Hi Egon, I am just curious about the impact or regression it might have. I support the idea but in my past experience, playing with CDK atom types was a challenging task!
Asad Sent from my iPhone On 4 May 2012, at 13:04, [email protected] wrote: > Send Cdk-user mailing list submissions to > [email protected] > > To subscribe or unsubscribe via the World Wide Web, visit > https://lists.sourceforge.net/lists/listinfo/cdk-user > or, via email, send a message with subject or body 'help' to > [email protected] > > You can reach the person managing the list at > [email protected] > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Cdk-user digest..." > > > Today's Topics: > > 1. updated atom type specification (Egon Willighagen) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Fri, 4 May 2012 13:44:38 +0200 > From: Egon Willighagen <[email protected]> > Subject: [Cdk-user] updated atom type specification > To: [email protected], [email protected] > Message-ID: > <CAMPqvY-=DLPw3ufmEMRjCP4AvY2MzG=8h296z23w+6ryzug...@mail.gmail.com> > Content-Type: text/plain; charset=ISO-8859-1 > > Hi all, > > for the deduce bond order work by Klas (Uppsala), we ran into the > situation that bondOrderSum and maxBondOrder were not defined for the > CDK atom types. To some extend this can be deduced, but it is nicer to > just have this info explicit... I just discussed this with a few > people and it seems to be useful for other algorithms too. > > So, I'm proposing this change: > > <at:AtomType rdf:ID="C.sp3"> > <at:categorizedAs rdf:resource="&cdkat;C.tetrahedral"/> > <at:hasElement rdf:resource="&elem;C"/> > <at:hybridization rdf:resource="&at;sp3"/> > <at:formalCharge>0</at:formalCharge> > <at:lonePairCount>0</at:lonePairCount> > - <at:formalNeighbourCount>4</at:formalNeighbourCount> > - <at:piBondCount>0</at:piBondCount> > + <at:formalBondType rdf:resource="&bo;single"/> > + <at:formalBondType rdf:resource="&bo;single"/> > + <at:formalBondType rdf:resource="&bo;single"/> > + <at:formalBondType rdf:resource="&bo;single"/> > </at:AtomType> > > The at:formalNeighbourCount and at:piBondCount properties follow from > the new at:formalBondType elements... but we now also cheaply get > maxBondOrder and bondOrderSum ... > > I have updated the OWLAtomTypeHandler accordingly and currently > supports both approaches. > > It will be some work to update all atom types, and it also means that > atom types like C.sp will need to be split up, as it currently matches > =C= and -C# ... I think that is actually a good thing. > > I'm moving forward with this, and write a patch against CDK 1.4.x, > because we'll need it for Bioclipse 2.6 (though Bioclipse can always > 'fork' in case in mainstream CDK we decide to put it only in > master)... if you have comments, suggestions, this would be a good > time. > > Egon > > -- > Dr E.L. Willighagen > Postdoctoral Researcher > Department of Bioinformatics - BiGCaT > Maastricht University (http://www.bigcat.unimaas.nl/) > Homepage: http://egonw.github.com/ > LinkedIn: http://se.linkedin.com/in/egonw > Blog: http://chem-bla-ics.blogspot.com/ > PubList: http://www.citeulike.org/user/egonw/tag/papers > > > > ------------------------------ > > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > > ------------------------------ > > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user > > > End of Cdk-user Digest, Vol 72, Issue 4 > *************************************** ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
