10 from __future__
import print_function, division, absolute_import
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():
19 pkg = __name__.rpartition(
'.')[0]
20 mname =
'.'.join((pkg,
'_IMP_npctransport')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_npctransport')
25 _IMP_npctransport = 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
33 fp, pathname, description = imp.find_module(
'_IMP_npctransport', [dirname(__file__)])
35 import _IMP_npctransport
36 return _IMP_npctransport
39 _mod = imp.load_module(
'_IMP_npctransport', fp, pathname, description)
43 _IMP_npctransport = swig_import_helper()
44 del swig_import_helper
46 import _IMP_npctransport
47 del _swig_python_version_info
49 _swig_property = property
54 import builtins
as __builtin__
58 def _swig_setattr_nondynamic(self, class_type, name, value, static=1):
59 if (name ==
"thisown"):
60 return self.this.own(value)
62 if type(value).__name__ ==
'SwigPyObject':
63 self.__dict__[name] = value
65 method = class_type.__swig_setmethods__.get(name,
None)
67 return method(self, value)
69 object.__setattr__(self, name, value)
71 raise AttributeError(
"You cannot add attributes to %s" % self)
74 def _swig_setattr(self, class_type, name, value):
75 return _swig_setattr_nondynamic(self, class_type, name, value, 0)
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)
84 raise AttributeError(
"'%s' object has no attribute '%s'" % (class_type.__name__, name))
89 strthis =
"proxy of " + self.this.__repr__()
90 except __builtin__.Exception:
92 return "<%s.%s; %s >" % (self.__class__.__module__, self.__class__.__name__, strthis,)
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)
102 raise AttributeError(
"You cannot add attributes to %s" % self)
108 weakref_proxy = weakref.proxy
109 except __builtin__.Exception:
110 weakref_proxy =
lambda x: x
113 class IMP_NPCTRANSPORT_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_NPCTRANSPORT_SwigPyIterator class."""
116 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
118 def __init__(self, *args, **kwargs):
119 raise AttributeError(
"No constructor defined - class is abstract")
120 __repr__ = _swig_repr
121 __swig_destroy__ = _IMP_npctransport.delete_IMP_NPCTRANSPORT_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
126 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_value(self)
131 incr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator
132 incr(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator
134 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_incr(self, n)
139 decr(IMP_NPCTRANSPORT_SwigPyIterator self, size_t n=1) -> IMP_NPCTRANSPORT_SwigPyIterator
140 decr(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator
142 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_distance(self, x)
151 """equal(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
152 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_equal(self, x)
156 """copy(IMP_NPCTRANSPORT_SwigPyIterator self) -> IMP_NPCTRANSPORT_SwigPyIterator"""
157 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_copy(self)
161 """next(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
162 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_next(self)
166 """__next__(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
167 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___next__(self)
171 """previous(IMP_NPCTRANSPORT_SwigPyIterator self) -> PyObject *"""
172 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
177 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
182 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> bool"""
187 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
192 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
197 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator"""
202 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, ptrdiff_t n) -> IMP_NPCTRANSPORT_SwigPyIterator
208 __sub__(IMP_NPCTRANSPORT_SwigPyIterator self, IMP_NPCTRANSPORT_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator___sub__(self, *args)
214 IMP_NPCTRANSPORT_SwigPyIterator_swigregister = _IMP_npctransport.IMP_NPCTRANSPORT_SwigPyIterator_swigregister
215 IMP_NPCTRANSPORT_SwigPyIterator_swigregister(IMP_NPCTRANSPORT_SwigPyIterator)
223 IMP_DEBUG = _IMP_npctransport.IMP_DEBUG
224 IMP_RELEASE = _IMP_npctransport.IMP_RELEASE
225 IMP_SILENT = _IMP_npctransport.IMP_SILENT
226 IMP_PROGRESS = _IMP_npctransport.IMP_PROGRESS
227 IMP_TERSE = _IMP_npctransport.IMP_TERSE
228 IMP_VERBOSE = _IMP_npctransport.IMP_VERBOSE
229 IMP_MEMORY = _IMP_npctransport.IMP_MEMORY
230 IMP_NONE = _IMP_npctransport.IMP_NONE
231 IMP_USAGE = _IMP_npctransport.IMP_USAGE
232 IMP_INTERNAL = _IMP_npctransport.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_npctransport.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_npctransport.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_npctransport.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_npctransport.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_NUMPY = _IMP_npctransport.IMP_KERNEL_HAS_NUMPY
239 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_npctransport.IMP_KERNEL_HAS_GPERFTOOLS
240 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
241 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_npctransport.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
242 IMPKERNEL_SHOW_WARNINGS = _IMP_npctransport.IMPKERNEL_SHOW_WARNINGS
245 class _DirectorObjects(object):
246 """@internal Simple class to keep references to director objects
247 to prevent premature deletion."""
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)
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]
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()
270 class _ostream(object):
271 """Proxy of C++ std::ostream class."""
273 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
275 def __init__(self, *args, **kwargs):
276 raise AttributeError(
"No constructor defined")
277 __repr__ = _swig_repr
279 def write(self, osa_buf):
280 """write(_ostream self, char const * osa_buf)"""
281 return _IMP_npctransport._ostream_write(self, osa_buf)
283 _ostream_swigregister = _IMP_npctransport._ostream_swigregister
284 _ostream_swigregister(_ostream)
286 IMP_COMPILER_HAS_OVERRIDE = _IMP_npctransport.IMP_COMPILER_HAS_OVERRIDE
287 IMP_COMPILER_HAS_FINAL = _IMP_npctransport.IMP_COMPILER_HAS_FINAL
288 IMP_HAS_NOEXCEPT = _IMP_npctransport.IMP_HAS_NOEXCEPT
289 IMP_C_OPEN_BINARY = _IMP_npctransport.IMP_C_OPEN_BINARY
291 IMP_BENCHMARK_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_FILESYSTEM
292 IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_PROGRAMOPTIONS
293 IMP_BENCHMARK_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_RANDOM
294 IMP_BENCHMARK_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_BENCHMARK_HAS_BOOST_SYSTEM
295 IMP_BENCHMARK_HAS_NUMPY = _IMP_npctransport.IMP_BENCHMARK_HAS_NUMPY
296 IMPBENCHMARK_SHOW_WARNINGS = _IMP_npctransport.IMPBENCHMARK_SHOW_WARNINGS
298 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_FILESYSTEM
299 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
300 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_RANDOM
301 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CGAL_HAS_BOOST_SYSTEM
302 IMP_CGAL_HAS_NUMPY = _IMP_npctransport.IMP_CGAL_HAS_NUMPY
303 IMPCGAL_SHOW_WARNINGS = _IMP_npctransport.IMPCGAL_SHOW_WARNINGS
305 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_IMP_CGAL
306 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
307 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
308 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_RANDOM
309 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ALGEBRA_HAS_BOOST_SYSTEM
310 IMP_ALGEBRA_HAS_CGAL = _IMP_npctransport.IMP_ALGEBRA_HAS_CGAL
311 IMP_ALGEBRA_HAS_NUMPY = _IMP_npctransport.IMP_ALGEBRA_HAS_NUMPY
312 IMP_ALGEBRA_HAS_ANN = _IMP_npctransport.IMP_ALGEBRA_HAS_ANN
313 IMPALGEBRA_SHOW_WARNINGS = _IMP_npctransport.IMPALGEBRA_SHOW_WARNINGS
315 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_IMP_CGAL
316 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
317 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
318 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_RANDOM
319 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_DISPLAY_HAS_BOOST_SYSTEM
320 IMP_DISPLAY_HAS_CGAL = _IMP_npctransport.IMP_DISPLAY_HAS_CGAL
321 IMP_DISPLAY_HAS_NUMPY = _IMP_npctransport.IMP_DISPLAY_HAS_NUMPY
322 IMPDISPLAY_SHOW_WARNINGS = _IMP_npctransport.IMPDISPLAY_SHOW_WARNINGS
324 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
325 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
326 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
327 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
328 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
329 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_CGAL
330 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_HDF5
331 IMP_SCORE_FUNCTOR_HAS_NUMPY = _IMP_npctransport.IMP_SCORE_FUNCTOR_HAS_NUMPY
332 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_npctransport.IMPSCOREFUNCTOR_SHOW_WARNINGS
334 IMP_STATISTICS_HAS_IMP_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_IMP_CGAL
335 IMP_STATISTICS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_FILESYSTEM
336 IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_PROGRAMOPTIONS
337 IMP_STATISTICS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_RANDOM
338 IMP_STATISTICS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_STATISTICS_HAS_BOOST_SYSTEM
339 IMP_STATISTICS_HAS_CGAL = _IMP_npctransport.IMP_STATISTICS_HAS_CGAL
340 IMP_STATISTICS_HAS_NUMPY = _IMP_npctransport.IMP_STATISTICS_HAS_NUMPY
341 IMPSTATISTICS_SHOW_WARNINGS = _IMP_npctransport.IMPSTATISTICS_SHOW_WARNINGS
343 IMP_CORE_HAS_IMP_CGAL = _IMP_npctransport.IMP_CORE_HAS_IMP_CGAL
344 IMP_CORE_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CORE_HAS_IMP_KERNEL
345 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_FILESYSTEM
346 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
347 IMP_CORE_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CORE_HAS_BOOST_RANDOM
348 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CORE_HAS_BOOST_SYSTEM
349 IMP_CORE_HAS_CGAL = _IMP_npctransport.IMP_CORE_HAS_CGAL
350 IMP_CORE_HAS_HDF5 = _IMP_npctransport.IMP_CORE_HAS_HDF5
351 IMP_CORE_HAS_NUMPY = _IMP_npctransport.IMP_CORE_HAS_NUMPY
352 IMPCORE_SHOW_WARNINGS = _IMP_npctransport.IMPCORE_SHOW_WARNINGS
354 IMP_CONTAINER_HAS_IMP_ALGEBRA = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_ALGEBRA
355 IMP_CONTAINER_HAS_IMP_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_CGAL
356 IMP_CONTAINER_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_DISPLAY
357 IMP_CONTAINER_HAS_IMP_KERNEL = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_KERNEL
358 IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_CONTAINER_HAS_IMP_SCORE_FUNCTOR
359 IMP_CONTAINER_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_FILESYSTEM
360 IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_PROGRAMOPTIONS
361 IMP_CONTAINER_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_RANDOM
362 IMP_CONTAINER_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_CONTAINER_HAS_BOOST_SYSTEM
363 IMP_CONTAINER_HAS_CGAL = _IMP_npctransport.IMP_CONTAINER_HAS_CGAL
364 IMP_CONTAINER_HAS_HDF5 = _IMP_npctransport.IMP_CONTAINER_HAS_HDF5
365 IMP_CONTAINER_HAS_NUMPY = _IMP_npctransport.IMP_CONTAINER_HAS_NUMPY
366 IMP_CONTAINER_HAS_PYTHON_IHM = _IMP_npctransport.IMP_CONTAINER_HAS_PYTHON_IHM
367 IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_GOOGLE_DENSE_HASH_MAP
368 IMP_CONTAINER_HAS_ROBIN_MAP = _IMP_npctransport.IMP_CONTAINER_HAS_ROBIN_MAP
369 IMPCONTAINER_SHOW_WARNINGS = _IMP_npctransport.IMPCONTAINER_SHOW_WARNINGS
371 IMP_ATOM_HAS_IMP_CGAL = _IMP_npctransport.IMP_ATOM_HAS_IMP_CGAL
372 IMP_ATOM_HAS_IMP_KERNEL = _IMP_npctransport.IMP_ATOM_HAS_IMP_KERNEL
373 IMP_ATOM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ATOM_HAS_IMP_SCORE_FUNCTOR
374 IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ATOM_HAS_BOOST_PROGRAMOPTIONS
375 IMP_ATOM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_RANDOM
376 IMP_ATOM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ATOM_HAS_BOOST_REGEX
377 IMP_ATOM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ATOM_HAS_BOOST_SYSTEM
378 IMP_ATOM_HAS_CGAL = _IMP_npctransport.IMP_ATOM_HAS_CGAL
379 IMP_ATOM_HAS_HDF5 = _IMP_npctransport.IMP_ATOM_HAS_HDF5
380 IMP_ATOM_HAS_NUMPY = _IMP_npctransport.IMP_ATOM_HAS_NUMPY
381 IMP_ATOM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ATOM_HAS_PYTHON_IHM
382 IMPATOM_SHOW_WARNINGS = _IMP_npctransport.IMPATOM_SHOW_WARNINGS
383 IMP_ATOM_TYPE_INDEX = _IMP_npctransport.IMP_ATOM_TYPE_INDEX
384 IMP_RESIDUE_TYPE_INDEX = _IMP_npctransport.IMP_RESIDUE_TYPE_INDEX
385 IMP_HIERARCHY_TYPE_INDEX = _IMP_npctransport.IMP_HIERARCHY_TYPE_INDEX
386 IMP_CHAIN_TYPE_INDEX = _IMP_npctransport.IMP_CHAIN_TYPE_INDEX
388 IMP_EM_HAS_IMP_CGAL = _IMP_npctransport.IMP_EM_HAS_IMP_CGAL
389 IMP_EM_HAS_IMP_CONTAINER = _IMP_npctransport.IMP_EM_HAS_IMP_CONTAINER
390 IMP_EM_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_EM_HAS_IMP_DISPLAY
391 IMP_EM_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_EM_HAS_IMP_SCORE_FUNCTOR
392 IMP_EM_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_EM_HAS_BOOST_FILESYSTEM
393 IMP_EM_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_EM_HAS_BOOST_PROGRAMOPTIONS
394 IMP_EM_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_EM_HAS_BOOST_RANDOM
395 IMP_EM_HAS_BOOST_REGEX = _IMP_npctransport.IMP_EM_HAS_BOOST_REGEX
396 IMP_EM_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_EM_HAS_BOOST_SYSTEM
397 IMP_EM_HAS_CGAL = _IMP_npctransport.IMP_EM_HAS_CGAL
398 IMP_EM_HAS_HDF5 = _IMP_npctransport.IMP_EM_HAS_HDF5
399 IMP_EM_HAS_NUMPY = _IMP_npctransport.IMP_EM_HAS_NUMPY
400 IMP_EM_HAS_PYTHON_IHM = _IMP_npctransport.IMP_EM_HAS_PYTHON_IHM
401 IMPEM_SHOW_WARNINGS = _IMP_npctransport.IMPEM_SHOW_WARNINGS
403 IMP_SAXS_HAS_IMP_CGAL = _IMP_npctransport.IMP_SAXS_HAS_IMP_CGAL
404 IMP_SAXS_HAS_IMP_CONTAINER = _IMP_npctransport.IMP_SAXS_HAS_IMP_CONTAINER
405 IMP_SAXS_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_SAXS_HAS_IMP_DISPLAY
406 IMP_SAXS_HAS_IMP_KERNEL = _IMP_npctransport.IMP_SAXS_HAS_IMP_KERNEL
407 IMP_SAXS_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_SAXS_HAS_IMP_SCORE_FUNCTOR
408 IMP_SAXS_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_FILESYSTEM
409 IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_SAXS_HAS_BOOST_PROGRAMOPTIONS
410 IMP_SAXS_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_RANDOM
411 IMP_SAXS_HAS_BOOST_REGEX = _IMP_npctransport.IMP_SAXS_HAS_BOOST_REGEX
412 IMP_SAXS_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_SAXS_HAS_BOOST_SYSTEM
413 IMP_SAXS_HAS_CGAL = _IMP_npctransport.IMP_SAXS_HAS_CGAL
414 IMP_SAXS_HAS_HDF5 = _IMP_npctransport.IMP_SAXS_HAS_HDF5
415 IMP_SAXS_HAS_NUMPY = _IMP_npctransport.IMP_SAXS_HAS_NUMPY
416 IMP_SAXS_HAS_PYTHON_IHM = _IMP_npctransport.IMP_SAXS_HAS_PYTHON_IHM
417 IMPSAXS_SHOW_WARNINGS = _IMP_npctransport.IMPSAXS_SHOW_WARNINGS
419 IMP_ISD_HAS_IMP_CGAL = _IMP_npctransport.IMP_ISD_HAS_IMP_CGAL
420 IMP_ISD_HAS_IMP_DISPLAY = _IMP_npctransport.IMP_ISD_HAS_IMP_DISPLAY
421 IMP_ISD_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_ISD_HAS_IMP_SCORE_FUNCTOR
422 IMP_ISD_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_ISD_HAS_BOOST_FILESYSTEM
423 IMP_ISD_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_ISD_HAS_BOOST_PROGRAMOPTIONS
424 IMP_ISD_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_ISD_HAS_BOOST_RANDOM
425 IMP_ISD_HAS_BOOST_REGEX = _IMP_npctransport.IMP_ISD_HAS_BOOST_REGEX
426 IMP_ISD_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_ISD_HAS_BOOST_SYSTEM
427 IMP_ISD_HAS_CGAL = _IMP_npctransport.IMP_ISD_HAS_CGAL
428 IMP_ISD_HAS_HDF5 = _IMP_npctransport.IMP_ISD_HAS_HDF5
429 IMP_ISD_HAS_NUMPY = _IMP_npctransport.IMP_ISD_HAS_NUMPY
430 IMP_ISD_HAS_PYTHON_IHM = _IMP_npctransport.IMP_ISD_HAS_PYTHON_IHM
431 IMPISD_SHOW_WARNINGS = _IMP_npctransport.IMPISD_SHOW_WARNINGS
433 IMP_RMF_HAS_IMP_CGAL = _IMP_npctransport.IMP_RMF_HAS_IMP_CGAL
434 IMP_RMF_HAS_IMP_EM = _IMP_npctransport.IMP_RMF_HAS_IMP_EM
435 IMP_RMF_HAS_IMP_SAXS = _IMP_npctransport.IMP_RMF_HAS_IMP_SAXS
436 IMP_RMF_HAS_IMP_SCORE_FUNCTOR = _IMP_npctransport.IMP_RMF_HAS_IMP_SCORE_FUNCTOR
437 IMP_RMF_HAS_IMP_STATISTICS = _IMP_npctransport.IMP_RMF_HAS_IMP_STATISTICS
438 IMP_RMF_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_FILESYSTEM
439 IMP_RMF_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_RMF_HAS_BOOST_PROGRAMOPTIONS
440 IMP_RMF_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_RMF_HAS_BOOST_RANDOM
441 IMP_RMF_HAS_BOOST_REGEX = _IMP_npctransport.IMP_RMF_HAS_BOOST_REGEX
442 IMP_RMF_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_RMF_HAS_BOOST_SYSTEM
443 IMP_RMF_HAS_CGAL = _IMP_npctransport.IMP_RMF_HAS_CGAL
444 IMP_RMF_HAS_HDF5 = _IMP_npctransport.IMP_RMF_HAS_HDF5
445 IMP_RMF_HAS_NUMPY = _IMP_npctransport.IMP_RMF_HAS_NUMPY
446 IMP_RMF_HAS_PYTHON_IHM = _IMP_npctransport.IMP_RMF_HAS_PYTHON_IHM
447 IMPRMF_SHOW_WARNINGS = _IMP_npctransport.IMPRMF_SHOW_WARNINGS
450 IMP_NPCTRANSPORT_HAS_IMP_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_CGAL
451 IMP_NPCTRANSPORT_HAS_IMP_EM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_EM
452 IMP_NPCTRANSPORT_HAS_IMP_ISD = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_ISD
453 IMP_NPCTRANSPORT_HAS_IMP_SAXS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_IMP_SAXS
454 IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_FILESYSTEM
455 IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_PROGRAMOPTIONS
456 IMP_NPCTRANSPORT_HAS_BOOST_RANDOM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_RANDOM
457 IMP_NPCTRANSPORT_HAS_BOOST_REGEX = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_REGEX
458 IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_BOOST_SYSTEM
459 IMP_NPCTRANSPORT_HAS_CGAL = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_CGAL
460 IMP_NPCTRANSPORT_HAS_HDF5 = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_HDF5
461 IMP_NPCTRANSPORT_HAS_NUMPY = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_NUMPY
462 IMP_NPCTRANSPORT_HAS_PYTHON_IHM = _IMP_npctransport.IMP_NPCTRANSPORT_HAS_PYTHON_IHM
463 IMPNPCTRANSPORT_SHOW_WARNINGS = _IMP_npctransport.IMPNPCTRANSPORT_SHOW_WARNINGS
465 _object_types.append(
"SitesPairScore")
468 def _object_cast_to_SitesPairScore(o):
469 """_object_cast_to_SitesPairScore(Object o) -> SitesPairScore"""
470 return _IMP_npctransport._object_cast_to_SitesPairScore(o)
472 _object_types.append(
"Scoring")
475 def _object_cast_to_Scoring(o):
476 """_object_cast_to_Scoring(Object o) -> Scoring"""
477 return _IMP_npctransport._object_cast_to_Scoring(o)
479 _object_types.append(
"BrownianDynamicsTAMDWithSlabSupport")
482 def _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o):
483 """_object_cast_to_BrownianDynamicsTAMDWithSlabSupport(Object o) -> BrownianDynamicsTAMDWithSlabSupport"""
484 return _IMP_npctransport._object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
486 _object_types.append(
"Statistics")
489 def _object_cast_to_Statistics(o):
490 """_object_cast_to_Statistics(Object o) -> Statistics"""
491 return _IMP_npctransport._object_cast_to_Statistics(o)
493 _object_types.append(
"SimulationData")
496 def _object_cast_to_SimulationData(o):
497 """_object_cast_to_SimulationData(Object o) -> SimulationData"""
498 return _IMP_npctransport._object_cast_to_SimulationData(o)
500 _object_types.append(
"SitesGeometry")
503 def _object_cast_to_SitesGeometry(o):
504 """_object_cast_to_SitesGeometry(Object o) -> SitesGeometry"""
505 return _IMP_npctransport._object_cast_to_SitesGeometry(o)
507 _object_types.append(
"TypedSitesGeometry")
510 def _object_cast_to_TypedSitesGeometry(o):
511 """_object_cast_to_TypedSitesGeometry(Object o) -> TypedSitesGeometry"""
512 return _IMP_npctransport._object_cast_to_TypedSitesGeometry(o)
514 _object_types.append(
"SlabWithCylindricalPorePairScore")
517 def _object_cast_to_SlabWithCylindricalPorePairScore(o):
518 """_object_cast_to_SlabWithCylindricalPorePairScore(Object o) -> SlabWithCylindricalPorePairScore"""
519 return _IMP_npctransport._object_cast_to_SlabWithCylindricalPorePairScore(o)
521 _object_types.append(
"SlabWithToroidalPorePairScore")
524 def _object_cast_to_SlabWithToroidalPorePairScore(o):
525 """_object_cast_to_SlabWithToroidalPorePairScore(Object o) -> SlabWithToroidalPorePairScore"""
526 return _IMP_npctransport._object_cast_to_SlabWithToroidalPorePairScore(o)
528 _object_types.append(
"PoreRadiusSingletonScore")
531 def _object_cast_to_PoreRadiusSingletonScore(o):
532 """_object_cast_to_PoreRadiusSingletonScore(Object o) -> PoreRadiusSingletonScore"""
533 return _IMP_npctransport._object_cast_to_PoreRadiusSingletonScore(o)
535 _object_types.append(
"ExcludeZRangeSingletonScore")
538 def _object_cast_to_ExcludeZRangeSingletonScore(o):
539 """_object_cast_to_ExcludeZRangeSingletonScore(Object o) -> ExcludeZRangeSingletonScore"""
540 return _IMP_npctransport._object_cast_to_ExcludeZRangeSingletonScore(o)
542 _object_types.append(
"ZBiasSingletonScore")
545 def _object_cast_to_ZBiasSingletonScore(o):
546 """_object_cast_to_ZBiasSingletonScore(Object o) -> ZBiasSingletonScore"""
547 return _IMP_npctransport._object_cast_to_ZBiasSingletonScore(o)
549 _object_types.append(
"SlabWithCylindricalPoreWireGeometry")
552 def _object_cast_to_SlabWithCylindricalPoreWireGeometry(o):
553 """_object_cast_to_SlabWithCylindricalPoreWireGeometry(Object o) -> SlabWithCylindricalPoreWireGeometry"""
554 return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
556 _object_types.append(
"SlabWithCylindricalPoreSurfaceGeometry")
559 def _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o):
560 """_object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(Object o) -> SlabWithCylindricalPoreSurfaceGeometry"""
561 return _IMP_npctransport._object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
563 _object_types.append(
"SlabWithToroidalPoreWireGeometry")
566 def _object_cast_to_SlabWithToroidalPoreWireGeometry(o):
567 """_object_cast_to_SlabWithToroidalPoreWireGeometry(Object o) -> SlabWithToroidalPoreWireGeometry"""
568 return _IMP_npctransport._object_cast_to_SlabWithToroidalPoreWireGeometry(o)
570 _object_types.append(
"LinearSoftSpherePairScore")
573 def _object_cast_to_LinearSoftSpherePairScore(o):
574 """_object_cast_to_LinearSoftSpherePairScore(Object o) -> LinearSoftSpherePairScore"""
575 return _IMP_npctransport._object_cast_to_LinearSoftSpherePairScore(o)
577 _object_types.append(
"FunctorLinearSoftSpherePairScore")
580 def _object_cast_to_FunctorLinearSoftSpherePairScore(o):
581 """_object_cast_to_FunctorLinearSoftSpherePairScore(Object o) -> FunctorLinearSoftSpherePairScore"""
582 return _IMP_npctransport._object_cast_to_FunctorLinearSoftSpherePairScore(o)
584 _object_types.append(
"LinearInteractionPairScore")
587 def _object_cast_to_LinearInteractionPairScore(o):
588 """_object_cast_to_LinearInteractionPairScore(Object o) -> LinearInteractionPairScore"""
589 return _IMP_npctransport._object_cast_to_LinearInteractionPairScore(o)
591 _object_types.append(
"FunctorLinearInteractionPairScore")
594 def _object_cast_to_FunctorLinearInteractionPairScore(o):
595 """_object_cast_to_FunctorLinearInteractionPairScore(Object o) -> FunctorLinearInteractionPairScore"""
596 return _IMP_npctransport._object_cast_to_FunctorLinearInteractionPairScore(o)
598 _object_types.append(
"LinearWellPairScore")
601 def _object_cast_to_LinearWellPairScore(o):
602 """_object_cast_to_LinearWellPairScore(Object o) -> LinearWellPairScore"""
603 return _IMP_npctransport._object_cast_to_LinearWellPairScore(o)
605 _object_types.append(
"HarmonicSpringSingletonScore")
608 def _object_cast_to_HarmonicSpringSingletonScore(o):
609 """_object_cast_to_HarmonicSpringSingletonScore(Object o) -> HarmonicSpringSingletonScore"""
610 return _IMP_npctransport._object_cast_to_HarmonicSpringSingletonScore(o)
612 _object_types.append(
"HierarchyWithSitesSaveLink")
615 def _object_cast_to_HierarchyWithSitesSaveLink(o):
616 """_object_cast_to_HierarchyWithSitesSaveLink(Object o) -> HierarchyWithSitesSaveLink"""
617 return _IMP_npctransport._object_cast_to_HierarchyWithSitesSaveLink(o)
619 _object_types.append(
"HierarchyWithSitesLoadLink")
622 def _object_cast_to_HierarchyWithSitesLoadLink(o):
623 """_object_cast_to_HierarchyWithSitesLoadLink(Object o) -> HierarchyWithSitesLoadLink"""
624 return _IMP_npctransport._object_cast_to_HierarchyWithSitesLoadLink(o)
626 _object_types.append(
"ChainStatisticsOptimizerState")
629 def _object_cast_to_ChainStatisticsOptimizerState(o):
630 """_object_cast_to_ChainStatisticsOptimizerState(Object o) -> ChainStatisticsOptimizerState"""
631 return _IMP_npctransport._object_cast_to_ChainStatisticsOptimizerState(o)
633 _object_types.append(
"BodyStatisticsOptimizerState")
636 def _object_cast_to_BodyStatisticsOptimizerState(o):
637 """_object_cast_to_BodyStatisticsOptimizerState(Object o) -> BodyStatisticsOptimizerState"""
638 return _IMP_npctransport._object_cast_to_BodyStatisticsOptimizerState(o)
640 _object_types.append(
"BipartitePairsStatisticsOptimizerState")
643 def _object_cast_to_BipartitePairsStatisticsOptimizerState(o):
644 """_object_cast_to_BipartitePairsStatisticsOptimizerState(Object o) -> BipartitePairsStatisticsOptimizerState"""
645 return _IMP_npctransport._object_cast_to_BipartitePairsStatisticsOptimizerState(o)
647 _object_types.append(
"ParticleTransportStatisticsOptimizerState")
650 def _object_cast_to_ParticleTransportStatisticsOptimizerState(o):
651 """_object_cast_to_ParticleTransportStatisticsOptimizerState(Object o) -> ParticleTransportStatisticsOptimizerState"""
652 return _IMP_npctransport._object_cast_to_ParticleTransportStatisticsOptimizerState(o)
654 _object_types.append(
"FGChain")
657 def _object_cast_to_FGChain(o):
658 """_object_cast_to_FGChain(Object o) -> FGChain"""
659 return _IMP_npctransport._object_cast_to_FGChain(o)
661 _object_types.append(
"ParticleFactory")
664 def _object_cast_to_ParticleFactory(o):
665 """_object_cast_to_ParticleFactory(Object o) -> ParticleFactory"""
666 return _IMP_npctransport._object_cast_to_ParticleFactory(o)
669 _plural_types.append(
"Avro2PBReaders")
670 _value_types.append(
"Avro2PBReader")
673 SitesPairScoreParametersList=list
674 _plural_types.append(
"SitesPairScoreParametersList")
675 _value_types.append(
"SitesPairScoreParameters")
678 def Transportings(l=[]):
679 return [Transporting(x)
for x
in l]
680 _plural_types.append(
"Transportings")
683 _value_types.append(
"Transporting")
686 def SlabWithPores(l=[]):
687 return [SlabWithPore(x)
for x
in l]
688 _plural_types.append(
"SlabWithPores")
691 _value_types.append(
"SlabWithPore")
694 def SlabWithCylindricalPores(l=[]):
695 return [SlabWithCylindricalPore(x)
for x
in l]
696 _plural_types.append(
"SlabWithCylindricalPores")
699 _value_types.append(
"SlabWithCylindricalPore")
702 def RelaxingSprings(l=[]):
703 return [RelaxingSpring(x)
for x
in l]
704 _plural_types.append(
"RelaxingSprings")
707 _value_types.append(
"RelaxingSpring")
710 def SlabWithToroidalPores(l=[]):
711 return [SlabWithToroidalPore(x)
for x
in l]
712 _plural_types.append(
"SlabWithToroidalPores")
715 _value_types.append(
"SlabWithToroidalPore")
717 class _DoubleParameter(object):
718 """Proxy of C++ IMP::npctransport::Parameter<(double)> class."""
