[MMTK] atom connectivity

Konrad Hinsen hinsen@cnrs-orleans.fr
22 Apr 2002 13:29:58 +0200

"Michael Sorich" <mike_sorich@hotmail.com> writes:

> I have a small molecule (not in the database) which I have loaded from a
> pdb file. I am trying to find out what atoms are bonded to an atom. When
> I call the bondedTo() function of an atom object, I am returned an empty
> list. Am I using the correct function? Is it possible to access

Yes, but you are asking for information that is not available. When
you construct a model from a PDB file, real molecule (or group)
objects can only be built for molecules/groups that are in the
database. For everything else you get AtomCluster objects, which just
group some atoms together, but contain no information about bonds,
atom types, force field parameters etc.

> connectivity information for an arbitary molecule with no database
> entry? 

No, because the connectivity information comes from the database.
MMTK does not try to guess it from the positions.

Konrad Hinsen                            | E-Mail: hinsen@cnrs-orleans.fr
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