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
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