#1374 InChITautomerGeneratorTest regressions

[Egon Willighagen]

See https://jenkins.bigcat.unimaas.nl/job/cdk/lastCompletedBuild/testReport/org.openscience.cdk.tautomers/InChITautomerGeneratorTest/

The problem does not seem to be that the AuxInfo is no longer calculated... that is, the following does not fix it:

diff --git a/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java b/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java
index 374ef4c..c790de8 100644
--- a/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java
+++ b/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java
@@ -71,7 +71,7 @@ public class InChITautomerGenerator {
*/
public List<IAtomContainer> getTautomers(IAtomContainer molecule) throws CDKException, CloneNotSupportedException {

• InChIGenerator gen = InChIGeneratorFactory.getInstance().getInChIGenerator(molecule);
• InChIGenerator gen = InChIGeneratorFactory.getInstance().getInChIGenerator(molecule, "");
  String inchi = gen.getInchi();
  if (inchi == null)
  throw new CDKException(InChIGenerator.class

[Egon Willighagen]

Just checking another new fail, and it seems to have to do with valencies not set... maybe due to the performance speed up in the atom typer?

[John May]

Hmm sounds very fragile. Maybe time I finish off this branch -
https://github.com/johnmay/cdk/tree/sd-tautomer.

Regards,
John W May
john.wilkinsonmay@gmail.com

On 22 November 2015 at 10:29, Egon Willighagen egonw@users.sf.net wrote:

Just checking another new fail, and it seems to have to do with valencies
not set... maybe due to the performance speed up in the atom typer?

---

• [bugs:#1374] http://sourceforge.net/p/cdk/bugs/1374/
  InChITautomerGeneratorTest regressions*

Status: open
Group: cdk-1.6.x
Created: Sun Nov 22, 2015 10:26 AM UTC by Egon Willighagen
Last Updated: Sun Nov 22, 2015 10:26 AM UTC
Owner: nobody

See
https://jenkins.bigcat.unimaas.nl/job/cdk/lastCompletedBuild/testReport/org.openscience.cdk.tautomers/InChITautomerGeneratorTest/

The problem does not seem to be that the AuxInfo is no longer
calculated... that is, the following does not fix it:

diff --git
a/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java
b/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java
index 374ef4c..c790de8 100644

---

a/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java
+++
b/tool/tautomer/src/main/java/org/openscience/cdk/tautomers/InChITautomerGenerator.java
@@ -71,7 +71,7 @@ public class InChITautomerGenerator {
*/
public List<IAtomContainer> getTautomers(IAtomContainer molecule) throws
CDKException, CloneNotSupportedException {

• InChIGenerator gen =
  InChIGeneratorFactory.getInstance().getInChIGenerator(molecule);
• InChIGenerator gen =
  InChIGeneratorFactory.getInstance().getInChIGenerator(molecule, "");
  String inchi = gen.getInchi();
  if (inchi == null)
  throw new CDKException(InChIGenerator.class

---

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[Egon Willighagen]

Not sure... several other tests are failing to, which seems to be caused by the same issue...

[John May]

Okay will hold off release for now. The SMILES failure I think is just a
clean needed on Jenkins. Will double check now though.

[John May]

Oh nope I goofed on the assertion. Ah well - I can prep release notes etc
and will get these fixed this week.

[John May]

Now resolved