Author: bugman
Date: Mon Jan 12 14:18:12 2009
New Revision: 8409
URL: http://svn.gna.org/viewcvs/relax?rev=8409&view=rev
Log:
Renamed __fill_object_from_pdb() to fill_object_from_pdb()
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=8409&r1=8408&r2=8409&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/internal.py (original)
+++ branches/multi_structure/generic_fns/structure/internal.py Mon Jan 12
14:18:12 2009
@@ -893,7 +893,7 @@
self.structural_data[-1].mol.add_item(mol_name=new_mol_name,
mol_cont=mol)
# Fill the molecular data object.
-
self.structural_data[-1].mol[-1].__fill_object_from_pdb(mol_records)
+
self.structural_data[-1].mol[-1].fill_object_from_pdb(mol_records)
# Increment the molecule index.
mol_index = mol_index + 1
@@ -1336,38 +1336,6 @@
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))
-
-
def atom_add(self, pdb_record=None, atom_num=None, atom_name=None,
res_name=None, chain_id=None, res_num=None, pos=[None, None, None],
segment_id=None, element=None):
"""Method for adding an atom to the structural data object.
@@ -1438,3 +1406,35 @@
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)
+
+
+ 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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