Author: bugman
Date: Tue Oct 6 11:22:21 2009
New Revision: 9568
URL: http://svn.gna.org/viewcvs/relax?rev=9568&view=rev
Log:
Added the spin_id_col arg to the rdc.read() user function.
This allows 2 different formats for spin identification - spin ID string or
mol name, res name and
num, and spin name and num.
Modified:
1.3/prompt/rdc.py
Modified: 1.3/prompt/rdc.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/prompt/rdc.py?rev=9568&r1=9567&r2=9568&view=diff
==============================================================================
--- 1.3/prompt/rdc.py (original)
+++ 1.3/prompt/rdc.py Tue Oct 6 11:22:21 2009
@@ -176,7 +176,7 @@
rdc.display(id=id)
- def read(self, id=None, file=None, dir=None, spin_id=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):
+ def read(self, id=None, file=None, dir=None, 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):
"""Read the RDC data from file.
Keyword Arguments
@@ -188,23 +188,36 @@
dir: The directory where the file is located.
+ spin_id_col: The spin identification string column (an alternative
to the mol, res, and
+ spin name and number columns).
+
+ mol_name_col: The molecule name column (alternative to the
spid_id_col).
+
+ res_num_col: The residue number column (alternative to the
spid_id_col).
+
+ res_name_col: The residue name column (alternative to the
spid_id_col).
+
+ spin_num_col: The spin number column (alternative to the
spid_id_col).
+
+ spin_name_col: The spin name column (alternative to the
spid_id_col).
+
+ data_col: The RDC data column.
+
+ error_col: The experimental error column.
+
+ sep: The column separator (the default is white space).
+
spin_id: The spin identification string.
- mol_name_col: The molecule name column (this defaults to no column).
-
- res_num_col: The residue number column (the default is 0, i.e. the
first column).
-
- res_name_col: The residue name column (the default is 1, i.e. the
second column).
-
- spin_num_col: The spin number column (this defaults to no column).
-
- spin_name_col: The spin name column (this defaults to no column).
-
- data_col: The RDC data column (the default is 2).
-
- error_col: The experimental error column (the default is 3).
-
- sep: The column separator (the default is white space).
+
+ Description
+ ~~~~~~~~~~~
+
+ The spin system can be identified in the file using two different
formats. The first is the
+ spin ID string column which can include the molecule name, the
residue name and number, and
+ the spin name and number. Alternatively the mol_name_col,
res_num_col, res_name_col,
+ spin_num_col, and/or spin_name_col arguments can be supplied
allowing this information to be
+ in separate columns. Note that the numbering of columns starts at
zero.
Examples
@@ -234,7 +247,7 @@
text = text + "id=" + repr(id)
text = text + ", file=" + repr(file)
text = text + ", dir=" + repr(dir)
- text = text + ", spin_id=" + repr(spin_id)
+ text = text + ", spin_id_col=" + repr(spin_id_col)
text = text + ", mol_name_col=" + repr(mol_name_col)
text = text + ", res_num_col=" + repr(res_num_col)
text = text + ", res_name_col=" + repr(res_name_col)
@@ -242,14 +255,15 @@
text = text + ", spin_name_col=" + repr(spin_name_col)
text = text + ", data_col=" + repr(data_col)
text = text + ", error_col=" + repr(error_col)
- text = text + ", sep=" + repr(sep) + ")"
+ text = text + ", sep=" + repr(sep)
+ text = text + ", spin_id=" + repr(spin_id) + ")"
print(text)
# The argument checks.
check.is_str(id, 'alignment identification string')
check.is_str(file, 'file name')
check.is_str(dir, 'directory name', can_be_none=True)
- check.is_str(spin_id, 'spin identification string', can_be_none=True)
+ check.is_int(spin_id_col, 'spin identification string column',
can_be_none=True)
check.is_int(mol_name_col, 'molecule name column', can_be_none=True)
check.is_int(res_num_col, 'residue number column', can_be_none=True)
check.is_int(res_name_col, 'residue name column', can_be_none=True)
@@ -258,9 +272,10 @@
check.is_int(data_col, 'data column', can_be_none=True)
check.is_int(error_col, 'error column', can_be_none=True)
check.is_str(sep, 'column separator', can_be_none=True)
-
- # Execute the functional code.
- rdc.read(id=id, file=file, dir=dir, spin_id=spin_id,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, data_col=data_col, error_col=error_col, sep=sep)
+ check.is_str(spin_id, 'spin identification string', can_be_none=True)
+
+ # Execute the functional code.
+ rdc.read(id=id, file=file, dir=dir, spin_id_col=spin_id_col,
mol_name_col=mol_name_col, res_num_col=res_num_col,
res_name_col=res_name_col, spin_num_col=spin_num_col,
spin_name_col=spin_name_col, data_col=data_col, error_col=error_col, sep=sep,
spin_id=spin_id)
def write(self, id=None, file=None, dir=None, force=False):
r9568 - /1.3/prompt/rdc.py