Author: bugman
Date: Fri Jan 18 12:21:25 2013
New Revision: 18217
URL: http://svn.gna.org/viewcvs/relax?rev=18217&view=rev
Log:
Implemented the pcs.set_error user function.
Modified:
trunk/generic_fns/pcs.py
trunk/user_functions/pcs.py
Modified: trunk/generic_fns/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/generic_fns/pcs.py?rev=18217&r1=18216&r2=18217&view=diff
==============================================================================
--- trunk/generic_fns/pcs.py (original)
+++ trunk/generic_fns/pcs.py Fri Jan 18 12:21:25 2013
@@ -668,6 +668,54 @@
cdp.pcs_ids.append(align_id)
+def set_errors(align_id=None, spin_id=None, sd=None):
+ """Set the PCS errors if not already present.
+
+ @keyword align_id: The optional alignment tensor ID string.
+ @type align_id: str
+ @keyword spin_id: The optional spin ID string.
+ @type spin_id: None or str
+ @keyword sd: The PCS standard deviation in ppm.
+ @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, 'pcs_ids') or (align_id and align_id not in
cdp.pcs_ids):
+ raise RelaxNoPCSError(align_id)
+
+ # Arg check.
+ if align_id and align_id not in cdp.pcs_ids:
+ raise RelaxError("The alignment ID '%s' is not in the PCS ID list
%s." % (align_id, cdp.pcs_ids))
+
+ # Convert the align IDs to an array, or take all IDs.
+ if align_id:
+ align_ids = [align_id]
+ else:
+ align_ids = cdp.pcs_ids
+
+ # Loop over the spins.
+ for spin in spin_loop(spin_id):
+ # Skip deselected spins.
+ if not spin.select:
+ continue
+
+ # Skip spins with no PCSs.
+ if not hasattr(spin, 'pcs') or (align_id and not align_id in
spin.pcs):
+ continue
+
+ # No data structure.
+ if not hasattr(spin, 'pcs_err'):
+ spin.pcs_err = {}
+
+ # Set the error.
+ for id in align_ids:
+ spin.pcs_err[id] = sd
+
+
def structural_noise(align_id=None, rmsd=0.2, sim_num=1000, file=None,
dir=None, force=False):
"""Determine the PCS error due to structural noise via simulation.
Modified: trunk/user_functions/pcs.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/pcs.py?rev=18217&r1=18216&r2=18217&view=diff
==============================================================================
--- trunk/user_functions/pcs.py (original)
+++ trunk/user_functions/pcs.py Fri Jan 18 12:21:25 2013
@@ -32,6 +32,7 @@
# relax module imports.
from generic_fns import align_tensor, pcs, pipes
+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
@@ -388,6 +389,45 @@
uf.gui_icon = "oxygen.actions.document-open"
uf.wizard_height_desc = 250
uf.wizard_size = (1000, 750)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
+
+
+# The pcs.set_errors user function.
+uf = uf_info.add_uf('pcs.set_errors')
+uf.title = "Set the errors for the PCSs."
+uf.title_short = "PCS 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_id",
+ py_type = "str",
+ arg_type = "spin ID",
+ desc_short = "spin ID string",
+ desc = "The optional spin ID string.",
+ #wiz_combo_iter = get_spin_ids,
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "sd",
+ default = 0.1,
+ py_type = "num",
+ desc_short = "PCS error (ppm)",
+ desc = "The PCS standard deviation value in ppm."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("If the PCS errors have not already been read from
a PCS data file or if they need to be changed, then the errors can be set via
this user function.")
+uf.backend = pcs.set_errors
+uf.menu_text = "&set_errors"
+uf.gui_icon = "oxygen.actions.edit-rename"
uf.wizard_image = WIZARD_IMAGE_PATH + 'align_tensor.png'
r18217 - in /trunk: generic_fns/pcs.py user_functions/pcs.py