Support for SMARTS extensions by MOE?
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Support for SMARTS extensions by MOE?
by Egon Willighagen-5
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Hi all (and the Dazhi/Rajarshi in particular),
I have playing with pKa prediction based on a JCIM paper release last Thursday [0] and ran into SMARTS parsing problems, because MOE extends the original specification in ways CDK does not support (yet): http://chem-bla-ics.blogspot.com/2008/10/pka-prediction-or-how-to-convert-jcim.html I identified at least the following constructs not supported: 1. [#G6] (or [#G7] etc) 2. [i] 3. [#X] Any possibility to see support for this in the CDK SMARTS engine? Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Rajarshi Guha-3
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On Oct 6, 2008, at 9:15 AM, Egon Willighagen wrote: > I identified at least the following constructs not supported: > > 1. [#G6] (or [#G7] etc) Shouldn't be difficult I expect > 2. [i] I'd rather support the OEChem version of this: C^2 means SP2. Also, OpenBabel supports this, so it's better than modifying our code to support just 1 application However, I disagree with your statement: "I'd rather see the CDK SMARTS engine support these industry adopted extensions" These extensions are just provided by one company, specific to their application. IMO, if I wanted to track extensions, I'd go for OpenEye. ------------------------------------------------------------------- Rajarshi Guha <rguha@...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- Q: What's yellow, linear, normed and complete? A: A Bananach space. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Egon Willighagen-5
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On Mon, Oct 6, 2008 at 3:41 PM, Rajarshi Guha <rguha@...> wrote:
> > On Oct 6, 2008, at 9:15 AM, Egon Willighagen wrote: > >> I identified at least the following constructs not supported: >> >> 1. [#G6] (or [#G7] etc) > > Shouldn't be difficult I expect > >> 2. [i] > > I'd rather support the OEChem version of this: C^2 means SP2. Also, > OpenBabel supports this, so it's better than modifying our code to support > just 1 application >From what the JCIM paper says, [i] != [C^2]... the former is a subset, really, of SP2 atoms involved in delocalized systems... so, stronger having electronic effects... > However, I disagree with your statement: > > "I'd rather see the CDK SMARTS engine support these industry adopted > extensions" > > These extensions are just provided by one company, specific to their > application. IMO, if I wanted to track extensions, I'd go for OpenEye. I'd most preferably see one fixed open standard, but I'd rather see support for these extensions *than* to have *approximating* SMARTS queries... that was my thought behind it... Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Rajarshi Guha-3
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On Oct 6, 2008, at 9:44 AM, Egon Willighagen wrote: > On Mon, Oct 6, 2008 at 3:41 PM, Rajarshi Guha <rguha@...> > wrote: >> >> On Oct 6, 2008, at 9:15 AM, Egon Willighagen wrote: >> >>> I identified at least the following constructs not supported: >>> >>> 1. [#G6] (or [#G7] etc) >> >> Shouldn't be difficult I expect Personally, I'd go for rewriting the above as an OR. Also if G6 indicates Group 6 of the periodic table then the elements are Cr, Mo, W so I'm not sure how it matches C, S etc Without MOE documentation, implementing these extensions is tricky. I'd rather not guess >> I'd most preferably see one fixed open standard, but I'd rather see > support for these extensions *than* to have *approximating* SMARTS > queries... that was my thought behind it... I see your point. We should also then publicize the CDK extension :) Specifically, the pharmacophore code allows you to do group wise OR's as P1|P2, where P1 and P2 are complete SMARTS patterns ------------------------------------------------------------------- Rajarshi Guha <rguha@...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- ...but there was no one in it....... - RG ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Egon Willighagen-5
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On Mon, Oct 6, 2008 at 4:02 PM, Rajarshi Guha <rguha@...> wrote:
>>>> 1. [#G6] (or [#G7] etc) >>> >>> Shouldn't be difficult I expect > > Personally, I'd go for rewriting the above as an OR. Yes, that's what I did... though it becomes rather long then... Moreover, there are a lot of variants (from my Perl script): $cdkSmarts =~ s/#G6H/#6H,#16H/g; $cdkSmarts =~ s/#G6;H/#6;H,#16;H/g; $cdkSmarts =~ s/#G4!H0/#4!H0,#14H0/g; I still have to check if I have rewritten the second and third variants correctly... > Also if G6 indicates Group 6 of the periodic table then the elements are Cr, > Mo, W so I'm not sure how it matches C, S etc Right... so my analysis that it meant 'Group' was so wrong... > Without MOE documentation, implementing these extensions is tricky. I'd > rather not guess Agreed. >>> I'd most preferably see one fixed open standard, but I'd rather see >> >> support for these extensions *than* to have *approximating* SMARTS >> queries... that was my thought behind it... > > I see your point. > > We should also then publicize the CDK extension :) Indeed :) I so only good in that... more papers, more citations :) BTW, can we parse a MQL query into a IQueryAtomContainer in the CDK already? Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Rajarshi Guha-3
