Author: bugman
Date: Fri Dec 12 12:22:03 2014
New Revision: 27107
URL: http://svn.gna.org/viewcvs/relax?rev=27107&view=rev
Log:
Improvement for the merge argument of the structure.read_pdb user function.
This argument is now overridden if the molecule to merge to does not exist.
This allows the merge
flag to be used together with read_mol and set_mol_name set to lists.
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=27107&r1=27106&r2=27107&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Fri Dec 12 12:22:03 2014
@@ -2334,16 +2334,25 @@
# Loop over the molecules.
for j in range(len(set_mol_name)):
+ # Override the merge argument if the molecule does not exist.
+ found = False
+ merge_new = True
+ for k in range(len(model.mol)):
+ if model.mol[k].mol_name == set_mol_name[j]:
+ found = True
+ if not found:
+ merge_new = False
+
# Printout.
if verbosity:
- if merge:
+ if merge_new:
print("Merging with model %s of molecule '%s' (from
the original molecule number %s of model %s)" % (set_model_num[i],
set_mol_name[j], orig_mol_num[j], orig_model_num[i]))
else:
print("Adding molecule '%s' to model %s (from the
original molecule number %s of model %s)" % (set_mol_name[j], set_model_num[i],
orig_mol_num[j], orig_model_num[i]))
# The index of the new molecule to add or merge.
index = len(model.mol)
- if merge:
+ if merge_new:
index -= 1
# Consistency check.
@@ -2351,7 +2360,7 @@
raise RelaxError("The new molecule name of '%s' in model
%s does not match the corresponding molecule's name of '%s' in model %s." %
(set_mol_name[j], set_model_num[i],
self.structural_data[0].mol[index].mol_name, self.structural_data[0].num))
# Pack the structures.
- if merge:
+ if merge_new:
mol = model.mol.merge_item(mol_name=set_mol_name[j],
mol_cont=data_matrix[i][j])
else:
mol = model.mol.add_item(mol_name=set_mol_name[j],
mol_cont=data_matrix[i][j])
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