720 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
721 __repr__ = _swig_repr
725 __init__(IMP::npctransport::Parameter<(double)> self) -> _DoubleParameter
726 __init__(IMP::npctransport::Parameter<(double)> self, double t) -> _DoubleParameter
728 this = _IMP_npctransport.new__DoubleParameter(*args)
730 self.this.append(this)
731 except __builtin__.Exception:
735 """get_value(_DoubleParameter self) -> double"""
736 return _IMP_npctransport._DoubleParameter_get_value(self)
740 """is_init(_DoubleParameter self) -> bool"""
741 return _IMP_npctransport._DoubleParameter_is_init(self)
743 __swig_destroy__ = _IMP_npctransport.delete__DoubleParameter
744 __del__ =
lambda self:
None
745 _DoubleParameter_swigregister = _IMP_npctransport._DoubleParameter_swigregister
746 _DoubleParameter_swigregister(_DoubleParameter)
748 class _IntParameter(object):
749 """Proxy of C++ IMP::npctransport::Parameter<(int)> class."""
751 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
752 __repr__ = _swig_repr
756 __init__(IMP::npctransport::Parameter<(int)> self) -> _IntParameter
757 __init__(IMP::npctransport::Parameter<(int)> self, int t) -> _IntParameter
759 this = _IMP_npctransport.new__IntParameter(*args)
761 self.this.append(this)
762 except __builtin__.Exception:
766 """get_value(_IntParameter self) -> int"""
767 return _IMP_npctransport._IntParameter_get_value(self)
771 """is_init(_IntParameter self) -> bool"""
772 return _IMP_npctransport._IntParameter_is_init(self)
774 __swig_destroy__ = _IMP_npctransport.delete__IntParameter
775 __del__ =
lambda self:
None
776 _IntParameter_swigregister = _IMP_npctransport._IntParameter_swigregister
777 _IntParameter_swigregister(_IntParameter)
779 class _BoolParameter(object):
780 """Proxy of C++ IMP::npctransport::Parameter<(bool)> class."""
782 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
783 __repr__ = _swig_repr
787 __init__(IMP::npctransport::Parameter<(bool)> self) -> _BoolParameter
788 __init__(IMP::npctransport::Parameter<(bool)> self, bool t) -> _BoolParameter
790 this = _IMP_npctransport.new__BoolParameter(*args)
792 self.this.append(this)
793 except __builtin__.Exception:
797 """get_value(_BoolParameter self) -> bool"""
798 return _IMP_npctransport._BoolParameter_get_value(self)
802 """is_init(_BoolParameter self) -> bool"""
803 return _IMP_npctransport._BoolParameter_is_init(self)
805 __swig_destroy__ = _IMP_npctransport.delete__BoolParameter
806 __del__ =
lambda self:
None
807 _BoolParameter_swigregister = _IMP_npctransport._BoolParameter_swigregister
808 _BoolParameter_swigregister(_BoolParameter)
812 """make_ordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
813 return _IMP_npctransport.make_ordered_interaction_type(t0, t1)
816 """make_unordered_interaction_type(ParticleType t0, ParticleType t1) -> IMP::npctransport::InteractionType"""
817 return _IMP_npctransport.make_unordered_interaction_type(t0, t1)
821 make_unordered_particle_index_pair(ParticleIndex pi0, ParticleIndex pi1) -> IMP::ParticleIndexPair
822 make_unordered_particle_index_pair(IMP::ParticleIndexPair pip) -> IMP::ParticleIndexPair
824 return _IMP_npctransport.make_unordered_particle_index_pair(*args)
826 """Proxy of C++ IMP::npctransport::LinearSoftSpherePairScore class."""
828 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
832 __init__(IMP::npctransport::LinearSoftSpherePairScore self, double k, std::string name) -> LinearSoftSpherePairScore
833 __init__(IMP::npctransport::LinearSoftSpherePairScore self, double k) -> LinearSoftSpherePairScore
835 this = _IMP_npctransport.new_LinearSoftSpherePairScore(*args)
837 self.this.append(this)
838 except __builtin__.Exception:
841 def do_get_inputs(self, m, pis):
842 """do_get_inputs(LinearSoftSpherePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
843 return _IMP_npctransport.LinearSoftSpherePairScore_do_get_inputs(self, m, pis)
847 """get_k(LinearSoftSpherePairScore self) -> double"""
848 return _IMP_npctransport.LinearSoftSpherePairScore_get_k(self)
851 def get_version_info(self):
852 """get_version_info(LinearSoftSpherePairScore self) -> VersionInfo"""
853 return _IMP_npctransport.LinearSoftSpherePairScore_get_version_info(self)
857 """__str__(LinearSoftSpherePairScore self) -> std::string"""
858 return _IMP_npctransport.LinearSoftSpherePairScore___str__(self)
862 """__repr__(LinearSoftSpherePairScore self) -> std::string"""
863 return _IMP_npctransport.LinearSoftSpherePairScore___repr__(self)
868 return _object_cast_to_LinearSoftSpherePairScore(o)
870 LinearSoftSpherePairScore_swigregister = _IMP_npctransport.LinearSoftSpherePairScore_swigregister
871 LinearSoftSpherePairScore_swigregister(LinearSoftSpherePairScore)
874 """Proxy of C++ IMP::npctransport::LinearInteractionPairScore class."""
876 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
880 __init__(IMP::npctransport::LinearInteractionPairScore self, double k_rep, double range_attr, double k_attr, std::string name) -> LinearInteractionPairScore
881 __init__(IMP::npctransport::LinearInteractionPairScore self, double k_rep, double range_attr, double k_attr) -> LinearInteractionPairScore
883 this = _IMP_npctransport.new_LinearInteractionPairScore(*args)
885 self.this.append(this)
886 except __builtin__.Exception:
889 def evaluate_if_good_index(self, *args):
891 evaluate_if_good_index(LinearInteractionPairScore self, Model m, IMP::ParticleIndexPair const & p, DerivativeAccumulator da, double max) -> double
892 evaluate_if_good_index(LinearInteractionPairScore self, Model m, IMP::ParticleIndexPairs const & p, DerivativeAccumulator da, double max, unsigned int lower_bound, unsigned int upper_bound) -> double
894 return _IMP_npctransport.LinearInteractionPairScore_evaluate_if_good_index(self, *args)
897 def do_get_inputs(self, m, pis):
898 """do_get_inputs(LinearInteractionPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
899 return _IMP_npctransport.LinearInteractionPairScore_do_get_inputs(self, m, pis)
902 def get_range_attraction(self):
903 """get_range_attraction(LinearInteractionPairScore self) -> double"""
904 return _IMP_npctransport.LinearInteractionPairScore_get_range_attraction(self)
907 def get_k_attraction(self):
908 """get_k_attraction(LinearInteractionPairScore self) -> double"""
909 return _IMP_npctransport.LinearInteractionPairScore_get_k_attraction(self)
912 def set_k_attraction(self, k_attr):
913 """set_k_attraction(LinearInteractionPairScore self, double k_attr)"""
914 return _IMP_npctransport.LinearInteractionPairScore_set_k_attraction(self, k_attr)
917 def get_k_repulsion(self):
918 """get_k_repulsion(LinearInteractionPairScore self) -> double"""
919 return _IMP_npctransport.LinearInteractionPairScore_get_k_repulsion(self)
922 def set_k_repulsion(self, k_rep):
923 """set_k_repulsion(LinearInteractionPairScore self, double k_rep)"""
924 return _IMP_npctransport.LinearInteractionPairScore_set_k_repulsion(self, k_rep)
927 def get_version_info(self):
928 """get_version_info(LinearInteractionPairScore self) -> VersionInfo"""
929 return _IMP_npctransport.LinearInteractionPairScore_get_version_info(self)
933 """__str__(LinearInteractionPairScore self) -> std::string"""
934 return _IMP_npctransport.LinearInteractionPairScore___str__(self)
938 """__repr__(LinearInteractionPairScore self) -> std::string"""
939 return _IMP_npctransport.LinearInteractionPairScore___repr__(self)
944 return _object_cast_to_LinearInteractionPairScore(o)
946 LinearInteractionPairScore_swigregister = _IMP_npctransport.LinearInteractionPairScore_swigregister
947 LinearInteractionPairScore_swigregister(LinearInteractionPairScore)
950 """Proxy of C++ IMP::npctransport::LinearWellPairScore class."""
952 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
956 __init__(IMP::npctransport::LinearWellPairScore self, double rest_length_factor, double k, std::string name) -> LinearWellPairScore
957 __init__(IMP::npctransport::LinearWellPairScore self, double rest_length_factor, double k) -> LinearWellPairScore
959 this = _IMP_npctransport.new_LinearWellPairScore(*args)
961 self.this.append(this)
962 except __builtin__.Exception:
965 def set_rest_length_factor(self, rest_length_factor):
966 """set_rest_length_factor(LinearWellPairScore self, double rest_length_factor)"""
967 return _IMP_npctransport.LinearWellPairScore_set_rest_length_factor(self, rest_length_factor)
970 def get_rest_length_factor(self):
971 """get_rest_length_factor(LinearWellPairScore self) -> double"""
972 return _IMP_npctransport.LinearWellPairScore_get_rest_length_factor(self)
976 """set_k(LinearWellPairScore self, double k)"""
977 return _IMP_npctransport.LinearWellPairScore_set_k(self, k)
981 """get_k(LinearWellPairScore self) -> double"""
982 return _IMP_npctransport.LinearWellPairScore_get_k(self)
985 def do_get_inputs(self, m, pis):
986 """do_get_inputs(LinearWellPairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
987 return _IMP_npctransport.LinearWellPairScore_do_get_inputs(self, m, pis)
990 def get_version_info(self):
991 """get_version_info(LinearWellPairScore self) -> VersionInfo"""
992 return _IMP_npctransport.LinearWellPairScore_get_version_info(self)
996 """__str__(LinearWellPairScore self) -> std::string"""
997 return _IMP_npctransport.LinearWellPairScore___str__(self)
1001 """__repr__(LinearWellPairScore self) -> std::string"""
1002 return _IMP_npctransport.LinearWellPairScore___repr__(self)
1007 return _object_cast_to_LinearWellPairScore(o)
1009 LinearWellPairScore_swigregister = _IMP_npctransport.LinearWellPairScore_swigregister
1010 LinearWellPairScore_swigregister(LinearWellPairScore)
1013 """Proxy of C++ IMP::npctransport::RelaxingSpring class."""
1015 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1019 __init__(IMP::npctransport::RelaxingSpring self) -> RelaxingSpring
1020 __init__(IMP::npctransport::RelaxingSpring self, Model m, ParticleIndex id) -> RelaxingSpring
1021 __init__(IMP::npctransport::RelaxingSpring self, _ParticleAdaptor d) -> RelaxingSpring
1023 this = _IMP_npctransport.new_RelaxingSpring(*args)
1025 self.this.append(this)
1026 except __builtin__.Exception:
1029 def show(self, *args):
1031 show(RelaxingSpring self, _ostream out)
1032 show(RelaxingSpring self)
1034 return _IMP_npctransport.RelaxingSpring_show(self, *args)
1037 def setup_particle(*args):
1039 setup_particle(Model m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1040 setup_particle(_ParticleAdaptor decorator, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1042 return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
1044 setup_particle = staticmethod(setup_particle)
1046 def get_is_setup(*args):
1048 get_is_setup(_ParticleAdaptor p) -> bool
1049 get_is_setup(Model m, ParticleIndex pi) -> bool
1051 return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
1053 get_is_setup = staticmethod(get_is_setup)
1055 def get_bonded_particle_0_key():
1056 """get_bonded_particle_0_key() -> ParticleIndexKey"""
1057 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0_key()
1059 get_bonded_particle_0_key = staticmethod(get_bonded_particle_0_key)
1061 def get_bonded_particle_1_key():
1062 """get_bonded_particle_1_key() -> ParticleIndexKey"""
1063 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1_key()
1065 get_bonded_particle_1_key = staticmethod(get_bonded_particle_1_key)
1067 def get_equilibrium_rest_length_factor_key():
1068 """get_equilibrium_rest_length_factor_key() -> FloatKey"""
1069 return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor_key()
1071 get_equilibrium_rest_length_factor_key = staticmethod(get_equilibrium_rest_length_factor_key)
1073 def get_rest_length_key():
1074 """get_rest_length_key() -> FloatKey"""
1075 return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1077 get_rest_length_key = staticmethod(get_rest_length_key)
1079 def get_rest_length_diffusion_coefficient_key():
1080 """get_rest_length_diffusion_coefficient_key() -> FloatKey"""
1081 return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient_key()
1083 get_rest_length_diffusion_coefficient_key = staticmethod(get_rest_length_diffusion_coefficient_key)
1085 def get_bonded_particle_0(self):
1086 """get_bonded_particle_0(RelaxingSpring self) -> Particle"""
1087 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0(self)
1090 def get_bonded_particle_1(self):
1091 """get_bonded_particle_1(RelaxingSpring self) -> Particle"""
1092 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1(self)
1095 def get_bonded_particle_index_0(self):
1096 """get_bonded_particle_index_0(RelaxingSpring self) -> ParticleIndex"""
1097 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_0(self)
1100 def get_bonded_particle_index_1(self):
1101 """get_bonded_particle_index_1(RelaxingSpring self) -> ParticleIndex"""
1102 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_index_1(self)
1105 def get_equilibrium_rest_length_factor(self):
1106 """get_equilibrium_rest_length_factor(RelaxingSpring self) -> IMP::Float"""
1107 return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor(self)
1110 def set_equilibrium_rest_length_factor(self, t):
1111 """set_equilibrium_rest_length_factor(RelaxingSpring self, IMP::Float t)"""
1112 return _IMP_npctransport.RelaxingSpring_set_equilibrium_rest_length_factor(self, t)
1115 def get_rest_length(self):
1116 """get_rest_length(RelaxingSpring self) -> IMP::Float"""
1117 return _IMP_npctransport.RelaxingSpring_get_rest_length(self)
1120 def set_rest_length(self, t):
1121 """set_rest_length(RelaxingSpring self, IMP::Float t)"""
1122 return _IMP_npctransport.RelaxingSpring_set_rest_length(self, t)
1125 def get_rest_length_diffusion_coefficient(self):
1126 """get_rest_length_diffusion_coefficient(RelaxingSpring self) -> IMP::Float"""
1127 return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient(self)
1130 def set_rest_length_diffusion_coefficient(self, t):
1131 """set_rest_length_diffusion_coefficient(RelaxingSpring self, IMP::Float t)"""
1132 return _IMP_npctransport.RelaxingSpring_set_rest_length_diffusion_coefficient(self, t)
1135 def add_to_rest_length_derivative(self, d, da):
1136 """add_to_rest_length_derivative(RelaxingSpring self, double d, DerivativeAccumulator da)"""
1137 return _IMP_npctransport.RelaxingSpring_add_to_rest_length_derivative(self, d, da)
1140 def get_rest_length_derivative(self):
1141 """get_rest_length_derivative(RelaxingSpring self) -> double"""
1142 return _IMP_npctransport.RelaxingSpring_get_rest_length_derivative(self)
1145 def add_attribute(self, *args):
1147 add_attribute(RelaxingSpring self, FloatKey k, IMP::Float v, bool opt)
1148 add_attribute(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1149 add_attribute(RelaxingSpring self, IntKey a0, IMP::Int a1)
1150 add_attribute(RelaxingSpring self, FloatsKey a0, IMP::Floats a1)
1151 add_attribute(RelaxingSpring self, IntsKey a0, IMP::Ints a1)
1152 add_attribute(RelaxingSpring self, StringKey a0, IMP::String a1)
1153 add_attribute(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1154 add_attribute(RelaxingSpring self, ObjectKey a0, Object a1)
1156 return _IMP_npctransport.RelaxingSpring_add_attribute(self, *args)
1159 def get_value(self, *args):
1161 get_value(RelaxingSpring self, FloatKey a0) -> IMP::Float
1162 get_value(RelaxingSpring self, IntKey a0) -> IMP::Int
1163 get_value(RelaxingSpring self, FloatsKey a0) -> IMP::Floats
1164 get_value(RelaxingSpring self, IntsKey a0) -> IMP::Ints
1165 get_value(RelaxingSpring self, StringKey a0) -> IMP::String
1166 get_value(RelaxingSpring self, ParticleIndexKey a0) -> Particle
1167 get_value(RelaxingSpring self, ObjectKey a0) -> Object
1169 return _IMP_npctransport.RelaxingSpring_get_value(self, *args)
1172 def set_value(self, *args):
1174 set_value(RelaxingSpring self, FloatKey a0, IMP::Float a1)
1175 set_value(RelaxingSpring self, IntKey a0, IMP::Int a1)
1176 set_value(RelaxingSpring self, FloatsKey a0, IMP::Floats a1)
1177 set_value(RelaxingSpring self, IntsKey a0, IMP::Ints a1)
1178 set_value(RelaxingSpring self, StringKey a0, IMP::String a1)
1179 set_value(RelaxingSpring self, ParticleIndexKey a0, Particle a1)
1180 set_value(RelaxingSpring self, ObjectKey a0, Object a1)
1182 return _IMP_npctransport.RelaxingSpring_set_value(self, *args)
1185 def remove_attribute(self, *args):
1187 remove_attribute(RelaxingSpring self, FloatKey a0)
1188 remove_attribute(RelaxingSpring self, IntKey a0)
1189 remove_attribute(RelaxingSpring self, FloatsKey a0)
1190 remove_attribute(RelaxingSpring self, IntsKey a0)
1191 remove_attribute(RelaxingSpring self, StringKey a0)
1192 remove_attribute(RelaxingSpring self, ParticleIndexKey a0)
1193 remove_attribute(RelaxingSpring self, ObjectKey a0)
1195 return _IMP_npctransport.RelaxingSpring_remove_attribute(self, *args)
1198 def has_attribute(self, *args):
1200 has_attribute(RelaxingSpring self, FloatKey a0) -> bool
1201 has_attribute(RelaxingSpring self, IntKey a0) -> bool
1202 has_attribute(RelaxingSpring self, FloatsKey a0) -> bool
1203 has_attribute(RelaxingSpring self, IntsKey a0) -> bool
1204 has_attribute(RelaxingSpring self, StringKey a0) -> bool
1205 has_attribute(RelaxingSpring self, ParticleIndexKey a0) -> bool
1206 has_attribute(RelaxingSpring self, ObjectKey a0) -> bool
1208 return _IMP_npctransport.RelaxingSpring_has_attribute(self, *args)
1211 def get_derivative(self, a0):
1212 """get_derivative(RelaxingSpring self, FloatKey a0) -> double"""
1213 return _IMP_npctransport.RelaxingSpring_get_derivative(self, a0)
1217 """get_name(RelaxingSpring self) -> std::string"""
1218 return _IMP_npctransport.RelaxingSpring_get_name(self)
1221 def clear_caches(self):
1222 """clear_caches(RelaxingSpring self)"""
1223 return _IMP_npctransport.RelaxingSpring_clear_caches(self)
1226 def set_name(self, a0):
1227 """set_name(RelaxingSpring self, std::string a0)"""
1228 return _IMP_npctransport.RelaxingSpring_set_name(self, a0)
1232 """set_check_level(RelaxingSpring self, IMP::CheckLevel a0)"""
1233 return _IMP_npctransport.RelaxingSpring_set_check_level(self, a0)
1236 def add_to_derivative(self, a0, a1, a2):
1237 """add_to_derivative(RelaxingSpring self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
1238 return _IMP_npctransport.RelaxingSpring_add_to_derivative(self, a0, a1, a2)
1241 def set_is_optimized(self, a0, a1):
1242 """set_is_optimized(RelaxingSpring self, FloatKey a0, bool a1)"""
1243 return _IMP_npctransport.RelaxingSpring_set_is_optimized(self, a0, a1)
1246 def get_is_optimized(self, a0):
1247 """get_is_optimized(RelaxingSpring self, FloatKey a0) -> bool"""
1248 return _IMP_npctransport.RelaxingSpring_get_is_optimized(self, a0)
1252 """get_check_level(RelaxingSpring self) -> IMP::CheckLevel"""
1253 return _IMP_npctransport.RelaxingSpring_get_check_level(self)
1256 def __eq__(self, *args):
1258 __eq__(RelaxingSpring self, RelaxingSpring o) -> bool
1259 __eq__(RelaxingSpring self, Particle d) -> bool
1261 return _IMP_npctransport.RelaxingSpring___eq__(self, *args)
1264 def __ne__(self, *args):
1266 __ne__(RelaxingSpring self, RelaxingSpring o) -> bool
1267 __ne__(RelaxingSpring self, Particle d) -> bool
1269 return _IMP_npctransport.RelaxingSpring___ne__(self, *args)
1272 def __le__(self, *args):
1274 __le__(RelaxingSpring self, RelaxingSpring o) -> bool
1275 __le__(RelaxingSpring self, Particle d) -> bool
1277 return _IMP_npctransport.RelaxingSpring___le__(self, *args)
1280 def __lt__(self, *args):
1282 __lt__(RelaxingSpring self, RelaxingSpring o) -> bool
1283 __lt__(RelaxingSpring self, Particle d) -> bool
1285 return _IMP_npctransport.RelaxingSpring___lt__(self, *args)
1288 def __ge__(self, *args):
1290 __ge__(RelaxingSpring self, RelaxingSpring o) -> bool
1291 __ge__(RelaxingSpring self, Particle d) -> bool
1293 return _IMP_npctransport.RelaxingSpring___ge__(self, *args)
1296 def __gt__(self, *args):
1298 __gt__(RelaxingSpring self, RelaxingSpring o) -> bool
1299 __gt__(RelaxingSpring self, Particle d) -> bool
1301 return _IMP_npctransport.RelaxingSpring___gt__(self, *args)
1305 """__hash__(RelaxingSpring self) -> std::size_t"""
1306 return _IMP_npctransport.RelaxingSpring___hash__(self)
1310 """__str__(RelaxingSpring self) -> std::string"""
1311 return _IMP_npctransport.RelaxingSpring___str__(self)
1315 """__repr__(RelaxingSpring self) -> std::string"""
1316 return _IMP_npctransport.RelaxingSpring___repr__(self)
1318 __swig_destroy__ = _IMP_npctransport.delete_RelaxingSpring
1319 __del__ =
lambda self:
None
1320 RelaxingSpring_swigregister = _IMP_npctransport.RelaxingSpring_swigregister
1321 RelaxingSpring_swigregister(RelaxingSpring)
1323 def RelaxingSpring_setup_particle(*args):
1325 setup_particle(Model m, ParticleIndex pi, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1326 RelaxingSpring_setup_particle(_ParticleAdaptor decorator, ParticleIndex bonded_pi0, ParticleIndex bonded_pi1, double equilibrium_rest_length_factor, double rest_length_diffusion_coefficient) -> RelaxingSpring
1328 return _IMP_npctransport.RelaxingSpring_setup_particle(*args)
1330 def RelaxingSpring_get_is_setup(*args):
1332 get_is_setup(_ParticleAdaptor p) -> bool
1333 RelaxingSpring_get_is_setup(Model m, ParticleIndex pi) -> bool
1335 return _IMP_npctransport.RelaxingSpring_get_is_setup(*args)
1337 def RelaxingSpring_get_bonded_particle_0_key():
1338 """RelaxingSpring_get_bonded_particle_0_key() -> ParticleIndexKey"""
1339 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_0_key()
1341 def RelaxingSpring_get_bonded_particle_1_key():
1342 """RelaxingSpring_get_bonded_particle_1_key() -> ParticleIndexKey"""
1343 return _IMP_npctransport.RelaxingSpring_get_bonded_particle_1_key()
1345 def RelaxingSpring_get_equilibrium_rest_length_factor_key():
1346 """RelaxingSpring_get_equilibrium_rest_length_factor_key() -> FloatKey"""
1347 return _IMP_npctransport.RelaxingSpring_get_equilibrium_rest_length_factor_key()
1349 def RelaxingSpring_get_rest_length_key():
1350 """RelaxingSpring_get_rest_length_key() -> FloatKey"""
1351 return _IMP_npctransport.RelaxingSpring_get_rest_length_key()
1353 def RelaxingSpring_get_rest_length_diffusion_coefficient_key():
1354 """RelaxingSpring_get_rest_length_diffusion_coefficient_key() -> FloatKey"""
1355 return _IMP_npctransport.RelaxingSpring_get_rest_length_diffusion_coefficient_key()
1358 """Proxy of C++ IMP::npctransport::HarmonicSpringSingletonScore class."""
