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_modeller')).lstrip(
'.')
22 return importlib.import_module(mname)
24 return importlib.import_module(
'_IMP_modeller')
25 _IMP_modeller = 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_modeller', [dirname(__file__)])
39 _mod = imp.load_module(
'_IMP_modeller', fp, pathname, description)
43 _IMP_modeller = swig_import_helper()
44 del swig_import_helper
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_MODELLER_SwigPyIterator(object):
114 """Proxy of C++ swig::IMP_MODELLER_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_modeller.delete_IMP_MODELLER_SwigPyIterator
122 __del__ =
lambda self:
None
125 """value(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
126 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_value(self)
131 incr(IMP_MODELLER_SwigPyIterator self, size_t n=1) -> IMP_MODELLER_SwigPyIterator
132 incr(IMP_MODELLER_SwigPyIterator self) -> IMP_MODELLER_SwigPyIterator
134 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_incr(self, n)
139 decr(IMP_MODELLER_SwigPyIterator self, size_t n=1) -> IMP_MODELLER_SwigPyIterator
140 decr(IMP_MODELLER_SwigPyIterator self) -> IMP_MODELLER_SwigPyIterator
142 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_decr(self, n)
145 def distance(self, x):
146 """distance(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> ptrdiff_t"""
147 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_distance(self, x)
151 """equal(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> bool"""
152 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_equal(self, x)
156 """copy(IMP_MODELLER_SwigPyIterator self) -> IMP_MODELLER_SwigPyIterator"""
157 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_copy(self)
161 """next(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
162 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_next(self)
166 """__next__(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
167 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___next__(self)
171 """previous(IMP_MODELLER_SwigPyIterator self) -> PyObject *"""
172 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_previous(self)
175 def advance(self, n):
176 """advance(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
177 return _IMP_modeller.IMP_MODELLER_SwigPyIterator_advance(self, n)
181 """__eq__(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> bool"""
182 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___eq__(self, x)
186 """__ne__(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> bool"""
187 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___ne__(self, x)
190 def __iadd__(self, n):
191 """__iadd__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
192 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___iadd__(self, n)
195 def __isub__(self, n):
196 """__isub__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
197 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___isub__(self, n)
200 def __add__(self, n):
201 """__add__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator"""
202 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___add__(self, n)
205 def __sub__(self, *args):
207 __sub__(IMP_MODELLER_SwigPyIterator self, ptrdiff_t n) -> IMP_MODELLER_SwigPyIterator
208 __sub__(IMP_MODELLER_SwigPyIterator self, IMP_MODELLER_SwigPyIterator x) -> ptrdiff_t
210 return _IMP_modeller.IMP_MODELLER_SwigPyIterator___sub__(self, *args)
214 IMP_MODELLER_SwigPyIterator_swigregister = _IMP_modeller.IMP_MODELLER_SwigPyIterator_swigregister
215 IMP_MODELLER_SwigPyIterator_swigregister(IMP_MODELLER_SwigPyIterator)
223 IMP_DEBUG = _IMP_modeller.IMP_DEBUG
224 IMP_RELEASE = _IMP_modeller.IMP_RELEASE
225 IMP_SILENT = _IMP_modeller.IMP_SILENT
226 IMP_PROGRESS = _IMP_modeller.IMP_PROGRESS
227 IMP_TERSE = _IMP_modeller.IMP_TERSE
228 IMP_VERBOSE = _IMP_modeller.IMP_VERBOSE
229 IMP_MEMORY = _IMP_modeller.IMP_MEMORY
230 IMP_NONE = _IMP_modeller.IMP_NONE
231 IMP_USAGE = _IMP_modeller.IMP_USAGE
232 IMP_INTERNAL = _IMP_modeller.IMP_INTERNAL
233 IMP_KERNEL_HAS_LOG4CXX = _IMP_modeller.IMP_KERNEL_HAS_LOG4CXX
234 IMP_COMPILER_HAS_AUTO = _IMP_modeller.IMP_COMPILER_HAS_AUTO
235 IMP_COMPILER_HAS_DEBUG_VECTOR = _IMP_modeller.IMP_COMPILER_HAS_DEBUG_VECTOR
236 IMP_COMPILER_HAS_UNIQUE_PTR = _IMP_modeller.IMP_COMPILER_HAS_UNIQUE_PTR
237 IMP_KERNEL_HAS_BOOST_RANDOM = _IMP_modeller.IMP_KERNEL_HAS_BOOST_RANDOM
238 IMP_KERNEL_HAS_GPERFTOOLS = _IMP_modeller.IMP_KERNEL_HAS_GPERFTOOLS
239 IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER = _IMP_modeller.IMP_KERNEL_HAS_TCMALLOC_HEAPCHECKER
240 IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER = _IMP_modeller.IMP_KERNEL_HAS_TCMALLOC_HEAPPROFILER
241 IMPKERNEL_SHOW_WARNINGS = _IMP_modeller.IMPKERNEL_SHOW_WARNINGS
244 class _DirectorObjects(object):
245 """@internal Simple class to keep references to director objects
246 to prevent premature deletion."""
