Author: bugman Date: Thu Feb 19 14:55:42 2015 New Revision: 27674 URL: http://svn.gna.org/viewcvs/relax?rev=27674&view=rev Log: Merged revisions 27673 via svnmerge from svn+ssh://bug...@svn.gna.org/svn/relax/trunk
........ r27673 | bugman | 2015-02-19 14:55:06 +0100 (Thu, 19 Feb 2015) | 9 lines Fix for bug #23293 (https://gna.org/bugs/?23293). This is the PDB HETATM loading error whereby the last HETATM record is sometimes not read from the PDB file. The problem was two-fold. Firstly the internal structural object _parse_mols_pdb() method for separating a PDB file into distinct molecules was terminating too early when a new molecule is found, so that the last PDB record is not appended to the records list for the molecule. Secondly the write_pdb() method was not handling the PDB sequential serial number correctly. ........ Modified: branches/nmrglue/ (props changed) branches/nmrglue/lib/structure/internal/object.py Propchange: branches/nmrglue/ ------------------------------------------------------------------------------ --- svnmerge-integrated (original) +++ svnmerge-integrated Thu Feb 19 14:55:42 2015 @@ -1 +1 @@ -/trunk:1-27670 +/trunk:1-27673 Modified: branches/nmrglue/lib/structure/internal/object.py URL: http://svn.gna.org/viewcvs/relax/branches/nmrglue/lib/structure/internal/object.py?rev=27674&r1=27673&r2=27674&view=diff ============================================================================== --- branches/nmrglue/lib/structure/internal/object.py (original) +++ branches/nmrglue/lib/structure/internal/object.py Thu Feb 19 14:55:42 2015 @@ -735,9 +735,6 @@ # Reset the flag. end = False - - # Skip the rest of this loop. - continue # The molecule number. chain_id = records[i][21] @@ -3040,7 +3037,6 @@ # Loop over the molecules. index = 0 - atom_serial = 0 for mol in model.mol_loop(): # Printout. if not model_records: @@ -3053,9 +3049,6 @@ if mol.pdb_record[i] in [None, 'ATOM']: atom_record = True - # The atom number. - atom_serial += 1 - # Handle the funky atom name alignment. From the PDB format documents: # "Alignment of one-letter atom name such as C starts at column 14, while two-letter atom name such as FE starts at column 13." if len(mol.atom_name[i]) == 1: @@ -3064,12 +3057,12 @@ atom_name = "%s" % mol.atom_name[i] # Write out. - pdb_write.atom(file, serial=atom_serial, name=atom_name, res_name=mol.res_name[i], chain_id=CHAIN_ID_LIST[index], res_seq=mol.res_num[i], x=mol.x[i], y=mol.y[i], z=mol.z[i], occupancy=1.0, temp_factor=0, element=mol.element[i]) + pdb_write.atom(file, serial=ser_num, name=atom_name, res_name=mol.res_name[i], chain_id=CHAIN_ID_LIST[index], res_seq=mol.res_num[i], x=mol.x[i], y=mol.y[i], z=mol.z[i], occupancy=1.0, temp_factor=0, element=mol.element[i]) num_atom += 1 ser_num += 1 # Info for the TER record. - ter_num = atom_serial + 1 + ter_num = ser_num + 1 ter_name = mol.res_name[i] ter_chain_id = CHAIN_ID_LIST[index] ter_res_num = mol.res_num[i] @@ -3085,14 +3078,9 @@ for i in range(len(mol.atom_name)): # Write the HETATM record. if mol.pdb_record[i] == 'HETATM': - # The atom number. - atom_serial += 1 - # Increment the atom number if a TER record was created. - if atom_record and atom_serial == ter_num: + if atom_record and ser_num == ter_num: count_shift = True - if atom_record and count_shift: - atom_serial += 1 # Write out. pdb_write.hetatm(file, serial=ser_num, name=self._translate(mol.atom_name[i]), res_name=mol.res_name[i], chain_id=CHAIN_ID_LIST[index], res_seq=mol.res_num[i], x=mol.x[i], y=mol.y[i], z=mol.z[i], occupancy=1.0, temp_factor=0.0, element=mol.element[i]) _______________________________________________ relax (http://www.nmr-relax.com) This is the relax-commits mailing list relax-commits@gna.org To unsubscribe from this list, get a password reminder, or change your subscription options, visit the list information page at https://mail.gna.org/listinfo/relax-commits
