normalization of chemical structures
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normalization of chemical structures
by Rajarshi Guha-3
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Hash: SHA1 based on recent discussions, it would be useful to have a method/ class that performs various levels of 'normalization' of a chemical structure. I'm wondering whether others are interested in this, and if so, what are the aspects that would be normalized? Some examples that come to mind: 1) aromaticity perception 2) perform atom typing (using CDK scheme) 3) If SMILES, convert certain fragments to a standard form (I see there's a file called fixsmiles.xml in the CDK, but I don't know where it's used) 4) hydrogen addition 5) tautomers - ------------------------------------------------------------------- Rajarshi Guha <rguha@...> GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 - ------------------------------------------------------------------- A committee is a group that keeps the minutes and loses hours. -- Milton Berle -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.8 (Darwin) iEYEARECAAYFAkh/dqQACgkQZqGSLFHnnoTzDACfZv189xjRQUNFF8Ku8SF+Sckt UJIAoIsywbc25fSd+bFmhJU/fh0Zubz2 =ApxF -----END PGP SIGNATURE----- ------------------------------------------------------------------------- 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: normalization of chemical structures
by Stefan Kuhn-3
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Have a look at org.openscience.cdk.tools.Normalizer. This was a first attempt
by me to do something like this. A more elaboreted normalization would be a valuable tool, I think. On Thursday 17 July 2008 17:43:16 Rajarshi Guha wrote: > based on recent discussions, it would be useful to have a method/ > class that performs various levels of 'normalization' of a chemical > structure. > > I'm wondering whether others are interested in this, and if so, what > are the aspects that would be normalized? > > Some examples that come to mind: > > 1) aromaticity perception > 2) perform atom typing (using CDK scheme) > 3) If SMILES, convert certain fragments to a standard form (I see > there's a file called fixsmiles.xml in the CDK, but I don't know > where it's used) > 4) hydrogen addition > 5) tautomers > > ------------------------------------------------------------------- > Rajarshi Guha <rguha@...> > GPG Fingerprint: D070 5427 CC5B 7938 929C DD13 66A1 922C 51E7 9E84 > ------------------------------------------------------------------- > A committee is a group that keeps the minutes and loses hours. > -- Milton Berle > > > > ------------------------------------------------------------------------- > 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 ------------------------------------------------------------------------- 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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