Author: bugman
Date: Tue Jun 19 10:54:07 2012
New Revision: 16945
URL: http://svn.gna.org/viewcvs/relax?rev=16945&view=rev
Log:
Created the spin.isotope user function.
This is designed to be a permanent replacement for the specific analysis API
'heteronuc_type' and
'proton_type' parameters.
Modified:
branches/interatomic/generic_fns/mol_res_spin.py
branches/interatomic/user_functions/spin.py
Modified: branches/interatomic/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/generic_fns/mol_res_spin.py?rev=16945&r1=16944&r2=16945&view=diff
==============================================================================
--- branches/interatomic/generic_fns/mol_res_spin.py (original)
+++ branches/interatomic/generic_fns/mol_res_spin.py Tue Jun 19 10:54:07 2012
@@ -2679,13 +2679,49 @@
if element not in valid_names:
raise(RelaxError("The element name '%s' is not valid and should be
one of the IUPAC names %s." % (element, valid_names)))
-
# Set the element name for the matching spins.
for spin, id in spin_loop(spin_id, return_id=True):
if hasattr(spin, 'element') and spin.element and not force:
warn(RelaxWarning("The element type of the spin '%s' is already
set. Set the force flag to True to rename." % id))
else:
spin.element = element
+
+
+def set_spin_isotope(spin_id=None, isotope=None, force=False):
+ """Set the nuclear isotope type of the spins.
+
+ @keyword spin_id: The spin identification string.
+ @type spin_id: str
+ @keyword isotope: The nuclear isotope type.
+ @type isotope: str
+ @keyword force: A flag which if True will cause the isotope type to
be changed.
+ @type force: bool
+ """
+
+ # Types currently supported in relax.
+ supported_types = [
+ '1H',
+ '2H',
+ '13C',
+ '14N',
+ '15N',
+ '17O',
+ '19F',
+ '23Na',
+ '31P',
+ '113Cd'
+ ]
+
+ # Check.
+ if isotope not in supported_types:
+ raise(RelaxError("The nuclear isotope type '%s' is currently not
supported." % isotope))
+
+ # Set the isotope type for the matching spins.
+ for spin, id in spin_loop(spin_id, return_id=True):
+ if hasattr(spin, 'isotope') and spin.isotope and not force:
+ warn(RelaxWarning("The nuclear isotope type of the spin '%s' is
already set. Change the force flag to True to reset." % id))
+ else:
+ spin.isotope = isotope
def spin_id_to_data_list(id):
Modified: branches/interatomic/user_functions/spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/interatomic/user_functions/spin.py?rev=16945&r1=16944&r2=16945&view=diff
==============================================================================
--- branches/interatomic/user_functions/spin.py (original)
+++ branches/interatomic/user_functions/spin.py Tue Jun 19 10:54:07 2012
@@ -24,7 +24,7 @@
"""The spin user function definitions."""
# relax module imports.
-from generic_fns.mol_res_spin import copy_spin, create_pseudo_spin,
create_spin, delete_spin, display_spin, get_molecule_names, get_residue_ids,
get_residue_names, get_residue_nums, get_spin_ids, id_string_doc, name_spin,
number_spin, set_spin_element
+from generic_fns.mol_res_spin import copy_spin, create_pseudo_spin,
create_spin, delete_spin, display_spin, get_molecule_names, get_residue_ids,
get_residue_names, get_residue_nums, get_spin_ids, id_string_doc, name_spin,
number_spin, set_spin_element, set_spin_isotope
from generic_fns import pipes
from graphics import WIZARD_IMAGE_PATH
from user_functions.data import Uf_info; uf_info = Uf_info()
@@ -326,6 +326,53 @@
uf.wizard_image = WIZARD_IMAGE_PATH + 'spin.png'
+# The spin.isotope user function.
+uf = uf_info.add_uf('spin.isotope')
+uf.title = "Set the spins' nuclear isotope type."
+uf.title_short = "Nuclear isotope type."
+uf.add_keyarg(
+ name = "isotope",
+ py_type = "str",
+ desc_short = "nuclear isotope name",
+ desc = "The nuclear isotope name in the AE notation - the atomic mass
number followed by the element symbol.",
+ wiz_element_type = "combo",
+ wiz_combo_choices = ["1H", "2H", "13C", "14N", "15N", "17O", "19F",
"23Na", "31P", "113Cd"],
+ wiz_read_only = False
+)
+uf.add_keyarg(
+ name = "spin_id",
+ py_type = "str",
+ desc_short = "spin ID string",
+ desc = "The spin identification string corresponding to one or more
spins.",
+ wiz_element_type = 'combo',
+ wiz_combo_iter = get_spin_ids,
+ can_be_none = True
+)
+uf.add_keyarg(
+ name = "force",
+ default = False,
+ py_type = "bool",
+ arg_type = "force flag",
+ desc_short = "force flag",
+ desc = "A flag which if True will cause the nuclear isotope to be
changed."
+)
+# Description.
+uf.desc.append(Desc_container())
+uf.desc[-1].add_paragraph("This allows the nuclear isotope type of the spins
to be set.")
+uf.desc.append(id_string_doc)
+# Prompt examples.
+uf.desc.append(Desc_container("Prompt examples"))
+uf.desc[-1].add_paragraph("The set all spins of residue 1 to the '13C'
nuclear isotope, type one of:")
+uf.desc[-1].add_prompt("relax> spin.isotope('@1', '13C', force=True)")
+uf.desc[-1].add_prompt("relax> spin.isotope(spin_id='@1', isotope='13C',
force=True)")
+uf.backend = set_spin_isotope
+uf.menu_text = "&isotope"
+uf.gui_icon = "relax.nuclear_symbol"
+uf.wizard_height_desc = 500
+uf.wizard_size = (1000, 750)
+uf.wizard_image = WIZARD_IMAGE_PATH + 'nuclear_symbol.png'
+
+
# The spin.name user function.
uf = uf_info.add_uf('spin.name')
uf.title = "Name the spins."
r16945 - in /branches/interatomic: generic_fns/mol_res_spin.py user_functions/spin.py