r8728 - /1.3/generic_fns/structure/scientific.py -- February 04, 2009 - 15:55

Author: bugman
Date: Wed Feb  4 15:55:49 2009
New Revision: 8728

URL: http://svn.gna.org/viewcvs/relax?rev=8728&view=rev
Log:
Fixes for the load_pdb() method.

Previously loaded structures were not being taken into account.


Modified:
    1.3/generic_fns/structure/scientific.py

Modified: 1.3/generic_fns/structure/scientific.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=8728&r1=8727&r2=8728&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Wed Feb  4 15:55:49 2009
@@ -41,6 +41,7 @@
 from generic_fns import pipes, relax_re
 from generic_fns.mol_res_spin import Selection, parse_token, tokenise
 from relax_errors import RelaxError, RelaxPdbLoadError
+from relax_io import file_root
 from relax_warnings import RelaxWarning, RelaxNoAtomWarning, 
RelaxNoPDBFileWarning, RelaxZeroVectorWarning
 
 
@@ -557,6 +558,17 @@
             mol_index = 0
             new_mol_name = []
 
+            # Set the target molecule number offset.
+            if set_mol_name:
+                mol_offset = [set_mol_name[mol_index]]
+            else:
+                # Number of structures already present for the model.
+                mol_offset = 0
+                for i in range(len(self.structural_data)):
+                    model_index = model_num - 1
+                    if not set_model_num or (model_index <= 
len(set_model_num) and set_model_num[model_index] == 
self.structural_data[i].num):
+                        mol_offset = len(self.structural_data[i].mol)
+
             # Store the original model number.
             orig_model_num.append(model_num)
 
@@ -571,7 +583,7 @@
                     mol_conts[-1].append(MolContainer())
                     mol_conts[-1][-1].data = mol
                     mol_conts[-1][-1].mol_type = 'protein'
-                    self.target_mol_name(set=set_mol_name, 
target=new_mol_name, index=mol_index, mol_num=mol_index+1, file=file)
+                    self.target_mol_name(set=set_mol_name, 
target=new_mol_name, index=mol_index, mol_num=mol_index+1+mol_offset, 
file=file)
                     mol_index = mol_index + 1
 
             # Then the nucleotide chains (generating the molecule names and 
incrementing the molecule index).
@@ -580,7 +592,7 @@
                     mol_conts[-1].append(MolContainer())
                     mol_conts[-1][-1].data = mol
                     mol_conts[-1][-1].mol_type = 'nucleic acid'
-                    self.target_mol_name(set=set_mol_name, 
target=new_mol_name, index=mol_index, mol_num=mol_index+1, file=file)
+                    self.target_mol_name(set=set_mol_name, 
target=new_mol_name, index=mol_index, mol_num=mol_index+1+mol_offset, 
file=file)
                     mol_index = mol_index + 1
 
             # Finally all other molecules (generating the molecule names and 
incrementing the molecule index).
@@ -596,7 +608,7 @@
                         mol_conts[-1][-1].data.append(mol)
 
                     # Update structures.
-                    self.target_mol_name(set=set_mol_name, 
target=new_mol_name, index=mol_index, mol_num=mol_index+1, file=file)
+                    self.target_mol_name(set=set_mol_name, 
target=new_mol_name, index=mol_index, mol_num=mol_index+1+mol_offset, 
file=file)
                     mol_index = mol_index + 1
 
             # Increment the model counter.