Author: bugman
Date: Thu Jan 15 10:01:00 2009
New Revision: 8449
URL: http://svn.gna.org/viewcvs/relax?rev=8449&view=rev
Log:
A number of bug fixes for the Scientific python structural object load_pdb()
method.
The molecules are now also taken from the peptide_chains and nucleotide_chains
structures, as the
molecules dictionary doesn't contain proteins or RNA!
Modified:
branches/multi_structure/generic_fns/structure/scientific.py
Modified: branches/multi_structure/generic_fns/structure/scientific.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/scientific.py?rev=8449&r1=8448&r2=8449&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/scientific.py (original)
+++ branches/multi_structure/generic_fns/structure/scientific.py Thu Jan 15
10:01:00 2009
@@ -603,12 +603,6 @@
if read_model and model_num not in read_model:
continue
- # Append an empty list to the molecule container structure for a
new model.
- mol_conts.append([])
-
- # Store the original model number.
- orig_model_num.append(model_num)
-
# Load the PDB file.
model = Scientific.IO.PDB.Structure(file_path, model_num)
@@ -627,11 +621,25 @@
del model
break
+ # Append an empty list to the molecule container structure for a
new model.
+ mol_conts.append([])
+
+ # Store the original model number.
+ orig_model_num.append(model_num)
+
# Print the PDB info.
if verbosity:
print model
- # Append the molecules.
+ # First add the peptide chains.
+ for mol in model.peptide_chains:
+ mol_conts[-1].append(mol)
+
+ # Then the nucleotide chains.
+ for mol in model.nucleotide_chains:
+ mol_conts[-1].append(mol)
+
+ # Finally all other molecules.
for key in model.molecules.keys():
mol_conts[-1].append(model.molecules[key])
@@ -639,7 +647,6 @@
model_num = model_num + 1
# Create the structural data data structures.
- print mol_conts
self.pack_structs(mol_conts, orig_model_num=orig_model_num,
set_model_num=set_model_num, orig_mol_num=range(1, len(mol_conts[0])),
set_mol_name=set_mol_name)
# Loading worked.
_______________________________________________
relax (http://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
