[MMTK] atom connectivity

Warren L. DeLano warren@sunesis.com
Mon, 22 Apr 2002 08:29:44 -0700 (PDT)


Michael,

You would be covering new ground, but you could use PyMOL's molecular
editor to assign the connectivity information from the PDB coordinates by
manually adjusting bond valences and adding hydrogens.  You could then
take that information into MMTK.

PyMOL can provide a native Python object [via cmd.get_model()]
which contains the molecular structure, connectivity, and properties, and
which could presumably be converted into a MMTK database entry via a
Python script.

I'm not saying it would be easy, but it would be a Python based solution.

However, you would still need to find a reasonable way of assigning
atom types and partial charges...

Cheers,
Warren

On 22 Apr 2002, Konrad Hinsen wrote:

> "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.
>