Author: bugman
Date: Fri Jan 16 13:43:37 2009
New Revision: 8494
URL: http://svn.gna.org/viewcvs/relax?rev=8494&view=rev
Log:
Support for models vs. molecules and elimination of struct_index in vectors().
Modified:
branches/multi_structure/generic_fns/structure/main.py
Modified: branches/multi_structure/generic_fns/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/branches/multi_structure/generic_fns/structure/main.py?rev=8494&r1=8493&r2=8494&view=diff
==============================================================================
--- branches/multi_structure/generic_fns/structure/main.py (original)
+++ branches/multi_structure/generic_fns/structure/main.py Fri Jan 16 13:43:37
2009
@@ -255,8 +255,8 @@
spin.xh_vect = xh_vect
-def vectors(attached=None, spin_id=None, struct_index=None, verbosity=1,
ave=True, unit=True):
- """Extract the bond vectors from the loaded structures.
+def vectors(attached=None, spin_id=None, model=None, verbosity=1, ave=True,
unit=True):
+ """Extract the bond vectors from the loaded structures and store them in
the spin container.
@keyword attached: The name of the atom attached to the spin, as
given in the structural
file. Regular expression can be used, for example
'H*'. This uses
@@ -264,9 +264,9 @@
@type attached: str
@keyword spin_id: The spin identifier string.
@type spin_id: str
- @keyword struct_index: The index of the structure to extract the vector
from. If None, all
+ @keyword model: The index of the structure to extract the vector
from. If None, all
vectors will be extracted.
- @type struct_index: str
+ @type model: str
@keyword verbosity: The higher the value, the more information is
printed to screen.
@type verbosity: int
@keyword ave: A flag which if True will cause the average of all
vectors to be
@@ -290,21 +290,21 @@
# Print out.
if verbosity:
- # Number of structures.
- num = cdp.structure.num_structures()
-
- # Multiple structures loaded.
- if num > 1:
- if struct_index:
- print "Extracting vectors for structure " + `struct_index` +
"."
+ # Number of models.
+ num_models = cdp.structure.num_models()
+
+ # Multiple models loaded.
+ if num_models > 1:
+ if model:
+ print "Extracting vectors for model '%s'." % model
else:
- print "Extracting vectors for all " + `num` + " structures."
+ print "Extracting vectors for all %s models." % num_models
if ave:
print "Averaging all vectors."
- # Single structure loaded.
- else:
- print "Extracting vectors from the single structure."
+ # Single model loaded.
+ else:
+ print "Extracting vectors from the single model."
# Unit vectors.
if unit:
@@ -333,12 +333,12 @@
if not spin.select:
continue
- # The spin identification string. The residue name is not included to
allow structures with point mutations to be used.
+ # The spin identification string. The residue name is not included to
allow molecules with point mutations to be used as different models.
id = generate_spin_id(mol_name=mol_name, res_num=res_num,
res_name=None, spin_num=spin.num, spin_name=spin.name)
# Test that the spin number or name are set (one or both are essential
for the identification of the atom).
if spin.num == None and spin.name == None:
- warn(RelaxWarning("Either the spin number or name must be set for
the spin " + `id` + " to identify the corresponding atom in the structure."))
+ warn(RelaxWarning("Either the spin number or name must be set for
the spin " + `id` + " to identify the corresponding atom in the molecule."))
continue
# The bond vector already exists.
@@ -349,7 +349,7 @@
continue
# Get the bond info.
- bond_vectors, attached_name, warnings =
cdp.structure.bond_vectors(atom_id=id, attached_atom=attached,
struct_index=struct_index, return_name=True, return_warnings=True)
+ bond_vectors, attached_name, warnings =
cdp.structure.bond_vectors(atom_id=id, attached_atom=attached, model=model,
return_name=True, return_warnings=True)
# No attached atom.
if not bond_vectors:
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