From: Egon W. <ego...@gm...> - 2008-07-27 15:46:49
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Hi all, the UniversalIsomorphismTester is in CDK's standard module, being so central to chemoinformatics. The isomorphism module, instead, contains code that uses this class for queries which involve IQueryAtomContainer's, using specialized IQueryAtom and IQueryBond implementations. For example, a SMARTS string gets converted into such queries, but one can easily write custom IQueryAtomContainers substructure queries without having to use the SMARTS parser. Now, I think that this isomorphism module is misnames, and I like to rename it to substruct instead. Anyone against this, or with a better name? Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Rajarshi G. <rg...@in...> - 2008-07-27 18:36:53
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Jul 27, 2008, at 11:46 AM, Egon Willighagen wrote: > Hi all, > > the UniversalIsomorphismTester is in CDK's standard module, being so > central to chemoinformatics. The isomorphism module, instead, contains > code that uses this class for queries which involve > IQueryAtomContainer's, using specialized IQueryAtom and IQueryBond > implementations. For example, a SMARTS string gets converted into such > queries, but one can easily write custom IQueryAtomContainers > substructure queries without having to use the SMARTS parser. > > Now, I think that this isomorphism module is misnames, and I like to > rename it to substruct instead. > > Anyone against this, or with a better name? It doesn't matter too much to me; however, I do prefer isomorphism since it is more generic and matches the notion that the UIT can do any type of isomorphism (whether it be substructure searches, pharmacophores etc). - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- A committee is a life form with six or more legs and no brain. -- Lazarus Long, "Time Enough For Love" -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkiMwD8ACgkQZqGSLFHnnoSfWQCcDW2GIBSfiShCQM9Sy9cGD37Z gKUAoLzvOkrnrbdQY5jHztFPISX/gTg8 =zpd7 -----END PGP SIGNATURE----- |
From: Egon W. <ego...@gm...> - 2008-07-27 21:02:37
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On Sun, Jul 27, 2008 at 8:36 PM, Rajarshi Guha <rg...@in...> wrote: > It doesn't matter too much to me; however, I do prefer isomorphism since it > is more generic and matches the notion that the UIT can do any type of > isomorphism (whether it be substructure searches, pharmacophores etc). Except that the UIT itself is *not* in the isomorphism module... Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Rajarshi G. <rg...@in...> - 2008-07-27 21:06:58
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Jul 27, 2008, at 5:02 PM, Egon Willighagen wrote: > On Sun, Jul 27, 2008 at 8:36 PM, Rajarshi Guha <rg...@in...> > wrote: >> It doesn't matter too much to me; however, I do prefer isomorphism >> since it >> is more generic and matches the notion that the UIT can do any >> type of >> isomorphism (whether it be substructure searches, pharmacophores >> etc). > > Except that the UIT itself is *not* in the isomorphism module... Aah! What is in the isomorphism module? - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- All great discoveries are made by mistake. -- Young -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkiM428ACgkQZqGSLFHnnoRW+ACg7rM79nGuJSCHtcWfLW2oR/D2 lzAAmgMSrYOvosoRExMv1rdku/u/IwMl =gPPU -----END PGP SIGNATURE----- |
From: Rajarshi G. <rg...@in...> - 2008-07-27 21:09:44
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Jul 27, 2008, at 5:02 PM, Egon Willighagen wrote: > On Sun, Jul 27, 2008 at 8:36 PM, Rajarshi Guha <rg...@in...> > wrote: >> It doesn't matter too much to me; however, I do prefer isomorphism >> since it >> is more generic and matches the notion that the UIT can do any >> type of >> isomorphism (whether it be substructure searches, pharmacophores >> etc). > > Except that the UIT itself is *not* in the isomorphism module... Hmm, looking at isomorphism.javafiles I see that it has org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java Shouldn't these be in the smarts module? And couldn't the remainder simply go into standard or core? At least QueryAtomContainer should be in core, since anything that uses the UIT will make use of this - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- "355/113 -- Not the famous irrational number PI, but an incredible simulation!" -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkiM5BcACgkQZqGSLFHnnoT02gCgn3VsxRz9D76pJZ1ODN7bR3H1 e4MAoIpMIj5WGVSNvD/Y0nC6PS/GCCuI =lrvl -----END PGP SIGNATURE----- |
From: Egon W. <ego...@gm...> - 2008-07-27 21:10:04
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On Sun, Jul 27, 2008 at 11:06 PM, Rajarshi Guha <rg...@in...> wrote: > On Jul 27, 2008, at 5:02 PM, Egon Willighagen wrote: >> >> On Sun, Jul 27, 2008 at 8:36 PM, Rajarshi Guha <rg...@in...> wrote: >>> >>> It doesn't matter too much to me; however, I do prefer isomorphism since >>> it >>> is more generic and matches the notion that the UIT can do any type of >>> isomorphism (whether it be substructure searches, pharmacophores etc). >> >> Except that the UIT itself is *not* in the isomorphism module... > > Aah! What is in the isomorphism module? cdk.isomorphism.smarts.matcher.* where smarts == query, and not really SMARTS More like smarts-like... If you know what I mean... :) Try: more build/isomorphism.javafiles Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Rajarshi G. <rg...@in...> - 2008-07-27 21:13:52
