Hi,
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.
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 :
- 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.
Nicolas
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