249 def register(self, obj):
250 """Take a reference to a director object; will only work for
251 refcounted C++ classes"""
252 if hasattr(obj,
'get_ref_count'):
253 self._objects.append(obj)
255 """Only drop our reference and allow cleanup by Python if no other
256 Python references exist (we hold 3 references: one in self._objects,
257 one in x, and one in the argument list for getrefcount) *and* no
258 other C++ references exist (the Python object always holds one)"""
259 objs = [x
for x
in self._objects
if sys.getrefcount(x) > 3 \
260 or x.get_ref_count() > 1]
264 def get_object_count(self):
265 """Get number of director objects (useful for testing only)"""
266 return len(self._objects)
267 _director_objects = _DirectorObjects()
269 class _ostream(object):
270 """Proxy of C++ std::ostream class."""
272 thisown = _swig_property(
lambda x: x.this.own(),
lambda x, v: x.this.own(v), doc=
'The membership flag')
274 def __init__(self, *args, **kwargs):
275 raise AttributeError(
"No constructor defined")
276 __repr__ = _swig_repr
278 def write(self, osa_buf):
279 """write(_ostream self, char const * osa_buf)"""
280 return _IMP_modeller._ostream_write(self, osa_buf)
282 _ostream_swigregister = _IMP_modeller._ostream_swigregister
283 _ostream_swigregister(_ostream)
285 IMP_COMPILER_HAS_OVERRIDE = _IMP_modeller.IMP_COMPILER_HAS_OVERRIDE
286 IMP_COMPILER_HAS_FINAL = _IMP_modeller.IMP_COMPILER_HAS_FINAL
287 IMP_HAS_NOEXCEPT = _IMP_modeller.IMP_HAS_NOEXCEPT
288 IMP_C_OPEN_BINARY = _IMP_modeller.IMP_C_OPEN_BINARY
290 IMP_CGAL_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_CGAL_HAS_BOOST_FILESYSTEM
291 IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_CGAL_HAS_BOOST_PROGRAMOPTIONS
292 IMP_CGAL_HAS_BOOST_RANDOM = _IMP_modeller.IMP_CGAL_HAS_BOOST_RANDOM
293 IMP_CGAL_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_CGAL_HAS_BOOST_SYSTEM
294 IMPCGAL_SHOW_WARNINGS = _IMP_modeller.IMPCGAL_SHOW_WARNINGS
296 IMP_ALGEBRA_HAS_IMP_CGAL = _IMP_modeller.IMP_ALGEBRA_HAS_IMP_CGAL
297 IMP_ALGEBRA_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_FILESYSTEM
298 IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_PROGRAMOPTIONS
299 IMP_ALGEBRA_HAS_BOOST_RANDOM = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_RANDOM
300 IMP_ALGEBRA_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_ALGEBRA_HAS_BOOST_SYSTEM
301 IMP_ALGEBRA_HAS_CGAL = _IMP_modeller.IMP_ALGEBRA_HAS_CGAL
302 IMP_ALGEBRA_HAS_ANN = _IMP_modeller.IMP_ALGEBRA_HAS_ANN
303 IMPALGEBRA_SHOW_WARNINGS = _IMP_modeller.IMPALGEBRA_SHOW_WARNINGS
305 IMP_DISPLAY_HAS_IMP_CGAL = _IMP_modeller.IMP_DISPLAY_HAS_IMP_CGAL
306 IMP_DISPLAY_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_FILESYSTEM
307 IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_PROGRAMOPTIONS
