[Rdkit-discuss] MolFromXYZ?

[Naeem Attari]

Hi,

Is it possible to generate rdkit mol object only from xyz coordinates?
It would be useful to connect rdkit with other tools.

Was asked earlier: http://sourceforge.net/p/rdkit/mailman/message/31601105/

Thanks
Kind Regards
Shaikh Naeem

[Dmitri Maziuk]

Post by Naeem Attari
Hi,
Is it possible to generate rdkit mol object only from xyz coordinates?
It would be useful to connect rdkit with other tools.

If you can't transform your xyz coordinates into pdb ATOM line, then
probably not.

Dima

[Greg Landrum]

Hi,

Without information about whether or not atoms are bonded, and the orders
of the bonds between them, there's no sensible way to get an XYZ file into
the RDKit. If you can combine the XYZ file with a SMILES (or some other
format that has bond information), then it should be no problem

-greg

Post by Naeem Attari
Hi,
Is it possible to generate rdkit mol object only from xyz coordinates?
It would be useful to connect rdkit with other tools.
http://sourceforge.net/p/rdkit/mailman/message/31601105/
Thanks
Kind Regards
Shaikh Naeem
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[Greg Landrum]

[adding the list back to the recipient list]

Can't we derive the bond order and connectivity information from distance
matrix (which can be derived from coordinates)?

Assuming all hydrogens and charges are present in the file, the geometry is
a good one, and the structure is made up of octet-complete atoms from the
"organic subset", getting >90% of the bonds correct is almost certainly
doable without too much effort. The last bit will be problematic. If you
remove any of the above constraints, you're left with a research problem.
Here's a recent publication on the topic:
http://pubs.acs.org/doi/abs/10.1021/ci300358c

This isn't an attempt to discourage you from doing an implementation for
your own purposes, just an explanation of why something that is seemingly
simple is not present in the RDKit.

-greg