Author: bugman
Date: Thu Feb 5 14:41:36 2009
New Revision: 8741
URL: http://svn.gna.org/viewcvs/relax?rev=8741&view=rev
Log:
Massive speed up of the bond_vectors() method.
The algorithm used was very, very poorly designed. Now when setting the
profile flag to 1 gives the
following. Before in one test:
11168736 function calls (10986641 primitive calls) in 76.750 CPU
seconds
ncalls tottime percall cumtime percall filename:lineno(function)
758954 12.160 0.000 51.060 0.000
/home/edau/relax/relax-1.3/generic_fns/relax_re.py:31(search)
141 0.890 0.006 67.620 0.480
/home/edau/relax/relax-1.3/generic_fns/structure/internal.py:444(bond_vectors)
All other function call info lines have been removed. After the changes:
2586419 function calls (2579305 primitive calls) in 21.370 CPU
seconds
ncalls tottime percall cumtime percall filename:lineno(function)
62803 1.180 0.000 5.020 0.000
/home/edau/relax/relax-1.3/generic_fns/relax_re.py:31(search)
141 0.060 0.000 12.020 0.085
/home/edau/relax/relax-1.3/generic_fns/structure/internal.py:444(bond_vectors)
The difference is that the selection object is no longer used, as it is
completely unnecessary.
Modified:
1.3/generic_fns/structure/internal.py
1.3/generic_fns/structure/main.py
Modified: 1.3/generic_fns/structure/internal.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/internal.py?rev=8741&r1=8740&r2=8741&view=diff
==============================================================================
--- 1.3/generic_fns/structure/internal.py (original)
+++ 1.3/generic_fns/structure/internal.py Thu Feb 5 14:41:36 2009
@@ -72,7 +72,7 @@
@param attached_atom: The name of the attached atom to return.
@type attached_atom: str
- @param index: The index of the atom which the attached
atom is attached to.
+ @param index: The index of the atom which the attached
atom is attached to.
@type index: int
@param mol: The molecule container.
@type mol: MolContainer instance
@@ -441,18 +441,25 @@
break
- def bond_vectors(self, atom_id=None, attached_atom=None, model_num=None,
return_name=False, return_warnings=False):
+ def bond_vectors(self, attached_atom=None, model_num=None,
mol_name=None, res_num=None, res_name=None, spin_num=None, spin_name=None,
return_name=False, return_warnings=False):
"""Find the bond vector between the atoms of 'attached_atom' and
'atom_id'.
- @keyword atom_id: The molecule, residue, and atom
identifier string. This must
- correspond to a single atom in the
system.
- @type atom_id: str
@keyword attached_atom: The name of the bonded atom.
@type attached_atom: str
@keyword model_num: The model of which to return the vectors
from. If not supplied
and multiple models exist, then vectors
from all models will be
returned.
@type model_num: None or int
+ @keyword mol_name: The name of the molecule that
attached_atom belongs to.
+ @type mol_name: str
+ @keyword res_num: The number of the residue that
attached_atom belongs to.
+ @type res_num: str
+ @keyword res_name: The name of the residue that
attached_atom belongs to.
+ @type res_name: str
+ @keyword spin_num: The number of the spin that
attached_atom is attached to.
+ @type spin_num: str
+ @keyword spin_name: The name of the spin that attached_atom
is attached to.
+ @type spin_name: str
@keyword return_name: A flag which if True will cause the name
of the attached atom to
be returned together with the bond
vectors.
@type return_name: bool
@@ -463,9 +470,6 @@
return_warnings are set)
"""
- # Generate the selection object.
- sel_obj = Selection(atom_id)
-
# Initialise some objects.
vectors = []
attached_name = None
@@ -480,28 +484,29 @@
# Loop over the molecules.
for mol in model.mol:
# Skip non-matching molecules.
- if sel_obj and not sel_obj.contains_mol(mol.mol_name):
+ if mol_name and mol_name != mol.mol_name:
continue
- # Init.
- atom_found = False
-
- # Loop over all atoms.
- for i in xrange(len(mol.atom_name)):
- # 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):
+ # Find the atomic index of the base atom.
+ index = None
+ for i in range(len(mol.atom_name)):
+ # Residues don't match.
+ if (res_num != None and mol.res_num[i] != res_num) or
(res_name != None and mol.res_name[i] != res_name):
continue
+ # Atoms don't match.
+ if (spin_num != None and mol.atom_num[i] != spin_num) or
(spin_name != None and mol.atom_name[i] != spin_name):
+ continue
+
# More than one matching atom!
- if atom_found:
+ if index != None:
raise RelaxError, "The atom_id argument " +
`atom_id` + " must correspond to a single atom."
- # The atom has been found, so store some info.
- atom_found = True
+ # Update the index.
index = i
# Found the atom.
- if atom_found:
+ if index != None:
# Get the atom bonded to this
model/molecule/residue/atom.
bonded_num, bonded_name, element, pos, attached_name,
warnings = self.__bonded_atom(attached_atom, index, mol)
Modified: 1.3/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/structure/main.py?rev=8741&r1=8740&r2=8741&view=diff
==============================================================================
--- 1.3/generic_fns/structure/main.py (original)
+++ 1.3/generic_fns/structure/main.py Thu Feb 5 14:41:36 2009
@@ -361,7 +361,7 @@
continue
# Get the bond info.
- bond_vectors, attached_name, warnings =
cdp.structure.bond_vectors(atom_id=id, attached_atom=attached,
model_num=model, return_name=True, return_warnings=True)
+ bond_vectors, attached_name, warnings =
cdp.structure.bond_vectors(attached_atom=attached, model_num=model,
mol_name=mol_name, res_num=res_num, res_name=res_name, spin_num=spin.num,
spin_name=spin.name, return_name=True, return_warnings=True)
# No attached atom.
if not bond_vectors:
r8741 - in /1.3/generic_fns/structure: internal.py main.py