308 IMP_DISPLAY_HAS_BOOST_RANDOM = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_RANDOM
309 IMP_DISPLAY_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_DISPLAY_HAS_BOOST_SYSTEM
310 IMP_DISPLAY_HAS_CGAL = _IMP_modeller.IMP_DISPLAY_HAS_CGAL
311 IMPDISPLAY_SHOW_WARNINGS = _IMP_modeller.IMPDISPLAY_SHOW_WARNINGS
313 IMP_SCORE_FUNCTOR_HAS_IMP_CGAL = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_IMP_CGAL
314 IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_FILESYSTEM
315 IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_PROGRAMOPTIONS
316 IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_RANDOM
317 IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_BOOST_SYSTEM
318 IMP_SCORE_FUNCTOR_HAS_CGAL = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_CGAL
319 IMP_SCORE_FUNCTOR_HAS_HDF5 = _IMP_modeller.IMP_SCORE_FUNCTOR_HAS_HDF5
320 IMPSCOREFUNCTOR_SHOW_WARNINGS = _IMP_modeller.IMPSCOREFUNCTOR_SHOW_WARNINGS
322 IMP_CORE_HAS_IMP_CGAL = _IMP_modeller.IMP_CORE_HAS_IMP_CGAL
323 IMP_CORE_HAS_IMP_KERNEL = _IMP_modeller.IMP_CORE_HAS_IMP_KERNEL
324 IMP_CORE_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_CORE_HAS_BOOST_FILESYSTEM
325 IMP_CORE_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_CORE_HAS_BOOST_PROGRAMOPTIONS
326 IMP_CORE_HAS_BOOST_RANDOM = _IMP_modeller.IMP_CORE_HAS_BOOST_RANDOM
327 IMP_CORE_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_CORE_HAS_BOOST_SYSTEM
328 IMP_CORE_HAS_CGAL = _IMP_modeller.IMP_CORE_HAS_CGAL
329 IMP_CORE_HAS_HDF5 = _IMP_modeller.IMP_CORE_HAS_HDF5
330 IMPCORE_SHOW_WARNINGS = _IMP_modeller.IMPCORE_SHOW_WARNINGS
332 IMP_MODELLER_HAS_IMP_ALGEBRA = _IMP_modeller.IMP_MODELLER_HAS_IMP_ALGEBRA
333 IMP_MODELLER_HAS_IMP_CGAL = _IMP_modeller.IMP_MODELLER_HAS_IMP_CGAL
334 IMP_MODELLER_HAS_IMP_DISPLAY = _IMP_modeller.IMP_MODELLER_HAS_IMP_DISPLAY
335 IMP_MODELLER_HAS_IMP_KERNEL = _IMP_modeller.IMP_MODELLER_HAS_IMP_KERNEL
336 IMP_MODELLER_HAS_IMP_SCORE_FUNCTOR = _IMP_modeller.IMP_MODELLER_HAS_IMP_SCORE_FUNCTOR
337 IMP_MODELLER_HAS_BOOST_FILESYSTEM = _IMP_modeller.IMP_MODELLER_HAS_BOOST_FILESYSTEM
338 IMP_MODELLER_HAS_BOOST_PROGRAMOPTIONS = _IMP_modeller.IMP_MODELLER_HAS_BOOST_PROGRAMOPTIONS
339 IMP_MODELLER_HAS_BOOST_RANDOM = _IMP_modeller.IMP_MODELLER_HAS_BOOST_RANDOM
340 IMP_MODELLER_HAS_BOOST_SYSTEM = _IMP_modeller.IMP_MODELLER_HAS_BOOST_SYSTEM
341 IMP_MODELLER_HAS_CGAL = _IMP_modeller.IMP_MODELLER_HAS_CGAL
342 IMP_MODELLER_HAS_HDF5 = _IMP_modeller.IMP_MODELLER_HAS_HDF5
343 IMP_MODELLER_HAS_PYTHON_IHM = _IMP_modeller.IMP_MODELLER_HAS_PYTHON_IHM
344 IMPMODELLER_SHOW_WARNINGS = _IMP_modeller.IMPMODELLER_SHOW_WARNINGS
355 import modeller.scripts
356 import modeller.optimizers
358 class _TempDir(object):
359 """Make a temporary directory that is deleted when the object is."""