1360 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1364 __init__(IMP::npctransport::HarmonicSpringSingletonScore self, double k1, double k2, std::string name) -> HarmonicSpringSingletonScore
1365 __init__(IMP::npctransport::HarmonicSpringSingletonScore self, double k1, double k2) -> HarmonicSpringSingletonScore
1367 this = _IMP_npctransport.new_HarmonicSpringSingletonScore(*args)
1369 self.this.append(this)
1370 except __builtin__.Exception:
1373 def set_k1(self, k1):
1374 """set_k1(HarmonicSpringSingletonScore self, double k1)"""
1375 return _IMP_npctransport.HarmonicSpringSingletonScore_set_k1(self, k1)
1379 """get_k1(HarmonicSpringSingletonScore self) -> double"""
1380 return _IMP_npctransport.HarmonicSpringSingletonScore_get_k1(self)
1383 def set_k2(self, k2):
1384 """set_k2(HarmonicSpringSingletonScore self, double k2)"""
1385 return _IMP_npctransport.HarmonicSpringSingletonScore_set_k2(self, k2)
1389 """get_k2(HarmonicSpringSingletonScore self) -> double"""
1390 return _IMP_npctransport.HarmonicSpringSingletonScore_get_k2(self)
1393 def do_get_inputs(self, m, pis):
1394 """do_get_inputs(HarmonicSpringSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1395 return _IMP_npctransport.HarmonicSpringSingletonScore_do_get_inputs(self, m, pis)
1398 def get_version_info(self):
1399 """get_version_info(HarmonicSpringSingletonScore self) -> VersionInfo"""
1400 return _IMP_npctransport.HarmonicSpringSingletonScore_get_version_info(self)
1404 """__str__(HarmonicSpringSingletonScore self) -> std::string"""
1405 return _IMP_npctransport.HarmonicSpringSingletonScore___str__(self)
1409 """__repr__(HarmonicSpringSingletonScore self) -> std::string"""
1410 return _IMP_npctransport.HarmonicSpringSingletonScore___repr__(self)
1415 return _object_cast_to_HarmonicSpringSingletonScore(o)
1417 HarmonicSpringSingletonScore_swigregister = _IMP_npctransport.HarmonicSpringSingletonScore_swigregister
1418 HarmonicSpringSingletonScore_swigregister(HarmonicSpringSingletonScore)
1420 class LinearInteraction(object):
1421 """Proxy of C++ IMP::npctransport::LinearInteraction class."""
1423 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1424 __repr__ = _swig_repr
1426 def __init__(self, krep, attr_range, kattr):
1427 """__init__(IMP::npctransport::LinearInteraction self, double krep, double attr_range, double kattr) -> LinearInteraction"""
1428 this = _IMP_npctransport.new_LinearInteraction(krep, attr_range, kattr)
1430 self.this.append(this)
1431 except __builtin__.Exception:
1434 def show(self, *args):
1436 show(LinearInteraction self, _ostream out)
1437 show(LinearInteraction self)
1439 return _IMP_npctransport.LinearInteraction_show(self, *args)
1441 __swig_destroy__ = _IMP_npctransport.delete_LinearInteraction
1442 __del__ =
lambda self:
None
1443 LinearInteraction_swigregister = _IMP_npctransport.LinearInteraction_swigregister
1444 LinearInteraction_swigregister(LinearInteraction)
1447 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> class."""
1449 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1450 __repr__ = _swig_repr
1454 __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > >::DistanceScore const & t0, std::string name) -> _DistancePairScoreForLinearSoftSphere
1455 __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearSoftSphereScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > >::DistanceScore const & t0) -> _DistancePairScoreForLinearSoftSphere
1457 this = _IMP_npctransport.new__DistancePairScoreForLinearSoftSphere(*args)
1459 self.this.append(this)
1460 except __builtin__.Exception:
1463 def do_get_inputs(self, m, pis):
1464 """do_get_inputs(_DistancePairScoreForLinearSoftSphere self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1465 return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_do_get_inputs(self, m, pis)
1468 def get_score_functor(self):
1469 """get_score_functor(_DistancePairScoreForLinearSoftSphere self) -> IMP::score_functor::SphereDistance< IMP::score_functor::LinearLowerBound > &"""
1470 return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_score_functor(self)
1473 def get_version_info(self):
1474 """get_version_info(_DistancePairScoreForLinearSoftSphere self) -> VersionInfo"""
1475 return _IMP_npctransport._DistancePairScoreForLinearSoftSphere_get_version_info(self)
1477 _DistancePairScoreForLinearSoftSphere_swigregister = _IMP_npctransport._DistancePairScoreForLinearSoftSphere_swigregister
1478 _DistancePairScoreForLinearSoftSphere_swigregister(_DistancePairScoreForLinearSoftSphere)
1480 class _DistancePairScoreForLinearInteraction(
IMP.PairScore):
1481 """Proxy of C++ IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> class."""
1483 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1484 __repr__ = _swig_repr
1488 __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0, std::string name) -> _DistancePairScoreForLinearInteraction
1489 __init__(IMP::score_functor::DistancePairScore<(IMP::npctransport::LinearInteractionScore)> self, IMP::score_functor::DistancePairScore< IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > >::DistanceScore const & t0) -> _DistancePairScoreForLinearInteraction
1491 this = _IMP_npctransport.new__DistancePairScoreForLinearInteraction(*args)
1493 self.this.append(this)
1494 except __builtin__.Exception:
1497 def do_get_inputs(self, m, pis):
1498 """do_get_inputs(_DistancePairScoreForLinearInteraction self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
1499 return _IMP_npctransport._DistancePairScoreForLinearInteraction_do_get_inputs(self, m, pis)
1502 def get_score_functor(self):
1503 """get_score_functor(_DistancePairScoreForLinearInteraction self) -> IMP::score_functor::SphereDistance< IMP::npctransport::LinearInteraction > &"""
1504 return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_score_functor(self)
1507 def get_version_info(self):
1508 """get_version_info(_DistancePairScoreForLinearInteraction self) -> VersionInfo"""
1509 return _IMP_npctransport._DistancePairScoreForLinearInteraction_get_version_info(self)
1511 _DistancePairScoreForLinearInteraction_swigregister = _IMP_npctransport._DistancePairScoreForLinearInteraction_swigregister
1512 _DistancePairScoreForLinearInteraction_swigregister(_DistancePairScoreForLinearInteraction)
1514 class FunctorLinearSoftSpherePairScore(_DistancePairScoreForLinearSoftSphere):
1515 """Proxy of C++ IMP::npctransport::FunctorLinearSoftSpherePairScore class."""
1517 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1521 __init__(IMP::npctransport::FunctorLinearSoftSpherePairScore self, double k, std::string name) -> FunctorLinearSoftSpherePairScore
1522 __init__(IMP::npctransport::FunctorLinearSoftSpherePairScore self, double k) -> FunctorLinearSoftSpherePairScore
1524 this = _IMP_npctransport.new_FunctorLinearSoftSpherePairScore(*args)
1526 self.this.append(this)
1527 except __builtin__.Exception:
1531 """__str__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1532 return _IMP_npctransport.FunctorLinearSoftSpherePairScore___str__(self)
1536 """__repr__(FunctorLinearSoftSpherePairScore self) -> std::string"""
1537 return _IMP_npctransport.FunctorLinearSoftSpherePairScore___repr__(self)
1542 return _object_cast_to_FunctorLinearSoftSpherePairScore(o)
1544 FunctorLinearSoftSpherePairScore_swigregister = _IMP_npctransport.FunctorLinearSoftSpherePairScore_swigregister
1545 FunctorLinearSoftSpherePairScore_swigregister(FunctorLinearSoftSpherePairScore)
1547 class FunctorLinearInteractionPairScore(_DistancePairScoreForLinearInteraction):
1548 """Proxy of C++ IMP::npctransport::FunctorLinearInteractionPairScore class."""
1550 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1554 __init__(IMP::npctransport::FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr, std::string name) -> FunctorLinearInteractionPairScore
1555 __init__(IMP::npctransport::FunctorLinearInteractionPairScore self, double krep, double attr_range, double kattr) -> FunctorLinearInteractionPairScore
1557 this = _IMP_npctransport.new_FunctorLinearInteractionPairScore(*args)
1559 self.this.append(this)
1560 except __builtin__.Exception:
1564 """__str__(FunctorLinearInteractionPairScore self) -> std::string"""
1565 return _IMP_npctransport.FunctorLinearInteractionPairScore___str__(self)
1569 """__repr__(FunctorLinearInteractionPairScore self) -> std::string"""
1570 return _IMP_npctransport.FunctorLinearInteractionPairScore___repr__(self)
1575 return _object_cast_to_FunctorLinearInteractionPairScore(o)
1577 FunctorLinearInteractionPairScore_swigregister = _IMP_npctransport.FunctorLinearInteractionPairScore_swigregister
1578 FunctorLinearInteractionPairScore_swigregister(FunctorLinearInteractionPairScore)
1581 """Proxy of C++ IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport class."""
1583 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1587 __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name, double wave_factor=1.0) -> BrownianDynamicsTAMDWithSlabSupport
1588 __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m, std::string name) -> BrownianDynamicsTAMDWithSlabSupport
1589 __init__(IMP::npctransport::BrownianDynamicsTAMDWithSlabSupport self, Model m) -> BrownianDynamicsTAMDWithSlabSupport
1591 this = _IMP_npctransport.new_BrownianDynamicsTAMDWithSlabSupport(*args)
1593 self.this.append(this)
1594 except __builtin__.Exception:
1598 """__str__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1599 return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___str__(self)
1603 """__repr__(BrownianDynamicsTAMDWithSlabSupport self) -> std::string"""
1604 return _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport___repr__(self)
1609 return _object_cast_to_BrownianDynamicsTAMDWithSlabSupport(o)
1611 __swig_destroy__ = _IMP_npctransport.delete_BrownianDynamicsTAMDWithSlabSupport
1612 __del__ =
lambda self:
None
1613 BrownianDynamicsTAMDWithSlabSupport_swigregister = _IMP_npctransport.BrownianDynamicsTAMDWithSlabSupport_swigregister
1614 BrownianDynamicsTAMDWithSlabSupport_swigregister(BrownianDynamicsTAMDWithSlabSupport)
1616 class SitesPairScoreParameters(object):
1617 """Proxy of C++ IMP::npctransport::SitesPairScoreParameters class."""
1619 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1620 r = _swig_property(_IMP_npctransport.SitesPairScoreParameters_r_get, _IMP_npctransport.SitesPairScoreParameters_r_set)
1621 k = _swig_property(_IMP_npctransport.SitesPairScoreParameters_k_get, _IMP_npctransport.SitesPairScoreParameters_k_set)
1622 r2 = _swig_property(_IMP_npctransport.SitesPairScoreParameters_r2_get, _IMP_npctransport.SitesPairScoreParameters_r2_set)
1623 kr = _swig_property(_IMP_npctransport.SitesPairScoreParameters_kr_get, _IMP_npctransport.SitesPairScoreParameters_kr_set)
1624 kr2 = _swig_property(_IMP_npctransport.SitesPairScoreParameters_kr2_get, _IMP_npctransport.SitesPairScoreParameters_kr2_set)
1625 cosSigma1_max = _swig_property(_IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma1_max_set)
1626 cosSigma2_max = _swig_property(_IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_get, _IMP_npctransport.SitesPairScoreParameters_cosSigma2_max_set)
1627 is_orientational = _swig_property(_IMP_npctransport.SitesPairScoreParameters_is_orientational_get, _IMP_npctransport.SitesPairScoreParameters_is_orientational_set)
1629 def __init__(self, range, k_coefficient, sigma1_max_deg=0.0, sigma2_max_deg=0.0):
1631 __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0, double sigma2_max_deg=0.0) -> SitesPairScoreParameters
1632 __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient, double sigma1_max_deg=0.0) -> SitesPairScoreParameters
1633 __init__(IMP::npctransport::SitesPairScoreParameters self, double range, double k_coefficient) -> SitesPairScoreParameters
1635 this = _IMP_npctransport.new_SitesPairScoreParameters(range, k_coefficient, sigma1_max_deg, sigma2_max_deg)
1637 self.this.append(this)
1638 except __builtin__.Exception:
1641 def set_range(self, r):
1642 """set_range(SitesPairScoreParameters self, double r)"""
1643 return _IMP_npctransport.SitesPairScoreParameters_set_range(self, r)
1646 def set_force_coefficient(self, k):
1647 """set_force_coefficient(SitesPairScoreParameters self, double k)"""
1648 return _IMP_npctransport.SitesPairScoreParameters_set_force_coefficient(self, k)
1651 def set_sigma1_max(self, sigma1_max_deg):
1652 """set_sigma1_max(SitesPairScoreParameters self, double sigma1_max_deg)"""
1653 return _IMP_npctransport.SitesPairScoreParameters_set_sigma1_max(self, sigma1_max_deg)
1656 def set_sigma2_max(self, sigma2_max_deg):
1657 """set_sigma2_max(SitesPairScoreParameters self, double sigma2_max_deg)"""
1658 return _IMP_npctransport.SitesPairScoreParameters_set_sigma2_max(self, sigma2_max_deg)
1661 def update_is_orientational(self):
1662 """update_is_orientational(SitesPairScoreParameters self)"""
1663 return _IMP_npctransport.SitesPairScoreParameters_update_is_orientational(self)
1666 def show(self, *args):
1668 show(SitesPairScoreParameters self, _ostream out)
1669 show(SitesPairScoreParameters self)
1671 return _IMP_npctransport.SitesPairScoreParameters_show(self, *args)
1675 """__str__(SitesPairScoreParameters self) -> std::string"""
1676 return _IMP_npctransport.SitesPairScoreParameters___str__(self)
1680 """__repr__(SitesPairScoreParameters self) -> std::string"""
1681 return _IMP_npctransport.SitesPairScoreParameters___repr__(self)
1683 __swig_destroy__ = _IMP_npctransport.delete_SitesPairScoreParameters
1684 __del__ =
lambda self:
None
1685 SitesPairScoreParameters_swigregister = _IMP_npctransport.SitesPairScoreParameters_swigregister
1686 SitesPairScoreParameters_swigregister(SitesPairScoreParameters)
1689 """Proxy of C++ IMP::npctransport::SitesGeometry class."""
1691 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1694 """__init__(IMP::npctransport::SitesGeometry self, Particle p, IMP::algebra::Sphere3Ds sites) -> SitesGeometry"""
1695 this = _IMP_npctransport.new_SitesGeometry(p, sites)
1697 self.this.append(this)
1698 except __builtin__.Exception:
1702 """__str__(SitesGeometry self) -> std::string"""
1703 return _IMP_npctransport.SitesGeometry___str__(self)
1707 """__repr__(SitesGeometry self) -> std::string"""
1708 return _IMP_npctransport.SitesGeometry___repr__(self)
1713 return _object_cast_to_SitesGeometry(o)
1715 SitesGeometry_swigregister = _IMP_npctransport.SitesGeometry_swigregister
1716 SitesGeometry_swigregister(SitesGeometry)
1719 """Proxy of C++ IMP::npctransport::TypedSitesGeometry class."""
1721 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1724 """__init__(IMP::npctransport::TypedSitesGeometry self, _SingletonContainerAdaptor sc) -> TypedSitesGeometry"""
1725 this = _IMP_npctransport.new_TypedSitesGeometry(sc)
1727 self.this.append(this)
1728 except __builtin__.Exception:
1731 def set_sites(self, t, s):
1732 """set_sites(TypedSitesGeometry self, ParticleType t, IMP::algebra::Sphere3Ds s)"""
1733 return _IMP_npctransport.TypedSitesGeometry_set_sites(self, t, s)
1736 def get_version_info(self):
1737 """get_version_info(TypedSitesGeometry self) -> VersionInfo"""
1738 return _IMP_npctransport.TypedSitesGeometry_get_version_info(self)
1742 """__str__(TypedSitesGeometry self) -> std::string"""
1743 return _IMP_npctransport.TypedSitesGeometry___str__(self)
1747 """__repr__(TypedSitesGeometry self) -> std::string"""
1748 return _IMP_npctransport.TypedSitesGeometry___repr__(self)
1753 return _object_cast_to_TypedSitesGeometry(o)
1755 TypedSitesGeometry_swigregister = _IMP_npctransport.TypedSitesGeometry_swigregister
1756 TypedSitesGeometry_swigregister(TypedSitesGeometry)
1758 class SitesPairScore(LinearInteractionPairScore):
1759 """Proxy of C++ IMP::npctransport::SitesPairScore class."""
1761 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1763 def __init__(self, range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1):
1764 """__init__(IMP::npctransport::SitesPairScore self, double range, double k, double sigma0_deg, double sigma1_deg, double range_nonspec_attraction, double k_nonspec_attraction, double k_nonspec_repulsion, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1) -> SitesPairScore"""
1765 this = _IMP_npctransport.new_SitesPairScore(range, k, sigma0_deg, sigma1_deg, range_nonspec_attraction, k_nonspec_attraction, k_nonspec_repulsion, sites0, sites1)
1767 self.this.append(this)
1768 except __builtin__.Exception:
1771 def get_sites_range(self):
1772 """get_sites_range(SitesPairScore self) -> double"""
1773 return _IMP_npctransport.SitesPairScore_get_sites_range(self)
1776 def get_sites_k(self):
1777 """get_sites_k(SitesPairScore self) -> double"""
1778 return _IMP_npctransport.SitesPairScore_get_sites_k(self)
1781 def get_parameters(self):
1782 """get_parameters(SitesPairScore self) -> SitesPairScoreParameters"""
1783 return _IMP_npctransport.SitesPairScore_get_parameters(self)
1786 def set_sites(self, sites0, sites1):
1787 """set_sites(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0, IMP::algebra::Sphere3Ds const & sites1)"""
1788 return _IMP_npctransport.SitesPairScore_set_sites(self, sites0, sites1)
1791 def set_sites0(self, sites0):
1792 """set_sites0(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites0)"""
1793 return _IMP_npctransport.SitesPairScore_set_sites0(self, sites0)
1796 def set_sites1(self, sites1):
1797 """set_sites1(SitesPairScore self, IMP::algebra::Sphere3Ds const & sites1)"""
1798 return _IMP_npctransport.SitesPairScore_set_sites1(self, sites1)
1802 """__str__(SitesPairScore self) -> std::string"""
1803 return _IMP_npctransport.SitesPairScore___str__(self)
1807 """__repr__(SitesPairScore self) -> std::string"""
1808 return _IMP_npctransport.SitesPairScore___repr__(self)
1813 return _object_cast_to_SitesPairScore(o)
1815 SitesPairScore_swigregister = _IMP_npctransport.SitesPairScore_swigregister
1816 SitesPairScore_swigregister(SitesPairScore)
1819 """Proxy of C++ IMP::npctransport::FGChain class."""
