Author: bugman
Date: Mon Jan 12 14:23:39 2009
New Revision: 8412
URL: http://svn.gna.org/viewcvs/relax?rev=8412&view=rev
Log:
Modified the atom_add() and atom_connect() methods to work within the
MolContainer.
Modified:
branches/multi_structure/generic_fns/structure/internal.py
Modified: branches/multi_structure/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/internal.py?rev=8412&r1=8411&r2=8412&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Mon Jan 12
14:23:39 2009
@@ -1362,25 +1362,19 @@
@type element: str or None
"""
- # Loop over the structures.
- for i in xrange(self.num):
- # Skip non-matching structures.
- if struct_index != None and struct_index != i:
- continue
-
- # Append to all the arrays.
- self.structural_data[i].atom_num.append(atom_num)
- self.structural_data[i].atom_name.append(atom_name)
- self.structural_data[i].bonded.append([])
- self.structural_data[i].chain_id.append(chain_id)
- self.structural_data[i].element.append(element)
- self.structural_data[i].pdb_record.append(pdb_record)
- self.structural_data[i].res_name.append(res_name)
- self.structural_data[i].res_num.append(res_num)
- self.structural_data[i].seg_id.append(segment_id)
- self.structural_data[i].x.append(pos[0])
- self.structural_data[i].y.append(pos[1])
- self.structural_data[i].z.append(pos[2])
+ # Append to all the arrays.
+ self.atom_num.append(atom_num)
+ self.atom_name.append(atom_name)
+ self.bonded.append([])
+ self.chain_id.append(chain_id)
+ self.element.append(element)
+ self.pdb_record.append(pdb_record)
+ self.res_name.append(res_name)
+ self.res_num.append(res_num)
+ self.seg_id.append(segment_id)
+ self.x.append(pos[0])
+ self.y.append(pos[1])
+ self.z.append(pos[2])
def atom_connect(self, index1=None, index2=None):
@@ -1395,17 +1389,11 @@
@type index2: int
"""
- # Loop over the structures.
- for i in xrange(self.num):
- # Skip non-matching structures.
- if struct_index != None and struct_index != i:
- continue
-
- # Update the bonded array structure, if necessary.
- if index2 not in self.structural_data[i].bonded[index1]:
- self.structural_data[i].bonded[index1].append(index2)
- if index1 not in self.structural_data[i].bonded[index2]:
- self.structural_data[i].bonded[index2].append(index1)
+ # Update the bonded array structure, if necessary.
+ if index2 not in self.bonded[index1]:
+ self.bonded[index1].append(index2)
+ if index1 not in self.bonded[index2]:
+ self.bonded[index2].append(index1)
def fill_object_from_pdb(self, records):
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