r5520 - /1.3/generic_fns/structure/scientific.py -- April 10, 2008 - 11:19

Author: bugman
Date: Thu Apr 10 11:19:07 2008
New Revision: 5520

URL: http://svn.gna.org/viewcvs/relax?rev=5520&view=rev
Log:
Updated the Scientific Python structural API atom_loop() method.

All the flags are now accepted, and the appropriate tuple is now built.


Modified:
    1.3/generic_fns/structure/scientific.py

Modified: 1.3/generic_fns/structure/scientific.py
URL: 
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/scientific.py?rev=5520&r1=5519&r2=5520&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Thu Apr 10 11:19:07 2008
@@ -51,20 +51,30 @@
     id = 'scientific'
 
 
-    def atom_loop(self, atom_id=None, pos=False):
+    def atom_loop(self, atom_id=None, mol_name=False, res_num=False, 
res_name=False, atom_num=False, atom_name=False, element=False, pos=False):
         """Generator function for looping over all atoms in the Scientific 
Python data objects.
 
         @keyword atom_id:   The molecule, residue, and atom identifier 
string.  Only atoms matching
                             this selection will be yielded.
         @type atom_id:      str
-        @keyword pos:       A flag which if True will cause the atom 
position to be yielded along
-                            with all the other information.
+        @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 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)
+        @return:            A tuple of atomic information, as described in 
the API method 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).
         """
 
         # Split up the selection string.
@@ -129,11 +139,25 @@
                         if atom_token and not (atom_name in atoms or 
atom_num in atoms):
                             continue
 
+                        # Build the tuple to be yielded.
+                        atomic_tuple = ()
+                        if mol_name:
+                            atomic_tuple = atomic_tuple + (mol_name,)
+                        if res_num:
+                            atomic_tuple = atomic_tuple + (res_num,)
+                        if res_name:
+                            atomic_tuple = atomic_tuple + (res_name,)
+                        if atom_num:
+                            atomic_tuple = atomic_tuple + (atom_num,)
+                        if atom_name:
+                            atomic_tuple = atomic_tuple + (atom_name,)
+                        if element:
+                            atomic_tuple = atomic_tuple + (element,)
+                        if pos:
+                            atomic_tuple = atomic_tuple + (pos,)
+
                         # Yield the information.
-                        if pos:
-                            yield mol_name, res_num, res_name, atom_num, 
atom_name, pos
-                        else:
-                            yield mol_name, res_num, res_name, atom_num, 
atom_name
+                        yield atomic_tuple
 
 
     def load_structures(self, file_path, model, verbosity=False):