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.
>
> It is really an ALPHA version (no much testing done), so try it at your own
> risk ;)
> If you want to try it, you will have to checkout the latest version from
> CVS and compile it.
> Comments are really welcome :)
>
> This command can be used for example for selecting groups of atoms
> corresponding to a pattern defined with SMILES description.
>
> For example:
> select substructure("C[NH2]")
> will select all atoms that are part of a structure CH3NH2.CDK has a fairly feature complete SMILES parser (no stereo), and also a partial SMARTS parser (SMARTS is the substructure definiation variant of SMILES). > A complete description of SMILES is available at > http://www.daylight.com/smiles/. > Currently, the substructure commande implements only a part of SMILES. > I have identified at least the following limitations : does is support ring systems? > - the atomic mass can be specified in the SMILES string but is not used for > the pattern matching (I didn't find the notion of atomic mass in Jmol) > - the chirality can not be specified in the SMILES string. I will probably > modify the parser to work when the chirality is specified, but, unless > someone really needs it, I don't plan to add it to the pattern matching > part. > - directional bonds can not be specified in the SMILES string. Same comment > as for chirality. > - aromaticity is not handled correctly (I didn't test it) : the definition > of aromatic bonds (':') should work but not the symbol in lower case. lower case element symbols != aromatic instead, lower case element symbols denote sp2 hybridization. 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...) Anyway, good to see this functionality... Egon ------------------------------------------------------- SF email is sponsored by - The IT Product Guide Read honest & candid reviews on hundreds of IT Products from real users. Discover which products truly live up to the hype. Start reading now. http://ads.osdn.com/?ad_id=6595&alloc_id=14396&op=click _______________________________________________ Jmol-developers mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/jmol-developers
