Author: bugman
Date: Wed Feb 25 13:58:45 2015
New Revision: 27719
URL: http://svn.gna.org/viewcvs/relax?rev=27719&view=rev
Log:
Implemented the new 'inv' argument for the selection() structural object method.
This allows for all atoms not matching the atom ID string to be selected. The
unit tests for this
argument now all pass, validating the implementation.
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=27719&r1=27718&r2=27719&view=diff
==============================================================================
--- trunk/lib/structure/internal/object.py (original)
+++ trunk/lib/structure/internal/object.py Wed Feb 25 13:58:45 2015
@@ -38,7 +38,7 @@
from lib.check_types import is_float
from lib.errors import RelaxError, RelaxFault, RelaxNoneIntError,
RelaxNoPdbError
from lib.io import file_root, open_read_file
-from lib.selection import Selection
+from lib.selection import Selection, tokenise
from lib.sequence import aa_codes_three_to_one
from lib.structure import pdb_read, pdb_write
from lib.structure.internal.displacements import Displacements
@@ -2627,17 +2627,22 @@
mol.z[i] = pos[2]
- def selection(self, atom_id=None):
+ def selection(self, atom_id=None, inv=False):
"""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
+ @keyword inv: A flag which if True will cause the selection to
be inverted.
+ @type inv: bool
@return: The internal structural selection object.
@rtype: Internal_selection instance
"""
# Initialise the internal structural selection object.
selection = Internal_selection()
+
+ # Split up the atom ID, to see if a molecule has been specified.
+ mol_token, res_token, spin_token = tokenise(atom_id)
# Generate the atom ID selection object.
sel_obj = None
@@ -2655,8 +2660,14 @@
mol = model.mol[mol_index]
# Skip non-matching molecules.
- if sel_obj and not sel_obj.contains_mol(mol.mol_name):
- continue
+ if not inv:
+ if sel_obj and not sel_obj.contains_mol(mol.mol_name):
+ continue
+
+ # Skip matching molecules.
+ else:
+ if (not sel_obj) or (mol_token != None and
sel_obj.contains_mol(mol.mol_name)):
+ continue
# Add the molecule index.
selection.add_mol(mol_index=mol_index)
@@ -2664,8 +2675,14 @@
# 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
+ if not inv:
+ 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
+
+ # Skip matching atoms.
+ else:
+ if (not sel_obj) or 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)
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