r5516 - /1.3/generic_fns/structure/api_base.py -- April 10, 2008 - 11:05

Author: bugman
Date: Thu Apr 10 11:05:05 2008
New Revision: 5516

URL: http://svn.gna.org/viewcvs/relax?rev=5516&view=rev
Log:
Made the structural API method atom_loop() much more flexible.

Each part of the tuple of atomic information can be individually selected to 
be yielded, and the
element name is now also returned.


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=5516&r1=5515&r2=5516&view=diff
==============================================================================
--- 1.3/generic_fns/structure/api_base.py (original)
+++ 1.3/generic_fns/structure/api_base.py Thu Apr 10 11:05:05 2008
@@ -88,23 +88,41 @@
         raise RelaxImplementError
 
 
-    def atom_loop(self, pos=False):
+    def atom_loop(self, mol_name=True, res_num=True, res_name=True, 
atom_num=True, atom_name=True, element=True, pos=True):
         """Prototype generator method stub for looping over all atoms in the 
structural data object.
 
         This method should be designed as a generator 
(http://www.python.org/dev/peps/pep-0255/).
-        It should loop over all atoms of the system yielding the molecule 
name, residue number and
-        name, and atom number and name.  If the pos argument is True, then 
the atom position should
-        also be yielded.
-
-
-        @keyword pos:   A flag which if True will cause the atom position to 
be yielded along with
-                        all the other information.
-        @type pos:      bool
-        @return:        A tuple consisting of the molecule name, residue 
number, residue name, atom
-                        number, and atom name.  If pos is True, then the 3D 
array of the atom
-                        position is also returned.
-        @rtype:         tuple (str, int, str, int, str) and if pos==True, 
(str, int, str, int, str,
-                        array of len 3)
+        It should loop over all atoms of the system yielding the following 
atomic information, if
+        the corresponding flag is True, in tuple form:
+
+            1.  Molecule name.
+            2.  Residue number.
+            3.  Residue name.
+            4.  Atom number.
+            5.  Atom name.
+            6.  The element name (its atomic symbol and optionally the 
isotope, e.g. 'N', 'Mg',
+                '17O', '13C', etc).
+            7.  The position of the atom in Euclidean space.
+
+
+        @keyword mol_name:  A flag which if True will cause the molecule 
name to be yielded.
+        @type mol_name:     bool
+        @keyword res_num:   A flag which if True will cause the residue 
number to be yielded.
+        @type res_num:      bool
+        @keyword res_name:  A flag which if True will cause the residue name 
to be yielded.
+        @type res_name:     bool
+        @keyword atom_num:  A flag which if True will cause the atom number 
to be yielded.
+        @type atom_num:     bool
+        @keyword atom_name: A flag which if True will cause the atom name to 
be yielded.
+        @type atom_name:    bool
+        @keyword element:   A flag which if True will cause the element name 
to be yielded.
+        @type element:      bool
+        @keyword pos:       A flag which if True will cause the atomic 
position to be yielded.
+        @type pos:          bool
+        @return:            A tuple of atomic information, as described in 
the docstring.
+        @rtype:             tuple with molecule name (str), residue number 
(int), residue name
+                            (str), atom number (int), atom name(str), 
element name (str), and atomic
+                            position (array of len 3).
         """
 
         # Raise the error.