Author: bugman
Date: Fri Dec 12 16:06:47 2014
New Revision: 27110
URL: http://svn.gna.org/viewcvs/relax?rev=27110&view=rev
Log:
Expanded the displace_id argument for the structure.align user function.
This can now be a list of atom IDs, so that any atoms can be rotated together
with the structure
being aligned. This is useful if the molecules argument is supplied.
Modified:
trunk/pipe_control/structure/main.py
trunk/user_functions/structure.py
Modified: trunk/pipe_control/structure/main.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/structure/main.py?rev=27110&r1=27109&r2=27110&view=diff
==============================================================================
--- trunk/pipe_control/structure/main.py (original)
+++ trunk/pipe_control/structure/main.py Fri Dec 12 16:06:47 2014
@@ -117,8 +117,8 @@
@type molecules: None or list of str
@keyword atom_id: The molecule, residue, and atom identifier string.
This matches the spin ID string format.
@type atom_id: str or None
- @keyword displace_id: The atom ID string for restricting the
displacement to a subset of all atoms. If not set, then all atoms will be
translated and rotated.
- @type displace_id: str or None
+ @keyword displace_id: The atom ID string for restricting the
displacement to a subset of all atoms. If not set, then all atoms will be
translated and rotated. This can be a list of atom IDs with each element
corresponding to one of the structures.
+ @type displace_id: None, str, or list of str
@keyword method: The superimposition method. It must be one of
'fit to mean' or 'fit to first'.
@type method: str
@keyword centre_type: The type of centre to superimpose over. This can
either be the standard centroid superimposition or the CoM could be used
instead.
@@ -153,15 +153,24 @@
# Loop over all pipes, models, and molecules.
i = 0
for pipe_index, model_num, mol_name in structure_loop(pipes=pipes,
molecules=molecules, models=models, atom_id=atom_id):
+ # The current displacement ID.
+ curr_displace_id = None
+ if isinstance(displace_id, str):
+ curr_displace_id = displace_id
+ elif isinstance(displace_id, list):
+ if len(displace_id) <= i:
+ raise RelaxError("Not enough displacement ID strings have been
provided.")
+ curr_displace_id = displace_id[i]
+
# Add the molecule name to the displacement ID if required.
- id = displace_id
+ id = curr_displace_id
if molecules != None:
- if displace_id == None:
+ if curr_displace_id == None:
id = '#%s' % mol_name
- elif search('#', displace_id):
- id = displace_id
+ elif search('#', curr_displace_id):
+ id = curr_displace_id
else:
- id = '#%s%s' % (mol_name, displace_id)
+ id = '#%s%s' % (mol_name, curr_displace_id)
# Translate the molecule first (the rotational pivot is defined in the
first model).
translate(T=T[i], model=model_num, pipe_name=pipes[pipe_index],
atom_id=id)
Modified: trunk/user_functions/structure.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/structure.py?rev=27110&r1=27109&r2=27110&view=diff
==============================================================================
--- trunk/user_functions/structure.py (original)
+++ trunk/user_functions/structure.py Fri Dec 12 16:06:47 2014
@@ -197,9 +197,9 @@
)
uf.add_keyarg(
name = "displace_id",
- py_type = "str",
- desc_short = "displacement ID string",
- desc = "The atom identification string for restricting the displacement to
a subset of all atoms. If not set, then all atoms will be translated and
rotated.",
+ py_type = "str_or_str_list",
+ desc_short = "displacement ID string(s)",
+ desc = "The atom identification string for restricting the displacement to
a subset of all atoms. If not set, then all atoms will be translated and
rotated. If supplied as a list of IDs, then the number of items must match the
number of structures.",
can_be_none = True
)
uf.add_keyarg(
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