r5584 - /1.3/generic_fns/structure/scientific.py -- April 11, 2008 - 16:30

Author: bugman
Date: Fri Apr 11 16:30:20 2008
New Revision: 5584

URL: http://svn.gna.org/viewcvs/relax?rev=5584&view=rev
Log:
Created the private __molecule_loop() method.

This is for looping over the individual molecules of the scientific data 
structures.


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=5584&r1=5583&r2=5584&view=diff
==============================================================================
--- 1.3/generic_fns/structure/scientific.py (original)
+++ 1.3/generic_fns/structure/scientific.py Fri Apr 11 16:30:20 2008
@@ -49,6 +49,64 @@
 
     # Identification string.
     id = 'scientific'
+
+
+    def __molecule_loop(self, struct, molecules):
+        """Generator function for looping over all molecules in the 
Scientific PDB data objects.
+
+        @param struct:      The individual structure object, the highest 
level Scientific Python PDB
+                            object.
+        @type struct:       Scientific Python PDB object
+        @param molecules:   A list of molecule names.  If non-empty, only 
molecules found in this
+                            list will be returned.
+        @type molecules:    list of str
+        @return:            A tuple of the Scientific Python PDB object 
representing a single
+                            molecule, the molecule name, and molecule type.
+        @rtype:             (Scientific Python PDB object, str, str)
+        """
+
+        # Protein.
+        if struct.peptide_chains:
+            for chain in struct.peptide_chains:
+                # The molecule name.
+                if hasattr(chain, 'chain_id') and chain.chain_id:
+                    mol_name = chain.chain_id
+                elif hasattr(chain, 'segment_id') and chain.segment_id:
+                    mol_name = chain.segment_id
+                else:
+                    mol_name = None
+
+                # Skip non-matching molecules.
+                if molecules and mol_name not in molecules:
+                    continue
+
+                # Yield the molecule and its name.
+                yield chain, mol_name, 'protein'
+
+        # RNA/DNA.
+        if struct.nucleotide_chains:
+            for chain in struct.nucleotide_chains:
+                # The molecule name.
+                if hasattr(chain, 'chain_id') and chain.chain_id:
+                    mol_name = chain.chain_id
+                elif hasattr(chain, 'segment_id') and chain.segment_id:
+                    mol_name = chain.segment_id
+                else:
+                    mol_name = None
+
+                # Skip non-matching molecules.
+                if molecules and mol_name not in molecules:
+                    continue
+
+                # Yield the molecule and its name.
+                yield chain, mol_name, 'nucleic acid'
+
+        # Other molecules.
+        if struct.molecules:
+            for key in struct.molecules:
+                for mol in struct.molecules[key]:
+                    # Yield the molecule and its name.
+                    yield mol, key, 'other'
 
 
     def atom_loop(self, atom_id=None, mol_name_flag=False, 
res_num_flag=False, res_name_flag=False, atom_num_flag=False, 
atom_name_flag=False, element_flag=False, pos_flag=False):