Dear Geoff,

the atom type list from OB has been on BODR SVN for some time now, and I want 
to make a start with converting this to CML so that I can add it to the BODR 
releases.

Could you please explain the four txt files in BODR SVN, i.e. aromatic.txt, 
atomtyp.txt, bondtyp.txt and types.txt and how they relate?

types.txt seems to indicate how atom types are interconverted, while 
atomtyp.txt seems to have the SMARTS queries to perceive atom types. 

About the atom type perception: what input does that require? In the CDK we 
have several kinds of input, with combinations of:
- no explicit hydrogens
- explicit hybridization
- missing bond orders

(Most notably, atom type perception in SMILES is tricky, where hydrogens are 
implicitly assumed (with unknown rules), missing bond orders, but with 
explicit hybridization states.)

Does OpenBabel perceive atom types, or just read them from files? If 
perception is done, do you rely simply on the SMARTS queries, and how well do 
those work with the above three types of missing input features?

Egon

-- 
[EMAIL PROTECTED]
Cologne University Bioinformatics Center (CUBIC)
Blog: http://chem-bla-ics.blogspot.com/
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