r22135 - /trunk/lib/structure/internal/object.py -- February 05, 2014 - 17:16

Author: bugman
Date: Wed Feb  5 17:16:11 2014
New Revision: 22135

URL: http://svn.gna.org/viewcvs/relax?rev=22135&view=rev
Log:
Converted the chain ID list in the internal structural object to the 
CHAIN_ID_LIST module variable.


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=22135&r1=22134&r2=22135&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Wed Feb  5 17:16:11 2014
@@ -45,6 +45,9 @@
 from lib.structure.internal.molecules import MolContainer
 from lib.warnings import RelaxWarning
 
+
+# Module variables.
+CHAIN_ID_LIST = 
'ABCDEFGHIJKLMNOPQRSTUVWXYZ0123456789abcdefghijklmnopqrstuvwxyz'
 
 
 class Internal:
@@ -2384,9 +2387,6 @@
             if hasattr(model, 'num') and model.num != None:
                 model_records = True
 
-        # Chain IDs.
-        chain_id_list = 'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
-
 
         ####################
         # Hetrogen section #
@@ -2414,7 +2414,7 @@
                 # If the residue is not already stored initialise a new 
het_data element.
                 # (residue number, residue name, chain ID, number of atoms, 
atom count array).
                 if not het_data[index] or not mol.res_num[i] == 
het_data[index][-1][0]:
-                    het_data[index].append([mol.res_num[i], mol.res_name[i], 
chain_id_list[index], 0, []])
+                    het_data[index].append([mol.res_num[i], mol.res_name[i], 
CHAIN_ID_LIST[index], 0, []])
 
                     # Catch missing chain_ids.
                     if het_data[index][-1][2] == None:
@@ -2617,19 +2617,19 @@
                             atom_name = "%s" % mol.atom_name[i]
 
                         # Write out.
-                        pdb_write.atom(file, serial=atom_num, 
name=atom_name, res_name=mol.res_name[i], chain_id=chain_id_list[index], 
res_seq=mol.res_num[i], x=mol.x[i], y=mol.y[i], z=mol.z[i], occupancy=1.0, 
temp_factor=0, element=mol.element[i])
+                        pdb_write.atom(file, serial=atom_num, 
name=atom_name, res_name=mol.res_name[i], chain_id=CHAIN_ID_LIST[index], 
res_seq=mol.res_num[i], x=mol.x[i], y=mol.y[i], z=mol.z[i], occupancy=1.0, 
temp_factor=0, element=mol.element[i])
                         num_atom += 1
                         ser_num += 1
 
                         # Info for the TER record.
                         ter_num = atom_num + 1
                         ter_name = mol.res_name[i]
-                        ter_chain_id = chain_id_list[index]
+                        ter_chain_id = CHAIN_ID_LIST[index]
                         ter_res_num = mol.res_num[i]
 
                 # Finish the ATOM section with the TER record.
                 if atom_record:
-                    pdb_write.ter(file, serial=ser_num, res_name=ter_name, 
chain_id=chain_id_list[index], res_seq=ter_res_num)
+                    pdb_write.ter(file, serial=ser_num, res_name=ter_name, 
chain_id=CHAIN_ID_LIST[index], res_seq=ter_res_num)
                     num_ter += 1
                     ser_num += 1
 
@@ -2650,7 +2650,7 @@
                             atom_num += 1
 
                         # Write out.
-                        pdb_write.hetatm(file, serial=ser_num, 
name=self._translate(mol.atom_name[i]), res_name=mol.res_name[i], 
chain_id=chain_id_list[index], res_seq=mol.res_num[i], x=mol.x[i], 
y=mol.y[i], z=mol.z[i], occupancy=1.0, temp_factor=0.0, 
element=mol.element[i])
+                        pdb_write.hetatm(file, serial=ser_num, 
name=self._translate(mol.atom_name[i]), res_name=mol.res_name[i], 
chain_id=CHAIN_ID_LIST[index], res_seq=mol.res_num[i], x=mol.x[i], 
y=mol.y[i], z=mol.z[i], occupancy=1.0, temp_factor=0.0, 
element=mol.element[i])
                         num_hetatm += 1
                         ser_num += 1