Author: bugman
Date: Tue May 20 18:46:40 2008
New Revision: 6168
URL: http://svn.gna.org/viewcvs/relax?rev=6168&view=rev
Log:
Updated the atom_add() method to handle multiple models.
Modified:
1.3/generic_fns/structure/internal.py
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=6168&r1=6167&r2=6168&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Tue May 20 18:46:40 2008
@@ -288,42 +288,52 @@
raise RelaxError, "The structural data is invalid."
- def atom_add(self, pdb_record=None, atom_name=None, res_name=None,
chain_id=None, res_num=None, pos=[None, None, None], segment_id=None,
element=None):
+ def atom_add(self, pdb_record=None, atom_name=None, res_name=None,
chain_id=None, res_num=None, pos=[None, None, None], segment_id=None,
element=None, model=None):
"""Method for adding an atom to the structural data object.
This method will create the key-value pair for the given atom.
- @param pdb_record: The optional PDB record name, e.g. 'ATOM',
'HETATM', or 'TER'.
- @type pdb_record: str or None
- @param atom_name: The atom name, e.g. 'H1'.
- @type atom_name: str or None
- @param res_name: The residue name.
- @type res_name: str or None
- @param chain_id: The chain identifier.
- @type chain_id: str or None
- @param res_num: The residue number.
- @type res_num: int or None
- @param pos: The position vector of coordinates.
- @type pos: list (length = 3)
- @param segment_id: The segment identifier.
- @type segment_id: str or None
- @param element: The element symbol.
- @type element: str or None
- """
-
- # Append to all the arrays.
- self.structural_data.atom_name.append(atom_name)
- self.structural_data.bonded.append([])
- self.structural_data.chain_id.append(chain_id)
- self.structural_data.element.append(element)
- self.structural_data.pdb_record.append(pdb_record)
- self.structural_data.res_name.append(res_name)
- self.structural_data.res_num.append(res_num)
- self.structural_data.seg_id.append(segment_id)
- self.structural_data.x.append(pos[0])
- self.structural_data.y.append(pos[1])
- self.structural_data.z.append(pos[2])
+ @keyword pdb_record: The optional PDB record name, e.g. 'ATOM',
'HETATM', or 'TER'.
+ @type pdb_record: str or None
+ @keyword atom_name: The atom name, e.g. 'H1'.
+ @type atom_name: str or None
+ @keyword res_name: The residue name.
+ @type res_name: str or None
+ @keyword chain_id: The chain identifier.
+ @type chain_id: str or None
+ @keyword res_num: The residue number.
+ @type res_num: int or None
+ @keyword pos: The position vector of coordinates.
+ @type pos: list (length = 3)
+ @keyword segment_id: The segment identifier.
+ @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:
+ continue
+
+ # Append to all the arrays.
+ 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])
def atom_connect(self, index1=None, index2=None):
r6168 - /1.3/generic_fns/structure/internal.py