def do_clustering(self, confs_RFs, max_rmsd):
"""
Cluster configurations for a model based on RMSD.
An IMP.ConfigurationSet is built using the reference frames for
of the components of the assembly for each solution
@param confs_RFs A lsit containing a tuples of reference frames.
Each tuple contains the reference frame for the rigid body
of one component of the assembly
@param max_rmsd Maximum RMSD tolerated when clustering
"""
model = IMP.Model()
assembly = representation.create_assembly(model, self.exp.fn_pdbs)
rbs = representation.create_rigid_bodies(assembly)
configuration_set = IMP.ConfigurationSet(model)
for RFs in confs_RFs:
representation.set_reference_frames(rbs, RFs)
configuration_set.save_configuration()
particles_container = container.ListSingletonContainer(model)
particles_container.add_particles(atom.get_leaves(assembly))
metric = stats.ConfigurationSetRMSDMetric(
configuration_set,particles_container, True)
log.info("Clustering ... ")
maximum_centrality = 10
self.pclus = stats.create_centrality_clustering( metric, max_rmsd,
maximum_centrality)
n = self.pclus.get_number_of_clusters()
log.info("Number of clusters found: %s", n)
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 = filter(
lambda m: not core.RigidBody.get_is_setup(
m.get_particle()), rb.get_members())
rn_members = filter(
lambda m: not core.RigidBody.get_is_setup(
m.get_particle()), rn.get_members())
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_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 buid 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 align_and_get_placement_scores(reference_rbs, rbs):
"""
reference_rbs - Reference rigid bodies.
The rigid bodies are aligned using their centroids.
NOTE: The function changes but restores the reference frames of rbs.
The rigid bodies refs_rbs of the reference are not changed.
"""
saved_refs = [rb.get_reference_frame() for rb in rbs]
best_rmsd, new_refs = \
alignments.get_reference_frames_aligning_rbs(rbs, reference_rbs)
representation.set_reference_frames(rbs, new_refs)
distances, angles = get_placement_scores(reference_rbs, rbs)
representation.set_reference_frames(rbs, saved_refs)
return distances, angles
