IMP_scratch.IMP_SCRATCH_HAS_IMP_SCORE_FUNCTOR
309 IMP_SCRATCH_HAS_BOOST_FILESYSTEM = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_FILESYSTEM
310 IMP_SCRATCH_HAS_BOOST_PROGRAMOPTIONS = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_PROGRAMOPTIONS
311 IMP_SCRATCH_HAS_BOOST_RANDOM = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_RANDOM
312 IMP_SCRATCH_HAS_BOOST_SYSTEM = _IMP_scratch.IMP_SCRATCH_HAS_BOOST_SYSTEM
313 IMP_SCRATCH_HAS_CGAL = _IMP_scratch.IMP_SCRATCH_HAS_CGAL
314 IMP_SCRATCH_HAS_HDF5 = _IMP_scratch.IMP_SCRATCH_HAS_HDF5
315 IMPSCRATCH_SHOW_WARNINGS = _IMP_scratch.IMPSCRATCH_SHOW_WARNINGS
316 
317 def get_module_version():
318  """get_module_version() -> std::string const"""
319  return _IMP_scratch.get_module_version()
320 
321 def get_example_path(*args):
322  """get_example_path(std::string fname) -> std::string"""
323  return _IMP_scratch.get_example_path(*args)
324 
325 def get_data_path(*args):
326  """get_data_path(std::string fname) -> std::string"""
327  return _IMP_scratch.get_data_path(*args)
328 from . import _version_check
329 _version_check.check_version(get_module_version())
330 
331 
332 
Various classes to hold sets of particles.
Make CGAL functionality available to IMP.
std::string get_data_path(std::string file_name)
Return the full path to installed data.
Low level functionality (logging, error handling, profiling, command line flags etc) that is used by ...
std::string get_example_path(std::string file_name)
Return the path to installed example data for this module.
Composable functors to implement scores via compile-time composition.
Base functionality and abstract base classes for representation, scoring and sampling.
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.