Author: bugman
Date: Wed Feb 25 14:16:04 2015
New Revision: 27721
URL: http://svn.gna.org/viewcvs/relax?rev=27721&view=rev
Log:
Added the new 'atom_id' argument to the frame_order.distribute user function.
This uses the new inverse selection functionality recently introduced into the
trunk to delete all
structural data not matching the atom_id from the copy of the loaded structural
data string prior to
generating the distribution of structures.
Modified:
branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
branches/frame_order_cleanup/user_functions/frame_order.py
Modified: branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/specific_analyses/frame_order/uf.py?rev=27721&r1=27720&r2=27721&view=diff
==============================================================================
--- branches/frame_order_cleanup/specific_analyses/frame_order/uf.py
(original)
+++ branches/frame_order_cleanup/specific_analyses/frame_order/uf.py Wed Feb
25 14:16:04 2015
@@ -47,13 +47,15 @@
from specific_analyses.frame_order.parameters import assemble_param_vector,
update_model
-def distribute(file="distribution.pdb.bz2", dir=None, total=1000,
max_rotations=100000, model=1, force=True):
+def distribute(file="distribution.pdb.bz2", dir=None, atom_id=None,
total=1000, max_rotations=100000, model=1, force=True):
"""Create a uniform distribution of structures for the frame order motions.
@keyword file: The PDB file for storing the frame order motional
distribution. The compression is determined automatically by the file
extensions '*.pdb', '*.pdb.gz', and '*.pdb.bz2'.
@type file: str
@keyword dir: The directory name to place the file into.
@type dir: str or None
+ @keyword atom_id: The atom identification string to allow the
distribution to be a subset of all atoms.
+ @type atom_id: None or str
@keyword total: The total number of states/model/structures in the
distribution.
@type total: int
@keyword max_rotations: The maximum number of rotations to generate the
distribution from. This prevents an execution for an infinite amount of time
when a frame order amplitude parameter is close to zero so that the subset of
all rotations within the distribution is close to zero.
@@ -108,6 +110,14 @@
# The motional eigenframe.
frame = generate_axis_system()
+
+ # Only work with a subset.
+ if atom_id:
+ # The inverted selection.
+ selection = structure.selection(atom_id=atom_id, inv=True)
+
+ # Delete the data.
+ structure.delete(selection=selection, verbosity=0)
# Create the distribution.
uniform_distribution(file=file, model=cdp.model, structure=structure,
parameters=params, eigenframe=frame, pivot=pivot, atom_id=domain_moving(),
total=total, max_rotations=max_rotations)
Modified: branches/frame_order_cleanup/user_functions/frame_order.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_cleanup/user_functions/frame_order.py?rev=27721&r1=27720&r2=27721&view=diff
==============================================================================
--- branches/frame_order_cleanup/user_functions/frame_order.py (original)
+++ branches/frame_order_cleanup/user_functions/frame_order.py Wed Feb 25
14:16:04 2015
@@ -83,6 +83,13 @@
arg_type = "dir",
desc_short = "directory name",
desc = "The directory where the files are to be located.",
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "atom_id",
+ py_type = "str",
+ desc_short = "atom identification string",
+ desc = "The atom identification string to allow the distribution to be a
subset of all atoms.",
can_be_none = True
)
uf.add_keyarg(
_______________________________________________
relax (http://www.nmr-relax.com)
This is the relax-commits mailing list
[email protected]
To unsubscribe from this list, get a password
reminder, or change your subscription options,
visit the list information page at
https://mail.gna.org/listinfo/relax-commits