362 self.tmpdir = tempfile.mkdtemp()
365 shutil.rmtree(self.tmpdir, ignore_errors=
True)
369 """A Modeller restraint which evaluates an IMP scoring function.
370 This can be used to incorporate IMP Restraints into an existing
371 comparative modeling pipeline, or to use Modeller optimizers or
375 _physical_type = modeller.physical.absposition
377 def __init__(self, particles, scoring_function=None):
379 @param particles A list of the IMP atoms (as Particle objects),
380 same order as the Modeller atoms.
381 @param scoring_function An IMP::ScoringFunction object that will
382 be incorporated into the Modeller score (molpdf).
383 @note since Modeller, unlike IMP, is sensitive to the ordering
384 of atoms, it usually makes sense to create the model in
385 Modeller and then use ModelLoader to load it into IMP,
386 since that will preserve the Modeller atom ordering in IMP.
388 modeller.terms.energy_term.__init__(self)
389 self._particles = particles
391 self._sf = scoring_function
393 self._sf = particles[0].get_model()
395 def eval(self, mdl, deriv, indats):
396 atoms = self.indices_to_atoms(mdl, indats)
397 _copy_modeller_coords_to_imp(atoms, self._particles)
398 if len(self._particles) == 0:
401 score = self._sf.evaluate(deriv)
403 dvx = [0.] * len(indats)
404 dvy = [0.] * len(indats)
405 dvz = [0.] * len(indats)
406 _get_imp_derivs(self._particles, dvx, dvy, dvz)
407 return (score, dvx, dvy, dvz)
413 """An IMP restraint using all defined Modeller restraints.
414 This is useful if you want to use Modeller restraints with an IMP
415 optimizer, or in combination with IMP restraints.
417 @note Currently only the coordinates of the atoms are translated
418 between Modeller and IMP; thus, a Modeller restraint which
419 uses any other attribute (e.g. charge) will not react if
420 this attribute is changed by IMP.
423 def __init__(self, model, modeller_model, particles):
425 @param model The IMP Model object.
426 @param modeller_model The Modeller model object.
427 @param particles A list of the IMP atoms (as Particle objects),
428 in the same order as the Modeller atoms.
429 @note since Modeller, unlike IMP, is sensitive to the ordering
430 of atoms, it usually makes sense to create the model in
431 Modeller and then use ModelLoader to load it into IMP,
432 since that will preserve the Modeller atom ordering in IMP.
435 if hasattr(x,
'get_particle'):
436 return x.get_particle()
439 IMP.Restraint.__init__(self, model,
"ModellerRestraints %1%")
440 self._modeller_model = modeller_model
441 self._particles = [get_particle(x)
for x
in particles]
443 def unprotected_evaluate(self, accum):
444 atoms = self._modeller_model.atoms
445 sel = modeller.selection(self._modeller_model)
446 _copy_imp_coords_to_modeller(self._particles, atoms)
447 energies = sel.energy()
449 _add_modeller_derivs_to_imp(atoms, self._particles, accum)
455 def do_show(self, fh):
456 fh.write(
"ModellerRestraints")
458 return self._particles
461 def _copy_imp_coords_to_modeller(particles, atoms):
462 """Copy atom coordinates from IMP to Modeller"""
466 for (num, at)
in enumerate(atoms):
467 at.x = particles[num].get_value(xkey)
468 at.y = particles[num].get_value(ykey)
469 at.z = particles[num].get_value(zkey)
472 def _copy_modeller_coords_to_imp(atoms, particles):
473 """Copy atom coordinates from Modeller to IMP"""
477 for (num, at)
in enumerate(atoms):
478 particles[num].set_value(xkey, at.x)
479 particles[num].set_value(ykey, at.y)
480 particles[num].set_value(zkey, at.z)
483 def _add_modeller_derivs_to_imp(atoms, particles, accum):
484 """Add atom derivatives from Modeller to IMP"""
485 for (num, at)
in enumerate(atoms):
487 xyz.add_to_derivative(0, at.dvx, accum)
488 xyz.add_to_derivative(1, at.dvy, accum)
489 xyz.add_to_derivative(2, at.dvz, accum)
492 def _get_imp_derivs(particles, dvx, dvy, dvz):
493 """Move atom derivatives from IMP to Modeller"""
497 for idx
