Author: bugman
Date: Fri Oct 14 10:21:50 2011
New Revision: 14869
URL: http://svn.gna.org/viewcvs/relax?rev=14869&view=rev
Log:
Fix for a problem introduced at r14810 - relax uses D and not 2D internally
for the RDCs.
This is only a problem if the rdc.read 'data_type' argument is used. This is
only a few days old so
will affect no one!
Modified:
1.3/generic_fns/rdc.py
1.3/prompt/rdc.py
Modified: 1.3/generic_fns/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/rdc.py?rev=14869&r1=14868&r2=14869&view=diff
==============================================================================
--- 1.3/generic_fns/rdc.py (original)
+++ 1.3/generic_fns/rdc.py Fri Oct 14 10:21:50 2011
@@ -122,7 +122,7 @@
@type value: float or None
@param align_id: The alignment tensor ID string.
@type align_id: str
- @keyword to_intern: A flag which if True will convert to the
internal 2D notation if needed, or if False will convert from the internal 2D
notation to the external D or 2D format.
+ @keyword to_intern: A flag which if True will convert to the
internal D notation if needed, or if False will convert from the internal D
notation to the external D or 2D format.
@type to_intern: bool
@return: The converted value.
@rtype: float or None
@@ -134,14 +134,14 @@
# The conversion factor.
factor = 1.0
- if hasattr(cdp, 'rdc_data_types') and
cdp.rdc_data_types.has_key(align_id) and cdp.rdc_data_types[align_id] == 'D':
+ if hasattr(cdp, 'rdc_data_types') and
cdp.rdc_data_types.has_key(align_id) and cdp.rdc_data_types[align_id] == '2D':
+ # Convert from 2D to D.
+ if to_intern:
+ factor = 2.0
+
# Convert from D to 2D.
- if to_intern:
+ else:
factor = 0.5
-
- # Convert from 2D to D.
- else:
- factor = 2.0
# Return the converted value.
return value * factor
@@ -358,7 +358,7 @@
cdp.q_rdc_norm2 = sqrt(cdp.q_rdc_norm2 / len(cdp.q_factors_rdc_norm2))
-def read(align_id=None, file=None, dir=None, file_data=None, data_type='2D',
spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None,
spin_num_col=None, spin_name_col=None, data_col=None, error_col=None,
sep=None, spin_id=None, neg_g_corr=False):
+def read(align_id=None, file=None, dir=None, file_data=None, data_type='D',
spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None,
spin_num_col=None, spin_name_col=None, data_col=None, error_col=None,
sep=None, spin_id=None, neg_g_corr=False):
"""Read the RDC data from file.
@keyword align_id: The alignment tensor ID string.
@@ -369,7 +369,7 @@
@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 '2D' means that the
splitting in the aligned sample was assumed to be J + 2D, or if set to 'D'
then the splitting was taken as J + D.
+ @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 spin_id_col: The column containing the spin ID strings. If
supplied, the mol_name_col, res_name_col, res_num_col, spin_name_col, and
spin_num_col arguments must be none.
@type spin_id_col: int or None
@keyword mol_name_col: The column containing the molecule name
information. If supplied, spin_id_col must be None.
Modified: 1.3/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/rdc.py?rev=14869&r1=14868&r2=14869&view=diff
==============================================================================
--- 1.3/prompt/rdc.py (original)
+++ 1.3/prompt/rdc.py Fri Oct 14 10:21:50 2011
@@ -1,6 +1,6 @@
###############################################################################
#
#
-# Copyright (C) 2003-2005,2007-2010 Edward d'Auvergne
#
+# Copyright (C) 2003-2011 Edward d'Auvergne
#
#
#
# This file is part of the program relax.
#
#
#
@@ -267,7 +267,7 @@
rdc.display(align_id=align_id)
- def read(self, align_id=None, file=None, dir=None, data_type='2D',
spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None,
spin_num_col=None, spin_name_col=None, data_col=None, error_col=None,
sep=None, spin_id=None, neg_g_corr=False):
+ def read(self, align_id=None, file=None, dir=None, data_type='D',
spin_id_col=None, mol_name_col=None, res_num_col=None, res_name_col=None,
spin_num_col=None, spin_name_col=None, data_col=None, error_col=None,
sep=None, spin_id=None, neg_g_corr=False):
"""Read the RDC data from file.
Keyword Arguments
@@ -279,7 +279,7 @@
dir: The directory where the file is located.
- data_type: Whether the RDC data is in the 2D or D format.
+ data_type: Whether the RDC data is in the D or 2D format.
spin_id_col: The spin ID string column (an alternative to the mol,
res, and spin name and
number columns).
@@ -311,10 +311,10 @@
The data_type argument is used to specify how the RDC is defined.
It is a string which can
be set to two values:
+ - 'D' means that the splitting in the aligned sample was taken
as J + D.
- '2D' means that the splitting in the aligned sample was
assumed to be J + 2D.
- - 'D' means that the splitting in the aligned sample was taken
as J + D.
-
- Internally, relax uses the 2D notation. Therefore if set to 'D',
the values will be halved
+
+ Internally, relax uses the D notation. Therefore if set to '2D',
the values will be doubled
when read in.
If neg_g_corr is set to True, a sign inversion will be applied to
all RDC values to be
r14869 - in /1.3: generic_fns/rdc.py prompt/rdc.py