Author: bugman
Date: Fri Jan 18 12:14:17 2013
New Revision: 18216
URL: http://svn.gna.org/viewcvs/relax?rev=18216&view=rev
Log:
Implemented the rdc.set_errors user function.
Modified:
trunk/generic_fns/rdc.py
trunk/user_functions/rdc.py
Modified: trunk/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/rdc.py?rev=18216&r1=18215&r2=18216&view=diff
==============================================================================
--- trunk/generic_fns/rdc.py (original)
+++ trunk/generic_fns/rdc.py Fri Jan 18 12:14:17 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2012 Edward d'Auvergne
#
+# Copyright (C) 2003-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -708,6 +708,48 @@
cdp.rdc_ids.append(align_id)
+def set_errors(align_id=None, spin_id1=None, spin_id2=None, sd=None):
+ """Set the RDC errors if not already present.
+
+ @keyword align_id: The optional alignment tensor ID string.
+ @type align_id: str
+ @keyword spin_id1: The optional spin ID string of the first spin.
+ @type spin_id1: None or str
+ @keyword spin_id2: The optional spin ID string of the second spin.
+ @type spin_id2: None or str
+ @keyword sd: The RDC standard deviation in Hz.
+ @type sd: float or int.
+ """
+
+ # Test if sequence data exists.
+ if not exists_mol_res_spin_data():
+ raise RelaxNoSequenceError
+
+ # Test if data corresponding to 'align_id' exists.
+ if not hasattr(cdp, 'rdc_ids') or (align_id and align_id not in
cdp.rdc_ids):
+ raise RelaxNoRDCError(align_id)
+
+ # Arg check.
+ if align_id and align_id not in cdp.rdc_ids:
+ raise RelaxError("The alignment ID '%s' is not in the RDC ID list
%s." % (align_id, cdp.rdc_ids))
+
+ # Convert the align IDs to an array, or take all IDs.
+ if align_id:
+ align_ids = [align_id]
+ else:
+ align_ids = cdp.rdc_ids
+
+ # Loop over the interatomic data.
+ for interatom in interatomic_loop(selection1=spin_id1,
selection2=spin_id2):
+ # No data structure.
+ if not hasattr(interatom, 'rdc_err'):
+ interatom.rdc_err = {}
+
+ # Set the error.
+ for id in align_ids:
+ interatom.rdc_err[id] = sd
+
+
def weight(align_id=None, spin_id=None, weight=1.0):
"""Set optimisation weights on the RDC data.
Modified: trunk/user_functions/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/rdc.py?rev=18216&r1=18215&r2=18216&view=diff
==============================================================================
--- trunk/user_functions/rdc.py (original)
+++ trunk/user_functions/rdc.py Fri Jan 18 12:14:17 2013
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2012 Edward d'Auvergne
#
+# Copyright (C) 2003-2013 Edward d'Auvergne
#
#
#
# This file is part of the program relax (http://www.nmr-relax.com).
#
#
#
@@ -32,6 +32,7 @@
# relax module imports.
from generic_fns import align_tensor, pipes, rdc
+from generic_fns.mol_res_spin import get_spin_ids
from graphics import WIZARD_IMAGE_PATH
from user_functions.data import Uf_info; uf_info = Uf_info()
from user_functions.objects import Desc_container
@@ -385,6 +386,54 @@
uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
+# The rdc.set_errors user function.
+uf = uf_info.add_uf('rdc.set_errors')
+uf.title = "Set the errors for the RDCs."
+uf.title_short = "RDC error setting."
+uf.add_keyarg(
+ name = "align_id",
+ py_type = "str",
+ desc_short = "alignment ID string",
+ desc = "The optional alignment ID string.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = align_tensor.get_ids,
+ wiz_read_only = True,
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_id1",
+ py_type = "str",
+ arg_type = "spin ID",
+ desc_short = "first spin ID string",
+ desc = "The optional spin ID string of the first spin.",
+ wiz_combo_iter = get_spin_ids,
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "spin_id2",
+ py_type = "str",
+ arg_type = "spin ID",
+ desc_short = "second spin ID string",
+ desc = "The optional spin ID string of the second spin.",
+ wiz_combo_iter = get_spin_ids,
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "sd",
+ default = 1.0,
+ py_type = "num",
+ desc_short = "RDC error (Hz)",
+ desc = "The RDC standard deviation value in Hertz."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("If the RDC errors have not already been read from
a RDC data file or if they need to be changed, then the errors can be set via
this user function.")
+uf.backend = rdc.set_errors
+uf.menu_text = "&set_errors"
+uf.gui_icon = "oxygen.actions.edit-rename"
+uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
+
+
# The rdc.weight user function.
uf = uf_info.add_uf('rdc.weight')
uf.title = "Set optimisation weights on the RDC data."
r18216 - in /trunk: generic_fns/rdc.py user_functions/rdc.py