Mannhold LogP descriptor
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Mannhold LogP descriptor
by Egon Willighagen-5
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Hi all,
over at FriendFeed there was a discussion on LogP and the ALogP [0] and XLogP implementations we have in the CDK. Particularly, the ALogP was somewhat off for the test compounds, including benzene and toluene, and there was mention of a recent paper by Mannhold et al. [1] describing a very simplistic equation which did very good on an overall set of 96 thousand compounds: logP = 1.46 + 0.11 * carbonAtoms - 0.11 * heteroAtoms Well, that is easy enough to implement and the result is available from this branch: http://github.com/egonw/cdk/tree/82-mannholdLogP It is a patch against CDK 1.3.x and I welcome very much review reports so that it can be applied to master soon. Egon PS. I have you have Open experimental LogP data, please contact Antony for contributing to ChemSpider, allowing him to build up an Open data set so that we can all make our favorite LogP prediction models. 0. http://friendfeed.com/chemspiderman/82577371/gathering-physicochemical-data-onto 1. http://dx.doi.org/10.1002/jps.21494 -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Mannhold LogP descriptor
by Rajarshi Guha-4
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On Oct 31, 2009, at 4:28 AM, Egon Willighagen wrote: > Hi all, > > over at FriendFeed there was a discussion on LogP and the ALogP [0] > and XLogP implementations we have in the CDK. Particularly, the ALogP > was somewhat off for the test compounds, including benzene and > toluene, and there was mention of a recent paper by Mannhold et al. > [1] describing a very simplistic equation which did very good on an > overall set of 96 thousand compounds: > > logP = 1.46 + 0.11 * carbonAtoms - 0.11 * heteroAtoms > > Well, that is easy enough to implement and the result is available > from this branch: > > http://github.com/egonw/cdk/tree/82-mannholdLogP > > It is a patch against CDK 1.3.x and I welcome very much review reports > so that it can be applied to master soon. Handy descriptor. The patch looks good to me ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Q: What do you get when you cross a mosquito with a mountain climber? A: Nothing. You can't cross a vector with a scaler. ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Mannhold LogP descriptor
by Egon Willighagen-5
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On Sat, Oct 31, 2009 at 1:40 PM, Rajarshi Guha <rajarshi.guha@...> wrote:
> On Oct 31, 2009, at 4:28 AM, Egon Willighagen wrote: >> It is a patch against CDK 1.3.x and I welcome very much review reports >> so that it can be applied to master soon. > > Handy descriptor. The patch looks good to me Do you want to sign off the patch, or shall I apply to master myself? Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Mannhold LogP descriptor
by Rajarshi Guha-4
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On Oct 31, 2009, at 11:14 AM, Egon Willighagen wrote: > On Sat, Oct 31, 2009 at 1:40 PM, Rajarshi Guha <rajarshi.guha@... > > wrote: >> On Oct 31, 2009, at 4:28 AM, Egon Willighagen wrote: >>> It is a patch against CDK 1.3.x and I welcome very much review >>> reports >>> so that it can be applied to master soon. >> >> Handy descriptor. The patch looks good to me > > Do you want to sign off the patch, or shall I apply to master myself? I pushed to master (though git pull didn't let me sign of) ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Chemistry professors never die, they just fail to react. ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Mannhold LogP descriptor
by Egon Willighagen-5
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On Sat, Oct 31, 2009 at 5:40 PM, Rajarshi Guha <rajarshi.guha@...> wrote:
> I pushed to master (though git pull didn't let me sign of) You tried: git commit --amend --signoff ? Thanx for reviewing and applying! Egon -- Post-doc @ Uppsala University Homepage: http://egonw.github.com/ Blog: http://chem-bla-ics.blogspot.com/ PubList: http://www.citeulike.org/user/egonw/tag/papers ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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Re: Mannhold LogP descriptor
by Rajarshi Guha-4
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On Nov 1, 2009, at 3:25 AM, Egon Willighagen wrote: > On Sat, Oct 31, 2009 at 5:40 PM, Rajarshi Guha <rajarshi.guha@... > > wrote: >> I pushed to master (though git pull didn't let me sign of) > > You tried: > > git commit --amend --signoff Aargh, forgot about --amend ---------------------------------------------------- Rajarshi Guha | NIH Chemical Genomics Center http://www.rguha.net | http://ncgc.nih.gov ---------------------------------------------------- Regular naps prevent old age.... especially if you take them while driving ------------------------------------------------------------------------------ Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference _______________________________________________ Cdk-devel mailing list Cdk-devel@... https://lists.sourceforge.net/lists/listinfo/cdk-devel |
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