in range(0, len(dvx)):
498 dvx[idx] = particles[idx].get_derivative(xkey)
499 dvy[idx] = particles[idx].get_derivative(ykey)
500 dvz[idx] = particles[idx].get_derivative(zkey)
504 def _HarmonicLowerBoundGenerator(parameters, modalities):
505 (mean, stdev) = parameters
509 def _HarmonicUpperBoundGenerator(parameters, modalities):
510 (mean, stdev) = parameters
514 def _HarmonicGenerator(parameters, modalities):
515 (mean, stdev) = parameters
519 def _CosineGenerator(parameters, modalities):
520 (phase, force_constant) = parameters
521 (periodicity,) = modalities
524 def _LinearGenerator(parameters, modalities):
525 (scale,) = parameters
528 def _SplineGenerator(parameters, modalities):
529 (open, low, high, delta, lowderiv, highderiv) = parameters[:6]
531 for v
in parameters[6:]:
539 _unary_func_generators = {
540 1: _HarmonicLowerBoundGenerator,
541 2: _HarmonicUpperBoundGenerator,
542 3: _HarmonicGenerator,
545 10: _SplineGenerator,
549 def _DistanceRestraintGenerator(form, modalities, atoms, parameters):
550 unary_func_gen = _unary_func_generators[form]
552 unary_func_gen(parameters, modalities),
555 def _AngleRestraintGenerator(form, modalities, atoms, parameters):
556 unary_func_gen = _unary_func_generators[form]
558 unary_func_gen(parameters, modalities),
559 atoms[0], atoms[1], atoms[2])
561 def _MultiBinormalGenerator(form, modalities, atoms, parameters):
562 nterms = modalities[0]
563 if len(parameters) != nterms * 6:
564 raise ValueError(
"Incorrect number of parameters (%d) for multiple "
565 "binormal restraint - expecting %d (%d terms * 6)" \
566 % (len(parameters), nterms * 6, nterms))
568 atoms[:4], atoms[4:8])
569 for i
in range(nterms):
571 t.set_weight(parameters[i])
572 t.set_means((parameters[nterms + i * 2],
573 parameters[nterms + i * 2 + 1]))
574 t.set_standard_deviations((parameters[nterms * 3 + i * 2],
575 parameters[nterms * 3 + i * 2 + 1]))
576 t.set_correlation(parameters[nterms * 5 + i])
580 def _DihedralRestraintGenerator(form, modalities, atoms, parameters):
582 return _MultiBinormalGenerator(form, modalities, atoms, parameters)
583 unary_func_gen = _unary_func_generators[form]
585 unary_func_gen(parameters, modalities),
586 atoms[0], atoms[1], atoms[2], atoms[3])
588 def _get_protein_atom_particles(protein):
589 """Given a protein particle, get the flattened list of all child atoms"""
591 for ichain
in range(protein.get_number_of_children()):
592 chain = protein.get_child(ichain)
593 for ires
in range(chain.get_number_of_children()):
594 residue = chain.get_child(ires)
595 for iatom
in range(residue.get_number_of_children()):
596 atom = residue.get_child(iatom)
597 atom_particles.append(atom.get_particle())
598 return atom_particles
600 def _load_restraints_line(line, atom_particles):
601 """Parse a single Modeller restraints file line and return the
602 corresponding IMP restraint."""
605 if typ ==
'MODELLER5':
608 raise NotImplementedError(
"Only 'R' lines currently read from " + \
609 "Modeller restraints files")
610 form = int(spl.pop(0))
611 modalities = [int(spl.pop(0))]
612 features = [int(spl.pop(0))]
615 natoms = [int(spl.pop(0))]
616 nparam = int(spl.pop(0))
617 nfeat = int(spl.pop(0))
618 for i
in range(nfeat - 1):
619 modalities.append(int(spl.pop(0)))
620 features.append(int(spl.pop(0)))
621 natoms.append(int(spl.pop(0)))
622 atoms = [int(spl.pop(0))
for x
in range(natoms[0])]
623 for i
in range(len(atoms)):
624 atoms[i] = atom_particles[atoms[i] - 1]
625 parameters = [float(spl.pop(0))
for x
in range(nparam)]
626 restraint_generators = {
627 1 : _DistanceRestraintGenerator,
628 2 : _AngleRestraintGenerator,
629 3 : _DihedralRestraintGenerator,
631 restraint_gen = restraint_generators[features[0]]
632 return restraint_gen(form, modalities, atoms, parameters)
635 def _load_entire_restraints_file(filename, protein):
636 """Yield a set of IMP restraints from a Modeller restraints file."""
