def get_restraints_for_native(self, restraints_names):
"""
Get values of the restraints for the native structure
@param restraints_names Names of the restraints requested
@return a list with the values of all scores, and the total score
"""
saved = [rb.get_reference_frame() for rb in self.components_rbs]
# Set the state of the model to native
for rb, rn in zip(self.components_rbs, self.native_rbs):
# remove sub-rigid bodies
rb_members = [m for m in rb.get_members()
if not core.RigidBody.get_is_setup(m.get_particle())]
rn_members = [m for m in rn.get_members()
if not core.RigidBody.get_is_setup(m.get_particle())]
rb_coords = [m.get_coordinates() for m in rb_members]
rn_coords = [m.get_coordinates() for m in rn_members]
# align and put rb in the position of rn
if len(rn_coords) != len(rb_coords):
raise ValueError("Mismatch in the number of members. "
"Reference %d Aligned %d " % (len(rn_coords), len(rb_coords)))
T = alg.get_transformation_aligning_first_to_second(rb_coords,
rn_coords)
t = rb.get_reference_frame().get_transformation_to()
new_t = alg.compose(T, t)
rb.set_reference_frame(alg.ReferenceFrame3D(new_t))
scores = []
for name in restraints_names:
scores.append(self.restraints[name].evaluate(False))
total_score = sum(scores)
representation.set_reference_frames(self.components_rbs, saved)
return scores, total_score
def get_restraints_for_native(self, restraints_names):
"""
Get values of the restraints for the native structure
@param restraints_names Names of the restraints requested
@return a list with the values of all scores, and the total score
"""
saved = [rb.get_reference_frame() for rb in self.components_rbs]
# Set the state of the model to native
for rb, rn in zip(self.components_rbs, self.native_rbs):
# remove sub-rigid bodies
rb_members = [m for m in rb.get_members()
if not core.RigidBody.get_is_setup(m.get_particle())]
rn_members = [m for m in rn.get_members()
if not core.RigidBody.get_is_setup(m.get_particle())]
rb_coords = [m.get_coordinates() for m in rb_members]
rn_coords = [m.get_coordinates() for m in rn_members]
# align and put rb in the position of rn
if len(rn_coords) != len(rb_coords):
raise ValueError("Mismatch in the number of members. "
"Reference %d Aligned %d " % (len(rn_coords), len(rb_coords)))
T = alg.get_transformation_aligning_first_to_second(rb_coords,
rn_coords)
t = rb.get_reference_frame().get_transformation_to()
new_t = alg.compose(T, t)
rb.set_reference_frame(alg.ReferenceFrame3D(new_t))
scores = []
for name in restraints_names:
scores.append(self.restraints[name].evaluate(False))
total_score = sum(scores)
representation.set_reference_frames(self.components_rbs, saved)
return scores, total_score
def write_pdb_for_reference_frames(self, RFs, fn_pdb):
"""
Write a PDB file with a solution given by a set of reference frames
@param RFs Reference frames for the elements of the complex
@param fn_pdb File to write the solution
"""
log.debug("Writting PDB %s for reference frames %s", fn_pdb, RFs)
representation.set_reference_frames(self.components_rbs, RFs)
atom.write_pdb(self.assembly, fn_pdb)
def write_pdb_for_reference_frames(self, RFs, fn_pdb):
"""
Write a PDB file with a solution given by a set of reference frames
@param RFs Reference frames for the elements of the complex
@param fn_pdb File to write the solution
"""
log.debug("Writting PDB %s for reference frames %s", fn_pdb, RFs)
representation.set_reference_frames(self.components_rbs, RFs)
atom.write_pdb(self.assembly, fn_pdb)
def write_pdbs_for_reference_frames(self, RFs, fn_base):
"""
Write a separate PDB for each of the elements
@param RFs Reference frames for the elements of the complex
@param fn_base base string to build the names of the PDBs files
"""
log.debug("Writting PDBs with basename %s", fn_base)
representation.set_reference_frames(self.components_rbs, RFs)
for i, ch in enumerate(self.assembly.get_children()):
atom.write_pdb(ch, fn_base + "component-%02d.pdb" % i)
def write_pdbs_for_reference_frames(self, RFs, fn_base):
"""
Write a separate PDB for each of the elements
@param RFs Reference frames for the elements of the complex
@param fn_base base string to build the names of the PDBs files
"""
log.debug("Writting PDBs with basename %s", fn_base)
representation.set_reference_frames(self.components_rbs, RFs)
for i, ch in enumerate(self.assembly.get_children()):
atom.write_pdb(ch, fn_base + "component-%02d.pdb" % i)