Author: bugman
Date: Wed Feb 11 10:48:24 2015
New Revision: 27626
URL: http://svn.gna.org/viewcvs/relax?rev=27626&view=rev
Log:
Modified the structure.read_pdb user function backend to skip water molecules.
All residues with the name 'HOH' are now skipped when loading PDB files. This
is implemented in the
MolContainer.fill_object_from_pdb() method, and a RelaxWarning is printed
listing the residue
numbers of all skipped waters.
Modified:
trunk/lib/structure/internal/molecules.py
Modified: trunk/lib/structure/internal/molecules.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/molecules.py?rev=27626&r1=27625&r2=27626&view=diff
==============================================================================
--- trunk/lib/structure/internal/molecules.py (original)
+++ trunk/lib/structure/internal/molecules.py Wed Feb 11 10:48:24 2015
@@ -388,6 +388,7 @@
"""
# Loop over the records.
+ water = []
for record in records:
# Nothing to do.
if not record or record == '\n':
@@ -401,6 +402,11 @@
if record[:6] == 'HETATM':
record_type, serial, name, alt_loc, res_name, chain_id,
res_seq, icode, x, y, z, occupancy, temp_factor, element, charge =
pdb_read.hetatm(record)
+ # Skip waters.
+ if res_name == 'HOH':
+ water.append(res_seq)
+ continue
+
# Handle the alternate locations.
if alt_loc != None:
# Don't know what to do.
@@ -435,6 +441,9 @@
# Make the connection.
self.atom_connect(index1=self._atom_index(serial),
index2=self._atom_index(bonded))
+
+ if len(water):
+ warn(RelaxWarning("Skipping the water molecules HOH %s." % water))
def fill_object_from_xyz(self, records):
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
[email protected]
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
