On 21 November 2015 at 15:08, <tlinnet@xxxxxxxxxxxxx> wrote:
Author: tlinnet
Date: Sat Nov 21 15:08:17 2015
New Revision: 28076
URL: http://svn.gna.org/viewcvs/relax?rev=28076&view=rev
Log:
Made additional check in sequence reading, that "nan" values are skipped.
Modified:
trunk/lib/sequence.py
Modified: trunk/lib/sequence.py
URL:
http://svn.gna.org/viewcvs/relax/trunk/lib/sequence.py?rev=28076&r1=28075&r2=28076&view=diff
==============================================================================
--- trunk/lib/sequence.py (original)
+++ trunk/lib/sequence.py Sat Nov 21 15:08:17 2015
@@ -24,6 +24,7 @@
"""Module for handling the molecule, residue, and spin sequence data."""
# Python module imports.
+from math import isnan
from warnings import warn
# relax module imports.
@@ -310,6 +311,11 @@
else:
value = float(line[data_col-1])
+ # If it a float, test if is nan.
+ if isnan(value):
+ warn(RelaxWarning("The value is 'nan', skipping
the line %s" % line))
+ continue
+
# Bad data.
except ValueError:
warn(RelaxWarning("Invalid data, skipping the line %s" %
line))
@@ -326,6 +332,11 @@
# A float.
else:
error = float(line[error_col-1])
+
+ # If it a float, test if is nan.
+ if isnan(error):
+ warn(RelaxWarning("The error is 'nan', skipping
the line %s" % line))
+ continue
# Bad data.
except ValueError:
Hi Troels,
For these changes, I would recommend using Gary's lib.float.isNaN()
function. The math.isnan() function is relatively recent and it
breaks our Python 2.5 compatibility. I believe that Gary's lib.float
code is also more advanced. For example even better would be to use
the isFinite() function, as that will simultaneously check for NaN and
+/- Inf. Or you could isNaN() followed by isInf() if you'd like
different warning messages for each number type.
Cheers,
Edward
Re: r28076 - /trunk/lib/sequence.py