Author: bugman
Date: Fri Feb 20 15:49:23 2015
New Revision: 27700
URL: http://svn.gna.org/viewcvs/relax?rev=27700&view=rev
Log:
Bug fix for the SHEET PDB records created by the structure.write_pdb user
function.
The current and previous atom parts of the record were not being correctly
formatted. This was
simply using the %4s formatting string. However the PDB atom format is
rather more complicated. To
handle this, the new _handle_atom_name() helper function has been added to the
lib.structure.pdb_write module. This is now used in the atom() and sheet()
functions for
consistently formatting the atom name field.
Modified:
trunk/lib/structure/internal/object.py
trunk/lib/structure/pdb_write.py
Modified: trunk/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=27700&r1=27699&r2=27700&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Fri Feb 20 15:49:23 2015
@@ -3070,15 +3070,8 @@
if mol.pdb_record[i] in [None, 'ATOM']:
atom_record = True
- # 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:
- atom_name = " %s" % mol.atom_name[i]
- else:
- atom_name = "%s" % mol.atom_name[i]
-
# Write out.
- 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])
+ pdb_write.atom(file, serial=ser_num,
name=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, element=mol.element[i])
num_atom += 1
ser_num += 1
Modified: trunk/lib/structure/pdb_write.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/pdb_write.py?rev=27700&r1=27699&r2=27700&view=diff
==============================================================================
--- trunk/lib/structure/pdb_write.py (original)
+++ trunk/lib/structure/pdb_write.py Fri Feb 20 15:49:23 2015
@@ -30,6 +30,40 @@
# relax module imports.
from lib.errors import RelaxError
+
+
+def _handle_atom_name(name):
+ """Handle the funky PDB 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."
+
+
+ @param name: The atom name.
+ @type name: str or None
+ @return: The whitespace padded and PDB formatted atom name. This
will be exactly 4 characters.
+ @rtype: str
+ """
+
+ # Handle none.
+ if name == None:
+ name = " "
+
+ # Single letter name.
+ if len(name) == 1:
+ name = " %s " % name
+
+ # Two letter name.
+ elif len(name) == 2:
+ name = "%s " % name
+
+ # Three letter name.
+ elif len(name) == 3:
+ name = "%s " % name
+
+ # Return the name.
+ return name
def _handle_none(value):
@@ -283,7 +317,7 @@
text = "%-6s%5s %-4s%1s%3s %1s%4s%1s %8.3f%8.3f%8.3f%6.2f%6.2f
%2s%2s" % (
'ATOM',
_handle_none(serial),
- _handle_none(name),
+ _handle_atom_name(name),
_handle_none(alt_loc),
_handle_none(res_name),
_handle_none(chain_id),
@@ -1725,12 +1759,12 @@
_handle_none(end_seq_num),
_handle_none(end_icode),
_handle_none(sense),
- _handle_none(cur_atom),
+ _handle_atom_name(cur_atom),
_handle_none(cur_res_name),
_handle_none(cur_chain_id),
_handle_none(cur_res_seq),
_handle_none(cur_icode),
- _handle_none(prev_atom),
+ _handle_atom_name(prev_atom),
_handle_none(prev_res_name),
_handle_none(prev_chain_id),
_handle_none(prev_res_seq),
r27700 - in /trunk/lib/structure: internal/object.py pdb_write.py