637 atoms = _get_protein_atom_particles(protein)
638 fh = open(filename,
'r')
641 rsr = _load_restraints_line(line, atoms)
644 except Exception
as err:
645 print(
"Cannot read restraints file line:\n" + line)
649 def _copy_residue(r, model):
650 """Copy residue information from modeller to imp"""
655 p.set_name(str(
"residue "+r.num));
659 def _copy_atom(a, model):
660 """Copy atom information from modeller"""
666 if hasattr(a,
'charge'):
668 if hasattr(a,
'type'):
670 ap.set_input_index(a.index)
673 def _copy_chain(c, model):
674 """Copy chain information from modeller"""
681 def _get_forcefield(submodel):
693 """Add radii to the hierarchy using the Modeller radius library, radii.lib.
694 Each radius is scaled by the given scale (Modeller usually scales radii
695 by a factor of 0.82). submodel specifies the topology submodel, which is
696 the column in radii.lib to use."""
700 for line
in open(filename):
701 if line.startswith(
'#'):
continue
704 radii[spl[0]] = float(spl[submodel])
705 atoms = IMP.atom.get_by_type(hierarchy, IMP.atom.ATOM_TYPE)
714 """Read a Modeller model into IMP. After creating this object, the atoms
715 in the Modeller model can be loaded into IMP using the load_atoms()
716 method, then optionally any Modeller static restraints can be read in
717 with load_static_restraints() or load_static_restraints_file().
719 This class can also be used to read Modeller alignment structures;
720 however, only load_atoms() will be useful in such a case (since
721 alignment structures don't have restraints or other information).
727 @param modeller_model The Modeller model or alignment structure
730 self._modeller_model = modeller_model
733 """Construct an IMP::atom::Hierarchy that contains the same atoms as
734 the Modeller model or alignment structure.
736 IMP atoms created from a Modeller model will be given charges and
737 CHARMM types, extracted from the model. Alignment structures don't
738 contain this information, so the IMP atoms won't either.
740 @param model The IMP::Model object in which the hierarchy will be
741 created. The highest level hierarchy node is a PROTEIN.
742 @return the newly-created root IMP::atom::Hierarchy.
747 for chain
in self._modeller_model.chains:
752 for residue
in chain.residues:
753 rp = _copy_residue(residue, model)
756 for atom
in residue.atoms:
757 ap = _copy_atom(atom, model)
760 self._atoms[atom.index] = ap
762 self._modeller_hierarchy = hpp
765 def _get_nonbonded_list(self, atoms, pair_filter, edat, distance):
770 if pair_filter
is None:
772 if edat.excl_local[0]:
773 pair_filter.set_bonds(list(self.
load_bonds()))
774 if edat.excl_local[1]:
776 if edat.excl_local[2]:
778 nbl.add_pair_filter(pair_filter)
782 """Load the Modeller bond topology into the IMP model. Each bond is
783 represented in IMP as an IMP::atom::Bond, with no defined length
784 or stiffness. These bonds are primarily useful as input to
785 IMP::atom::StereochemistryPairFilter, to exclude bond interactions
786 from the nonbonded list. Typically the contribution to the scoring
787 function from the bonds is included in the Modeller static restraints
788 (use load_static_restraints() or load_static_restraints_file() to
789 load these). If you want to regenerate the stereochemistry in IMP,
790 do not use these functions (as then stereochemistry scoring terms
791 and exclusions would be double-counted) and instead use the
792 IMP::atom::CHARMMTopology class.
794 You must call load_atoms() prior to using this function.
795 @see load_angles(), load_dihedrals(), load_impropers()
796 @return A generator listing all of the bonds.
798 if not hasattr(self,
'_modeller_hierarchy'):
799 raise ValueError(
"Call load_atoms() first.")
800 for (maa, mab)
in self._modeller_model.bonds:
801 pa = self._atoms[maa.index]
802 pb = self._atoms[mab.index]
812 IMP.atom.Bond.SINGLE).get_particle()
815 """Load the Modeller angle topology into the IMP model.
