Author: bugman
Date: Thu Jan 15 18:30:08 2009
New Revision: 8485
URL: http://svn.gna.org/viewcvs/relax?rev=8485&view=rev
Log:
The internal PDB reader now has rudimentary support for element determination
if that column is missing.
Modified:
branches/multi_structure/generic_fns/structure/internal.py
Modified: branches/multi_structure/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8485&r1=8484&r2=8485&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Thu Jan 15
18:30:08 2009
@@ -28,7 +28,7 @@
import os
from os import F_OK, access
from re import search
-from string import split, strip, upper
+from string import digits, split, strip, upper
from warnings import warn
# relax module imports.
@@ -1321,6 +1321,29 @@
self.bonded[index2].append(index1)
+ def __det_pdb_element(self, atom_name):
+ """Try to determine the element from the PDB atom name.
+
+ @param atom_name: The PDB atom name.
+ @type atom_name: str
+ @return: The element name, or None if unsuccessful.
+ @rtype: str or None
+ """
+
+ # Strip away atom numbering, from the front and end.
+ element = strip(atom_name, digits)
+
+ # Allowed element list.
+ elements = ['H', 'C', 'N', 'O', 'F', 'P']
+
+ # Return the element, if in the list.
+ if element in elements:
+ return element
+
+ # Else, throw a warning.
+ warn(RelaxWarning("Cannot determine the element associated with atom
'%s'." % atom_name))
+
+
def fill_object_from_pdb(self, records):
"""Method for generating a complete Structure_container object from
the given PDB records.
@@ -1339,7 +1362,13 @@
# Add the atom.
if record[0] == 'ATOM' or record[0] == 'HETATM':
- self.atom_add(pdb_record=record[0], atom_num=record[1],
atom_name=record[2], res_name=record[4], chain_id=record[5], res_num=record[6],
pos=[record[8], record[9], record[10]], segment_id=record[13],
element=record[14])
+ # Attempt at determining the element, if missing.
+ element = record[14]
+ if not element:
+ element = self.__det_pdb_element(record[2])
+
+ # Add.
+ self.atom_add(pdb_record=record[0], atom_num=record[1],
atom_name=record[2], res_name=record[4], chain_id=record[5], res_num=record[6],
pos=[record[8], record[9], record[10]], segment_id=record[13], element=element)
# Connect atoms.
if record[0] == 'CONECT':
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