1821 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1825 __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0, std::string name) -> FGChain
1826 __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0, double rest_length_factor=1.0) -> FGChain
1827 __init__(IMP::npctransport::FGChain self, Particle root, double backbone_k=0.0) -> FGChain
1828 __init__(IMP::npctransport::FGChain self, Particle root) -> FGChain
1830 this = _IMP_npctransport.new_FGChain(*args)
1832 self.this.append(this)
1833 except __builtin__.Exception:
1837 """get_root(FGChain self) -> Hierarchy"""
1838 return _IMP_npctransport.FGChain_get_root(self)
1841 def get_beads(self):
1842 """get_beads(FGChain self) -> IMP::ParticlesTemp"""
1843 return _IMP_npctransport.FGChain_get_beads(self)
1846 def get_bead(self, i):
1847 """get_bead(FGChain self, unsigned int i) -> Particle"""
1848 return _IMP_npctransport.FGChain_get_bead(self, i)
1851 def get_bead_index(self, i):
1852 """get_bead_index(FGChain self, unsigned int i) -> ParticleIndex"""
1853 return _IMP_npctransport.FGChain_get_bead_index(self, i)
1856 def get_number_of_beads(self):
1857 """get_number_of_beads(FGChain self) -> unsigned int"""
1858 return _IMP_npctransport.FGChain_get_number_of_beads(self)
1861 def get_chain_restraints(self, scoring_manager):
1862 """get_chain_restraints(FGChain self, Scoring scoring_manager) -> IMP::Restraints"""
1863 return _IMP_npctransport.FGChain_get_chain_restraints(self, scoring_manager)
1866 def set_rest_length_factor(self, rlf):
1867 """set_rest_length_factor(FGChain self, double rlf)"""
1868 return _IMP_npctransport.FGChain_set_rest_length_factor(self, rlf)
1871 def set_backbone_k(self, k):
1872 """set_backbone_k(FGChain self, double k)"""
1873 return _IMP_npctransport.FGChain_set_backbone_k(self, k)
1876 def get_rest_length_factor(self):
1877 """get_rest_length_factor(FGChain self) -> double"""
1878 return _IMP_npctransport.FGChain_get_rest_length_factor(self)
1881 def get_backbone_k(self):
1882 """get_backbone_k(FGChain self) -> double"""
1883 return _IMP_npctransport.FGChain_get_backbone_k(self)
1886 def get_version_info(self):
1887 """get_version_info(FGChain self) -> VersionInfo"""
1888 return _IMP_npctransport.FGChain_get_version_info(self)
1892 """__str__(FGChain self) -> std::string"""
1893 return _IMP_npctransport.FGChain___str__(self)
1897 """__repr__(FGChain self) -> std::string"""
1898 return _IMP_npctransport.FGChain___repr__(self)
1903 return _object_cast_to_FGChain(o)
1905 FGChain_swigregister = _IMP_npctransport.FGChain_swigregister
1906 FGChain_swigregister(FGChain)
1910 """create_fg_chain(SimulationData sd, Hierarchy parent, ::npctransport_proto::Assignment_FGAssignment const & fg_data, Color c) -> FGChain"""
1911 return _IMP_npctransport.create_fg_chain(sd, parent, fg_data, c)
1915 get_fg_chain(Hierarchy root) -> FGChain
1916 get_fg_chain(Particle p_root) -> FGChain
1918 return _IMP_npctransport.get_fg_chain(*args)
1920 """Proxy of C++ IMP::npctransport::Scoring class."""
1922 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
1924 def __init__(self, owner_sd, data):
1925 """__init__(IMP::npctransport::Scoring self, SimulationData owner_sd, ::npctransport_proto::Assignment const & data) -> Scoring"""
1926 this = _IMP_npctransport.new_Scoring(owner_sd, data)
1928 self.this.append(this)
1929 except __builtin__.Exception:
1932 def get_scoring_function(self, force_update=False):
1934 get_scoring_function(Scoring self, bool force_update=False) -> ScoringFunction
1935 get_scoring_function(Scoring self) -> ScoringFunction
1937 return _IMP_npctransport.Scoring_get_scoring_function(self, force_update)
1940 def get_scoring_function_restraints(self, force_update=False):
1942 get_scoring_function_restraints(Scoring self, bool force_update=False) -> IMP::Restraints
1943 get_scoring_function_restraints(Scoring self) -> IMP::Restraints
1945 return _IMP_npctransport.Scoring_get_scoring_function_restraints(self, force_update)
1948 def get_custom_scoring_function(self, *args):
1950 get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, _SingletonContainerAdaptor non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=True) -> ScoringFunction
1951 get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, _SingletonContainerAdaptor non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> ScoringFunction
1952 get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads, bool is_attr_interactions_on=True) -> ScoringFunction
1953 get_custom_scoring_function(Scoring self, IMP::RestraintsTemp const & extra_restraints, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> ScoringFunction
1955 return _IMP_npctransport.Scoring_get_custom_scoring_function(self, *args)
1958 def get_close_beads_container(self, update=False):
1960 get_close_beads_container(Scoring self, bool update=False) -> PairContainer
1961 get_close_beads_container(Scoring self) -> PairContainer
1963 return _IMP_npctransport.Scoring_get_close_beads_container(self, update)
1966 def get_predicates_pair_restraint(self, update=False):
1968 get_predicates_pair_restraint(Scoring self, bool update=False) -> PredicatePairsRestraint
1969 get_predicates_pair_restraint(Scoring self) -> PredicatePairsRestraint
1971 return _IMP_npctransport.Scoring_get_predicates_pair_restraint(self, update)
1974 def get_bounding_volume_restraint(self, update=False):
1976 get_bounding_volume_restraint(Scoring self, bool update=False) -> Restraint
1977 get_bounding_volume_restraint(Scoring self) -> Restraint
1979 return _IMP_npctransport.Scoring_get_bounding_volume_restraint(self, update)
1982 def get_slab_restraint(self, update=False):
1984 get_slab_restraint(Scoring self, bool update=False) -> Restraint
1985 get_slab_restraint(Scoring self) -> Restraint
1987 return _IMP_npctransport.Scoring_get_slab_restraint(self, update)
1990 def add_interaction(self, idata):
1991 """add_interaction(Scoring self, ::npctransport_proto::Assignment_InteractionAssignment const & idata)"""
1992 return _IMP_npctransport.Scoring_add_interaction(self, idata)
1995 def create_close_beads_container(self, *args):
1997 create_close_beads_container(Scoring self, _SingletonContainerAdaptor non_optimiziable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
1998 create_close_beads_container(Scoring self, IMP::ParticleIndexes non_optimizable_beads, _SingletonContainerAdaptor optimizable_beads) -> PairContainer
2000 return _IMP_npctransport.Scoring_create_close_beads_container(self, *args)
2003 def create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on=True):
2005 create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs, bool is_attr_interactions_on=True) -> PredicatePairsRestraint
2006 create_predicates_pair_restraint(Scoring self, PairContainer bead_pairs) -> PredicatePairsRestraint
2008 return _IMP_npctransport.Scoring_create_predicates_pair_restraint(self, bead_pairs, is_attr_interactions_on)
2011 def create_bounding_volume_restraint(self, beads):
2012 """create_bounding_volume_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
2013 return _IMP_npctransport.Scoring_create_bounding_volume_restraint(self, beads)
2016 def create_slab_restraint(self, beads):
2017 """create_slab_restraint(Scoring self, _SingletonContainerAdaptor beads) -> Restraint"""
2018 return _IMP_npctransport.Scoring_create_slab_restraint(self, beads)
2021 def get_model(self):
2022 """get_model(Scoring self) -> Model"""
2023 return _IMP_npctransport.Scoring_get_model(self)
2027 """get_sd(Scoring self) -> SimulationData"""
2028 return _IMP_npctransport.Scoring_get_sd(self)
2031 def get_has_bounding_box(self):
2032 """get_has_bounding_box(Scoring self) -> bool"""
2033 return _IMP_npctransport.Scoring_get_has_bounding_box(self)
2036 def get_has_bounding_sphere(self):
2037 """get_has_bounding_sphere(Scoring self) -> bool"""
2038 return _IMP_npctransport.Scoring_get_has_bounding_sphere(self)
2041 def get_has_bounding_volume(self):
2042 """get_has_bounding_volume(Scoring self) -> bool"""
2043 return _IMP_npctransport.Scoring_get_has_bounding_volume(self)
2046 def get_default_backbone_k(self):
2047 """get_default_backbone_k(Scoring self) -> double"""
2048 return _IMP_npctransport.Scoring_get_default_backbone_k(self)
2051 def get_is_backbone_harmonic(self):
2052 """get_is_backbone_harmonic(Scoring self) -> bool"""
2053 return _IMP_npctransport.Scoring_get_is_backbone_harmonic(self)
2056 def get_excluded_volume_k(self):
2057 """get_excluded_volume_k(Scoring self) -> double"""
2058 return _IMP_npctransport.Scoring_get_excluded_volume_k(self)
2061 def get_interaction_k(self):
2062 """get_interaction_k(Scoring self) -> double"""
2063 return _IMP_npctransport.Scoring_get_interaction_k(self)
2066 def get_predicate_pair_score(self, *args):
2068 get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
2069 get_predicate_pair_score(Scoring self, ParticleType t1, ParticleType t2) -> PairScore
2071 return _IMP_npctransport.Scoring_get_predicate_pair_score(self, *args)
2074 def get_interaction_range_for(self, t1, t2, site_specific=True, non_specific=False):
2076 get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True, bool non_specific=False) -> double
2077 get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2, bool site_specific=True) -> double
2078 get_interaction_range_for(Scoring self, ParticleType t1, ParticleType t2) -> double
2080 return _IMP_npctransport.Scoring_get_interaction_range_for(self, t1, t2, site_specific, non_specific)
2083 def get_ordered_type_pair_predicate(self):
2084 """get_ordered_type_pair_predicate(Scoring self) -> OrderedTypePairPredicate"""
2085 return _IMP_npctransport.Scoring_get_ordered_type_pair_predicate(self)
2088 def add_chain_restraints(self, chain):
2089 """add_chain_restraints(Scoring self, FGChain chain)"""
2090 return _IMP_npctransport.Scoring_add_chain_restraints(self, chain)
2093 def get_chain_restraints_on(self, beads):
2094 """get_chain_restraints_on(Scoring self, _SingletonContainerAdaptor beads) -> IMP::Restraints"""
2095 return _IMP_npctransport.Scoring_get_chain_restraints_on(self, beads)
2098 def get_all_chain_restraints(self):
2099 """get_all_chain_restraints(Scoring self) -> IMP::Restraints"""
2100 return _IMP_npctransport.Scoring_get_all_chain_restraints(self)
2103 def remove_particle_type(self, pt):
2104 """remove_particle_type(Scoring self, ParticleType pt)"""
2105 return _IMP_npctransport.Scoring_remove_particle_type(self, pt)
2108 def add_z_bias_restraint(self, *args):
2110 add_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k)
2111 add_z_bias_restraint(Scoring self, Particle p, double k)
2113 return _IMP_npctransport.Scoring_add_z_bias_restraint(self, *args)
2116 def get_z_bias_restraints(self):
2117 """get_z_bias_restraints(Scoring self) -> IMP::Restraints"""
2118 return _IMP_npctransport.Scoring_get_z_bias_restraints(self)
2121 def create_z_bias_restraint(self, ps, k):
2122 """create_z_bias_restraint(Scoring self, _SingletonContainerAdaptor ps, double k) -> Restraint"""
2123 return _IMP_npctransport.Scoring_create_z_bias_restraint(self, ps, k)
2126 def add_custom_restraint(self, r):
2127 """add_custom_restraint(Scoring self, Restraint r)"""
2128 return _IMP_npctransport.Scoring_add_custom_restraint(self, r)
2131 def add_custom_restraints(self, R):
2132 """add_custom_restraints(Scoring self, IMP::Restraints R)"""
2133 return _IMP_npctransport.Scoring_add_custom_restraints(self, R)
2136 def clear_custom_restraints(self):
2137 """clear_custom_restraints(Scoring self)"""
2138 return _IMP_npctransport.Scoring_clear_custom_restraints(self)
2141 def get_custom_restraints(self):
2142 """get_custom_restraints(Scoring self) -> IMP::Restraints"""
2143 return _IMP_npctransport.Scoring_get_custom_restraints(self)
2146 def add_restrained_anchor_bead(self, p):
2147 """add_restrained_anchor_bead(Scoring self, Particle p)"""
2148 return _IMP_npctransport.Scoring_add_restrained_anchor_bead(self, p)
2151 def get_pore_radius_restraint(self):
2152 """get_pore_radius_restraint(Scoring self) -> Restraint"""
2153 return _IMP_npctransport.Scoring_get_pore_radius_restraint(self)
2156 def get_range(self):
2157 """get_range(Scoring self) -> double"""
2158 return _IMP_npctransport.Scoring_get_range(self)
2161 def set_interaction_range_factor(self, type, value):
2162 """set_interaction_range_factor(Scoring self, ParticleType type, double value)"""
2163 return _IMP_npctransport.Scoring_set_interaction_range_factor(self, type, value)
2166 def set_interaction_k_factor(self, type, value):
2167 """set_interaction_k_factor(Scoring self, ParticleType type, double value)"""
2168 return _IMP_npctransport.Scoring_set_interaction_k_factor(self, type, value)
2171 def get_version_info(self):
2172 """get_version_info(Scoring self) -> VersionInfo"""
2173 return _IMP_npctransport.Scoring_get_version_info(self)
2177 """__str__(Scoring self) -> std::string"""
2178 return _IMP_npctransport.Scoring___str__(self)
2182 """__repr__(Scoring self) -> std::string"""
2183 return _IMP_npctransport.Scoring___repr__(self)
2188 return _object_cast_to_Scoring(o)
2190 Scoring_swigregister = _IMP_npctransport.Scoring_swigregister
2191 Scoring_swigregister(Scoring)
2193 class timer(object):
2194 """Proxy of C++ boost::timer class."""
2196 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2197 __repr__ = _swig_repr
2200 """__init__(boost::timer self) -> timer"""
2201 this = _IMP_npctransport.new_timer()
2203 self.this.append(this)
2204 except __builtin__.Exception:
2206 __swig_destroy__ = _IMP_npctransport.delete_timer
2207 __del__ =
lambda self:
None
2208 timer_swigregister = _IMP_npctransport.timer_swigregister
2209 timer_swigregister(timer)
2212 """Proxy of C++ IMP::npctransport::Statistics class."""
2214 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2216 def remove_particle_type(self, pt):
2217 """remove_particle_type(Statistics self, ParticleType pt)"""
2218 return _IMP_npctransport.Statistics_remove_particle_type(self, pt)
2221 def __init__(self, sd, statistics_interval_frames, output_file_name):
2222 """__init__(IMP::npctransport::Statistics self, SimulationData sd, unsigned int statistics_interval_frames, std::string output_file_name) -> Statistics"""
2223 this = _IMP_npctransport.new_Statistics(sd, statistics_interval_frames, output_file_name)
2225 self.this.append(this)
2226 except __builtin__.Exception:
2229 def add_fg_chain_stats(self, fg_chain):
2230 """add_fg_chain_stats(Statistics self, FGChain fg_chain)"""
2231 return _IMP_npctransport.Statistics_add_fg_chain_stats(self, fg_chain)
2234 def add_floater_stats(self, p):
2235 """add_floater_stats(Statistics self, Particle p)"""
2236 return _IMP_npctransport.Statistics_add_floater_stats(self, p)
2239 def add_interaction_stats(self, type0, type1):
2240 """add_interaction_stats(Statistics self, ParticleType type0, ParticleType type1)"""
2241 return _IMP_npctransport.Statistics_add_interaction_stats(self, type0, type1)
2244 def add_optimizer_states(self, o=None):
2246 add_optimizer_states(Statistics self, Optimizer o=None) -> IMP::OptimizerStates
2247 add_optimizer_states(Statistics self) -> IMP::OptimizerStates
2249 return _IMP_npctransport.Statistics_add_optimizer_states(self, o)
2252 def update_particle_type_zr_distribution_map(self, p):
2253 """update_particle_type_zr_distribution_map(Statistics self, Particle p)"""
2254 return _IMP_npctransport.Statistics_update_particle_type_zr_distribution_map(self, p)
2257 def update_particle_type_xyz_distribution_map(self, p):
2258 """update_particle_type_xyz_distribution_map(Statistics self, Particle p)"""
2259 return _IMP_npctransport.Statistics_update_particle_type_xyz_distribution_map(self, p)
2262 def update(self, timer, nf_new=1):
2264 update(Statistics self, timer timer, unsigned int nf_new=1)
2265 update(Statistics self, timer timer)
2267 return _IMP_npctransport.Statistics_update(self, timer, nf_new)
2270 def reset_statistics_optimizer_states(self):
2271 """reset_statistics_optimizer_states(Statistics self)"""
2272 return _IMP_npctransport.Statistics_reset_statistics_optimizer_states(self)
2275 def set_interrupted(self, tf):
2276 """set_interrupted(Statistics self, bool tf)"""
2277 return _IMP_npctransport.Statistics_set_interrupted(self, tf)
2280 def get_model(self):
2281 """get_model(Statistics self) -> Model"""
2282 return _IMP_npctransport.Statistics_get_model(self)
2286 """get_sd(Statistics self) -> SimulationData"""
2287 return _IMP_npctransport.Statistics_get_sd(self)
2290 def get_is_activated(self):
2291 """get_is_activated(Statistics self) -> bool"""
2292 return _IMP_npctransport.Statistics_get_is_activated(self)
2295 def get_output_file_name(self):
2296 """get_output_file_name(Statistics self) -> std::string"""
2297 return _IMP_npctransport.Statistics_get_output_file_name(self)
2300 def get_version_info(self):
2301 """get_version_info(Statistics self) -> VersionInfo"""
2302 return _IMP_npctransport.Statistics_get_version_info(self)
2306 """__str__(Statistics self) -> std::string"""
2307 return _IMP_npctransport.Statistics___str__(self)
2311 """__repr__(Statistics self) -> std::string"""
2312 return _IMP_npctransport.Statistics___repr__(self)
2317 return _object_cast_to_Statistics(o)
2319 Statistics_swigregister = _IMP_npctransport.Statistics_swigregister
2320 Statistics_swigregister(Statistics)
2323 def create_boost_timer():
2324 """create_boost_timer() -> timer"""
2325 return _IMP_npctransport.create_boost_timer()
2326 IMPNPCTRANSPORT_VERSION = _IMP_npctransport.IMPNPCTRANSPORT_VERSION
2328 """Proxy of C++ IMP::npctransport::SimulationData class."""
2330 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2332 def get_output_npctransport_version(self):
2333 """get_output_npctransport_version(SimulationData self) -> double"""
2334 return _IMP_npctransport.SimulationData_get_output_npctransport_version(self)
2337 def get_range(self):
2338 """get_range(SimulationData self) -> double"""
2339 return _IMP_npctransport.SimulationData_get_range(self)
2342 def get_output_statistics_interval_frames(self):
2343 """get_output_statistics_interval_frames(SimulationData self) -> int"""
2344 return _IMP_npctransport.SimulationData_get_output_statistics_interval_frames(self)
2347 def get_is_exclude_floaters_from_slab_initially(self):
2348 """get_is_exclude_floaters_from_slab_initially(SimulationData self) -> bool"""
2349 return _IMP_npctransport.SimulationData_get_is_exclude_floaters_from_slab_initially(self)
2352 def get_are_floaters_on_one_slab_side(self):
2353 """get_are_floaters_on_one_slab_side(SimulationData self) -> bool"""
2354 return _IMP_npctransport.SimulationData_get_are_floaters_on_one_slab_side(self)
2357 def get_is_xyz_hist_stats(self):
2358 """get_is_xyz_hist_stats(SimulationData self) -> bool"""
2359 return _IMP_npctransport.SimulationData_get_is_xyz_hist_stats(self)
2362 def get_angular_d_factor(self):
2363 """get_angular_d_factor(SimulationData self) -> double"""
2364 return _IMP_npctransport.SimulationData_get_angular_d_factor(self)
2369 __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name, std::string new_output_file) -> SimulationData
2370 __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick, std::string rmf_file_name) -> SimulationData
2371 __init__(IMP::npctransport::SimulationData self, std::string prev_output_file, bool quick) -> SimulationData
2373 this = _IMP_npctransport.new_SimulationData(*args)
2375 self.this.append(this)
2376 except __builtin__.Exception:
2379 def get_model(self):
2380 """get_model(SimulationData self) -> Model"""
2381 return _IMP_npctransport.SimulationData_get_model(self)
2384 def get_scoring(self):
2385 """get_scoring(SimulationData self) -> Scoring"""
2386 return _IMP_npctransport.SimulationData_get_scoring(self)
2389 def get_statistics(self):
2390 """get_statistics(SimulationData self) -> Statistics"""
2391 return _IMP_npctransport.SimulationData_get_statistics(self)
2394 def get_bd(self, recreate=False):
2396 get_bd(SimulationData self, bool recreate=False) -> BrownianDynamics
2397 get_bd(SimulationData self) -> BrownianDynamics
2399 return _IMP_npctransport.SimulationData_get_bd(self, recreate)
2402 def activate_statistics(self):
2403 """activate_statistics(SimulationData self)"""
2404 return _IMP_npctransport.SimulationData_activate_statistics(self)
2407 def get_statistics_fraction(self):
2408 """get_statistics_fraction(SimulationData self) -> double"""
2409 return _IMP_npctransport.SimulationData_get_statistics_fraction(self)
2412 def get_is_fg_bead(self, *args):
2414 get_is_fg_bead(SimulationData self, ParticleIndex pi) -> bool
2415 get_is_fg_bead(SimulationData self, ParticleType pt) -> bool
2417 return _IMP_npctransport.SimulationData_get_is_fg_bead(self, *args)
2420 def get_is_fg_chain(self, *args):
2422 get_is_fg_chain(SimulationData self, ParticleIndex pi) -> bool
2423 get_is_fg_chain(SimulationData self, ParticleType pt) -> bool
2425 return _IMP_npctransport.SimulationData_get_is_fg_chain(self, *args)
2428 def get_fg_bead_types(self):
2429 """get_fg_bead_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2430 return _IMP_npctransport.SimulationData_get_fg_bead_types(self)
2433 def get_fg_chain_types(self):
2434 """get_fg_chain_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2435 return _IMP_npctransport.SimulationData_get_fg_chain_types(self)
2438 def get_floater_types(self):
2439 """get_floater_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2440 return _IMP_npctransport.SimulationData_get_floater_types(self)
2443 def get_obstacle_types(self):
2444 """get_obstacle_types(SimulationData self) -> IMP::npctransport::ParticleTypeSet const &"""
2445 return _IMP_npctransport.SimulationData_get_obstacle_types(self)
2448 def get_fg_chain_roots(self):
2449 """get_fg_chain_roots(SimulationData self) -> IMP::atom::Hierarchies"""
2450 return _IMP_npctransport.SimulationData_get_fg_chain_roots(self)
2453 def get_fg_chains(self):
2454 """get_fg_chains(SimulationData self) -> IMP::atom::Hierarchies"""
2455 return _IMP_npctransport.SimulationData_get_fg_chains(self)
2458 def get_obstacle_particles(self):
2459 """get_obstacle_particles(SimulationData self) -> IMP::ParticlesTemp"""
2460 return _IMP_npctransport.SimulationData_get_obstacle_particles(self)
2463 def get_beads(self):
2464 """get_beads(SimulationData self) -> IMP::ParticlesTemp"""
2465 return _IMP_npctransport.SimulationData_get_beads(self)
2468 def get_optimizable_beads(self):
2469 """get_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2470 return _IMP_npctransport.SimulationData_get_optimizable_beads(self)
2473 def get_non_optimizable_beads(self):
2474 """get_non_optimizable_beads(SimulationData self) -> IMP::ParticlesTemp"""
2475 return _IMP_npctransport.SimulationData_get_non_optimizable_beads(self)
2478 def get_is_backbone_harmonic(self):
2479 """get_is_backbone_harmonic(SimulationData self) -> bool"""
2480 return _IMP_npctransport.SimulationData_get_is_backbone_harmonic(self)
2483 def get_backbone_tau_ns(self):
2484 """get_backbone_tau_ns(SimulationData self) -> double"""
2485 return _IMP_npctransport.SimulationData_get_backbone_tau_ns(self)
2488 def get_temperature_k(self):
2489 """get_temperature_k(SimulationData self) -> double"""
2490 return _IMP_npctransport.SimulationData_get_temperature_k(self)
2493 def get_initial_simulation_time_ns(self):
2494 """get_initial_simulation_time_ns(SimulationData self) -> double"""
2495 return _IMP_npctransport.SimulationData_get_initial_simulation_time_ns(self)
2498 def get_site_centers(self, t0):
2499 """get_site_centers(SimulationData self, ParticleType t0) -> IMP::algebra::Vector3Ds"""
2500 return _IMP_npctransport.SimulationData_get_site_centers(self, t0)
2503 def get_sites(self, t0):
2504 """get_sites(SimulationData self, ParticleType t0) -> IMP::algebra::Sphere3Ds"""
2505 return _IMP_npctransport.SimulationData_get_sites(self, t0)
2508 def set_sites(self, *args):
2510 set_sites(SimulationData self, ParticleType t0, int n, double r, double sr)
2511 set_sites(SimulationData self, ParticleType t0, IMP::algebra::Sphere3Ds const & sites)
2513 return _IMP_npctransport.SimulationData_set_sites(self, *args)
2516 def get_site_display_radius(self, arg2):
2517 """get_site_display_radius(SimulationData self, ParticleType arg2) -> double"""
2518 return _IMP_npctransport.SimulationData_get_site_display_radius(self, arg2)
2521 def get_maximum_number_of_minutes(self):
2522 """get_maximum_number_of_minutes(SimulationData self) -> double"""
2523 return _IMP_npctransport.SimulationData_get_maximum_number_of_minutes(self)
2526 def remove_particle_type(self, pt):
2527 """remove_particle_type(SimulationData self, ParticleType pt)"""
2528 return _IMP_npctransport.SimulationData_remove_particle_type(self, pt)
2531 def remove_fgs_with_prefix(self, s_fg_type):
2532 """remove_fgs_with_prefix(SimulationData self, std::string s_fg_type)"""
2533 return _IMP_npctransport.SimulationData_remove_fgs_with_prefix(self, s_fg_type)
2536 def get_bounding_box(self):
2537 """get_bounding_box(SimulationData self) -> BoundingBox3D"""
2538 return _IMP_npctransport.SimulationData_get_bounding_box(self)
2541 def get_bounding_sphere(self):
2542 """get_bounding_sphere(SimulationData self) -> Sphere3D"""
2543 return _IMP_npctransport.SimulationData_get_bounding_sphere(self)
2546 def get_bounding_box_size(self):
2547 """get_bounding_box_size(SimulationData self) -> double"""
2548 return _IMP_npctransport.SimulationData_get_bounding_box_size(self)
2551 def set_bounding_box_size(self, box_size):
2552 """set_bounding_box_size(SimulationData self, double box_size)"""
