Author: scooter
Date: 2013-02-21 15:40:03 -0800 (Thu, 21 Feb 2013)
New Revision: 31131
Removed:
csplugins/trunk/ucsf/scooter/chemViz/lib/cdk+smsd-1.4.17.jar
Modified:
csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
Log:
Remove 1.4.17 jar and add an extra attempt at
parsing SMILES strings
Deleted: csplugins/trunk/ucsf/scooter/chemViz/lib/cdk+smsd-1.4.17.jar
===================================================================
(Binary files differ)
Modified: csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
===================================================================
--- csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2013-02-21 20:09:25 UTC (rev 31130)
+++ csplugins/trunk/ucsf/scooter/chemViz/src/chemViz/model/Compound.java
2013-02-21 23:40:03 UTC (rev 31131)
@@ -403,7 +403,14 @@
} catch (InvalidSmilesException e) {
iMolecule = null;
logger.warning("Unable to parse SMILES:
"+smilesStr+" for "+source.getIdentifier()+": "+e.getMessage());
- return;
+ // Something's a little flakey with the
SmilesParser in 1.5.1, so try again
+ sp = new
SmilesParser(DefaultChemObjectBuilder.getInstance());
+ try {
+ iMolecule =
sp.parseSmiles(this.smilesStr);
+ } catch (InvalidSmilesException e2) {
+ // No reason to tell the user again
+ return;
+ }
}
}
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