Author: bugman Date: Tue Jan 27 10:50:56 2015 New Revision: 27322 URL: http://svn.gna.org/viewcvs/relax?rev=27322&view=rev Log: Bug fix for the PDB secondary sheet handling when combining multiple PDB structures. The helix and sheet metadata now converts the original chain IDs into molecule indices, shifted to new values based on the currently loaded data, when the structure.read_pdb user function is executed. When the structure.write_pdb user function is executed, the molecule indices are converted into new chain IDs. This allows the chain IDs in the HELIX and SHEET records to match those of the ATOM and HETATOM records. Modified: trunk/lib/structure/internal/object.py Modified: trunk/lib/structure/internal/object.py URL: http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=27322&r1=27321&r2=27322&view=diff ============================================================================== --- trunk/lib/structure/internal/object.py (original) +++ trunk/lib/structure/internal/object.py Tue Jan 27 10:50:56 2015 @@ -487,6 +487,12 @@ 'TURN ' ] + # The number of pre-existing molecules. + if not len(self.structural_data): + mol_num = 0 + else: + mol_num = len(self.structural_data[0].mol) + # Loop over the lines. for i in range(len(lines)): # No match, therefore assume to be out of the secondary structure section. @@ -498,34 +504,56 @@ # Parse the record. record_type, ser_num, helix_id, init_res_name, init_chain_id, init_seq_num, init_icode, end_res_name, end_chain_id, end_seq_num, end_icode, helix_class, comment, length = pdb_read.helix(lines[i]) + # The molecule indices. + mol_init_index = self._pdb_chain_id_to_mol_index(init_chain_id) + mol_end_index = self._pdb_chain_id_to_mol_index(end_chain_id) + # Only load the desired molecule. if read_mol != None: - if self._pdb_chain_id_to_mol_index(init_chain_id)+1 not in read_mol: + if mol_init_index + 1 not in read_mol: continue - if self._pdb_chain_id_to_mol_index(end_chain_id)+1 not in read_mol: + if mol_end_index + 1 not in read_mol: continue + + # New molecule indices based on currently loaded data. + mol_init_index += mol_num + mol_end_index += mol_num # Store the data. if not hasattr(self, 'helices'): self.helices = [] - self.helices.append([helix_id, init_chain_id, init_res_name, init_seq_num, end_chain_id, end_res_name, end_seq_num, helix_class, length]) + self.helices.append([helix_id, mol_init_index, init_res_name, init_seq_num, mol_end_index, end_res_name, end_seq_num, helix_class, length]) # A sheet. if lines[i][:5] == 'SHEET': # Parse the record. record_type, strand, sheet_id, num_strands, init_res_name, init_chain_id, init_seq_num, init_icode, end_res_name, end_chain_id, end_seq_num, end_icode, sense, cur_atom, cur_res_name, cur_chain_id, cur_res_seq, cur_icode, prev_atom, prev_res_name, prev_chain_id, prev_res_seq, prev_icode = pdb_read.sheet(lines[i]) + # The molecule indices. + mol_init_index = self._pdb_chain_id_to_mol_index(init_chain_id) + mol_end_index = self._pdb_chain_id_to_mol_index(end_chain_id) + # Only load the desired molecule. if read_mol != None: - if self._pdb_chain_id_to_mol_index(init_chain_id)+1 not in read_mol: + if mol_init_index + 1 not in read_mol: continue - if self._pdb_chain_id_to_mol_index(end_chain_id)+1 not in read_mol: + if mol_end_index + 1 not in read_mol: continue + + # New molecule indices based on currently loaded data. + mol_init_index += mol_num + mol_end_index += mol_num + mol_cur_index = None + if cur_chain_id: + mol_cur_index = self._pdb_chain_id_to_mol_index(cur_chain_id) + mol_num + mol_prev_index = None + if prev_chain_id: + mol_prev_index = self._pdb_chain_id_to_mol_index(prev_chain_id) + mol_num # Store the data. if not hasattr(self, 'sheets'): self.sheets = [] - self.sheets.append([strand, sheet_id, num_strands, init_res_name, init_chain_id, init_seq_num, init_icode, end_res_name, end_chain_id, end_seq_num, end_icode, sense, cur_atom, cur_res_name, cur_chain_id, cur_res_seq, cur_icode, prev_atom, prev_res_name, prev_chain_id, prev_res_seq, prev_icode]) + self.sheets.append([strand, sheet_id, num_strands, init_res_name, mol_init_index, init_seq_num, init_icode, end_res_name, mol_end_index, end_seq_num, end_icode, sense, cur_atom, cur_res_name, mol_cur_index, cur_res_seq, cur_icode, prev_atom, prev_res_name, mol_prev_index, prev_res_seq, prev_icode]) # Return the remaining lines. return lines[i:] @@ -2865,8 +2893,8 @@ # Loop over and unpack the helix data. index = 1 - for helix_id, init_chain_id, init_res_name, init_seq_num, end_chain_id, end_res_name, end_seq_num, helix_class, length in self.helices: - pdb_write.helix(file, ser_num=index, helix_id=helix_id, init_chain_id=init_chain_id, init_res_name=init_res_name, init_seq_num=init_seq_num, end_chain_id=end_chain_id, end_res_name=end_res_name, end_seq_num=end_seq_num, helix_class=helix_class, length=length) + for helix_id, mol_init_index, init_res_name, init_seq_num, mol_end_index, end_res_name, end_seq_num, helix_class, length in self.helices: + pdb_write.helix(file, ser_num=index, helix_id=helix_id, init_chain_id=CHAIN_ID_LIST[mol_init_index], init_res_name=init_res_name, init_seq_num=init_seq_num, end_chain_id=CHAIN_ID_LIST[mol_end_index], end_res_name=end_res_name, end_seq_num=end_seq_num, helix_class=helix_class, length=length) index += 1 # The SHEET records. @@ -2878,7 +2906,18 @@ # Loop over and unpack the helix data. index = 1 - for strand, sheet_id, num_strands, init_res_name, init_chain_id, init_seq_num, init_icode, end_res_name, end_chain_id, end_seq_num, end_icode, sense, cur_atom, cur_res_name, cur_chain_id, cur_res_seq, cur_icode, prev_atom, prev_res_name, prev_chain_id, prev_res_seq, prev_icode in self.sheets: + for strand, sheet_id, num_strands, init_res_name, mol_init_index, init_seq_num, init_icode, end_res_name, mol_end_index, end_seq_num, end_icode, sense, cur_atom, cur_res_name, mol_cur_index, cur_res_seq, cur_icode, prev_atom, prev_res_name, mol_prev_index, prev_res_seq, prev_icode in self.sheets: + # Translate molecule indices to chain IDs. + init_chain_id = CHAIN_ID_LIST[mol_init_index] + end_chain_id = CHAIN_ID_LIST[mol_end_index] + cur_chain_id = None + if mol_cur_index != None: + cur_chain_id = CHAIN_ID_LIST[mol_cur_index] + prev_chain_id = None + if mol_prev_index != None: + prev_chain_id = CHAIN_ID_LIST[mol_prev_index] + + # Write out. pdb_write.sheet(file, strand=strand, sheet_id=sheet_id, num_strands=num_strands, init_res_name=init_res_name, init_chain_id=init_chain_id, init_seq_num=init_seq_num, init_icode=init_icode, end_res_name=end_res_name, end_chain_id=end_chain_id, end_seq_num=end_seq_num, end_icode=end_icode, sense=sense, cur_atom=cur_atom, cur_res_name=cur_res_name, cur_chain_id=cur_chain_id, cur_res_seq=cur_res_seq, cur_icode=cur_icode, prev_atom=prev_atom, prev_res_name=prev_res_name, prev_chain_id=prev_chain_id, prev_res_seq=prev_res_seq, prev_icode=prev_icode) index += 1