Author: bugman
Date: Fri Jul 2 10:53:18 2010
New Revision: 11275
URL: http://svn.gna.org/viewcvs/relax?rev=11275&view=rev
Log:
The fix flag is now accepted by the paramag.centre() user function.
Modified:
1.3/generic_fns/paramag.py
1.3/prompt/paramag.py
Modified: 1.3/generic_fns/paramag.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/paramag.py?rev=11275&r1=11274&r2=11275&view=diff
==============================================================================
--- 1.3/generic_fns/paramag.py (original)
+++ 1.3/generic_fns/paramag.py Fri Jul 2 10:53:18 2010
@@ -37,7 +37,7 @@
from relax_warnings import RelaxWarning
-def centre(pos=None, atom_id=None, pipe=None, verbosity=1, ave_pos=False,
force=False):
+def centre(pos=None, atom_id=None, pipe=None, verbosity=1, fix=True,
ave_pos=False, force=False):
"""Specify the atom in the loaded structure corresponding to the
paramagnetic centre.
@keyword pos: The atomic position. If set, the atom_id string
will be ignored.
@@ -48,9 +48,12 @@
@type pipe: None or str
@keyword verbosity: The amount of information to print out. The bigger
the number, the more information.
@type verbosity: int
+ @keyword fix: A flag which if False causes the paramagnetic centre
to be optimised during minimisation.
+ @type fix: bool
@keyword ave_pos: A flag which if True causes the atomic positions
from multiple models to be averaged.
@type ave_pos: bool
@keyword force: A flag which if True will cause the current
paramagnetic centre to be overwritten.
+ @type force: bool
"""
# The data pipe.
@@ -124,3 +127,6 @@
if verbosity:
print("\nUsing all paramagnetic positions.")
cdp.paramagnetic_centre = full_pos_list
+
+ # The fixed flag.
+ cdp.paramag_centre_fix = fix
Modified: 1.3/prompt/paramag.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/paramag.py?rev=11275&r1=11274&r2=11275&view=diff
==============================================================================
--- 1.3/prompt/paramag.py (original)
+++ 1.3/prompt/paramag.py Fri Jul 2 10:53:18 2010
@@ -34,7 +34,7 @@
class PCS(User_fn_class):
"""Class for handling paramagnetic information."""
- def centre(self, pos=None, atom_id=None, pipe=None, verbosity=1,
ave_pos=True, force=False):
+ def centre(self, pos=None, atom_id=None, pipe=None, verbosity=1,
fix=True, ave_pos=True, force=False):
"""Specify which atom is the paramagnetic centre.
Keyword Arguments
@@ -47,6 +47,8 @@
pipe: The data pipe containing the structures to extract the centre
from.
verbosity: The amount of information to print out.
+
+ fix: A flag specifying if the paramagnetic centre should be fixed
during optimisation.
ave_pos: A flag specifying if the position of the atom is to be
averaged across all models.
@@ -89,6 +91,10 @@
relax> pcs.centre([0.136, 12.543, 4.356])
relax> pcs.centre(pos=[0.136, 12.543, 4.356])
+
+ To find an unknown paramagnetic centre, type:
+
+ relax> pcs.centre(fix=False)
"""
# Function intro text.
@@ -98,6 +104,7 @@
text = text + ", atom_id=" + repr(atom_id)
text = text + ", pipe=" + repr(pipe)
text = text + ", verbosity=" + repr(verbosity)
+ text = text + ", fix=" + repr(fix)
text = text + ", ave_pos=" + repr(ave_pos)
text = text + ", force=" + repr(force) + ")"
print(text)
@@ -107,8 +114,9 @@
arg_check.is_str(atom_id, 'atom ID string', can_be_none=True)
arg_check.is_str(pipe, 'data pipe', can_be_none=True)
arg_check.is_int(verbosity, 'verbosity level')
+ arg_check.is_bool(fix, 'fix flag')
arg_check.is_bool(ave_pos, 'average position flag')
arg_check.is_bool(force, 'force flag')
# Execute the functional code.
- paramag.centre(pos=pos, atom_id=atom_id, pipe=pipe,
verbosity=verbosity, ave_pos=ave_pos, force=force)
+ paramag.centre(pos=pos, atom_id=atom_id, pipe=pipe,
verbosity=verbosity, fix=fix, ave_pos=ave_pos, force=force)
r11275 - in /1.3: generic_fns/paramag.py prompt/paramag.py