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
[adding the list back to the recipient list]
On Mon, Jan 19, 2015 at 10:02 AM, Naeem Attari naeemraz...@gmail.com
wrote:
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
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
On 1/17/2015 8:57 AM, Naeem Attari wrote:
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
Dear Sereina,
No, I have just a table of 3D coordinates (generated by cclib). This
is equivalent to having an xyz file.
I know that this conversion is possible with OpenBabel, but I would
like to avoid using it for this particular purpose.
It seems that the simplest way is to hardcode generation
Hi Michal,
Well, if you have your 3D coordinates as a PDB file, you can read them in
with the new PDB parser and assign the bond orders based on a template
(generated from the SMILES of your molecule):
tmp = Chem.MolFromPDBFile(yourfilename)
template = Chem.MolFromSmiles(yoursmiles)
mol =
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