Author: bugman
Date: Tue Oct 6 15:46:25 2009
New Revision: 9583
URL: http://svn.gna.org/viewcvs/relax?rev=9583&view=rev
Log:
The relax_io.read_spin_data_file() function now calls
generic_fns.sequence.validate_sequence().
This is a more advanced check of the sequence information. The
validate_sequence() function has
also been modified to handle single data lines.
Modified:
1.3/generic_fns/sequence.py
1.3/relax_io.py
Modified: 1.3/generic_fns/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/generic_fns/sequence.py?rev=9583&r1=9582&r2=9583&view=diff
==============================================================================
--- 1.3/generic_fns/sequence.py (original)
+++ 1.3/generic_fns/sequence.py Tue Oct 6 15:46:25 2009
@@ -323,7 +323,7 @@
def validate_sequence(data, mol_name_col=None, res_num_col=None,
res_name_col=None, spin_num_col=None, spin_name_col=None):
- """Function for testing if the sequence data is valid.
+ """Test if the sequence data is valid.
The only function this performs is to raise a RelaxError if the data is
invalid.
@@ -342,56 +342,54 @@
@type spin_num_col: int or None
"""
- # Loop over the data.
- for i in xrange(len(data)):
- # Molecule name data.
- if mol_name_col != None:
- try:
- data[i][mol_name_col]
- except IndexError:
- raise RelaxInvalidSeqError(data[i])
-
- # Residue number data.
- if res_num_col != None:
- # No data in column.
- try:
- data[i][res_num_col]
- except IndexError:
- raise RelaxInvalidSeqError(data[i])
-
- # Bad data in column.
- try:
- int(data[i][res_num_col])
- except ValueError:
- raise RelaxInvalidSeqError(data[i])
-
- # Residue name data.
- if res_name_col != None:
- try:
- data[i][res_name_col]
- except IndexError:
- raise RelaxInvalidSeqError(data[i])
-
- # Spin number data.
- if spin_num_col != None:
- # No data in column.
- try:
- data[i][spin_num_col]
- except IndexError:
- raise RelaxInvalidSeqError(data[i])
-
- # Bad data in column.
- try:
- int(data[i][spin_num_col])
- except ValueError:
- raise RelaxInvalidSeqError(data[i])
-
- # Spin name data.
- if spin_name_col != None:
- try:
- data[i][spin_name_col]
- except IndexError:
- raise RelaxInvalidSeqError(data[i])
+ # Molecule name data.
+ if mol_name_col:
+ try:
+ data[mol_name_col]
+ except IndexError:
+ raise RelaxInvalidSeqError(data)
+
+ # Residue number data.
+ if res_num_col:
+ # No data in column.
+ try:
+ data[res_num_col]
+ except IndexError:
+ raise RelaxInvalidSeqError(data)
+
+ # Bad data in column.
+ try:
+ int(data[res_num_col])
+ except ValueError:
+ raise RelaxInvalidSeqError(data)
+
+ # Residue name data.
+ if res_name_col:
+ try:
+ data[res_name_col]
+ except IndexError:
+ raise RelaxInvalidSeqError(data)
+
+ # Spin number data.
+ if spin_num_col:
+ # No data in column.
+ try:
+ data[spin_num_col]
+ except IndexError:
+ raise RelaxInvalidSeqError(data)
+
+ # Bad data in column.
+ try:
+ int(data[spin_num_col])
+ except ValueError:
+ raise RelaxInvalidSeqError(data)
+
+ # Spin name data.
+ if spin_name_col:
+ try:
+ data[spin_name_col]
+ except IndexError:
+ raise RelaxInvalidSeqError(data)
def write(file, dir=None, sep=None, mol_name_flag=False, res_num_flag=False,
res_name_flag=False, spin_num_flag=False, spin_name_flag=False, force=False):
Modified: 1.3/relax_io.py
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax_io.py?rev=9583&r1=9582&r2=9583&view=diff
==============================================================================
--- 1.3/relax_io.py (original)
+++ 1.3/relax_io.py Tue Oct 6 15:46:25 2009
@@ -45,6 +45,7 @@
from sys import stdin, stdout, stderr
# relax module imports.
+import generic_fns
from generic_fns.mol_res_spin import generate_spin_id_data_array
from relax_errors import RelaxError, RelaxFileError, RelaxFileEmptyError,
RelaxFileOverwriteError, RelaxMissingBinaryError, RelaxNoInPathError,
RelaxNonExecError
from relax_warnings import RelaxWarning
@@ -544,27 +545,17 @@
# Test the validity of the data.
if data_col or error_col:
missing = True
- for i in xrange(len(file_data)):
+ for line in file_data:
# Skip missing data.
- if len(file_data[i]) < min_col_num:
+ if len(line) < min_col_num:
continue
- elif data_col and file_data[i][data_col-1] == 'None':
+ elif data_col and line[data_col-1] == 'None':
continue
- elif error_col and file_data[i][error_col-1] == 'None':
+ elif error_col and line[error_col-1] == 'None':
continue
- # Test that the data are numbers.
- try:
- if res_num_col:
- int(file_data[i][res_num_col-1])
- if spin_num_col:
- int(file_data[i][spin_num_col-1])
- if data_col:
- float(file_data[i][data_col-1])
- if error_col:
- float(file_data[i][error_col-1])
- except ValueError:
- raise RelaxError("The data in the line " +
repr(file_data[i]) + " is invalid.")
+ # Validate the sequence.
+ 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)
# Right, data is OK and exists.
missing = False
r9583 - in /1.3: generic_fns/sequence.py relax_io.py