2553 return _IMP_npctransport.SimulationData_set_bounding_box_size(self, box_size)
2556 def get_bounding_sphere_radius(self):
2557 """get_bounding_sphere_radius(SimulationData self) -> double"""
2558 return _IMP_npctransport.SimulationData_get_bounding_sphere_radius(self)
2561 def set_bounding_sphere_radius(self, sphere_radius):
2562 """set_bounding_sphere_radius(SimulationData self, double sphere_radius)"""
2563 return _IMP_npctransport.SimulationData_set_bounding_sphere_radius(self, sphere_radius)
2566 def get_bounding_volume(self):
2567 """get_bounding_volume(SimulationData self) -> double"""
2568 return _IMP_npctransport.SimulationData_get_bounding_volume(self)
2571 def set_bounding_volume(self, volume_A3):
2572 """set_bounding_volume(SimulationData self, double volume_A3)"""
2573 return _IMP_npctransport.SimulationData_set_bounding_volume(self, volume_A3)
2576 def get_has_slab(self):
2577 """get_has_slab(SimulationData self) -> bool"""
2578 return _IMP_npctransport.SimulationData_get_has_slab(self)
2581 def get_is_slab_with_cylindrical_pore(self):
2582 """get_is_slab_with_cylindrical_pore(SimulationData self) -> bool"""
2583 return _IMP_npctransport.SimulationData_get_is_slab_with_cylindrical_pore(self)
2586 def get_is_slab_with_toroidal_pore(self):
2587 """get_is_slab_with_toroidal_pore(SimulationData self) -> bool"""
2588 return _IMP_npctransport.SimulationData_get_is_slab_with_toroidal_pore(self)
2591 def get_slab_particle(self):
2592 """get_slab_particle(SimulationData self) -> Particle"""
2593 return _IMP_npctransport.SimulationData_get_slab_particle(self)
2596 def get_cylinder(self):
2597 """get_cylinder(SimulationData self) -> Cylinder3D"""
2598 return _IMP_npctransport.SimulationData_get_cylinder(self)
2601 def get_has_bounding_box(self):
2602 """get_has_bounding_box(SimulationData self) -> bool"""
2603 return _IMP_npctransport.SimulationData_get_has_bounding_box(self)
2606 def get_has_bounding_sphere(self):
2607 """get_has_bounding_sphere(SimulationData self) -> bool"""
2608 return _IMP_npctransport.SimulationData_get_has_bounding_sphere(self)
2611 def get_has_bounding_volume(self):
2612 """get_has_bounding_volume(SimulationData self) -> bool"""
2613 return _IMP_npctransport.SimulationData_get_has_bounding_volume(self)
2616 def initialize_positions_from_rmf(self, fh, frame_number=-1):
2618 initialize_positions_from_rmf(SimulationData self, FileConstHandle fh, int frame_number=-1)
2619 initialize_positions_from_rmf(SimulationData self, FileConstHandle fh)
2621 return _IMP_npctransport.SimulationData_initialize_positions_from_rmf(self, fh, frame_number)
2624 def link_rmf_file_handle(self, fh, is_restraints=True):
2626 link_rmf_file_handle(SimulationData self, FileHandle fh, bool is_restraints=True)
2627 link_rmf_file_handle(SimulationData self, FileHandle fh)
2629 return _IMP_npctransport.SimulationData_link_rmf_file_handle(self, fh, is_restraints)
2632 def get_rmf_sos_writer(self):
2633 """get_rmf_sos_writer(SimulationData self) -> SaveOptimizerState"""
2634 return _IMP_npctransport.SimulationData_get_rmf_sos_writer(self)
2637 def reset_rmf(self):
2638 """reset_rmf(SimulationData self)"""
2639 return _IMP_npctransport.SimulationData_reset_rmf(self)
2642 def switch_suspend_rmf(self, suspend):
2643 """switch_suspend_rmf(SimulationData self, bool suspend)"""
2644 return _IMP_npctransport.SimulationData_switch_suspend_rmf(self, suspend)
2647 def write_geometry(self, out):
2648 """write_geometry(SimulationData self, std::string out)"""
2649 return _IMP_npctransport.SimulationData_write_geometry(self, out)
2652 def dump_geometry(self):
2653 """dump_geometry(SimulationData self)"""
2654 return _IMP_npctransport.SimulationData_dump_geometry(self)
2657 def get_root_of_type(self, type):
2658 """get_root_of_type(SimulationData self, ParticleType type) -> Hierarchy"""
2659 return _IMP_npctransport.SimulationData_get_root_of_type(self, type)
2663 """get_number_of_frames(SimulationData self) -> unsigned int"""
2664 return _IMP_npctransport.SimulationData_get_number_of_frames(self)
2667 def get_number_of_trials(self):
2668 """get_number_of_trials(SimulationData self) -> unsigned int"""
2669 return _IMP_npctransport.SimulationData_get_number_of_trials(self)
2673 """get_root(SimulationData self) -> Hierarchy"""
2674 return _IMP_npctransport.SimulationData_get_root(self)
2677 def get_slab_thickness(self):
2678 """get_slab_thickness(SimulationData self) -> double"""
2679 return _IMP_npctransport.SimulationData_get_slab_thickness(self)
2682 def get_tunnel_radius(self):
2683 """get_tunnel_radius(SimulationData self) -> double"""
2684 return _IMP_npctransport.SimulationData_get_tunnel_radius(self)
2687 def get_pore_radius(self):
2688 """get_pore_radius(SimulationData self) -> double"""
2689 return _IMP_npctransport.SimulationData_get_pore_radius(self)
2692 def get_tunnel_radius_k(self):
2693 """get_tunnel_radius_k(SimulationData self) -> double"""
2694 return _IMP_npctransport.SimulationData_get_tunnel_radius_k(self)
2697 def get_pore_radius_k(self):
2698 """get_pore_radius_k(SimulationData self) -> double"""
2699 return _IMP_npctransport.SimulationData_get_pore_radius_k(self)
2702 def get_is_pore_radius_dynamic(self):
2703 """get_is_pore_radius_dynamic(SimulationData self) -> bool"""
2704 return _IMP_npctransport.SimulationData_get_is_pore_radius_dynamic(self)
2707 def get_pore_anchored_beads_k(self):
2708 """get_pore_anchored_beads_k(SimulationData self) -> double"""
2709 return _IMP_npctransport.SimulationData_get_pore_anchored_beads_k(self)
2712 def get_static_geometry(self):
2713 """get_static_geometry(SimulationData self) -> Geometry"""
2714 return _IMP_npctransport.SimulationData_get_static_geometry(self)
2717 def get_rmf_dump_interval_frames(self):
2718 """get_rmf_dump_interval_frames(SimulationData self) -> int"""
2719 return _IMP_npctransport.SimulationData_get_rmf_dump_interval_frames(self)
2722 def get_rmf_file_name(self):
2723 """get_rmf_file_name(SimulationData self) -> std::string"""
2724 return _IMP_npctransport.SimulationData_get_rmf_file_name(self)
2727 def set_rmf_file(self, new_name, is_save_restraints_to_rmf=True, is_force_restart=False):
2729 set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True, bool is_force_restart=False)
2730 set_rmf_file(SimulationData self, std::string const & new_name, bool is_save_restraints_to_rmf=True)
2731 set_rmf_file(SimulationData self, std::string const & new_name)
2733 return _IMP_npctransport.SimulationData_set_rmf_file(self, new_name, is_save_restraints_to_rmf, is_force_restart)
2736 def get_version_info(self):
2737 """get_version_info(SimulationData self) -> VersionInfo"""
2738 return _IMP_npctransport.SimulationData_get_version_info(self)
2742 """__str__(SimulationData self) -> std::string"""
2743 return _IMP_npctransport.SimulationData___str__(self)
2747 """__repr__(SimulationData self) -> std::string"""
2748 return _IMP_npctransport.SimulationData___repr__(self)
2753 return _object_cast_to_SimulationData(o)
2755 SimulationData_swigregister = _IMP_npctransport.SimulationData_swigregister
2756 SimulationData_swigregister(SimulationData)
2759 def get_simulation_data_key():
2760 """get_simulation_data_key() -> IMP::WeakObjectKey"""
2761 return _IMP_npctransport.get_simulation_data_key()
2763 def write_geometry(kaps, kap_sites, chains, chain_sites, rs, out):
2764 """write_geometry(IMP::ParticlesTemp const & kaps, IMP::algebra::Sphere3Ds const & kap_sites, IMP::ParticlesTemp const & chains, IMP::algebra::Sphere3Ds const & chain_sites, IMP::RestraintsTemp const & rs, Writer out)"""
2765 return _IMP_npctransport.write_geometry(kaps, kap_sites, chains, chain_sites, rs, out)
2767 """Proxy of C++ IMP::npctransport::ParticleFactory class."""
2769 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2770 sd_ = _swig_property(_IMP_npctransport.ParticleFactory_sd__get, _IMP_npctransport.ParticleFactory_sd__set)
2771 radius_ = _swig_property(_IMP_npctransport.ParticleFactory_radius__get, _IMP_npctransport.ParticleFactory_radius__set)
2772 D_factor_ = _swig_property(_IMP_npctransport.ParticleFactory_D_factor__get, _IMP_npctransport.ParticleFactory_D_factor__set)
2773 angular_D_factor_ = _swig_property(_IMP_npctransport.ParticleFactory_angular_D_factor__get, _IMP_npctransport.ParticleFactory_angular_D_factor__set)
2774 color_ = _swig_property(_IMP_npctransport.ParticleFactory_color__get, _IMP_npctransport.ParticleFactory_color__set)
2775 type_ = _swig_property(_IMP_npctransport.ParticleFactory_type__get, _IMP_npctransport.ParticleFactory_type__set)
2779 __init__(IMP::npctransport::ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type, std::string name) -> ParticleFactory
2780 __init__(IMP::npctransport::ParticleFactory self, SimulationData sd, double radius, double D_factor, double angular_D_factor, Color color, ParticleType type) -> ParticleFactory
2782 this = _IMP_npctransport.new_ParticleFactory(*args)
2784 self.this.append(this)
2785 except __builtin__.Exception:
2788 def create(self, *args):
2790 create(ParticleFactory self, std::string name) -> Particle
2791 create(ParticleFactory self) -> Particle
2793 return _IMP_npctransport.ParticleFactory_create(self, *args)
2796 def get_model(self):
2797 """get_model(ParticleFactory self) -> Model"""
2798 return _IMP_npctransport.ParticleFactory_get_model(self)
2801 def get_simulation_data(self):
2802 """get_simulation_data(ParticleFactory self) -> SimulationData"""
2803 return _IMP_npctransport.ParticleFactory_get_simulation_data(self)
2806 def get_radius(self):
2807 """get_radius(ParticleFactory self) -> double"""
2808 return _IMP_npctransport.ParticleFactory_get_radius(self)
2811 def get_version_info(self):
2812 """get_version_info(ParticleFactory self) -> VersionInfo"""
2813 return _IMP_npctransport.ParticleFactory_get_version_info(self)
2817 """__str__(ParticleFactory self) -> std::string"""
2818 return _IMP_npctransport.ParticleFactory___str__(self)
2822 """__repr__(ParticleFactory self) -> std::string"""
2823 return _IMP_npctransport.ParticleFactory___repr__(self)
2828 return _object_cast_to_ParticleFactory(o)
2830 ParticleFactory_swigregister = _IMP_npctransport.ParticleFactory_swigregister
2831 ParticleFactory_swigregister(ParticleFactory)
2834 """Proxy of C++ IMP::npctransport::HierarchyWithSitesLoadLink class."""
2836 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2839 """__init__(IMP::npctransport::HierarchyWithSitesLoadLink self, FileConstHandle fh) -> HierarchyWithSitesLoadLink"""
2840 this = _IMP_npctransport.new_HierarchyWithSitesLoadLink(fh)
2842 self.this.append(this)
2843 except __builtin__.Exception:
2847 """get_name() -> char const *"""
2848 return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
2850 get_name = staticmethod(get_name)
2853 """__str__(HierarchyWithSitesLoadLink self) -> std::string"""
2854 return _IMP_npctransport.HierarchyWithSitesLoadLink___str__(self)
2858 """__repr__(HierarchyWithSitesLoadLink self) -> std::string"""
2859 return _IMP_npctransport.HierarchyWithSitesLoadLink___repr__(self)
2864 return _object_cast_to_HierarchyWithSitesLoadLink(o)
2866 __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesLoadLink
2867 __del__ =
lambda self:
None
2868 HierarchyWithSitesLoadLink_swigregister = _IMP_npctransport.HierarchyWithSitesLoadLink_swigregister
2869 HierarchyWithSitesLoadLink_swigregister(HierarchyWithSitesLoadLink)
2871 def HierarchyWithSitesLoadLink_get_name():
2872 """HierarchyWithSitesLoadLink_get_name() -> char const *"""
2873 return _IMP_npctransport.HierarchyWithSitesLoadLink_get_name()
2876 """Proxy of C++ IMP::npctransport::HierarchyWithSitesSaveLink class."""
2878 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2881 """__init__(IMP::npctransport::HierarchyWithSitesSaveLink self, FileHandle fh) -> HierarchyWithSitesSaveLink"""
2882 this = _IMP_npctransport.new_HierarchyWithSitesSaveLink(fh)
2884 self.this.append(this)
2885 except __builtin__.Exception:
2889 """get_name() -> char const *"""
2890 return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
2892 get_name = staticmethod(get_name)
2895 """__str__(HierarchyWithSitesSaveLink self) -> std::string"""
2896 return _IMP_npctransport.HierarchyWithSitesSaveLink___str__(self)
2900 """__repr__(HierarchyWithSitesSaveLink self) -> std::string"""
2901 return _IMP_npctransport.HierarchyWithSitesSaveLink___repr__(self)
2906 return _object_cast_to_HierarchyWithSitesSaveLink(o)
2908 __swig_destroy__ = _IMP_npctransport.delete_HierarchyWithSitesSaveLink
2909 __del__ =
lambda self:
None
2910 HierarchyWithSitesSaveLink_swigregister = _IMP_npctransport.HierarchyWithSitesSaveLink_swigregister
2911 HierarchyWithSitesSaveLink_swigregister(HierarchyWithSitesSaveLink)
2913 def HierarchyWithSitesSaveLink_get_name():
2914 """HierarchyWithSitesSaveLink_get_name() -> char const *"""
2915 return _IMP_npctransport.HierarchyWithSitesSaveLink_get_name()
2920 add_test_sites(FileHandle fh, ParticleType t, double display_radius, IMP::algebra::Vector3Ds sites)
2921 add_test_sites(FileHandle fh, ParticleType t, IMP::algebra::Sphere3Ds sites)
2923 return _IMP_npctransport.add_test_sites(*args)
2927 add_hierarchies_with_sites(FileHandle fh, IMP::atom::Hierarchies const & hs)
2928 add_hierarchies_with_sites(NodeHandle fh, IMP::atom::Hierarchies const & hs)
2930 return _IMP_npctransport.add_hierarchies_with_sites(*args)
2933 """add_hierarchy_with_sites(FileHandle fh, Hierarchy hs)"""
2934 return _IMP_npctransport.add_hierarchy_with_sites(fh, hs)
2937 """create_hierarchies_with_sites(FileConstHandle fh, Model m) -> IMP::atom::Hierarchies"""
2938 return _IMP_npctransport.create_hierarchies_with_sites(fh, m)
2941 """link_hierarchies_with_sites(FileConstHandle fh, IMP::atom::Hierarchies const & hs)"""
2942 return _IMP_npctransport.link_hierarchies_with_sites(fh, hs)
2944 """Proxy of C++ IMP::npctransport::Transporting class."""
2946 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
2950 __init__(IMP::npctransport::Transporting self) -> Transporting
2951 __init__(IMP::npctransport::Transporting self, Model m, ParticleIndex id) -> Transporting
2952 __init__(IMP::npctransport::Transporting self, _ParticleAdaptor d) -> Transporting
2954 this = _IMP_npctransport.new_Transporting(*args)
2956 self.this.append(this)
2957 except __builtin__.Exception:
2960 def show(self, *args):
2962 show(Transporting self, _ostream out)
2963 show(Transporting self)
2965 return _IMP_npctransport.Transporting_show(self, *args)
2968 def setup_particle(*args):
2970 setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
2971 setup_particle(Model m, ParticleIndex pi) -> Transporting
2972 setup_particle(_ParticleAdaptor decorator, bool is_last_entry_from_top=False) -> Transporting
2973 setup_particle(_ParticleAdaptor decorator) -> Transporting
2975 return _IMP_npctransport.Transporting_setup_particle(*args)
2977 setup_particle = staticmethod(setup_particle)
2979 def get_is_setup(*args):
2981 get_is_setup(_ParticleAdaptor p) -> bool
2982 get_is_setup(Model m, ParticleIndex pi) -> bool
2984 return _IMP_npctransport.Transporting_get_is_setup(*args)
2986 get_is_setup = staticmethod(get_is_setup)
2988 def set_is_last_entry_from_top(self, is_last_entry_from_top):
2989 """set_is_last_entry_from_top(Transporting self, bool is_last_entry_from_top)"""
2990 return _IMP_npctransport.Transporting_set_is_last_entry_from_top(self, is_last_entry_from_top)
2993 def get_is_last_entry_from_top(self):
2994 """get_is_last_entry_from_top(Transporting self) -> bool"""
2995 return _IMP_npctransport.Transporting_get_is_last_entry_from_top(self)
2998 def get_is_last_entry_from_top_key():
2999 """get_is_last_entry_from_top_key() -> IntKey"""
3000 return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
3002 get_is_last_entry_from_top_key = staticmethod(get_is_last_entry_from_top_key)
3004 def set_last_tracked_z(self, last_tracked_z):
3005 """set_last_tracked_z(Transporting self, double last_tracked_z)"""
3006 return _IMP_npctransport.Transporting_set_last_tracked_z(self, last_tracked_z)
3009 def get_last_tracked_z(self):
3010 """get_last_tracked_z(Transporting self) -> double"""
3011 return _IMP_npctransport.Transporting_get_last_tracked_z(self)
3014 def get_last_tracked_z_key():
3015 """get_last_tracked_z_key() -> FloatKey"""
3016 return _IMP_npctransport.Transporting_get_last_tracked_z_key()
3018 get_last_tracked_z_key = staticmethod(get_last_tracked_z_key)
3020 def set_n_entries_bottom(self, n):
3021 """set_n_entries_bottom(Transporting self, int n)"""
3022 return _IMP_npctransport.Transporting_set_n_entries_bottom(self, n)
3025 def get_n_entries_bottom(self):
3026 """get_n_entries_bottom(Transporting self) -> int"""
3027 return _IMP_npctransport.Transporting_get_n_entries_bottom(self)
3030 def get_n_entries_bottom_key():
3031 """get_n_entries_bottom_key() -> IntKey"""
3032 return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
3034 get_n_entries_bottom_key = staticmethod(get_n_entries_bottom_key)
3036 def set_n_entries_top(self, n):
3037 """set_n_entries_top(Transporting self, int n)"""
3038 return _IMP_npctransport.Transporting_set_n_entries_top(self, n)
3041 def get_n_entries_top(self):
3042 """get_n_entries_top(Transporting self) -> int"""
3043 return _IMP_npctransport.Transporting_get_n_entries_top(self)
3046 def get_n_entries_top_key():
3047 """get_n_entries_top_key() -> IntKey"""
3048 return _IMP_npctransport.Transporting_get_n_entries_top_key()
3050 get_n_entries_top_key = staticmethod(get_n_entries_top_key)
3052 def add_attribute(self, *args):
3054 add_attribute(Transporting self, FloatKey k, IMP::Float v, bool opt)
3055 add_attribute(Transporting self, FloatKey a0, IMP::Float a1)
3056 add_attribute(Transporting self, IntKey a0, IMP::Int a1)
3057 add_attribute(Transporting self, FloatsKey a0, IMP::Floats a1)
3058 add_attribute(Transporting self, IntsKey a0, IMP::Ints a1)
3059 add_attribute(Transporting self, StringKey a0, IMP::String a1)
3060 add_attribute(Transporting self, ParticleIndexKey a0, Particle a1)
3061 add_attribute(Transporting self, ObjectKey a0, Object a1)
3063 return _IMP_npctransport.Transporting_add_attribute(self, *args)
3066 def get_value(self, *args):
3068 get_value(Transporting self, FloatKey a0) -> IMP::Float
3069 get_value(Transporting self, IntKey a0) -> IMP::Int
3070 get_value(Transporting self, FloatsKey a0) -> IMP::Floats
3071 get_value(Transporting self, IntsKey a0) -> IMP::Ints
3072 get_value(Transporting self, StringKey a0) -> IMP::String
3073 get_value(Transporting self, ParticleIndexKey a0) -> Particle
3074 get_value(Transporting self, ObjectKey a0) -> Object
3076 return _IMP_npctransport.Transporting_get_value(self, *args)
3079 def set_value(self, *args):
3081 set_value(Transporting self, FloatKey a0, IMP::Float a1)
3082 set_value(Transporting self, IntKey a0, IMP::Int a1)
3083 set_value(Transporting self, FloatsKey a0, IMP::Floats a1)
3084 set_value(Transporting self, IntsKey a0, IMP::Ints a1)
3085 set_value(Transporting self, StringKey a0, IMP::String a1)
3086 set_value(Transporting self, ParticleIndexKey a0, Particle a1)
3087 set_value(Transporting self, ObjectKey a0, Object a1)
3089 return _IMP_npctransport.Transporting_set_value(self, *args)
3092 def remove_attribute(self, *args):
3094 remove_attribute(Transporting self, FloatKey a0)
3095 remove_attribute(Transporting self, IntKey a0)
3096 remove_attribute(Transporting self, FloatsKey a0)
3097 remove_attribute(Transporting self, IntsKey a0)
3098 remove_attribute(Transporting self, StringKey a0)
3099 remove_attribute(Transporting self, ParticleIndexKey a0)
3100 remove_attribute(Transporting self, ObjectKey a0)
3102 return _IMP_npctransport.Transporting_remove_attribute(self, *args)
3105 def has_attribute(self, *args):
3107 has_attribute(Transporting self, FloatKey a0) -> bool
3108 has_attribute(Transporting self, IntKey a0) -> bool
3109 has_attribute(Transporting self, FloatsKey a0) -> bool
3110 has_attribute(Transporting self, IntsKey a0) -> bool
3111 has_attribute(Transporting self, StringKey a0) -> bool
3112 has_attribute(Transporting self, ParticleIndexKey a0) -> bool
3113 has_attribute(Transporting self, ObjectKey a0) -> bool
3115 return _IMP_npctransport.Transporting_has_attribute(self, *args)
3118 def get_derivative(self, a0):
3119 """get_derivative(Transporting self, FloatKey a0) -> double"""
3120 return _IMP_npctransport.Transporting_get_derivative(self, a0)
3124 """get_name(Transporting self) -> std::string"""
3125 return _IMP_npctransport.Transporting_get_name(self)
3128 def clear_caches(self):
3129 """clear_caches(Transporting self)"""
3130 return _IMP_npctransport.Transporting_clear_caches(self)
3133 def set_name(self, a0):
3134 """set_name(Transporting self, std::string a0)"""
3135 return _IMP_npctransport.Transporting_set_name(self, a0)
3139 """set_check_level(Transporting self, IMP::CheckLevel a0)"""
3140 return _IMP_npctransport.Transporting_set_check_level(self, a0)
3143 def add_to_derivative(self, a0, a1, a2):
3144 """add_to_derivative(Transporting self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3145 return _IMP_npctransport.Transporting_add_to_derivative(self, a0, a1, a2)
3148 def set_is_optimized(self, a0, a1):
3149 """set_is_optimized(Transporting self, FloatKey a0, bool a1)"""
3150 return _IMP_npctransport.Transporting_set_is_optimized(self, a0, a1)
3153 def get_is_optimized(self, a0):
3154 """get_is_optimized(Transporting self, FloatKey a0) -> bool"""
3155 return _IMP_npctransport.Transporting_get_is_optimized(self, a0)
3159 """get_check_level(Transporting self) -> IMP::CheckLevel"""
3160 return _IMP_npctransport.Transporting_get_check_level(self)
3163 def __eq__(self, *args):
3165 __eq__(Transporting self, Transporting o) -> bool
3166 __eq__(Transporting self, Particle d) -> bool
3168 return _IMP_npctransport.Transporting___eq__(self, *args)
3171 def __ne__(self, *args):
3173 __ne__(Transporting self, Transporting o) -> bool
3174 __ne__(Transporting self, Particle d) -> bool
3176 return _IMP_npctransport.Transporting___ne__(self, *args)
3179 def __le__(self, *args):
3181 __le__(Transporting self, Transporting o) -> bool
3182 __le__(Transporting self, Particle d) -> bool
3184 return _IMP_npctransport.Transporting___le__(self, *args)
3187 def __lt__(self, *args):
3189 __lt__(Transporting self, Transporting o) -> bool
3190 __lt__(Transporting self, Particle d) -> bool
3192 return _IMP_npctransport.Transporting___lt__(self, *args)
3195 def __ge__(self, *args):
3197 __ge__(Transporting self, Transporting o) -> bool
3198 __ge__(Transporting self, Particle d) -> bool
3200 return _IMP_npctransport.Transporting___ge__(self, *args)
3203 def __gt__(self, *args):
3205 __gt__(Transporting self, Transporting o) -> bool
3206 __gt__(Transporting self, Particle d) -> bool
3208 return _IMP_npctransport.Transporting___gt__(self, *args)
3212 """__hash__(Transporting self) -> std::size_t"""
3213 return _IMP_npctransport.Transporting___hash__(self)
3217 """__str__(Transporting self) -> std::string"""
3218 return _IMP_npctransport.Transporting___str__(self)
3222 """__repr__(Transporting self) -> std::string"""
3223 return _IMP_npctransport.Transporting___repr__(self)
3225 __swig_destroy__ = _IMP_npctransport.delete_Transporting
3226 __del__ =
lambda self:
None
3227 Transporting_swigregister = _IMP_npctransport.Transporting_swigregister
3228 Transporting_swigregister(Transporting)
3230 def Transporting_setup_particle(*args):
3232 setup_particle(Model m, ParticleIndex pi, bool is_last_entry_from_top=False) -> Transporting
3233 setup_particle(Model m, ParticleIndex pi) -> Transporting
3234 setup_particle(_ParticleAdaptor decorator, bool is_last_entry_from_top=False) -> Transporting
3235 Transporting_setup_particle(_ParticleAdaptor decorator) -> Transporting
3237 return _IMP_npctransport.Transporting_setup_particle(*args)
3239 def Transporting_get_is_setup(*args):
3241 get_is_setup(_ParticleAdaptor p) -> bool
3242 Transporting_get_is_setup(Model m, ParticleIndex pi) -> bool
3244 return _IMP_npctransport.Transporting_get_is_setup(*args)
3246 def Transporting_get_is_last_entry_from_top_key():
3247 """Transporting_get_is_last_entry_from_top_key() -> IntKey"""
3248 return _IMP_npctransport.Transporting_get_is_last_entry_from_top_key()
3250 def Transporting_get_last_tracked_z_key():
3251 """Transporting_get_last_tracked_z_key() -> FloatKey"""
3252 return _IMP_npctransport.Transporting_get_last_tracked_z_key()
3254 def Transporting_get_n_entries_bottom_key():
3255 """Transporting_get_n_entries_bottom_key() -> IntKey"""
3256 return _IMP_npctransport.Transporting_get_n_entries_bottom_key()
3258 def Transporting_get_n_entries_top_key():
3259 """Transporting_get_n_entries_top_key() -> IntKey"""
3260 return _IMP_npctransport.Transporting_get_n_entries_top_key()
3263 def show_ranges(fname):
3264 """show_ranges(std::string fname)"""
3265 return _IMP_npctransport.show_ranges(fname)
3267 def assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed):
3268 """assign_ranges(std::string input_config_fname, std::string output_assignment_fname, unsigned int work_unit, bool show_steps, boost::uint64_t random_seed) -> int"""
3269 return _IMP_npctransport.assign_ranges(input_config_fname, output_assignment_fname, work_unit, show_steps, random_seed)
3271 def get_number_of_work_units(configuration_file):
3272 """get_number_of_work_units(std::string configuration_file) -> int"""
3273 return _IMP_npctransport.get_number_of_work_units(configuration_file)
3275 """Proxy of C++ IMP::npctransport::SlabWithPore class."""
