On Monday 21 March 2005 10:38 pm, Nicolas Vervelle wrote: > I have just committed under CVS the first version of the substructure() > command for the script language.
<snip/>
I have been thinking of having a plugins for certain functionality like this... I can imagine a plugin which provides new script commands, e.g. this match command, allowing for example the CDK to be used for these kind of algorithms. My worries are that this is at least the third independent SMILES implementation to be implemented (CDK and JOElib to be the others...)
[crossposted to CDK...]
As a user I also have this concern. I need substructure search for two separate tools at least:
- atom-atom mapping in reactions (MACiE database)
- substructure search in collections of molecules
I am leaning towards doing some of this through webservices or other wrapped functionality (which avoids jar problems). At present we use OpenBabel for brute-force SMARTS and it does ca 10,000 searches/min. Personally I do not want to implement more than one and I particualrly want a consistent interface. The input is probably not a major problem but the output other than boolean yes/no is non-trivial. So I'm neutral on where it comes from, but it should be relatively lightweight or alternatively be easily encapsulated.
BTW I think that for extended searches we need to have AtomMatcher and BondMatcher classes (we've discussed this before)
P.
Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 Fax: +44 1223 763076
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