816 See load_bonds() for more details."""
817 return self._internal_load_angles(self._modeller_model.angles,
821 """Load the Modeller dihedral topology into the IMP model.
822 See load_bonds() for more details."""
823 return self._internal_load_angles(self._modeller_model.dihedrals,
827 """Load the Modeller improper topology into the IMP model.
828 See load_bonds() for more details."""
829 return self._internal_load_angles(self._modeller_model.impropers,
832 def _internal_load_angles(self, angles, angle_class):
833 if not hasattr(self,
'_modeller_hierarchy'):
834 raise ValueError(
"Call load_atoms() first.")
835 for modeller_atoms
in angles:
836 imp_particles = [self._atoms[x.index]
for x
in modeller_atoms]
838 a = angle_class.setup_particle(p,
840 yield a.get_particle()
843 """Convert a Modeller static restraints file into equivalent
844 IMP::Restraints. load_atoms() must have been called first to read
845 in the atoms that the restraints will act upon.
846 @param filename Name of the Modeller restraints file. The restraints
847 in this file are assumed to act upon the model read in by
848 load_atoms(); no checking is done to enforce this.
849 @return A Python generator of the newly-created IMP::Restraint
852 if not hasattr(self,
'_modeller_hierarchy'):
853 raise ValueError(
"Call load_atoms() first.")
854 return _load_entire_restraints_file(filename, self._modeller_hierarchy)
858 """Convert the current set of Modeller static restraints into equivalent
859 IMP::Restraints. load_atoms() must have been called first to read
860 in the atoms that the restraints will act upon.
861 @return A Python generator of the newly-created IMP::Restraint
864 class _RestraintGenerator(object):
865 """Simple generator wrapper"""
868 def __iter__(self, *args, **keys):
870 def close(self, *args, **keys):
871 return self._gen.close(*args, **keys)
873 return next(self._gen)
875 def send(self, *args, **keys):
876 return self._gen.send(*args, **keys)
877 def throw(self, *args, **keys):
878 return self._gen.throw(*args, **keys)
881 rsrfile = os.path.join(t.tmpdir,
'restraints.rsr')
882 self._modeller_model.restraints.write(file=rsrfile)
885 wrap = _RestraintGenerator(gen)
891 """Convert Modeller dynamic restraints into IMP::Restraint objects.
893 For each currently active Modeller dynamic restraint
894 (e.g. soft-sphere, electrostatics) an equivalent IMP::Restraint
896 load_atoms() must have been called first to read
897 in the atoms that the restraints will act upon.
899 If pair_filter is given, it is an IMP::PairFilter object to exclude
900 pairs from the nonbonded lists used by the dynamic restraints.
901 Otherwise, an IMP::atom::StereochemistryPairFilter object is created
902 to exclude Modeller bonds, angles and dihedrals, as specified by
903 edat.excl_local. (Note that this calls load_bonds(), load_angles()
904 and load_dihedrals(), so will create duplicate lists of bonds if
905 those methods are called manually as well.)
907 @note Currently only soft-sphere, electrostatic and Lennard-Jones
908 restraints are loaded.
909 @return A Python generator of the newly-created IMP::Restraint
912 if not hasattr(self,
'_modeller_hierarchy'):
913 raise ValueError(
"Call load_atoms() first.")
914 edat = self._modeller_model.env.edat
915 libs = self._modeller_model.env.libs
917 m = atoms[0].get_model()
920 if edat.dynamic_sphere:
923 nbl = self._get_nonbonded_list(atoms, pair_filter, edat, 0.)
926 libs.topology.submodel, edat.radii_factor)
933 if edat.dynamic_lennard
or edat.dynamic_coulomb:
935 d = max(edat.contact_shell - 3.0, 0.0)
936 nbl = self._get_nonbonded_list(atoms, pair_filter, edat, d)
937 ff = _get_forcefield(libs.topology.submodel)
938 ff.add_radii(self._modeller_hierarchy)
940 if edat.dynamic_lennard:
941 ff.add_well_depths(self._modeller_hierarchy)
943 edat.lennard_jones_switch[1])
947 if edat.dynamic_coulomb:
949 edat.coulomb_switch[1])
951 ps.set_relative_dielectric(edat.relative_dielectric)
956 def get_module_version():
957 """get_module_version() -> std::string const"""
958 return _IMP_modeller.get_module_version()
961 """get_example_path(std::string fname) -> std::string"""
962 return _IMP_modeller.get_example_path(fname)
965 """get_data_path(std::string fname) -> std::string"""
966 return _IMP_modeller.get_data_path(fname)
968 from .
