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[Cdk-devel] [ cdk-Patches-2686065 ] pharmacophore update
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From: SourceForge.net <no...@so...> - 2009-04-27 06:15:34
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Patches item #2686065, was opened at 2009-03-13 12:22 Message generated for change (Comment added) made by egonw You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=2686065&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: None >Group: Accepted >Status: Closed >Resolution: Accepted Priority: 5 Private: No Submitted By: Rajarshi Guha (rajarshi) Assigned to: Egon Willighagen (egonw) Summary: pharmacophore update Initial Comment: been updating the pharmcophore code a bit. The primary change is to create a subclass of QueryAtomContainer called PharmacophoreQuery that will allow us ot consider things such as excluded volumes. The previous form of the code did not allow us to do this. While it does add a new class, code that uses the pharmacophore classes only needs to be updated by changing QueryAtomContainer (or IQueryAtomContainer) to PharmacophoreQuery. Everything else should stay the same. Other changes also include updating to JDK 1.5 idioms and addition of tests and annotations. This branch is based of the SF master, so I request a review and subsequent merge into master. You can pull these updates from me by doing git pull git://rguha.ath.cx/cdk pcore ---------------------------------------------------------------------- >Comment By: Egon Willighagen (egonw) Date: 2009-04-27 08:15 Message: Applied to master. ---------------------------------------------------------------------- Comment By: Rajarshi Guha (rajarshi) Date: 2009-04-27 07:35 Message: OK. The uploaded patch fixes issues raised in your comments (and should be applied after the original patch) ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2009-04-27 07:22 Message: That's the patch I was refering too... ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2009-04-27 07:22 Message: commit 7870121695663b1c64c9ad6505e551e037b63765 Author: Rajarshi Guha <raj...@gm...> Date: Thu Mar 12 15:39:57 2009 -0400 Updated the toString tests diff --git a/src/test/org/openscience/cdk/pharmacophore/PharmacophoreQueryAngleBondTest.java b/src/test/org/openscience/cdk/p index a8f5b4b..5936fed 100644 --- a/src/test/org/openscience/cdk/pharmacophore/PharmacophoreQueryAngleBondTest.java +++ b/src/test/org/openscience/cdk/pharmacophore/PharmacophoreQueryAngleBondTest.java @@ -83,6 +83,6 @@ public class PharmacophoreQueryAngleBondTest { PharmacophoreQueryAtom qatom3 = new PharmacophoreQueryAtom("blah", "C"); PharmacophoreQueryAngleBond qbond1 = new PharmacophoreQueryAngleBond(qatom1, qatom2, qatom3, 54.735); String repr = qbond1.toString(); - Assert.assertEquals("AC::Amine [[CX2]N]::aromatic [c1ccccc1]::blah [C]::[54.74 - 54.74]", repr); + Assert.assertEquals(0, repr.indexOf("AC::Amine [[CX2]N]::aromatic [c1ccccc1]::blah [C]::[54.74 - 54.74]")); } } \ No newline at end of file diff --git a/src/test/org/openscience/cdk/pharmacophore/PharmacophoreQueryBondTest.java b/src/test/org/openscience/cdk/pharma index c3baca3..74a72bf 100644 --- a/src/test/org/openscience/cdk/pharmacophore/PharmacophoreQueryBondTest.java +++ b/src/test/org/openscience/cdk/pharmacophore/PharmacophoreQueryBondTest.java @@ -78,7 +78,7 @@ public class PharmacophoreQueryBondTest { PharmacophoreQueryAtom qatom1 = new PharmacophoreQueryAtom("Amine", "[CX2]N"); PharmacophoreQueryAtom qatom2 = new PharmacophoreQueryAtom("aromatic", "c1ccccc1"); PharmacophoreQueryBond qbond1 = new PharmacophoreQueryBond(qatom1, qatom2, 1.0, 2.0); - String repr = qbond1.toString(); - Assert.assertEquals("DC::Amine [[CX2]N]::aromatic [c1ccccc1]::[1.0 - 2.0]", repr); + String repr = qbond1.toString(); + Assert.assertEquals(0, repr.indexOf("DC::Amine [[CX2]N]::aromatic [c1ccccc1]::[1.0 - 2.0]")); } } ---------------------------------------------------------------------- Comment By: Rajarshi Guha (rajarshi) Date: 2009-04-27 07:19 Message: Addressed your comments (except the one about full package names in Javadocs - see my previous comment). The attached patch should be applied on top of the original patch ---------------------------------------------------------------------- Comment By: Rajarshi Guha (rajarshi) Date: 2009-04-24 19:03 Message: > Ad 7870121695663b1c64c9ad6505e551e037b63765: > can you explain that change? Would an equals not be more precise? Since I pulled from pele, I don't have the whole history here. So I don't know which code you're referring to. Can you provide the diff for this query? > Also, can't you just import PharmacophoreQuery so you do not need to have > all those org.openscience.cdk.pharmacophore in the JavaDoc {@link }'s and > @see's...? as in: I thought of that - but this happens when that class is not used anywhere in that source file. By forcing an import, we unnecessarily improt a class that will not be used. While I realzie that some other class will likely use the imported class, it seem ineffcieint to import classes that don't get used just to make documentation neater I've addressed the other concers - I'll wait to hear about the two issues above and then post a patch to be applied after the current changes have been applied ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2009-04-24 17:57 Message: Ad f99d0a0def3013450104e35a3bf731d5fc5b79e3: appending one char can be done as char, e.g. '[' instead of "[" Ad 7870121695663b1c64c9ad6505e551e037b63765: can you explain that change? Would an equals not be more precise? Ad de3ad6edba5979b8bd2e37a225b5b2689779631c: please fix this example code in one of the JavaDocs (missing bracket): - * List<IQueryAtomContainer> defs = readPharmacophoreDefinitions"mydefs.xml"); + * List<PharmacophoreQuery> defs = readPharmacophoreDefinitions"mydefs.xml"); Also, can't you just import PharmacophoreQuery so you do not need to have all those org.openscience.cdk.pharmacophore in the JavaDoc {@link }'s and @see's...? as in: - * @return A list of {@link IQueryAtomContainer} objects + * @return A list of {@link org.openscience.cdk.pharmacophore.PharmacophoreQuery} objects ---------------------------------------------------------------------- Comment By: Egon Willighagen (egonw) Date: 2009-04-13 00:15 Message: Rajarshi asked me to put up the branch on a machine here in Uppsala, as his ath.cx machine is going down, so please check the patch from: git pull http://pele.farmbio.uu.se/git/rajarshi.git/ pcore ---------------------------------------------------------------------- You can respond by visiting: https://sourceforge.net/tracker/?func=detail&atid=320024&aid=2686065&group_id=20024 |