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On Oct 6, 2008, at 10:11 AM, Egon Willighagen wrote: > BTW, can we parse a MQL query into a IQueryAtomContainer in the CDK > already? Dazhi mentioned something on these lines sometime back, but I don't know for sure. My understanding is that it'd be difficult, since MQL goes beyond what SMARTS provides ------------------------------------------------------------------- Rajarshi Guha <rguha@...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- The Heineken Uncertainty Principle: You can never be sure how many beers you had last night. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Egon Willighagen-5
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On Mon, Oct 6, 2008 at 4:14 PM, Rajarshi Guha <rguha@...> wrote:
> On Oct 6, 2008, at 10:11 AM, Egon Willighagen wrote: >> BTW, can we parse a MQL query into a IQueryAtomContainer in the CDK >> already? > > Dazhi mentioned something on these lines sometime back, but I don't know for > sure. My understanding is that it'd be difficult, since MQL goes beyond what > SMARTS provides Ah, that would be translating MQL into SMARTS... I was wondering about MQL directly into IQueryAtomContainer... Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Rajarshi Guha-3
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On Oct 6, 2008, at 10:16 AM, Egon Willighagen wrote: > On Mon, Oct 6, 2008 at 4:14 PM, Rajarshi Guha <rguha@...> > wrote: >> On Oct 6, 2008, at 10:11 AM, Egon Willighagen wrote: >>> BTW, can we parse a MQL query into a IQueryAtomContainer in the CDK >>> already? >> >> Dazhi mentioned something on these lines sometime back, but I >> don't know for >> sure. My understanding is that it'd be difficult, since MQL goes >> beyond what >> SMARTS provides > > Ah, that would be translating MQL into SMARTS... I was wondering about > MQL directly into IQueryAtomContainer... Oh, OK. Don't know about that ------------------------------------------------------------------- Rajarshi Guha <rguha@...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- Q: What's purple and commutes? A: An abelian grape. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Nina Jeliazkova
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Hi all,
I would also be interested in finding a solution to the MOE SMARTS extensions. Does MOE documentation come only with their products? With the supporting info the implementation is pretty quick and straightforward (here is mine from Friday evening :) https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-descriptors/src/main/java/ambit2/descriptors/PKASmartsDescriptor.java Regards, Nina Egon Willighagen wrote: > Hi all (and the Dazhi/Rajarshi in particular), > > I have playing with pKa prediction based on a JCIM paper release last > Thursday [0] and ran into SMARTS parsing problems, because MOE extends > the original specification in ways CDK does not support (yet): > > http://chem-bla-ics.blogspot.com/2008/10/pka-prediction-or-how-to-convert-jcim.html > > I identified at least the following constructs not supported: > > 1. [#G6] (or [#G7] etc) > 2. [i] > 3. [#X] > > Any possibility to see support for this in the CDK SMARTS engine? > > Egon > > > ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Rajarshi Guha-3
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On Oct 6, 2008, at 10:48 AM, Nina Jeliazkova wrote: > Hi all, > > I would also be interested in finding a solution to the MOE SMARTS > extensions. Does MOE documentation come only with their products? Apparently so. I've asked Adam if he can shed some light. AFAICS, the G? identifier means group of periodic table, since they have a entry in the table where they say G7 is a halogen. But the MOE implementation is not using IUPAC group numbering system. So G6 does mean C,S etc - but it's referring to VIB and VIA ------------------------------------------------------------------- Rajarshi Guha <rguha@...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- A beer delayed is a beer denied. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Egon Willighagen-5
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On Mon, Oct 6, 2008 at 4:48 PM, Nina Jeliazkova <nina@...> wrote:
