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[Cdk-devel] [ cdk-Patches-3037137 ] SMSD 1.0.2 code with updates
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From: SourceForge.net <no...@so...> - 2010-08-08 11:54:45
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Patches item #3037137, was opened at 2010-07-30 14:43 Message generated for change (Comment added) made by gilleain You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3037137&group_id=20024 Please note that this message will contain a full copy of the comment thread, including the initial issue submission, for this request, not just the latest update. Category: master Group: Needs Review Status: Open Resolution: None Priority: 5 Private: No Submitted By: Asad (asadrahman) Assigned to: Nobody/Anonymous (nobody) Summary: SMSD 1.0.2 code with updates Initial Comment: SMSD core code moved as .jar Main class is called Isomorphism.java Bugs are fixed IQueryAtomConatiner supported for SMARTS Test class updated ---------------------------------------------------------------------- Comment By: gilleain maclean torrance (gilleain) Date: 2010-08-08 11:54 Message: Oh, I found an email from Irilenia Nobeli on this: https://sourceforge.net/mailarchive/forum.php?thread_name=Pine.LNX.4.44.0506151947560.2289-100000%40ginger.ebi.ac.uk&forum_name=cdk-user Which suggests the problem is to do with doing aromaticity detection multiple times, and flags not getting cleared properly... ---------------------------------------------------------------------- Comment By: gilleain maclean torrance (gilleain) Date: 2010-08-08 11:44 Message: Right. I still have the problem with MolHandler, but the errors reported by test-module are now just one: Testcase: testSFBug1208740(org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSTest): FAILED expected:<8> but was:<9> junit.framework.AssertionFailedError: expected:<8> but was:<9> at org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSTest.testSFBug1208740(CDKMCSTest.java:279) Which refers to a 'bug report' : https://sourceforge.net/tracker/index.php?func=detail&aid=1208740&group_id=20024&atid=120024 that is a bit confusing, as it doesn't mention the specific test. ---------------------------------------------------------------------- Comment By: Asad (asadrahman) Date: 2010-08-06 21:37 Message: Thanks gilleain, I have updated the patches. please try again! Asad ---------------------------------------------------------------------- Comment By: gilleain maclean torrance (gilleain) Date: 2010-08-06 17:20 Message: I got a rejected hunk in MolHandler when applying the first patch, which I worked around. However, the following errors turned up in the report when running module test: Testcase: testSMSD(org.openscience.cdk.smsd.SMSDBondSensitiveTest): Caused an ERROR null java.lang.NullPointerException at org.openscience.cdk.smsd.SMSDBondSensitiveTest.testSMSD(SMSDBondSensitiveTest.java:155) Testcase: testSMSDBondSensitive(org.openscience.cdk.smsd.SMSDBondSensitiveTest): FAILED expected:<6> but was:<2> junit.framework.AssertionFailedError: expected:<6> but was:<2> at org.openscience.cdk.smsd.SMSDBondSensitiveTest.testSMSDBondSensitive(SMSDBondSensitiveTest.java:200) Testcase: testItShouldMatchHexaneToHexane(org.openscience.cdk.smsd.algorithm.vflib.VFLibTest): FAILED null junit.framework.AssertionFailedError: null at org.openscience.cdk.smsd.algorithm.vflib.VFLibTest.testItShouldMatchHexaneToHexane(VFLibTest.java:205) Testcase: testItShouldFindTwoMapsFromHexaneToHexane(org.openscience.cdk.smsd.algorithm.vflib.VFLibTest): FAILED expected:<6> but was:<0> junit.framework.AssertionFailedError: expected:<6> but was:<0> at org.openscience.cdk.smsd.algorithm.vflib.VFLibTest.testItShouldFindTwoMapsFromHexaneToHexane(VFLibTest.java:221) Testcase: testSFBug1208740(org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSTest): FAILED expected:<8> but was:<9> junit.framework.AssertionFailedError: expected:<8> but was:<9> at org.openscience.cdk.smsd.algorithm.rgraph.CDKMCSTest.testSFBug1208740(CDKMCSTest.java:282) I've been working on the first of these, and it seems like the bonds never match (cylohexane to benzene) because the Is_Aromatic flag in the cyclohexane bonds are always false. ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2010-08-05 10:33 Message: Thanx! ---------------------------------------------------------------------- Comment By: Asad (asadrahman) Date: 2010-08-05 10:09 Message: Here is a new set of patches without removing the core smsd lib. ---------------------------------------------------------------------- Comment By: Asad (asadrahman) Date: 2010-08-02 11:55 Message: kindly download the patches from http://github.com/downloads/asad/cdk/patches.zip ---------------------------------------------------------------------- Comment By: Asad (asadrahman) Date: 2010-07-30 14:50 Message: Patches can be download from http://github.com/downloads/asad/cdk/patches.zip as they are very big. SF refuses to lead them! ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=3037137&group_id=20024 |