def get_rmsd_from_start(self): if self.rmsd_from_start is not None: return self.rmsd_from_start # calculate rmsd self.rmsd_from_start = ssb.calculate_rmsd_smart( self.original_boxed_hierarchy, self.model.get_hierarchy(), backbone_only=True) return self.rmsd_from_start
def get_rmsd_from_start(self): if self.rmsd_from_start is not None: return self.rmsd_from_start # calculate rmsd self.rmsd_from_start = ssb.calculate_rmsd_smart( self.original_boxed_hierarchy, self.whole_pdb_h, backbone_only=True) return self.rmsd_from_start
def exercise_00(prefix="exercise_00"): "Build poly-ALA alpha helix" ph = ssb.secondary_structure_from_sequence( alpha_helix_template, "".join(["A"]*12)) ph.atoms().reset_i_seq() #ph.write_pdb_file(file_name="%s_result.pdb"%prefix) sites_1 = ph.atoms().extract_xyz() sites_2 = iotbx.pdb.input(source_info=None, lines=alpha_helix_answer).construct_hierarchy().atoms().extract_xyz() #of = open("1.pdb","w") #print >> of, alpha_helix_answer #of.close() assert sites_1.size()==sites_2.size(), [sites_1.size(),sites_2.size()] d1 = flex.sqrt((sites_1 - sites_2).dot()) rmsd = ssb.calculate_rmsd_smart(ph, iotbx.pdb.input(source_info=None, lines=alpha_helix_answer).construct_hierarchy()) assert rmsd < 0.1, rmsd
def get_rmsd_from_start2(self): return ssb.calculate_rmsd_smart(self.original_boxed_hierarchy, self.model.get_hierarchy(), backbone_only=False)
def get_rmsd_from_start2(self): return ssb.calculate_rmsd_smart( self.original_boxed_hierarchy, self.whole_pdb_h, backbone_only=False)