3277 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3281 __init__(IMP::npctransport::SlabWithPore self) -> SlabWithPore
3282 __init__(IMP::npctransport::SlabWithPore self, Model m, ParticleIndex id) -> SlabWithPore
3283 __init__(IMP::npctransport::SlabWithPore self, _ParticleAdaptor d) -> SlabWithPore
3285 this = _IMP_npctransport.new_SlabWithPore(*args)
3287 self.this.append(this)
3288 except __builtin__.Exception:
3291 def show(self, *args):
3293 show(SlabWithPore self, _ostream out)
3294 show(SlabWithPore self)
3296 return _IMP_npctransport.SlabWithPore_show(self, *args)
3299 def setup_particle(*args):
3301 setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
3302 setup_particle(_ParticleAdaptor decorator, double thickness, double pore_radius) -> SlabWithPore
3304 return _IMP_npctransport.SlabWithPore_setup_particle(*args)
3306 setup_particle = staticmethod(setup_particle)
3308 def get_is_setup(*args):
3310 get_is_setup(_ParticleAdaptor p) -> bool
3311 get_is_setup(Model m, ParticleIndex pi) -> bool
3313 return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
3315 get_is_setup = staticmethod(get_is_setup)
3317 def set_thickness(self, thickness):
3318 """set_thickness(SlabWithPore self, double thickness)"""
3319 return _IMP_npctransport.SlabWithPore_set_thickness(self, thickness)
3322 def get_thickness(self):
3323 """get_thickness(SlabWithPore self) -> IMP::Float"""
3324 return _IMP_npctransport.SlabWithPore_get_thickness(self)
3327 def get_pore_radius(self):
3328 """get_pore_radius(SlabWithPore self) -> IMP::Float"""
3329 return _IMP_npctransport.SlabWithPore_get_pore_radius(self)
3332 def set_pore_radius(self, r):
3333 """set_pore_radius(SlabWithPore self, double r)"""
3334 return _IMP_npctransport.SlabWithPore_set_pore_radius(self, r)
3337 def add_to_pore_radius_derivative(self, v, d):
3338 """add_to_pore_radius_derivative(SlabWithPore self, double v, DerivativeAccumulator d)"""
3339 return _IMP_npctransport.SlabWithPore_add_to_pore_radius_derivative(self, v, d)
3342 def get_pore_radius_is_optimized(self):
3343 """get_pore_radius_is_optimized(SlabWithPore self) -> bool"""
3344 return _IMP_npctransport.SlabWithPore_get_pore_radius_is_optimized(self)
3347 def set_pore_radius_is_optimized(self, tf):
3348 """set_pore_radius_is_optimized(SlabWithPore self, bool tf)"""
3349 return _IMP_npctransport.SlabWithPore_set_pore_radius_is_optimized(self, tf)
3352 def get_thickness_key():
3353 """get_thickness_key() -> FloatKey"""
3354 return _IMP_npctransport.SlabWithPore_get_thickness_key()
3356 get_thickness_key = staticmethod(get_thickness_key)
3358 def get_pore_radius_key():
3359 """get_pore_radius_key() -> FloatKey"""
3360 return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
3362 get_pore_radius_key = staticmethod(get_pore_radius_key)
3364 def add_attribute(self, *args):
3366 add_attribute(SlabWithPore self, FloatKey k, IMP::Float v, bool opt)
3367 add_attribute(SlabWithPore self, FloatKey a0, IMP::Float a1)
3368 add_attribute(SlabWithPore self, IntKey a0, IMP::Int a1)
3369 add_attribute(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
3370 add_attribute(SlabWithPore self, IntsKey a0, IMP::Ints a1)
3371 add_attribute(SlabWithPore self, StringKey a0, IMP::String a1)
3372 add_attribute(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3373 add_attribute(SlabWithPore self, ObjectKey a0, Object a1)
3375 return _IMP_npctransport.SlabWithPore_add_attribute(self, *args)
3378 def get_value(self, *args):
3380 get_value(SlabWithPore self, FloatKey a0) -> IMP::Float
3381 get_value(SlabWithPore self, IntKey a0) -> IMP::Int
3382 get_value(SlabWithPore self, FloatsKey a0) -> IMP::Floats
3383 get_value(SlabWithPore self, IntsKey a0) -> IMP::Ints
3384 get_value(SlabWithPore self, StringKey a0) -> IMP::String
3385 get_value(SlabWithPore self, ParticleIndexKey a0) -> Particle
3386 get_value(SlabWithPore self, ObjectKey a0) -> Object
3388 return _IMP_npctransport.SlabWithPore_get_value(self, *args)
3391 def set_value(self, *args):
3393 set_value(SlabWithPore self, FloatKey a0, IMP::Float a1)
3394 set_value(SlabWithPore self, IntKey a0, IMP::Int a1)
3395 set_value(SlabWithPore self, FloatsKey a0, IMP::Floats a1)
3396 set_value(SlabWithPore self, IntsKey a0, IMP::Ints a1)
3397 set_value(SlabWithPore self, StringKey a0, IMP::String a1)
3398 set_value(SlabWithPore self, ParticleIndexKey a0, Particle a1)
3399 set_value(SlabWithPore self, ObjectKey a0, Object a1)
3401 return _IMP_npctransport.SlabWithPore_set_value(self, *args)
3404 def remove_attribute(self, *args):
3406 remove_attribute(SlabWithPore self, FloatKey a0)
3407 remove_attribute(SlabWithPore self, IntKey a0)
3408 remove_attribute(SlabWithPore self, FloatsKey a0)
3409 remove_attribute(SlabWithPore self, IntsKey a0)
3410 remove_attribute(SlabWithPore self, StringKey a0)
3411 remove_attribute(SlabWithPore self, ParticleIndexKey a0)
3412 remove_attribute(SlabWithPore self, ObjectKey a0)
3414 return _IMP_npctransport.SlabWithPore_remove_attribute(self, *args)
3417 def has_attribute(self, *args):
3419 has_attribute(SlabWithPore self, FloatKey a0) -> bool
3420 has_attribute(SlabWithPore self, IntKey a0) -> bool
3421 has_attribute(SlabWithPore self, FloatsKey a0) -> bool
3422 has_attribute(SlabWithPore self, IntsKey a0) -> bool
3423 has_attribute(SlabWithPore self, StringKey a0) -> bool
3424 has_attribute(SlabWithPore self, ParticleIndexKey a0) -> bool
3425 has_attribute(SlabWithPore self, ObjectKey a0) -> bool
3427 return _IMP_npctransport.SlabWithPore_has_attribute(self, *args)
3430 def get_derivative(self, a0):
3431 """get_derivative(SlabWithPore self, FloatKey a0) -> double"""
3432 return _IMP_npctransport.SlabWithPore_get_derivative(self, a0)
3436 """get_name(SlabWithPore self) -> std::string"""
3437 return _IMP_npctransport.SlabWithPore_get_name(self)
3440 def clear_caches(self):
3441 """clear_caches(SlabWithPore self)"""
3442 return _IMP_npctransport.SlabWithPore_clear_caches(self)
3445 def set_name(self, a0):
3446 """set_name(SlabWithPore self, std::string a0)"""
3447 return _IMP_npctransport.SlabWithPore_set_name(self, a0)
3451 """set_check_level(SlabWithPore self, IMP::CheckLevel a0)"""
3452 return _IMP_npctransport.SlabWithPore_set_check_level(self, a0)
3455 def add_to_derivative(self, a0, a1, a2):
3456 """add_to_derivative(SlabWithPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3457 return _IMP_npctransport.SlabWithPore_add_to_derivative(self, a0, a1, a2)
3460 def set_is_optimized(self, a0, a1):
3461 """set_is_optimized(SlabWithPore self, FloatKey a0, bool a1)"""
3462 return _IMP_npctransport.SlabWithPore_set_is_optimized(self, a0, a1)
3465 def get_is_optimized(self, a0):
3466 """get_is_optimized(SlabWithPore self, FloatKey a0) -> bool"""
3467 return _IMP_npctransport.SlabWithPore_get_is_optimized(self, a0)
3471 """get_check_level(SlabWithPore self) -> IMP::CheckLevel"""
3472 return _IMP_npctransport.SlabWithPore_get_check_level(self)
3475 def __eq__(self, *args):
3477 __eq__(SlabWithPore self, SlabWithPore o) -> bool
3478 __eq__(SlabWithPore self, Particle d) -> bool
3480 return _IMP_npctransport.SlabWithPore___eq__(self, *args)
3483 def __ne__(self, *args):
3485 __ne__(SlabWithPore self, SlabWithPore o) -> bool
3486 __ne__(SlabWithPore self, Particle d) -> bool
3488 return _IMP_npctransport.SlabWithPore___ne__(self, *args)
3491 def __le__(self, *args):
3493 __le__(SlabWithPore self, SlabWithPore o) -> bool
3494 __le__(SlabWithPore self, Particle d) -> bool
3496 return _IMP_npctransport.SlabWithPore___le__(self, *args)
3499 def __lt__(self, *args):
3501 __lt__(SlabWithPore self, SlabWithPore o) -> bool
3502 __lt__(SlabWithPore self, Particle d) -> bool
3504 return _IMP_npctransport.SlabWithPore___lt__(self, *args)
3507 def __ge__(self, *args):
3509 __ge__(SlabWithPore self, SlabWithPore o) -> bool
3510 __ge__(SlabWithPore self, Particle d) -> bool
3512 return _IMP_npctransport.SlabWithPore___ge__(self, *args)
3515 def __gt__(self, *args):
3517 __gt__(SlabWithPore self, SlabWithPore o) -> bool
3518 __gt__(SlabWithPore self, Particle d) -> bool
3520 return _IMP_npctransport.SlabWithPore___gt__(self, *args)
3524 """__hash__(SlabWithPore self) -> std::size_t"""
3525 return _IMP_npctransport.SlabWithPore___hash__(self)
3529 """__str__(SlabWithPore self) -> std::string"""
3530 return _IMP_npctransport.SlabWithPore___str__(self)
3534 """__repr__(SlabWithPore self) -> std::string"""
3535 return _IMP_npctransport.SlabWithPore___repr__(self)
3537 __swig_destroy__ = _IMP_npctransport.delete_SlabWithPore
3538 __del__ =
lambda self:
None
3539 SlabWithPore_swigregister = _IMP_npctransport.SlabWithPore_swigregister
3540 SlabWithPore_swigregister(SlabWithPore)
3542 def SlabWithPore_setup_particle(*args):
3544 setup_particle(Model m, ParticleIndex pi, double thickness, double pore_radius) -> SlabWithPore
3545 SlabWithPore_setup_particle(_ParticleAdaptor decorator, double thickness, double pore_radius) -> SlabWithPore
3547 return _IMP_npctransport.SlabWithPore_setup_particle(*args)
3549 def SlabWithPore_get_is_setup(*args):
3551 get_is_setup(_ParticleAdaptor p) -> bool
3552 SlabWithPore_get_is_setup(Model m, ParticleIndex pi) -> bool
3554 return _IMP_npctransport.SlabWithPore_get_is_setup(*args)
3556 def SlabWithPore_get_thickness_key():
3557 """SlabWithPore_get_thickness_key() -> FloatKey"""
3558 return _IMP_npctransport.SlabWithPore_get_thickness_key()
3560 def SlabWithPore_get_pore_radius_key():
3561 """SlabWithPore_get_pore_radius_key() -> FloatKey"""
3562 return _IMP_npctransport.SlabWithPore_get_pore_radius_key()
3564 class SlabWithCylindricalPore(SlabWithPore):
3565 """Proxy of C++ IMP::npctransport::SlabWithCylindricalPore class."""
3567 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3571 __init__(IMP::npctransport::SlabWithCylindricalPore self) -> SlabWithCylindricalPore
3572 __init__(IMP::npctransport::SlabWithCylindricalPore self, Model m, ParticleIndex id) -> SlabWithCylindricalPore
3573 __init__(IMP::npctransport::SlabWithCylindricalPore self, _ParticleAdaptor d) -> SlabWithCylindricalPore
3575 this = _IMP_npctransport.new_SlabWithCylindricalPore(*args)
3577 self.this.append(this)
3578 except __builtin__.Exception:
3581 def show(self, *args):
3583 show(SlabWithCylindricalPore self, _ostream out)
3584 show(SlabWithCylindricalPore self)
3586 return _IMP_npctransport.SlabWithCylindricalPore_show(self, *args)
3589 def setup_particle(*args):
3591 setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3592 setup_particle(_ParticleAdaptor decorator, double thickness, double radius) -> SlabWithCylindricalPore
3594 return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3596 setup_particle = staticmethod(setup_particle)
3598 def get_is_setup(*args):
3600 get_is_setup(_ParticleAdaptor p) -> bool
3601 get_is_setup(Model m, ParticleIndex pi) -> bool
3603 return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3605 get_is_setup = staticmethod(get_is_setup)
3607 def get_cylindrical_pore_key():
3608 """get_cylindrical_pore_key() -> IntKey"""
3609 return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3611 get_cylindrical_pore_key = staticmethod(get_cylindrical_pore_key)
3613 def add_attribute(self, *args):
3615 add_attribute(SlabWithCylindricalPore self, FloatKey k, IMP::Float v, bool opt)
3616 add_attribute(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3617 add_attribute(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3618 add_attribute(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
3619 add_attribute(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
3620 add_attribute(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3621 add_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3622 add_attribute(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3624 return _IMP_npctransport.SlabWithCylindricalPore_add_attribute(self, *args)
3627 def get_value(self, *args):
3629 get_value(SlabWithCylindricalPore self, FloatKey a0) -> IMP::Float
3630 get_value(SlabWithCylindricalPore self, IntKey a0) -> IMP::Int
3631 get_value(SlabWithCylindricalPore self, FloatsKey a0) -> IMP::Floats
3632 get_value(SlabWithCylindricalPore self, IntsKey a0) -> IMP::Ints
3633 get_value(SlabWithCylindricalPore self, StringKey a0) -> IMP::String
3634 get_value(SlabWithCylindricalPore self, ParticleIndexKey a0) -> Particle
3635 get_value(SlabWithCylindricalPore self, ObjectKey a0) -> Object
3637 return _IMP_npctransport.SlabWithCylindricalPore_get_value(self, *args)
3640 def set_value(self, *args):
3642 set_value(SlabWithCylindricalPore self, FloatKey a0, IMP::Float a1)
3643 set_value(SlabWithCylindricalPore self, IntKey a0, IMP::Int a1)
3644 set_value(SlabWithCylindricalPore self, FloatsKey a0, IMP::Floats a1)
3645 set_value(SlabWithCylindricalPore self, IntsKey a0, IMP::Ints a1)
3646 set_value(SlabWithCylindricalPore self, StringKey a0, IMP::String a1)
3647 set_value(SlabWithCylindricalPore self, ParticleIndexKey a0, Particle a1)
3648 set_value(SlabWithCylindricalPore self, ObjectKey a0, Object a1)
3650 return _IMP_npctransport.SlabWithCylindricalPore_set_value(self, *args)
3653 def remove_attribute(self, *args):
3655 remove_attribute(SlabWithCylindricalPore self, FloatKey a0)
3656 remove_attribute(SlabWithCylindricalPore self, IntKey a0)
3657 remove_attribute(SlabWithCylindricalPore self, FloatsKey a0)
3658 remove_attribute(SlabWithCylindricalPore self, IntsKey a0)
3659 remove_attribute(SlabWithCylindricalPore self, StringKey a0)
3660 remove_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0)
3661 remove_attribute(SlabWithCylindricalPore self, ObjectKey a0)
3663 return _IMP_npctransport.SlabWithCylindricalPore_remove_attribute(self, *args)
3666 def has_attribute(self, *args):
3668 has_attribute(SlabWithCylindricalPore self, FloatKey a0) -> bool
3669 has_attribute(SlabWithCylindricalPore self, IntKey a0) -> bool
3670 has_attribute(SlabWithCylindricalPore self, FloatsKey a0) -> bool
3671 has_attribute(SlabWithCylindricalPore self, IntsKey a0) -> bool
3672 has_attribute(SlabWithCylindricalPore self, StringKey a0) -> bool
3673 has_attribute(SlabWithCylindricalPore self, ParticleIndexKey a0) -> bool
3674 has_attribute(SlabWithCylindricalPore self, ObjectKey a0) -> bool
3676 return _IMP_npctransport.SlabWithCylindricalPore_has_attribute(self, *args)
3679 def get_derivative(self, a0):
3680 """get_derivative(SlabWithCylindricalPore self, FloatKey a0) -> double"""
3681 return _IMP_npctransport.SlabWithCylindricalPore_get_derivative(self, a0)
3685 """get_name(SlabWithCylindricalPore self) -> std::string"""
3686 return _IMP_npctransport.SlabWithCylindricalPore_get_name(self)
3689 def clear_caches(self):
3690 """clear_caches(SlabWithCylindricalPore self)"""
3691 return _IMP_npctransport.SlabWithCylindricalPore_clear_caches(self)
3694 def set_name(self, a0):
3695 """set_name(SlabWithCylindricalPore self, std::string a0)"""
3696 return _IMP_npctransport.SlabWithCylindricalPore_set_name(self, a0)
3700 """set_check_level(SlabWithCylindricalPore self, IMP::CheckLevel a0)"""
3701 return _IMP_npctransport.SlabWithCylindricalPore_set_check_level(self, a0)
3704 def add_to_derivative(self, a0, a1, a2):
3705 """add_to_derivative(SlabWithCylindricalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3706 return _IMP_npctransport.SlabWithCylindricalPore_add_to_derivative(self, a0, a1, a2)
3709 def set_is_optimized(self, a0, a1):
3710 """set_is_optimized(SlabWithCylindricalPore self, FloatKey a0, bool a1)"""
3711 return _IMP_npctransport.SlabWithCylindricalPore_set_is_optimized(self, a0, a1)
3714 def get_is_optimized(self, a0):
3715 """get_is_optimized(SlabWithCylindricalPore self, FloatKey a0) -> bool"""
3716 return _IMP_npctransport.SlabWithCylindricalPore_get_is_optimized(self, a0)
3720 """get_check_level(SlabWithCylindricalPore self) -> IMP::CheckLevel"""
3721 return _IMP_npctransport.SlabWithCylindricalPore_get_check_level(self)
3724 def __eq__(self, *args):
3726 __eq__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3727 __eq__(SlabWithCylindricalPore self, Particle d) -> bool
3729 return _IMP_npctransport.SlabWithCylindricalPore___eq__(self, *args)
3732 def __ne__(self, *args):
3734 __ne__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3735 __ne__(SlabWithCylindricalPore self, Particle d) -> bool
3737 return _IMP_npctransport.SlabWithCylindricalPore___ne__(self, *args)
3740 def __le__(self, *args):
3742 __le__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3743 __le__(SlabWithCylindricalPore self, Particle d) -> bool
3745 return _IMP_npctransport.SlabWithCylindricalPore___le__(self, *args)
3748 def __lt__(self, *args):
3750 __lt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3751 __lt__(SlabWithCylindricalPore self, Particle d) -> bool
3753 return _IMP_npctransport.SlabWithCylindricalPore___lt__(self, *args)
3756 def __ge__(self, *args):
3758 __ge__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3759 __ge__(SlabWithCylindricalPore self, Particle d) -> bool
3761 return _IMP_npctransport.SlabWithCylindricalPore___ge__(self, *args)
3764 def __gt__(self, *args):
3766 __gt__(SlabWithCylindricalPore self, SlabWithCylindricalPore o) -> bool
3767 __gt__(SlabWithCylindricalPore self, Particle d) -> bool
3769 return _IMP_npctransport.SlabWithCylindricalPore___gt__(self, *args)
3773 """__hash__(SlabWithCylindricalPore self) -> std::size_t"""
3774 return _IMP_npctransport.SlabWithCylindricalPore___hash__(self)
3778 """__str__(SlabWithCylindricalPore self) -> std::string"""
3779 return _IMP_npctransport.SlabWithCylindricalPore___str__(self)
3783 """__repr__(SlabWithCylindricalPore self) -> std::string"""
3784 return _IMP_npctransport.SlabWithCylindricalPore___repr__(self)
3786 __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPore
3787 __del__ =
lambda self:
None
3788 SlabWithCylindricalPore_swigregister = _IMP_npctransport.SlabWithCylindricalPore_swigregister
3789 SlabWithCylindricalPore_swigregister(SlabWithCylindricalPore)
3791 def SlabWithCylindricalPore_setup_particle(*args):
3793 setup_particle(Model m, ParticleIndex pi, double thickness, double radius) -> SlabWithCylindricalPore
3794 SlabWithCylindricalPore_setup_particle(_ParticleAdaptor decorator, double thickness, double radius) -> SlabWithCylindricalPore
3796 return _IMP_npctransport.SlabWithCylindricalPore_setup_particle(*args)
3798 def SlabWithCylindricalPore_get_is_setup(*args):
3800 get_is_setup(_ParticleAdaptor p) -> bool
3801 SlabWithCylindricalPore_get_is_setup(Model m, ParticleIndex pi) -> bool
3803 return _IMP_npctransport.SlabWithCylindricalPore_get_is_setup(*args)
3805 def SlabWithCylindricalPore_get_cylindrical_pore_key():
3806 """SlabWithCylindricalPore_get_cylindrical_pore_key() -> IntKey"""
3807 return _IMP_npctransport.SlabWithCylindricalPore_get_cylindrical_pore_key()
3809 class SlabWithToroidalPore(SlabWithPore):
3810 """Proxy of C++ IMP::npctransport::SlabWithToroidalPore class."""
