Author: bugman
Date: Tue Sep 23 18:05:23 2014
New Revision: 25972
URL: http://svn.gna.org/viewcvs/relax?rev=25972&view=rev
Log:
Added the selection() method to the internal structural object.
This parses the atom ID string using the lib.selection module, loops over the
molecules and atoms,
performs matches using re.search() via lib.selection, and populates and returns
the new
Internal_selection object. This can be used to pre-process the atom ID string
to save huge amounts
of time.
Modified:
trunk/lib/structure/internal/object.py
Modified: trunk/lib/structure/internal/object.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/structure/internal/object.py?rev=25972&r1=25971&r2=25972&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Tue Sep 23 18:05:23 2014
@@ -2322,6 +2322,53 @@
mol.z[i] = pos[2]
+ def selection(self, atom_id=None):
+ """Convert the atom ID string into a special internal selection object
for speed.
+
+ @keyword atom_id: The molecule, residue, and atom identifier string.
Only atoms matching this selection will be used.
+ @type atom_id: str or None
+ @return: The internal structural selection object.
+ @rtype: Internal_selection instance
+ """
+
+ # Initialise the internal structural selection object.
+ selection = Internal_selection()
+
+ # Generate the atom ID selection object.
+ sel_obj = None
+ if atom_id:
+ sel_obj = Selection(atom_id)
+
+ # Validate the models.
+ self.validate_models(verbosity=0)
+
+ # Obtain all data from the first model (except the position data).
+ model = self.structural_data[0]
+
+ # Loop over the molecules.
+ for mol_index in range(len(model.mol)):
+ mol = model.mol[mol_index]
+
+ # Skip non-matching molecules.
+ if sel_obj and not sel_obj.contains_mol(mol.mol_name):
+ continue
+
+ # Add the molecule index.
+ selection.add_mol(mol_index=mol_index)
+
+ # Loop over the atoms.
+ for i in range(len(mol.atom_num)):
+ # Skip non-matching atoms.
+ if sel_obj and not sel_obj.contains_spin(mol.atom_num[i],
mol.atom_name[i], mol.res_num[i], mol.res_name[i], mol.mol_name):
+ continue
+
+ # Add the atom index.
+ selection.add_atom(mol_index=mol_index, atom_index=i)
+
+ # Return the object.
+ return selection
+
+
def set_model(self, model_orig=None, model_new=None):
"""Set or reset the model number.
@keyword model_orig: The original model number. Leave as None if
no models are currently present.
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