def add_native_record(self, assignment, RFs, total_score,
restraints_scores):
"""
Add a record for the native structure to the database
see add_record() for the meaning of the parameters
"""
words = [io.ReferenceFrameToText(ref).get_text() for ref in RFs]
RFs_txt = unit_delim.join(words)
solution_id = 0
record = [solution_id, assignment, RFs_txt, total_score] + \
restraints_scores
measures = [0, 0, 0] # ["drms", "cdrms", "crmsd"]
record = record + measures
self.store_data(self.native_table_name, [record])
def add_record(self, solution_id, assignment, RFs, total_score,
restraints_scores, measures):
"""
Add a recorde to the database
@param solution_id The key for the solution
@param assignment The assigment for the solution provided by
domino
@param RFs Reference frames of the rigid bodies of the components
of the assembly in the solution
@param total_score Total value of the scoring function
@param restraints_scores A list with all the values for the
restraints
@param measures A list with the values of all the measures for
benchmark
"""
words = [io.ReferenceFrameToText(ref).get_text() for ref in RFs]
RFs_txt = unit_delim.join(words)
record = [solution_id, assignment, RFs_txt, total_score] + \
restraints_scores
if measures is not None:
record = record + measures
self.records.append(record)
def get_assignment_and_RFs(self, assignment, subset):
"""
Return a line with texts for an assignment and the
the reference frames of the RigidBodies in the subset.
@param subset Subset of components of the assembly
@param assignment Assignment class with the states for the subset
@note: see the get_assignment_assignment_text() note.
"""
ordered_assignment = []
RFs = []
for rb in self.components_rbs:
for i, particle in enumerate(subset):
if rb.get_particle() == particle:
j = assignment[i]
ordered_assignment.append(j)
pstates = self.rb_states_table.get_particle_states(rb)
pstates.load_particle_state(j, rb.get_particle())
RFs.append(rb.get_reference_frame())
RFs_text = unit_delim.join(
[io.ReferenceFrameToText(ref).get_text() for ref in RFs])
assignment_numbers = "|".join([str(i) for i in ordered_assignment])
return [assignment_numbers, RFs_text]