3812 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
3816 __init__(IMP::npctransport::SlabWithToroidalPore self) -> SlabWithToroidalPore
3817 __init__(IMP::npctransport::SlabWithToroidalPore self, Model m, ParticleIndex id) -> SlabWithToroidalPore
3818 __init__(IMP::npctransport::SlabWithToroidalPore self, _ParticleAdaptor d) -> SlabWithToroidalPore
3820 this = _IMP_npctransport.new_SlabWithToroidalPore(*args)
3822 self.this.append(this)
3823 except __builtin__.Exception:
3826 def show(self, *args):
3828 show(SlabWithToroidalPore self, _ostream out)
3829 show(SlabWithToroidalPore self)
3831 return _IMP_npctransport.SlabWithToroidalPore_show(self, *args)
3834 def setup_particle(*args):
3836 setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
3837 setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius) -> SlabWithToroidalPore
3838 setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3839 setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
3841 return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
3843 setup_particle = staticmethod(setup_particle)
3845 def get_is_setup(*args):
3847 get_is_setup(_ParticleAdaptor p) -> bool
3848 get_is_setup(Model m, ParticleIndex pi) -> bool
3850 return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
3852 get_is_setup = staticmethod(get_is_setup)
3854 def set_minor_radius_h2v_aspect_ratio(self, aspect_ratio):
3855 """set_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self, double aspect_ratio)"""
3856 return _IMP_npctransport.SlabWithToroidalPore_set_minor_radius_h2v_aspect_ratio(self, aspect_ratio)
3859 def get_minor_radius_h2v_aspect_ratio(self):
3860 """get_minor_radius_h2v_aspect_ratio(SlabWithToroidalPore self) -> double"""
3861 return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio(self)
3864 def get_vertical_minor_radius(self):
3865 """get_vertical_minor_radius(SlabWithToroidalPore self) -> double"""
3866 return _IMP_npctransport.SlabWithToroidalPore_get_vertical_minor_radius(self)
3869 def set_vertical_minor_radius(self, rv):
3870 """set_vertical_minor_radius(SlabWithToroidalPore self, double rv)"""
3871 return _IMP_npctransport.SlabWithToroidalPore_set_vertical_minor_radius(self, rv)
3874 def get_horizontal_minor_radius(self):
3875 """get_horizontal_minor_radius(SlabWithToroidalPore self) -> double"""
3876 return _IMP_npctransport.SlabWithToroidalPore_get_horizontal_minor_radius(self)
3879 def set_horizontal_minor_radius(self, rh):
3880 """set_horizontal_minor_radius(SlabWithToroidalPore self, double rh)"""
3881 return _IMP_npctransport.SlabWithToroidalPore_set_horizontal_minor_radius(self, rh)
3884 def get_minor_radius_h2v_aspect_ratio_key():
3885 """get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
3886 return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
3888 get_minor_radius_h2v_aspect_ratio_key = staticmethod(get_minor_radius_h2v_aspect_ratio_key)
3890 def get_toroidal_pore_key():
3891 """get_toroidal_pore_key() -> IntKey"""
3892 return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
3894 get_toroidal_pore_key = staticmethod(get_toroidal_pore_key)
3896 def add_attribute(self, *args):
3898 add_attribute(SlabWithToroidalPore self, FloatKey k, IMP::Float v, bool opt)
3899 add_attribute(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3900 add_attribute(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3901 add_attribute(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
3902 add_attribute(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
3903 add_attribute(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3904 add_attribute(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3905 add_attribute(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3907 return _IMP_npctransport.SlabWithToroidalPore_add_attribute(self, *args)
3910 def get_value(self, *args):
3912 get_value(SlabWithToroidalPore self, FloatKey a0) -> IMP::Float
3913 get_value(SlabWithToroidalPore self, IntKey a0) -> IMP::Int
3914 get_value(SlabWithToroidalPore self, FloatsKey a0) -> IMP::Floats
3915 get_value(SlabWithToroidalPore self, IntsKey a0) -> IMP::Ints
3916 get_value(SlabWithToroidalPore self, StringKey a0) -> IMP::String
3917 get_value(SlabWithToroidalPore self, ParticleIndexKey a0) -> Particle
3918 get_value(SlabWithToroidalPore self, ObjectKey a0) -> Object
3920 return _IMP_npctransport.SlabWithToroidalPore_get_value(self, *args)
3923 def set_value(self, *args):
3925 set_value(SlabWithToroidalPore self, FloatKey a0, IMP::Float a1)
3926 set_value(SlabWithToroidalPore self, IntKey a0, IMP::Int a1)
3927 set_value(SlabWithToroidalPore self, FloatsKey a0, IMP::Floats a1)
3928 set_value(SlabWithToroidalPore self, IntsKey a0, IMP::Ints a1)
3929 set_value(SlabWithToroidalPore self, StringKey a0, IMP::String a1)
3930 set_value(SlabWithToroidalPore self, ParticleIndexKey a0, Particle a1)
3931 set_value(SlabWithToroidalPore self, ObjectKey a0, Object a1)
3933 return _IMP_npctransport.SlabWithToroidalPore_set_value(self, *args)
3936 def remove_attribute(self, *args):
3938 remove_attribute(SlabWithToroidalPore self, FloatKey a0)
3939 remove_attribute(SlabWithToroidalPore self, IntKey a0)
3940 remove_attribute(SlabWithToroidalPore self, FloatsKey a0)
3941 remove_attribute(SlabWithToroidalPore self, IntsKey a0)
3942 remove_attribute(SlabWithToroidalPore self, StringKey a0)
3943 remove_attribute(SlabWithToroidalPore self, ParticleIndexKey a0)
3944 remove_attribute(SlabWithToroidalPore self, ObjectKey a0)
3946 return _IMP_npctransport.SlabWithToroidalPore_remove_attribute(self, *args)
3949 def has_attribute(self, *args):
3951 has_attribute(SlabWithToroidalPore self, FloatKey a0) -> bool
3952 has_attribute(SlabWithToroidalPore self, IntKey a0) -> bool
3953 has_attribute(SlabWithToroidalPore self, FloatsKey a0) -> bool
3954 has_attribute(SlabWithToroidalPore self, IntsKey a0) -> bool
3955 has_attribute(SlabWithToroidalPore self, StringKey a0) -> bool
3956 has_attribute(SlabWithToroidalPore self, ParticleIndexKey a0) -> bool
3957 has_attribute(SlabWithToroidalPore self, ObjectKey a0) -> bool
3959 return _IMP_npctransport.SlabWithToroidalPore_has_attribute(self, *args)
3962 def get_derivative(self, a0):
3963 """get_derivative(SlabWithToroidalPore self, FloatKey a0) -> double"""
3964 return _IMP_npctransport.SlabWithToroidalPore_get_derivative(self, a0)
3968 """get_name(SlabWithToroidalPore self) -> std::string"""
3969 return _IMP_npctransport.SlabWithToroidalPore_get_name(self)
3972 def clear_caches(self):
3973 """clear_caches(SlabWithToroidalPore self)"""
3974 return _IMP_npctransport.SlabWithToroidalPore_clear_caches(self)
3977 def set_name(self, a0):
3978 """set_name(SlabWithToroidalPore self, std::string a0)"""
3979 return _IMP_npctransport.SlabWithToroidalPore_set_name(self, a0)
3983 """set_check_level(SlabWithToroidalPore self, IMP::CheckLevel a0)"""
3984 return _IMP_npctransport.SlabWithToroidalPore_set_check_level(self, a0)
3987 def add_to_derivative(self, a0, a1, a2):
3988 """add_to_derivative(SlabWithToroidalPore self, FloatKey a0, double a1, DerivativeAccumulator a2)"""
3989 return _IMP_npctransport.SlabWithToroidalPore_add_to_derivative(self, a0, a1, a2)
3992 def set_is_optimized(self, a0, a1):
3993 """set_is_optimized(SlabWithToroidalPore self, FloatKey a0, bool a1)"""
3994 return _IMP_npctransport.SlabWithToroidalPore_set_is_optimized(self, a0, a1)
3997 def get_is_optimized(self, a0):
3998 """get_is_optimized(SlabWithToroidalPore self, FloatKey a0) -> bool"""
3999 return _IMP_npctransport.SlabWithToroidalPore_get_is_optimized(self, a0)
4003 """get_check_level(SlabWithToroidalPore self) -> IMP::CheckLevel"""
4004 return _IMP_npctransport.SlabWithToroidalPore_get_check_level(self)
4007 def __eq__(self, *args):
4009 __eq__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4010 __eq__(SlabWithToroidalPore self, Particle d) -> bool
4012 return _IMP_npctransport.SlabWithToroidalPore___eq__(self, *args)
4015 def __ne__(self, *args):
4017 __ne__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4018 __ne__(SlabWithToroidalPore self, Particle d) -> bool
4020 return _IMP_npctransport.SlabWithToroidalPore___ne__(self, *args)
4023 def __le__(self, *args):
4025 __le__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4026 __le__(SlabWithToroidalPore self, Particle d) -> bool
4028 return _IMP_npctransport.SlabWithToroidalPore___le__(self, *args)
4031 def __lt__(self, *args):
4033 __lt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4034 __lt__(SlabWithToroidalPore self, Particle d) -> bool
4036 return _IMP_npctransport.SlabWithToroidalPore___lt__(self, *args)
4039 def __ge__(self, *args):
4041 __ge__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4042 __ge__(SlabWithToroidalPore self, Particle d) -> bool
4044 return _IMP_npctransport.SlabWithToroidalPore___ge__(self, *args)
4047 def __gt__(self, *args):
4049 __gt__(SlabWithToroidalPore self, SlabWithToroidalPore o) -> bool
4050 __gt__(SlabWithToroidalPore self, Particle d) -> bool
4052 return _IMP_npctransport.SlabWithToroidalPore___gt__(self, *args)
4056 """__hash__(SlabWithToroidalPore self) -> std::size_t"""
4057 return _IMP_npctransport.SlabWithToroidalPore___hash__(self)
4061 """__str__(SlabWithToroidalPore self) -> std::string"""
4062 return _IMP_npctransport.SlabWithToroidalPore___str__(self)
4066 """__repr__(SlabWithToroidalPore self) -> std::string"""
4067 return _IMP_npctransport.SlabWithToroidalPore___repr__(self)
4069 __swig_destroy__ = _IMP_npctransport.delete_SlabWithToroidalPore
4070 __del__ =
lambda self:
None
4071 SlabWithToroidalPore_swigregister = _IMP_npctransport.SlabWithToroidalPore_swigregister
4072 SlabWithToroidalPore_swigregister(SlabWithToroidalPore)
4074 def SlabWithToroidalPore_setup_particle(*args):
4076 setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius) -> SlabWithToroidalPore
4077 setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius) -> SlabWithToroidalPore
4078 setup_particle(Model m, ParticleIndex pi, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
4079 SlabWithToroidalPore_setup_particle(_ParticleAdaptor decorator, double thickness, double major_radius, double minor_radius_h2v_aspect_ratio) -> SlabWithToroidalPore
4081 return _IMP_npctransport.SlabWithToroidalPore_setup_particle(*args)
4083 def SlabWithToroidalPore_get_is_setup(*args):
4085 get_is_setup(_ParticleAdaptor p) -> bool
4086 SlabWithToroidalPore_get_is_setup(Model m, ParticleIndex pi) -> bool
4088 return _IMP_npctransport.SlabWithToroidalPore_get_is_setup(*args)
4090 def SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key():
4091 """SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key() -> FloatKey"""
4092 return _IMP_npctransport.SlabWithToroidalPore_get_minor_radius_h2v_aspect_ratio_key()
4094 def SlabWithToroidalPore_get_toroidal_pore_key():
4095 """SlabWithToroidalPore_get_toroidal_pore_key() -> IntKey"""
4096 return _IMP_npctransport.SlabWithToroidalPore_get_toroidal_pore_key()
4099 def __lshift__(*args):
4101 __lshift__(_ostream out, RelaxingSpring n) -> _ostream
4102 __lshift__(_ostream out, Transporting n) -> _ostream
4103 __lshift__(_ostream out, SlabWithPore n) -> _ostream
4104 __lshift__(_ostream out, SlabWithCylindricalPore n) -> _ostream
4105 __lshift__(_ostream out, SlabWithToroidalPore n) -> _ostream
4107 return _IMP_npctransport.__lshift__(*args)
4109 """Proxy of C++ IMP::npctransport::SlabWithCylindricalPorePairScore class."""
4111 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4114 """__init__(IMP::npctransport::SlabWithCylindricalPorePairScore self, double k) -> SlabWithCylindricalPorePairScore"""
4115 this = _IMP_npctransport.new_SlabWithCylindricalPorePairScore(k)
4117 self.this.append(this)
4118 except __builtin__.Exception:
4121 def get_displacement_direction(self, slab, v):
4122 """get_displacement_direction(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> Vector3D"""
4123 return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_direction(self, slab, v)
4126 def get_displacement_magnitude(self, slab, v):
4127 """get_displacement_magnitude(SlabWithCylindricalPorePairScore self, SlabWithCylindricalPore slab, Vector3D v) -> double"""
4128 return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_displacement_magnitude(self, slab, v)
4131 def do_get_inputs(self, m, pis):
4132 """do_get_inputs(SlabWithCylindricalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4133 return _IMP_npctransport.SlabWithCylindricalPorePairScore_do_get_inputs(self, m, pis)
4136 def get_version_info(self):
4137 """get_version_info(SlabWithCylindricalPorePairScore self) -> VersionInfo"""
4138 return _IMP_npctransport.SlabWithCylindricalPorePairScore_get_version_info(self)
4142 """__str__(SlabWithCylindricalPorePairScore self) -> std::string"""
4143 return _IMP_npctransport.SlabWithCylindricalPorePairScore___str__(self)
4147 """__repr__(SlabWithCylindricalPorePairScore self) -> std::string"""
4148 return _IMP_npctransport.SlabWithCylindricalPorePairScore___repr__(self)
4153 return _object_cast_to_SlabWithCylindricalPorePairScore(o)
4155 SlabWithCylindricalPorePairScore_swigregister = _IMP_npctransport.SlabWithCylindricalPorePairScore_swigregister
4156 SlabWithCylindricalPorePairScore_swigregister(SlabWithCylindricalPorePairScore)
4159 """Proxy of C++ IMP::npctransport::SlabWithToroidalPorePairScore class."""
4161 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4164 """__init__(IMP::npctransport::SlabWithToroidalPorePairScore self, double k) -> SlabWithToroidalPorePairScore"""
4165 this = _IMP_npctransport.new_SlabWithToroidalPorePairScore(k)
4167 self.this.append(this)
4168 except __builtin__.Exception:
4171 def do_get_inputs(self, m, pis):
4172 """do_get_inputs(SlabWithToroidalPorePairScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4173 return _IMP_npctransport.SlabWithToroidalPorePairScore_do_get_inputs(self, m, pis)
4176 def get_version_info(self):
4177 """get_version_info(SlabWithToroidalPorePairScore self) -> VersionInfo"""
4178 return _IMP_npctransport.SlabWithToroidalPorePairScore_get_version_info(self)
4182 """__str__(SlabWithToroidalPorePairScore self) -> std::string"""
4183 return _IMP_npctransport.SlabWithToroidalPorePairScore___str__(self)
4187 """__repr__(SlabWithToroidalPorePairScore self) -> std::string"""
4188 return _IMP_npctransport.SlabWithToroidalPorePairScore___repr__(self)
4193 return _object_cast_to_SlabWithToroidalPorePairScore(o)
4195 SlabWithToroidalPorePairScore_swigregister = _IMP_npctransport.SlabWithToroidalPorePairScore_swigregister
4196 SlabWithToroidalPorePairScore_swigregister(SlabWithToroidalPorePairScore)
4199 """Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreWireGeometry class."""
4201 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4203 def __init__(self, height, radius, length):
4204 """__init__(IMP::npctransport::SlabWithCylindricalPoreWireGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreWireGeometry"""
4205 this = _IMP_npctransport.new_SlabWithCylindricalPoreWireGeometry(height, radius, length)
4207 self.this.append(this)
4208 except __builtin__.Exception:
4211 def get_version_info(self):
4212 """get_version_info(SlabWithCylindricalPoreWireGeometry self) -> VersionInfo"""
4213 return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_get_version_info(self)
4217 """__str__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
4218 return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___str__(self)
4222 """__repr__(SlabWithCylindricalPoreWireGeometry self) -> std::string"""
4223 return _IMP_npctransport.SlabWithCylindricalPoreWireGeometry___repr__(self)
4228 return _object_cast_to_SlabWithCylindricalPoreWireGeometry(o)
4230 SlabWithCylindricalPoreWireGeometry_swigregister = _IMP_npctransport.SlabWithCylindricalPoreWireGeometry_swigregister
4231 SlabWithCylindricalPoreWireGeometry_swigregister(SlabWithCylindricalPoreWireGeometry)
4234 """Proxy of C++ IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry class."""
4236 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4238 def __init__(self, height, radius, length):
4239 """__init__(IMP::npctransport::SlabWithCylindricalPoreSurfaceGeometry self, double height, double radius, double length) -> SlabWithCylindricalPoreSurfaceGeometry"""
4240 this = _IMP_npctransport.new_SlabWithCylindricalPoreSurfaceGeometry(height, radius, length)
4242 self.this.append(this)
4243 except __builtin__.Exception:
4247 """__str__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
4248 return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___str__(self)
4252 """__repr__(SlabWithCylindricalPoreSurfaceGeometry self) -> std::string"""
4253 return _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry___repr__(self)
4258 return _object_cast_to_SlabWithCylindricalPoreSurfaceGeometry(o)
4260 __swig_destroy__ = _IMP_npctransport.delete_SlabWithCylindricalPoreSurfaceGeometry
4261 __del__ =
lambda self:
None
4262 SlabWithCylindricalPoreSurfaceGeometry_swigregister = _IMP_npctransport.SlabWithCylindricalPoreSurfaceGeometry_swigregister
4263 SlabWithCylindricalPoreSurfaceGeometry_swigregister(SlabWithCylindricalPoreSurfaceGeometry)
4266 """Proxy of C++ IMP::npctransport::SlabWithToroidalPoreWireGeometry class."""
4268 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4272 __init__(IMP::npctransport::SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double horizontal_semiaxis, double slab_length) -> SlabWithToroidalPoreWireGeometry
4273 __init__(IMP::npctransport::SlabWithToroidalPoreWireGeometry self, double slab_height, double major_radius, double slab_length) -> SlabWithToroidalPoreWireGeometry
4275 this = _IMP_npctransport.new_SlabWithToroidalPoreWireGeometry(*args)
4277 self.this.append(this)
4278 except __builtin__.Exception:
4281 def get_version_info(self):
4282 """get_version_info(SlabWithToroidalPoreWireGeometry self) -> VersionInfo"""
4283 return _IMP_npctransport.SlabWithToroidalPoreWireGeometry_get_version_info(self)
4287 """__str__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
4288 return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___str__(self)
4292 """__repr__(SlabWithToroidalPoreWireGeometry self) -> std::string"""
4293 return _IMP_npctransport.SlabWithToroidalPoreWireGeometry___repr__(self)
4298 return _object_cast_to_SlabWithToroidalPoreWireGeometry(o)
4300 SlabWithToroidalPoreWireGeometry_swigregister = _IMP_npctransport.SlabWithToroidalPoreWireGeometry_swigregister
4301 SlabWithToroidalPoreWireGeometry_swigregister(SlabWithToroidalPoreWireGeometry)
4304 """Proxy of C++ IMP::core::GenericAttributeSingletonScore<(IMP::core::Harmonic)> class."""
4306 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4307 __repr__ = _swig_repr
4310 """__init__(IMP::core::GenericAttributeSingletonScore<(IMP::core::Harmonic)> self, Harmonic f, FloatKey k) -> _GenericAttributeSingletonScoreForPoreRadus"""
4311 this = _IMP_npctransport.new__GenericAttributeSingletonScoreForPoreRadus(f, k)
4313 self.this.append(this)
4314 except __builtin__.Exception:
4317 def do_get_inputs(self, m, pis):
4318 """do_get_inputs(_GenericAttributeSingletonScoreForPoreRadus self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4319 return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_do_get_inputs(self, m, pis)
4322 def get_unary_function(self):
4323 """get_unary_function(_GenericAttributeSingletonScoreForPoreRadus self) -> Harmonic"""
4324 return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_unary_function(self)
4327 def get_version_info(self):
4328 """get_version_info(_GenericAttributeSingletonScoreForPoreRadus self) -> VersionInfo"""
4329 return _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_get_version_info(self)
4331 _GenericAttributeSingletonScoreForPoreRadus_swigregister = _IMP_npctransport._GenericAttributeSingletonScoreForPoreRadus_swigregister
4332 _GenericAttributeSingletonScoreForPoreRadus_swigregister(_GenericAttributeSingletonScoreForPoreRadus)
4334 class PoreRadiusSingletonScore(_GenericAttributeSingletonScoreForPoreRadus):
4335 """Proxy of C++ IMP::npctransport::PoreRadiusSingletonScore class."""
4337 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4340 """__init__(IMP::npctransport::PoreRadiusSingletonScore self, IMP::Float mean, IMP::Float k) -> PoreRadiusSingletonScore"""
4341 this = _IMP_npctransport.new_PoreRadiusSingletonScore(mean, k)
4343 self.this.append(this)
4344 except __builtin__.Exception:
4348 """set_k(PoreRadiusSingletonScore self, double k)"""
4349 return _IMP_npctransport.PoreRadiusSingletonScore_set_k(self, k)
4353 """__str__(PoreRadiusSingletonScore self) -> std::string"""
4354 return _IMP_npctransport.PoreRadiusSingletonScore___str__(self)
4358 """__repr__(PoreRadiusSingletonScore self) -> std::string"""
4359 return _IMP_npctransport.PoreRadiusSingletonScore___repr__(self)
4364 return _object_cast_to_PoreRadiusSingletonScore(o)
4366 PoreRadiusSingletonScore_swigregister = _IMP_npctransport.PoreRadiusSingletonScore_swigregister
4367 PoreRadiusSingletonScore_swigregister(PoreRadiusSingletonScore)
4370 """Proxy of C++ IMP::npctransport::ExcludeZRangeSingletonScore class."""
4372 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4374 def __init__(self, bottom, top, k):
4375 """__init__(IMP::npctransport::ExcludeZRangeSingletonScore self, double bottom, double top, double k) -> ExcludeZRangeSingletonScore"""
4376 this = _IMP_npctransport.new_ExcludeZRangeSingletonScore(bottom, top, k)
4378 self.this.append(this)
4379 except __builtin__.Exception:
4382 def get_bottom_z(self):
4383 """get_bottom_z(ExcludeZRangeSingletonScore self) -> double"""
4384 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_bottom_z(self)
4387 def get_top_z(self):
4388 """get_top_z(ExcludeZRangeSingletonScore self) -> double"""
4389 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_top_z(self)
4393 """get_k(ExcludeZRangeSingletonScore self) -> double"""
4394 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_k(self)
4397 def do_get_inputs(self, m, pis):
4398 """do_get_inputs(ExcludeZRangeSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4399 return _IMP_npctransport.ExcludeZRangeSingletonScore_do_get_inputs(self, m, pis)
4402 def get_version_info(self):
4403 """get_version_info(ExcludeZRangeSingletonScore self) -> VersionInfo"""
4404 return _IMP_npctransport.ExcludeZRangeSingletonScore_get_version_info(self)
4408 """__str__(ExcludeZRangeSingletonScore self) -> std::string"""
4409 return _IMP_npctransport.ExcludeZRangeSingletonScore___str__(self)
4413 """__repr__(ExcludeZRangeSingletonScore self) -> std::string"""
4414 return _IMP_npctransport.ExcludeZRangeSingletonScore___repr__(self)
4419 return _object_cast_to_ExcludeZRangeSingletonScore(o)
4421 ExcludeZRangeSingletonScore_swigregister = _IMP_npctransport.ExcludeZRangeSingletonScore_swigregister
4422 ExcludeZRangeSingletonScore_swigregister(ExcludeZRangeSingletonScore)
4425 """Proxy of C++ IMP::npctransport::ZBiasSingletonScore class."""
