Author: bugman
Date: Fri Jul 4 17:58:14 2008
New Revision: 6678
URL: http://svn.gna.org/viewcvs/relax?rev=6678&view=rev
Log:
Bug fix for the loading of multiple files.
Each time a new file was loaded, all its atoms would be appended to all other
presently loaded
structures. This would cause large slow downs of the atom_loop() function,
and a few other
problems. Now structures are referenced by structure index rather than model
number.
Modified:
branches/rdc_analysis/generic_fns/structure/internal.py
Modified: branches/rdc_analysis/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/branches/rdc_analysis/generic_fns/structure/internal.py?rev=6678&r1=6677&r2=6678&view=diff
==============================================================================
--- branches/rdc_analysis/generic_fns/structure/internal.py (original)
+++ branches/rdc_analysis/generic_fns/structure/internal.py Fri Jul 4
17:58:14 2008
@@ -49,34 +49,27 @@
id = 'internal'
- def __fill_object_from_pdb(self, records, model=None):
+ def __fill_object_from_pdb(self, records, struct_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
- @keyword model: The model to add the data to. If not supplied
and multiple models
- exist, then the data will be added to all models.
- @type model: None or int
- """
-
- # Loop over the models.
- for struct in self.structural_data:
- # Skip non-matching models.
- if model != None and model != struct.model:
- continue
-
- # 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=model)
+ @param records: A list of structural PDB records.
+ @type records: list of str
+ @param struct_index: The index of the structural container to add
the data to.
+ @type struct_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], struct_index=struct_index)
def __get_chemical_name(self, hetID):
@@ -297,7 +290,7 @@
raise RelaxError, "The structural data is invalid."
- 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, model=None):
+ 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, struct_index=None):
"""Method for adding an atom to the structural data object.
This method will create the key-value pair for the given atom.
@@ -321,31 +314,32 @@
@type segment_id: str or None
@keyword element: The element symbol.
@type element: str or None
- @keyword model: The model to add the atom to. If not
supplied and multiple models
- exist, then the atom will be added to all
models.
- @type model: None or int
- """
-
-
- # Loop over the models.
- for struct in self.structural_data:
- # Skip non-matching models.
- if model != None and model != struct.model:
+ @keyword struct_index: The index of the structure to add the atom
to. If not supplied and
+ multiple structures or models are loaded,
then the atom will be
+ added to all structures.
+ @type struct_index: None or int
+ """
+
+
+ # Loop over the structures.
+ for i in xrange(len(self.structural_data)):
+ # Skip non-matching structures.
+ if struct_index != None and struct_index != i:
continue
# Append to all the arrays.
- struct.atom_num.append(atom_num)
- struct.atom_name.append(atom_name)
- struct.bonded.append([])
- struct.chain_id.append(chain_id)
- struct.element.append(element)
- struct.pdb_record.append(pdb_record)
- struct.res_name.append(res_name)
- struct.res_num.append(res_num)
- struct.seg_id.append(segment_id)
- struct.x.append(pos[0])
- struct.y.append(pos[1])
- struct.z.append(pos[2])
+ 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])
def atom_connect(self, index1=None, index2=None, model=None):
@@ -551,7 +545,7 @@
# Initialise and fill the structural data object.
self.structural_data.append(Structure_container())
self.structural_data[-1].model = model_num
- self.__fill_object_from_pdb(records, model_num)
+ self.__fill_object_from_pdb(records, len(self.structural_data)-1)
def terminate(self, model=None):
r6678 - /branches/rdc_analysis/generic_fns/structure/internal.py