Author: bugman
Date: Fri Jun 14 11:44:55 2013
New Revision: 20115
URL: http://svn.gna.org/viewcvs/relax?rev=20115&view=rev
Log:
The rdc.read user function can now handle T = J+D type data.
Support for this in the specific analyses is yet to be added.
Modified:
trunk/pipe_control/rdc.py
trunk/user_functions/rdc.py
Modified: trunk/pipe_control/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/pipe_control/rdc.py?rev=20115&r1=20114&r2=20115&view=diff
==============================================================================
--- trunk/pipe_control/rdc.py (original)
+++ trunk/pipe_control/rdc.py Fri Jun 14 11:44:55 2013
@@ -553,7 +553,7 @@
@type dir: str or None
@keyword file_data: An alternative to opening a file, if the data
already exists in the correct format. The format is a list of lists where
the first index corresponds to the row and the second the column.
@type file_data: list of lists
- @keyword data_type: A string which is set to 'D' means that the
splitting in the aligned sample was assumed to be J + D, or if set to '2D'
then the splitting was taken as J + 2D.
+ @keyword data_type: A string which is set to 'D' means that the
splitting in the aligned sample was assumed to be J + D, or if set to '2D'
then the splitting was taken as J + 2D. If set to 'T', then the data will be
marked as being J+D values.
@keyword spin_id1_col: The column containing the spin ID strings of the
first spin.
@type spin_id1_col: int
@keyword spin_id2_col: The column containing the spin ID strings of the
second spin.
@@ -578,7 +578,7 @@
raise RelaxError("One of either the data or error column must be
supplied.")
# Check the data types.
- rdc_types = ['D', '2D']
+ rdc_types = ['D', '2D', 'T']
if data_type not in rdc_types:
raise RelaxError("The RDC data type '%s' must be one of %s." %
(data_type, rdc_types))
Modified: trunk/user_functions/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/user_functions/rdc.py?rev=20115&r1=20114&r2=20115&view=diff
==============================================================================
--- trunk/user_functions/rdc.py (original)
+++ trunk/user_functions/rdc.py Fri Jun 14 11:44:55 2013
@@ -299,9 +299,9 @@
default = "D",
py_type = "str",
desc_short = "data type",
- desc = "Specify if the RDC data is in the D or 2D format.",
+ desc = "Specify if the RDC data is in the D or 2D format, or the T = J +
D format.",
wiz_element_type = "combo",
- wiz_combo_choices = ["D", "2D"],
+ wiz_combo_choices = ["D", "2D", "T"],
wiz_read_only = True
)
uf.add_keyarg(
@@ -362,10 +362,11 @@
# Description.
uf.desc.append(Desc_container())
uf.desc[-1].add_paragraph("This will read RDC data from a file and associate
it with an alignment ID, either a new ID or a preexisting one with no RDC
data.")
-uf.desc[-1].add_paragraph("The data type is used to specify how the RDC is
defined. It can be set to two values:")
+uf.desc[-1].add_paragraph("The data type is used to specify how the RDC is
defined. It can be set to a number of values:")
uf.desc[-1].add_list_element("'D' means that the splitting in the aligned
sample was taken as J + D.")
uf.desc[-1].add_list_element("'2D' means that the splitting in the aligned
sample was assumed to be J + 2D.")
-uf.desc[-1].add_paragraph("Internally, relax uses the D notation. Therefore
if set to '2D', the values will be doubled when read in.")
+uf.desc[-1].add_list_element("'T' means that the file contains T = J + D
values.")
+uf.desc[-1].add_paragraph("Internally, relax uses the D notation. Therefore
if set to '2D', the values will be doubled when read in. If the 'T' data
type is specified, then J couplings must be present for this data to be of
any use.")
uf.desc[-1].add_paragraph("If the negative gyromagnetic ratio correction
flag is set, a sign inversion will be applied to all RDC values to be loaded.
This is sometimes needed for 15N if the data is not compensated for the
negative gyromagnetic ratio.")
uf.desc[-1].add_paragraph("The absolute RDCs flag is used for RDCs in which
the sign is unknown. All absolute RDCs loaded will be converted to positive
values.")
# Prompt examples.
r20115 - in /trunk: pipe_control/rdc.py user_functions/rdc.py