4427 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4431 __init__(IMP::npctransport::ZBiasSingletonScore self, double k, double max_r) -> ZBiasSingletonScore
4432 __init__(IMP::npctransport::ZBiasSingletonScore self, double k) -> ZBiasSingletonScore
4434 this = _IMP_npctransport.new_ZBiasSingletonScore(*args)
4436 self.this.append(this)
4437 except __builtin__.Exception:
4441 """get_k(ZBiasSingletonScore self) -> double"""
4442 return _IMP_npctransport.ZBiasSingletonScore_get_k(self)
4446 """set_k(ZBiasSingletonScore self, double k)"""
4447 return _IMP_npctransport.ZBiasSingletonScore_set_k(self, k)
4450 def do_get_inputs(self, m, pis):
4451 """do_get_inputs(ZBiasSingletonScore self, Model m, IMP::ParticleIndexes const & pis) -> IMP::ModelObjectsTemp"""
4452 return _IMP_npctransport.ZBiasSingletonScore_do_get_inputs(self, m, pis)
4455 def get_version_info(self):
4456 """get_version_info(ZBiasSingletonScore self) -> VersionInfo"""
4457 return _IMP_npctransport.ZBiasSingletonScore_get_version_info(self)
4461 """__str__(ZBiasSingletonScore self) -> std::string"""
4462 return _IMP_npctransport.ZBiasSingletonScore___str__(self)
4466 """__repr__(ZBiasSingletonScore self) -> std::string"""
4467 return _IMP_npctransport.ZBiasSingletonScore___repr__(self)
4472 return _object_cast_to_ZBiasSingletonScore(o)
4474 ZBiasSingletonScore_swigregister = _IMP_npctransport.ZBiasSingletonScore_swigregister
4475 ZBiasSingletonScore_swigregister(ZBiasSingletonScore)
4478 """Proxy of C++ IMP::npctransport::BodyStatisticsOptimizerState class."""
4480 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4482 def __init__(self, p, statistics_manager=None, periodicity=1):
4484 __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None, unsigned int periodicity=1) -> BodyStatisticsOptimizerState
4485 __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p, Statistics statistics_manager=None) -> BodyStatisticsOptimizerState
4486 __init__(IMP::npctransport::BodyStatisticsOptimizerState self, Particle p) -> BodyStatisticsOptimizerState
4488 this = _IMP_npctransport.new_BodyStatisticsOptimizerState(p, statistics_manager, periodicity)
4490 self.this.append(this)
4491 except __builtin__.Exception:
4494 def get_correlation_time(self):
4495 """get_correlation_time(BodyStatisticsOptimizerState self) -> double"""
4496 return _IMP_npctransport.BodyStatisticsOptimizerState_get_correlation_time(self)
4500 """get_diffusion_coefficient(BodyStatisticsOptimizerState self) -> double"""
4501 return _IMP_npctransport.BodyStatisticsOptimizerState_get_diffusion_coefficient(self)
4504 def update_particle_type_zr_distribution_map(self):
4505 """update_particle_type_zr_distribution_map(BodyStatisticsOptimizerState self)"""
4506 return _IMP_npctransport.BodyStatisticsOptimizerState_update_particle_type_zr_distribution_map(self)
4509 def do_update(self, call_num):
4510 """do_update(BodyStatisticsOptimizerState self, unsigned int call_num)"""
4511 return _IMP_npctransport.BodyStatisticsOptimizerState_do_update(self, call_num)
4514 def get_version_info(self):
4515 """get_version_info(BodyStatisticsOptimizerState self) -> VersionInfo"""
4516 return _IMP_npctransport.BodyStatisticsOptimizerState_get_version_info(self)
4520 """__str__(BodyStatisticsOptimizerState self) -> std::string"""
4521 return _IMP_npctransport.BodyStatisticsOptimizerState___str__(self)
4525 """__repr__(BodyStatisticsOptimizerState self) -> std::string"""
4526 return _IMP_npctransport.BodyStatisticsOptimizerState___repr__(self)
4531 return _object_cast_to_BodyStatisticsOptimizerState(o)
4533 BodyStatisticsOptimizerState_swigregister = _IMP_npctransport.BodyStatisticsOptimizerState_swigregister
4534 BodyStatisticsOptimizerState_swigregister(BodyStatisticsOptimizerState)
4537 """Proxy of C++ IMP::npctransport::ParticleTransportStatisticsOptimizerState class."""
4539 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4541 def __init__(self, p, bottom_z, top_z, statistics_manager=0, owner=0):
4543 __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z, WeakPointer< IMP::npctransport::Statistics > statistics_manager=0, WeakPointer< IMP::atom::Simulator > owner=0) -> ParticleTransportStatisticsOptimizerState
4544 __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z, WeakPointer< IMP::npctransport::Statistics > statistics_manager=0) -> ParticleTransportStatisticsOptimizerState
4545 __init__(IMP::npctransport::ParticleTransportStatisticsOptimizerState self, Particle p, IMP::Float bottom_z, IMP::Float top_z) -> ParticleTransportStatisticsOptimizerState
4547 this = _IMP_npctransport.new_ParticleTransportStatisticsOptimizerState(p, bottom_z, top_z, statistics_manager, owner)
4549 self.this.append(this)
4550 except __builtin__.Exception:
4553 def set_owner(self, owner):
4554 """set_owner(ParticleTransportStatisticsOptimizerState self, WeakPointer< IMP::atom::Simulator > owner)"""
4555 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_set_owner(self, owner)
4558 def get_owner(self):
4559 """get_owner(ParticleTransportStatisticsOptimizerState self) -> WeakPointer< IMP::atom::Simulator >"""
4560 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_owner(self)
4563 def get_n_transports_up(self):
4564 """get_n_transports_up(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4565 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_up(self)
4568 def get_n_transports_down(self):
4569 """get_n_transports_down(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4570 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_n_transports_down(self)
4573 def get_total_n_transports(self):
4574 """get_total_n_transports(ParticleTransportStatisticsOptimizerState self) -> unsigned int"""
4575 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_total_n_transports(self)
4578 def get_transport_time_points_in_ns(self):
4579 """get_transport_time_points_in_ns(ParticleTransportStatisticsOptimizerState self) -> IMP::Floats const &"""
4580 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_transport_time_points_in_ns(self)
4583 def do_update(self, call_num):
4584 """do_update(ParticleTransportStatisticsOptimizerState self, unsigned int call_num)"""
4585 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_do_update(self, call_num)
4588 def get_version_info(self):
4589 """get_version_info(ParticleTransportStatisticsOptimizerState self) -> VersionInfo"""
4590 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState_get_version_info(self)
4594 """__str__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4595 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___str__(self)
4599 """__repr__(ParticleTransportStatisticsOptimizerState self) -> std::string"""
4600 return _IMP_npctransport.ParticleTransportStatisticsOptimizerState___repr__(self)
4605 return _object_cast_to_ParticleTransportStatisticsOptimizerState(o)
4607 ParticleTransportStatisticsOptimizerState_swigregister = _IMP_npctransport.ParticleTransportStatisticsOptimizerState_swigregister
4608 ParticleTransportStatisticsOptimizerState_swigregister(ParticleTransportStatisticsOptimizerState)
4611 """Proxy of C++ IMP::npctransport::ChainStatisticsOptimizerState class."""
4613 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4615 def __init__(self, ps, periodicity=1):
4617 __init__(IMP::npctransport::ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps, unsigned int periodicity=1) -> ChainStatisticsOptimizerState
4618 __init__(IMP::npctransport::ChainStatisticsOptimizerState self, IMP::ParticlesTemp const & ps) -> ChainStatisticsOptimizerState
4620 this = _IMP_npctransport.new_ChainStatisticsOptimizerState(ps, periodicity)
4622 self.this.append(this)
4623 except __builtin__.Exception:
4626 def get_correlation_time(self):
4627 """get_correlation_time(ChainStatisticsOptimizerState self) -> double"""
4628 return _IMP_npctransport.ChainStatisticsOptimizerState_get_correlation_time(self)
4631 def get_local_diffusion_coefficients(self):
4632 """get_local_diffusion_coefficients(ChainStatisticsOptimizerState self) -> IMP::Floats"""
4633 return _IMP_npctransport.ChainStatisticsOptimizerState_get_local_diffusion_coefficients(self)
4637 """get_diffusion_coefficient(ChainStatisticsOptimizerState self) -> double"""
4638 return _IMP_npctransport.ChainStatisticsOptimizerState_get_diffusion_coefficient(self)
4641 def get_mean_radius_of_gyration(self):
4642 """get_mean_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4643 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_radius_of_gyration(self)
4646 def get_mean_square_radius_of_gyration(self):
4647 """get_mean_square_radius_of_gyration(ChainStatisticsOptimizerState self) -> double"""
4648 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_radius_of_gyration(self)
4651 def get_mean_end_to_end_distance(self):
4652 """get_mean_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4653 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_end_to_end_distance(self)
4656 def get_mean_square_end_to_end_distance(self):
4657 """get_mean_square_end_to_end_distance(ChainStatisticsOptimizerState self) -> double"""
4658 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_end_to_end_distance(self)
4661 def get_mean_bond_distance(self):
4662 """get_mean_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4663 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_bond_distance(self)
4666 def get_mean_square_bond_distance(self):
4667 """get_mean_square_bond_distance(ChainStatisticsOptimizerState self) -> double"""
4668 return _IMP_npctransport.ChainStatisticsOptimizerState_get_mean_square_bond_distance(self)
4671 def do_update(self, call_num):
4672 """do_update(ChainStatisticsOptimizerState self, unsigned int call_num)"""
4673 return _IMP_npctransport.ChainStatisticsOptimizerState_do_update(self, call_num)
4676 def get_version_info(self):
4677 """get_version_info(ChainStatisticsOptimizerState self) -> VersionInfo"""
4678 return _IMP_npctransport.ChainStatisticsOptimizerState_get_version_info(self)
4682 """__str__(ChainStatisticsOptimizerState self) -> std::string"""
4683 return _IMP_npctransport.ChainStatisticsOptimizerState___str__(self)
4687 """__repr__(ChainStatisticsOptimizerState self) -> std::string"""
4688 return _IMP_npctransport.ChainStatisticsOptimizerState___repr__(self)
4693 return _object_cast_to_ChainStatisticsOptimizerState(o)
4695 ChainStatisticsOptimizerState_swigregister = _IMP_npctransport.ChainStatisticsOptimizerState_swigregister
4696 ChainStatisticsOptimizerState_swigregister(ChainStatisticsOptimizerState)
4699 """Proxy of C++ IMP::npctransport::BipartitePairsStatisticsOptimizerState class."""
4701 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4703 def __init__(self, statistics_manager, interaction_type, particlesI, particlesII, contact_range=1.0, slack=1.0):
4705 __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII, double contact_range=1.0, double slack=1.0) -> BipartitePairsStatisticsOptimizerState
4706 __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII, double contact_range=1.0) -> BipartitePairsStatisticsOptimizerState
4707 __init__(IMP::npctransport::BipartitePairsStatisticsOptimizerState self, Statistics statistics_manager, IMP::npctransport::InteractionType interaction_type, IMP::ParticlesTemp const & particlesI, IMP::ParticlesTemp const & particlesII) -> BipartitePairsStatisticsOptimizerState
4709 this = _IMP_npctransport.new_BipartitePairsStatisticsOptimizerState(statistics_manager, interaction_type, particlesI, particlesII, contact_range, slack)
4711 self.this.append(this)
4712 except __builtin__.Exception:
4715 def get_interaction_type(self):
4716 """get_interaction_type(BipartitePairsStatisticsOptimizerState self) -> IMP::npctransport::InteractionType"""
4717 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_interaction_type(self)
4720 def get_average_number_of_contacts(self):
4721 """get_average_number_of_contacts(BipartitePairsStatisticsOptimizerState self) -> double"""
4722 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_number_of_contacts(self)
4725 def get_average_off_per_contact_per_ns(self):
4726 """get_average_off_per_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4727 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_contact_per_ns(self)
4730 def get_average_off_per_bound_I_per_ns(self):
4731 """get_average_off_per_bound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4732 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_I_per_ns(self)
4735 def get_average_off_per_bound_II_per_ns(self):
4736 """get_average_off_per_bound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4737 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_off_per_bound_II_per_ns(self)
4740 def get_average_on_per_missing_contact_per_ns(self):
4741 """get_average_on_per_missing_contact_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4742 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_missing_contact_per_ns(self)
4745 def get_average_on_per_unbound_I_per_ns(self):
4746 """get_average_on_per_unbound_I_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4747 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_I_per_ns(self)
4750 def get_average_on_per_unbound_II_per_ns(self):
4751 """get_average_on_per_unbound_II_per_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4752 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_on_per_unbound_II_per_ns(self)
4755 def get_average_fraction_bound_particles_I(self):
4756 """get_average_fraction_bound_particles_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4757 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_I(self)
4760 def get_average_fraction_bound_particles_II(self):
4761 """get_average_fraction_bound_particles_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4762 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particles_II(self)
4765 def get_average_fraction_bound_particle_sites_I(self):
4766 """get_average_fraction_bound_particle_sites_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4767 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_I(self)
4770 def get_average_fraction_bound_particle_sites_II(self):
4771 """get_average_fraction_bound_particle_sites_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4772 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_bound_particle_sites_II(self)
4775 def get_average_fraction_nonspecific_interactions_I(self):
4776 """get_average_fraction_nonspecific_interactions_I(BipartitePairsStatisticsOptimizerState self) -> double"""
4777 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_I(self)
4780 def get_average_fraction_nonspecific_interactions_II(self):
4781 """get_average_fraction_nonspecific_interactions_II(BipartitePairsStatisticsOptimizerState self) -> double"""
4782 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_average_fraction_nonspecific_interactions_II(self)
4785 def get_number_of_particles_1(self):
4786 """get_number_of_particles_1(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4787 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_1(self)
4790 def get_number_of_particles_2(self):
4791 """get_number_of_particles_2(BipartitePairsStatisticsOptimizerState self) -> IMP::Int"""
4792 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_number_of_particles_2(self)
4795 def get_misc_stats_period_ns(self):
4796 """get_misc_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4797 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_misc_stats_period_ns(self)
4800 def get_off_stats_period_ns(self):
4801 """get_off_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4802 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_stats_period_ns(self)
4805 def get_off_I_stats_period_ns(self):
4806 """get_off_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4807 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_I_stats_period_ns(self)
4810 def get_off_II_stats_period_ns(self):
4811 """get_off_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4812 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_off_II_stats_period_ns(self)
4815 def get_on_stats_period_ns(self):
4816 """get_on_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4817 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_stats_period_ns(self)
4820 def get_on_I_stats_period_ns(self):
4821 """get_on_I_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4822 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_I_stats_period_ns(self)
4825 def get_on_II_stats_period_ns(self):
4826 """get_on_II_stats_period_ns(BipartitePairsStatisticsOptimizerState self) -> double"""
4827 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_on_II_stats_period_ns(self)
4830 def get_version_info(self):
4831 """get_version_info(BipartitePairsStatisticsOptimizerState self) -> VersionInfo"""
4832 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState_get_version_info(self)
4836 """__str__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4837 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___str__(self)
4841 """__repr__(BipartitePairsStatisticsOptimizerState self) -> std::string"""
4842 return _IMP_npctransport.BipartitePairsStatisticsOptimizerState___repr__(self)
4847 return _object_cast_to_BipartitePairsStatisticsOptimizerState(o)
4849 BipartitePairsStatisticsOptimizerState_swigregister = _IMP_npctransport.BipartitePairsStatisticsOptimizerState_swigregister
4850 BipartitePairsStatisticsOptimizerState_swigregister(BipartitePairsStatisticsOptimizerState)
4853 def get_close_pairs_range(*args):
4855 get_close_pairs_range(double max_range, double max_range_factor) -> double
4856 get_close_pairs_range(::npctransport_proto::Assignment const & config) -> double
4858 return _IMP_npctransport.get_close_pairs_range(*args)
4862 get_time_step(double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1, double time_step_factor=1.0) -> double
4863 get_time_step(double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1) -> double
4864 get_time_step(double max_d_factor, double max_k, double min_radius, double min_range) -> double
4865 get_time_step(::npctransport_proto::Assignment const & config, double max_trans_relative_to_radius=0.1) -> double
4866 get_time_step(::npctransport_proto::Assignment const & config) -> double
4868 return _IMP_npctransport.get_time_step(*args)
4871 """get_frames_from_ns(double ns, double time_step) -> int"""
4872 return _IMP_npctransport.get_frames_from_ns(ns, time_step)
4875 """get_number_of_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4876 return _IMP_npctransport.get_number_of_frames(config, time_step)
4879 """get_dump_interval_in_frames(::npctransport_proto::Assignment const & config, double time_step) -> int"""
4880 return _IMP_npctransport.get_dump_interval_in_frames(config, time_step)
4884 get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=0.1) -> int
4885 get_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step) -> int
4887 return _IMP_npctransport.get_statistics_interval_in_frames(assign, time_step, default_value_ns)
4891 get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step, double default_value_ns=1.0) -> int
4892 get_output_statistics_interval_in_frames(::npctransport_proto::Assignment const & assign, double time_step) -> int
4894 return _IMP_npctransport.get_output_statistics_interval_in_frames(assign, time_step, default_value_ns)
4898 initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0, bool is_disable_randomize=False, bool are_fgs_pre_initialized=False)
4899 initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0, bool is_disable_randomize=False)
4900 initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False, double short_init_factor=1.0)
4901 initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints, bool debug=False)
4902 initialize_positions(SimulationData sd, IMP::RestraintsTemp const & extra_restraints)
4903 initialize_positions(SimulationData sd)
4905 return _IMP_npctransport.initialize_positions(*args)
4906 class Avro2PBReader(object):
4907 """Proxy of C++ IMP::npctransport::Avro2PBReader class."""
4909 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
4913 __init__(IMP::npctransport::Avro2PBReader self, IMP::Strings const & avro_filenames) -> Avro2PBReader
4914 __init__(IMP::npctransport::Avro2PBReader self, std::string avro_filename) -> Avro2PBReader
4916 this = _IMP_npctransport.new_Avro2PBReader(*args)
4918 self.this.append(this)
4919 except __builtin__.Exception:
4921 __swig_destroy__ = _IMP_npctransport.delete_Avro2PBReader
4922 __del__ =
lambda self:
None
4924 def read_next(self):
4925 """read_next(Avro2PBReader self) -> IMP::npctransport::Avro2PBReader::ByteBuffer"""
4926 return _IMP_npctransport.Avro2PBReader_read_next(self)
4929 def get_is_valid(self):
4930 """get_is_valid(Avro2PBReader self) -> bool"""
4931 return _IMP_npctransport.Avro2PBReader_get_is_valid(self)
4934 def get_cur_file_name(self):
4935 """get_cur_file_name(Avro2PBReader self) -> std::string"""
4936 return _IMP_npctransport.Avro2PBReader_get_cur_file_name(self)
4939 def show(self, *args):
4941 show(Avro2PBReader self, _ostream out)
4942 show(Avro2PBReader self)
4944 return _IMP_npctransport.Avro2PBReader_show(self, *args)
4948 """__str__(Avro2PBReader self) -> std::string"""
4949 return _IMP_npctransport.Avro2PBReader___str__(self)
4953 """__repr__(Avro2PBReader self) -> std::string"""
4954 return _IMP_npctransport.Avro2PBReader___repr__(self)
4956 Avro2PBReader_swigregister = _IMP_npctransport.Avro2PBReader_swigregister
4957 Avro2PBReader_swigregister(Avro2PBReader)
4961 """get_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4962 return _IMP_npctransport.get_optimizable_particles(particles)
4965 """get_non_optimizable_particles(IMP::ParticlesTemp const & particles) -> IMP::ParticlesTemp"""
4966 return _IMP_npctransport.get_non_optimizable_particles(particles)
4969 """get_particle_indexes(IMP::ParticlesTemp const & particles) -> IMP::ParticleIndexes"""
4970 return _IMP_npctransport.get_particle_indexes(particles)
4973 """get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)"""
4974 return _IMP_npctransport.get_protobuf_configuration_from_text(config_txt, config_pb)
4977 """get_spheres_from_vectors(IMP::algebra::Vector3Ds const & vs, double radius) -> IMP::algebra::Sphere3Ds"""
4978 return _IMP_npctransport.get_spheres_from_vectors(vs, radius)
4980 def get_spheres_centers(spheres):
4981 """get_spheres_centers(IMP::algebra::Sphere3Ds const & spheres) -> IMP::algebra::Vector3Ds"""
4982 return _IMP_npctransport.get_spheres_centers(spheres)
4985 """copy_particle_reference_frame_if_applicable(Particle src_p, Particle trg_p)"""
4986 return _IMP_npctransport.copy_particle_reference_frame_if_applicable(src_p, trg_p)
4989 """copy_hierarchy_reference_frame_recursive(Particle src_p, Particle trg_p)"""
4990 return _IMP_npctransport.copy_hierarchy_reference_frame_recursive(src_p, trg_p)
4993 """copy_FGs_coordinates(SimulationData src_sd, SimulationData trg_sd)"""
4994 return _IMP_npctransport.copy_FGs_coordinates(src_sd, trg_sd)
4997 from .npctransport_pb2
import *
4998 import google.protobuf
5000 print(
"no protobuf support in python")
5001 from ._configuration
import *
5005 """get_module_version() -> std::string const"""
5006 return _IMP_npctransport.get_module_version()
5009 """get_example_path(std::string fname) -> std::string"""
5010 return _IMP_npctransport.get_example_path(fname)
5013 """get_data_path(std::string fname) -> std::string"""
5014 return _IMP_npctransport.get_data_path(fname)
5016 from .
import _version_check
Abstract class for scoring object(s) of type ParticleIndexPair.
CheckLevel get_check_level()
Get the current audit mode.
FGChain * create_fg_chain(IMP::npctransport::SimulationData *sd, atom::Hierarchy parent, const ::npctransport_proto::Assignment_FGAssignment &fg_data, display::Color c)
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
void add_hierarchy_with_sites(RMF::FileHandle fh, atom::Hierarchy hs)
Various classes to hold sets of particles.
int assign_ranges(std::string input_config_fname, std::string output_assignment_fname, unsigned int work_unit, bool show_steps, boost::uint64_t random_seed)
The base class for geometry.
int get_output_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=1.0)
IMP::ParticleIndexPair make_unordered_particle_index_pair(IMP::ParticleIndex pi0, IMP::ParticleIndex pi1)
A base class for geometry from a set of particles.
double get_time_step(double max_d_factor, double max_k, double min_radius, double min_range, double max_trans_relative_to_radius=0.1, double time_step_factor=1.0)
Make CGAL functionality available to IMP.
void copy_FGs_coordinates(SimulationData const *src_sd, SimulationData *trg_sd)
copy coordinates of src_sd to trg_sd for FG repeats only
std::string get_module_version()
Return the version of this module, as a string.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
int get_statistics_interval_in_frames(const ::npctransport_proto::Assignment &assign, double time_step, double default_value_ns=0.1)
void get_protobuf_configuration_from_text(std::string config_txt, std::string config_pb)
void copy_hierarchy_reference_frame_recursive(Particle *src_p, Particle *trg_p)
Simple Brownian dynamics simulator.
Composable functors to implement scores via compile-time composition.
Code to compute statistical measures.
void link_hierarchies_with_sites(RMF::FileConstHandle fh, const atom::Hierarchies &hs)
ParticlesTemp get_non_optimizable_particles(ParticlesTemp const &particles)
void copy_particle_reference_frame_if_applicable(Particle *src_p, Particle *trg_p)
Common base class for heavy weight IMP objects.
ParticleIndexes get_particle_indexes(ParticlesTemp const &particles)
int get_number_of_frames(const ::npctransport_proto::Assignment &config, double time_step)
Abstract class for scoring object(s) of type ParticleIndex.
int get_frames_from_ns(double ns, double time_step)
Basic utilities for handling cryo-electron microscopy 3D density maps.
void initialize_positions(SimulationData *sd, const RestraintsTemp &extra_restraints=RestraintsTemp(), bool debug=false, double short_init_factor=1.0, bool is_disable_randomize=false, bool are_fgs_pre_initialized=false)
Interface to specialized Particle types (e.g. atoms)
std::ostream & show(Hierarchy h, std::ostream &out=std::cout)
Print the hierarchy using a given decorator to display each node.
ParticlesTemp get_optimizable_particles(ParticlesTemp const &particles)
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...
int get_dump_interval_in_frames(const ::npctransport_proto::Assignment &config, double time_step)
atom::Hierarchies create_hierarchies_with_sites(RMF::FileConstHandle fh, Model *m)
Shared optimizer state that is invoked upon commitment of new coordinates.
Hierarchy get_root(Hierarchy h)
Return the root of the hierarchy.
void add_hierarchies_with_sites(RMF::FileHandle fh, const atom::Hierarchies &hs)
InteractionType make_unordered_interaction_type(IMP::core::ParticleType t0, IMP::core::ParticleType t1)
double get_diffusion_coefficient(const algebra::Vector3Ds &displacements, double dt)
FGChain * get_fg_chain(atom::Hierarchy root)
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
Support for developing and analyzing benchmarks of IMP code.
InteractionType make_ordered_interaction_type(IMP::core::ParticleType t0, IMP::core::ParticleType t1)
convenience method for creating and interaction type in swig
Support for the RMF file format for storing hierarchical molecular data and markup.
Support for small angle X-ray scattering (SAXS) data.
void set_check_level(CheckLevel tf)
Control runtime checks in the code.
Display an IMP::core::XYZR particle as a ball.
void add_test_sites(RMF::FileHandle fh, core::ParticleType t, double display_radius, algebra::Vector3Ds sites)
Inferential scoring building on methods developed as part of the Inferential Structure Determination ...
algebra::Sphere3Ds get_spheres_from_vectors(V3iter first, V3iter last, double radius)
convert vectors to spheres of passed radius