Author: bugman
Date: Fri Jul 29 19:08:13 2011
New Revision: 14013
URL: http://svn.gna.org/viewcvs/relax?rev=14013&view=rev
Log:
The relax_io.read_spin_data() function no longer skips short lines so that a
warning is given for it.
Modified:
1.3/relax_io.py
Modified: 1.3/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax_io.py?rev=14013&r1=14012&r2=14013&view=diff
==============================================================================
--- 1.3/relax_io.py (original)
+++ 1.3/relax_io.py Fri Jul 29 19:08:13 2011
@@ -473,38 +473,26 @@
Description
===========
- This function reads a columnar formatted file where each line
corresponds to a spin system.
- Spin identification is either through a spin ID string or through
columns containing the
- molecule name, residue name and number, and/or spin name and number.
+ This function reads a columnar formatted file where each line
corresponds to a spin system. Spin identification is either through a spin ID
string or through columns containing the molecule name, residue name and
number, and/or spin name and number.
@keyword file: The name of the file to open.
@type file: str
- @keyword dir: The directory containing the file (defaults to
the current directory
- if None).
+ @keyword dir: The directory containing the file (defaults to
the current directory if None).
@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.
+ @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 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.
+ @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.
+ @keyword mol_name_col: The column containing the molecule name
information. If supplied, spin_id_col must be None.
@type mol_name_col: int or None
- @keyword res_name_col: The column containing the residue name
information. If supplied,
- spin_id_col must be None.
+ @keyword res_name_col: The column containing the residue name
information. If supplied, spin_id_col must be None.
@type res_name_col: int or None
- @keyword res_num_col: The column containing the residue number
information. If supplied,
- spin_id_col must be None.
+ @keyword res_num_col: The column containing the residue number
information. If supplied, spin_id_col must be None.
@type res_num_col: int or None
- @keyword spin_name_col: The column containing the spin name information.
If supplied,
- spin_id_col must be None.
+ @keyword spin_name_col: The column containing the spin name information.
If supplied, spin_id_col must be None.
@type spin_name_col: int or None
- @keyword spin_num_col: The column containing the spin number
information. If supplied,
- spin_id_col must be None.
+ @keyword spin_num_col: The column containing the spin number
information. If supplied, spin_id_col must be None.
@type spin_num_col: int or None
@keyword data_col: The column containing the data.
@type data_col: int or None
@@ -512,13 +500,9 @@
@type error_col: int or None
@keyword sep: The column separator which, if None, defaults to
whitespace.
@type sep: str or None
- @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all
- spins.
+ @keyword spin_id: The spin ID string used to restrict data loading
to a subset of all spins.
@type spin_id: None or str
- @return: A list of the spin specific data is yielded.
The format is a list
- consisting of the spin ID string, the data value
(if data_col is give),
- and the error value (if error_col is given). If
both data_col and
- error_col are None, then the spin ID string is
simply yielded.
+ @return: A list of the spin specific data is yielded.
The format is a list consisting of the spin ID string, the data value (if
data_col is give), and the error value (if error_col is given). If both
data_col and error_col are None, then the spin ID string is simply yielded.
@rtype: str, list of [str, float], or list of [str,
float, float]
"""
@@ -550,10 +534,6 @@
# Yield the data, spin by spin.
missing_data = True
for line in file_data:
- # Skip missing data.
- if len(line) < min_col_num:
- continue
-
# Validate the sequence.
try:
generic_fns.sequence.validate_sequence(line,
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)
r14013 - /1.3/relax_io.py