Author: bugman
Date: Tue May 20 18:54:06 2008
New Revision: 6171
URL: http://svn.gna.org/viewcvs/relax?rev=6171&view=rev
Log:
Updated the atom_add(), atom_connect(), and terminate() API base class
methods for the model arg.
Modified:
1.3/generic_fns/structure/api_base.py
Modified: 1.3/generic_fns/structure/api_base.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/api_base.py?rev=6171&r1=6170&r2=6171&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Tue May 20 18:54:06 2008
@@ -49,44 +49,50 @@
self.structural_data = []
- 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):
"""Prototype method stub 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 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
- """
-
- # Raise the error.
- raise RelaxImplementError
-
-
- def atom_connect(self, index1=None, index2=None):
+ @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
+ """
+
+ # Raise the error.
+ raise RelaxImplementError
+
+
+ def atom_connect(self, index1=None, index2=None, model=None):
"""Prototype method stub for connecting two atoms within the data
structure object.
This method should connect the atoms corresponding to the two
indecies.
- @param index1: The index of the first atom.
- @type index1: int
- @param index2: The index of the second atom.
- @type index2: int
+ @keyword index1: The index of the first atom.
+ @type index1: int
+ @keyword index2: The index of the second atom.
+ @type index2: int
+ @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
"""
# Raise the error.
@@ -213,8 +219,13 @@
return len(self.structural_data)
- def terminate(self):
- """Prototype method stub for terminating the structural chain."""
+ def terminate(self, model=None):
+ """Prototype method stub for terminating the structural chain.
+
+ @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
+ """
# Raise the error.
raise RelaxImplementError
r6171 - /1.3/generic_fns/structure/api_base.py