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Jul 27, 2008, at 5:10 PM, Egon Willighagen wrote: > On Sun, Jul 27, 2008 at 11:06 PM, Rajarshi Guha <rg...@in...> > wrote: >> On Jul 27, 2008, at 5:02 PM, Egon Willighagen wrote: >>> >>> On Sun, Jul 27, 2008 at 8:36 PM, Rajarshi Guha >>> <rg...@in...> wrote: >>>> >>>> It doesn't matter too much to me; however, I do prefer >>>> isomorphism since >>>> it >>>> is more generic and matches the notion that the UIT can do any >>>> type of >>>> isomorphism (whether it be substructure searches, pharmacophores >>>> etc). >>> >>> Except that the UIT itself is *not* in the isomorphism module... >> >> Aah! What is in the isomorphism module? > > cdk.isomorphism.smarts.matcher.* > > where smarts == query, and not really SMARTS > > More like smarts-like... > > If you know what I mean... :) You totally lost me :) It seems to be that org/openscience/cdk/isomorphism/matchers/smarts/* should go in the smarts module - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- All science is either physics or stamp collecting. -- Ernest Rutherford -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkiM5Q8ACgkQZqGSLFHnnoSdAwCfTDWb90eZ83KR2hloUBRHDqnf qQoAoLApjz2TEt2w2XF9HWIYqb30Eq82 =mpKQ -----END PGP SIGNATURE----- |
From: Egon W. <ego...@gm...> - 2008-07-27 21:13:18
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On Sun, Jul 27, 2008 at 11:09 PM, Rajarshi Guha <rg...@in...> wrote: > Hmm, looking at isomorphism.javafiles I see that it has > > org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java > org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java > org/openscience/cdk/isomorphism/matchers/smarts/AromaticQueryBond.java > org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java > org/openscience/cdk/isomorphism/matchers/smarts/AnyOrderQueryBond.java > org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java > > Shouldn't these be in the smarts module? Why should they? These classes are not restricted to the SMARTS syntax... SMARTS is nothing more than a line notation language for flexible molecular queries, just like MQL... (Maybe Dzaio can use JJTree for parsing MQL? Because the opensource MQL library is not LGPL compatible.) > And couldn't the remainder simply go into standard or core? At least QueryAtomContainer should be in core, No, because it least currently it depends on the data module... (QAC extends AC) > since anything that uses the UIT will make use of this Actually not. The second argument *may* be an IQueryAtomContainer, but may be also just an IAtomContainer, as in the original UIT implementation. Egon -- ---- http://chem-bla-ics.blogspot.com/ |
From: Rajarshi G. <rg...@in...> - 2008-07-27 21:15:47
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Jul 27, 2008, at 5:13 PM, Egon Willighagen wrote: > On Sun, Jul 27, 2008 at 11:09 PM, Rajarshi Guha <rg...@in...> > wrote: >> Hmm, looking at isomorphism.javafiles I see that it has >> >> org/openscience/cdk/isomorphism/matchers/smarts/SMARTSBond.java >> org/openscience/cdk/isomorphism/matchers/smarts/SMARTSAtom.java >> org/openscience/cdk/isomorphism/matchers/smarts/ >> AromaticQueryBond.java >> org/openscience/cdk/isomorphism/matchers/smarts/AromaticAtom.java >> org/openscience/cdk/isomorphism/matchers/smarts/ >> AnyOrderQueryBond.java >> org/openscience/cdk/isomorphism/matchers/smarts/AnyAtom.java >> >> Shouldn't these be in the smarts module? > > Why should they? These classes are not restricted to the SMARTS > syntax... I'd suggest a rename of the SMARTS*.java files if they are not specific to SMARTS > >> And couldn't the remainder simply go into standard or core? At >> least QueryAtomContainer should be in core, > > No, because it least currently it depends on the data module... > (QAC extends AC) OK >> since anything that uses the UIT will make use of this > > Actually not. The second argument *may* be an IQueryAtomContainer, but > may be also just an IAtomContainer, as in the original UIT > implementation. OK - ------------------------------------------------------------------- Rajarshi Guha <rg...@in...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- Chemistry professors never die, they just fail to react. -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkiM5YIACgkQZqGSLFHnnoQgFQCg5xg/lrNmpdMYJiwsIEqpHjpu +GsAoMXNdwl8J3vOkSp43XLPaZR1pqGJ =UnqW -----END PGP SIGNATURE----- |
From: Daniel Z. <Zah...@ma...> - 2008-07-29 14:03:30
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Egon, Is there a reason why you removed the public IMolecule cmlMoleculeTocdkAtomContainer(CMLMolecule mol) method in this file (revision 11753, 7/25/08). I'm happy to move it else where or implement it in a different way, but I do need that functionality. DanZ /******************************************** Daniel Zaharevitz Chief, Information Technology Branch National Cancer Institute zah...@dt... ********************************************/ |
From: Egon W. <ego...@gm...> - 2008-07-29 15:31:53
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On Tue, Jul 29, 2008 at 4:03 PM, Daniel Zaharevitz <Zah...@ma...> wrote: > Is there a reason why you removed the > public IMolecule cmlMoleculeTocdkAtomContainer(CMLMolecule mol) method in > this file (revision 11753, 7/25/08). I'm happy to move it else where or > implement it in a different way, but I do need that functionality. It was not used, as I could see, and the CMLReader is available for that kind of functionality. Should have checked when it was added, and why. Sorry about that. Would using the new CMLReader(new StringReader(myCMLMoleculeString)).read(new Molecule()) do for you? Egon -- ---- http://chem-bla-ics.blogspot.com/ |