import _version_check
969 _version_check.check_version(get_module_version())
970 __version__ = get_module_version()
static CHARMMAtom setup_particle(Model *m, ParticleIndex pi, String charmm_type)
static Charged setup_particle(Model *m, ParticleIndex pi, Float charge)
Lower bound harmonic function (non-zero when feature < mean)
def load_static_restraints
Convert the current set of Modeller static restraints into equivalent IMP::Restraints.
std::string get_example_path(std::string file_name)
Return the full path to one of this module's example files.
def load_bonds
Load the Modeller bond topology into the IMP model.
A Modeller restraint which evaluates an IMP scoring function.
Coulomb (electrostatic) score between a pair of particles.
static Atom setup_particle(Model *m, ParticleIndex pi, Atom other)
Various classes to hold sets of particles.
Upper bound harmonic function (non-zero when feature > mean)
static XYZR setup_particle(Model *m, ParticleIndex pi)
A decorator for a particle which has bonds.
def load_impropers
Load the Modeller improper topology into the IMP model.
Make CGAL functionality available to IMP.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Dihedral restraint between four particles.
def load_static_restraints_file
Convert a Modeller static restraints file into equivalent IMP::Restraints.
A score on the distance between the surfaces of two spheres.
Return all close unordered pairs of particles taken from the SingletonContainer.
static Residue setup_particle(Model *m, ParticleIndex pi, ResidueType t, int index, int insertion_code)
A single binormal term in a MultipleBinormalRestraint.
def load_dynamic_restraints
Convert Modeller dynamic restraints into IMP::Restraint objects.
Distance restraint between two particles.
static XYZ setup_particle(Model *m, ParticleIndex pi)
Composable functors to implement scores via compile-time composition.
An IMP restraint using all defined Modeller restraints.
CHARMM force field parameters.
Bond create_bond(Bonded a, Bonded b, Bond o)
Connect the two wrapped particles by a custom bond.
def load_dihedrals
Load the Modeller dihedral topology into the IMP model.
static Float get_k_from_standard_deviation(Float sd, Float t=297.15)
Return the k to use for a given Gaussian standard deviation.
Angle restraint between three particles.
static Hierarchy setup_particle(Model *m, ParticleIndex pi, ParticleIndexesAdaptor children=ParticleIndexesAdaptor())
Create a Hierarchy of level t by adding the needed attributes.
ParticleIndexPairs get_indexes(const ParticlePairsTemp &ps)
Lennard-Jones score between a pair of particles.
A particle that describes an angle between three particles.
The standard decorator for manipulating molecular structures.
Store a list of ParticleIndexes.
static Bonded setup_particle(Model *m, ParticleIndex pi)
def load_atoms
Construct an IMP::atom::Hierarchy that contains the same atoms as the Modeller model or alignment str...
Version and module information for Objects.
A decorator for a particle with x,y,z coordinates.
Modeller-style multiple binormal (phi/psi) restraint.
def add_soft_sphere_radii
Add radii to the hierarchy using the Modeller radius library, radii.lib.
A particle that describes a dihedral angle between four particles.
def load_angles
Load the Modeller angle topology into the IMP model.
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...
static bool get_is_setup(const IMP::ParticleAdaptor &p)
virtual VersionInfo get_version_info() const
Get information about the module and version of the object.
A filter that excludes bonds, angles and dihedrals.
Read a Modeller model into IMP.
Class to handle individual particles of a Model object.
std::string get_data_path(std::string file_name)
Return the full path to one of this module's data files.
Smooth interaction scores by switching the derivatives (force switch).
Output IMP model data in various file formats.
Functionality for loading, creating, manipulating and scoring atomic structures.
static Chain setup_particle(Model *m, ParticleIndex pi, std::string id)
Hierarchies get_leaves(const Selection &h)
Applies a PairScore to each Pair in a list.
virtual ModelObjectsTemp do_get_inputs() const =0
Closed cubic spline function.
A decorator for an atom that has a defined CHARMM type.
A restraint is a term in an IMP ScoringFunction.
Harmonic function (symmetric about the mean)