Author: bugman
Date: Thu Feb 19 14:55:06 2015
New Revision: 27673
URL: http://svn.gna.org/viewcvs/relax?rev=27673&view=rev
Log:
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:
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=27673&r1=27672&r2=27673&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Thu Feb 19 14:55:06 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])
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