From: "Egon Willighagen" <[EMAIL PROTECTED]>
> On Monday 28 March 2005 14:37, Nicolas Vervelle wrote:
> > I have completed a few parts of the substructure() command.
> > It can be used in select or restrict commands to select atoms matching a
> > pattern.
> > restrict not substructure("O")
> > will hide H20 molecules.
>
> Intuitively this should hide proteins too! "O" is a substructure of every
> peptide bond. Can you explain?Yes, I can In SMILES specifications, there are two ways of specifying atoms in the pattern : - between []: it is the full form where you can specify all informations (atomic mass, chirality, hydrogen count, charge). In this form, the hydrogen atoms must be counted explicitely. For example [O] means an oxygen atom. - without []: it is a simplified version where you can't specify all informations. In this form, hydrogen atoms are automatically added to the atom to match the lowest normal valence of the atom. So O means oxygen bonded with two hydrogens, H2O (valence of O is 2) Different ways to write H2O in SMILES: - O - [OH2] - [H][O][H] - [O](H)H ... Nicolas ------------------------------------------------------- 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
