r6160 - /1.3/generic_fns/structure/api_base.py -- May 20, 2008 - 16:05

Author: bugman
Date: Tue May 20 15:44:03 2008
New Revision: 6160

URL: http://svn.gna.org/viewcvs/relax?rev=6160&view=rev
Log:
Updated the API stub methods atom_add() and atom_connect().


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=6160&r1=6159&r2=6160&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Tue May 20 15:44:03 2008
@@ -49,46 +49,44 @@
         self.structural_data = []
 
 
-    def atom_add(self, atom_id=None, record_name='', atom_name='', 
res_name='', chain_id='', res_num=None, pos=[None, None, None], 
segment_id='', element=''):
+    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):
         """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 atom_id:     The atom identifier.  This is used as the key 
within the dictionary.
-        @type atom_id:      str
-        @param record_name: The record name, e.g. 'ATOM', 'HETATM', or 'TER'.
-        @type record_name:  str
+        @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
+        @type atom_name:    str or None
         @param res_name:    The residue name.
-        @type res_name:     str
+        @type res_name:     str or None
         @param chain_id:    The chain identifier.
-        @type chain_id:     str
+        @type chain_id:     str or None
         @param res_num:     The residue number.
-        @type res_num:      int
+        @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
+        @type segment_id:   str or None
         @param element:     The element symbol.
-        @type element:      str
-        """
-
-        # Raise the error.
-        raise RelaxImplementError
-
-
-    def atom_connect(self, atom_id=None, bonded_id=None):
+        @type element:      str or None
+        """
+
+        # Raise the error.
+        raise RelaxImplementError
+
+
+    def atom_connect(self, index1=None, index2=None):
         """Prototype method stub for connecting two atoms within the data 
structure object.
 
-        This method will connect the atoms corresponding to atom_id and 
bonded_id.
-
-
-        @param atom_id:     The atom identifier.
-        @type atom_id:      str
-        @param bonded_id:   The second atom identifier.
-        @type bonded_id:    str
+        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
         """
 
         # Raise the error.