Author: bugman
Date: Mon Jan 12 14:13:02 2009
New Revision: 8406
URL: http://svn.gna.org/viewcvs/relax?rev=8406&view=rev
Log:
Shifted __fill_object_from_pdb() from the Internal class to 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=8406&r1=8405&r2=8406&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Mon Jan 12
14:13:02 2009
@@ -192,42 +192,6 @@
# Return the information.
return bonded_num, bonded_name, element, pos, attached_name, None
-
-
- def __fill_object_from_pdb(self, records, model_index, mol_index):
- """Method for generating a complete Structure_container object from
the given PDB records.
-
- @param records: A list of structural PDB records.
- @type records: list of str
- @param model_index: The model index.
- @type model_index: int
- @param mol_index: The molecule index.
- @type mol_index: int
- """
-
- # Loop over the records.
- for record in records:
- # Parse the record.
- record = self.__parse_pdb_record(record)
-
- # Nothing to do.
- if not record:
- continue
-
- # Add the atom.
- if record[0] == 'ATOM' or record[0] == 'HETATM':
- self.atom_add(pdb_record=record[0], atom_num=record[1],
atom_name=record[2], res_name=record[4], chain_id=record[5], res_num=record[6],
pos=[record[8], record[9], record[10]], segment_id=record[13],
element=record[14], model_index=model_index, mol_index=mol_index)
-
- # Connect atoms.
- if record[0] == 'CONECT':
- # Loop over the atoms of the record.
- for i in xrange(len(record)-2):
- # Skip if there is no record.
- if record[i+2] == None:
- continue
-
- # Make the connection.
- self.atom_connect(index1=self.__atom_index(record[1],
struct_index), index2=self.__atom_index(record[i+2], struct_index),
struct_index=struct_index)
def __find_bonded_atoms(self, index, struct_index, radius=1.2):
@@ -1009,7 +973,7 @@
self.structural_data[-1].mol.add_item(mol_name=new_mol_name,
mol_cont=mol)
# Fill the molecular data object.
- self.__fill_object_from_pdb(mol_records,
model_index=len(self.structural_data),
mol_index=len(self.structural_data[-1].mol))
+
self.structural_data[-1].mol[-1].__fill_object_from_pdb(mol_records)
# Increment the molecule index.
mol_index = mol_index + 1
@@ -1450,3 +1414,35 @@
# The z coordinate (array of float).
self.z = []
+
+
+ def __fill_object_from_pdb(self, records):
+ """Method for generating a complete Structure_container object from
the given PDB records.
+
+ @param records: A list of structural PDB records.
+ @type records: list of str
+ """
+
+ # Loop over the records.
+ for record in records:
+ # Parse the record.
+ record = self.__parse_pdb_record(record)
+
+ # Nothing to do.
+ if not record:
+ continue
+
+ # Add the atom.
+ if record[0] == 'ATOM' or record[0] == 'HETATM':
+ self.atom_add(pdb_record=record[0], atom_num=record[1],
atom_name=record[2], res_name=record[4], chain_id=record[5], res_num=record[6],
pos=[record[8], record[9], record[10]], segment_id=record[13],
element=record[14])
+
+ # Connect atoms.
+ if record[0] == 'CONECT':
+ # Loop over the atoms of the record.
+ for i in xrange(len(record)-2):
+ # Skip if there is no record.
+ if record[i+2] == None:
+ continue
+
+ # Make the connection.
+ self.atom_connect(index1=self.__atom_index(record[1],
struct_index), index2=self.__atom_index(record[i+2], struct_index))
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