> I would also be interested in finding a solution to the MOE SMARTS > extensions. Does MOE documentation come only with their products? > > With the supporting info the implementation is pretty quick and > straightforward (here is mine from Friday evening :) > https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-descriptors/src/main/java/ambit2/descriptors/PKASmartsDescriptor.java At least I got first post :) Are your PkaNode use the SMARTSQueryTool too? How did you deal with the difficult SMARTS? Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Egon Willighagen-5
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On Mon, Oct 6, 2008 at 4:02 PM, Rajarshi Guha <rguha@...> wrote:
> > On Oct 6, 2008, at 9:44 AM, Egon Willighagen wrote: > >> On Mon, Oct 6, 2008 at 3:41 PM, Rajarshi Guha <rguha@...> wrote: >>> >>> On Oct 6, 2008, at 9:15 AM, Egon Willighagen wrote: >>> >>>> I identified at least the following constructs not supported: >>>> >>>> 1. [#G6] (or [#G7] etc) >>> >>> Shouldn't be difficult I expect > > Personally, I'd go for rewriting the above as an OR. > > Also if G6 indicates Group 6 of the periodic table then the elements are Cr, > Mo, W so I'm not sure how it matches C, S etc Maybe Group VI of the main group elements? [1] describes [#G7!F] as "halogens (other than fluorine)"... Egon 1.http://www.chemcomp.com/journal/sdtools.htm -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Nina Jeliazkova
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:)On Mon, Oct 6, 2008 at 4:48 PM, Nina Jeliazkova nina@... wrote:I would also be interested in finding a solution to the MOE SMARTS extensions. Does MOE documentation come only with their products? With the supporting info the implementation is pretty quick and straightforward (here is mine from Friday evening :) https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-descriptors/src/main/java/ambit2/descriptors/PKASmartsDescriptor.javaAt least I got first post :) https://ambit.svn.sourceforge.net/svnroot/ambit/trunk/ambit2-all/ambit2-descriptors/src/main/java/ambit2/descriptors/PKANode.javaAre your PkaNode use the SMARTSQueryTool too? How did you deal with Actually it uses Smarts implementation written by my colleague. But nevertheless, difficult smiles are not dealt yet - too much to expect from a quick implementation. I hope it will be possible to rewrite the smarts, given MOE documentation.the difficult SMARTS? Regards, Nina Egon ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Rajarshi Guha-3
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On Oct 6, 2008, at 9:15 AM, Egon Willighagen wrote: > 1. [#G6] (or [#G7] etc) This is now support in 1.2.x. It's slightly different from the above, in that you'd write [G6] or [G7]. Also the number used in the CDK is based on the IUPAC group numbering. So MOE's [#G6] is actually [G14] in the CDK SMARTS implementation ------------------------------------------------------------------- Rajarshi Guha <rguha@...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- All science is either physics or stamp collecting. -- Ernest Rutherford ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Egon Willighagen-5
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On Tue, Oct 14, 2008 at 5:21 AM, Rajarshi Guha <rguha@...> wrote:
> This is now support in 1.2.x. It's slightly different from the above, in > that you'd write [G6] or [G7]. Also the number used in the CDK is based on > the IUPAC group numbering. So MOE's [#G6] is actually [G14] in the CDK > SMARTS implementation Thanx! Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Andrew Dalke
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On Oct 14, 2008, at 5:21 AM, Rajarshi Guha wrote:
> This is now support in 1.2.x. It's slightly different from the above, > in that you'd write [G6] or [G7]. Also the number used in the CDK is > based on the IUPAC group numbering. So MOE's [#G6] is actually [G14] > in the CDK SMARTS implementation Cool! Is this documented somewhere as a list of CDK extensions to SMARTS? Andrew dalke@... ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
by Rajarshi Guha-3
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On Oct 14, 2008, at 12:23 PM, Andrew Dalke wrote: > On Oct 14, 2008, at 5:21 AM, Rajarshi Guha wrote: >> This is now support in 1.2.x. It's slightly different from the above, >> in that you'd write [G6] or [G7]. Also the number used in the CDK is >> based on the IUPAC group numbering. So MOE's [#G6] is actually [G14] >> in the CDK SMARTS implementation > > Cool! Is this documented somewhere as a list of CDK extensions > to SMARTS? It's documented in the Javadocs for SMARTSQueryTool http://cheminfo.informatics.indiana.edu/~rguha/code/java/nightly/api/ org/openscience/cdk/smiles/smarts/SMARTSQueryTool.html (It'll be updated after the afternoon build completes, about 20 min) ------------------------------------------------------------------- Rajarshi Guha <rguha@...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 ------------------------------------------------------------------- Chemistry professors never die, they just fail to react. ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Support for SMARTS extensions by MOE?
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