Hi Eric,
I may be a bit late, but here's a gist that shows how to convert a
molecule in XYZ format to an RDKit molecule with bond orders taken from
SMILES retaining hydrogens if originally present.
https://gist.github.com/ptosco/4844d3635cf14d11e5e14381993915c1
Disclaimer: I have tested it on the single molecule that I used as example.
Cheers,
p.
On 10/04/18 22:36, Eric Jonas wrote:
Thanks both Patrick and Maria, this is incredibly helpful. Is there
any easy way to inside of RDKit go from a list of molecules to a pdb
file? Right now I'm writing an .xyz file and doing a xyz->pdb pass via
a command-line callout to openbabel, but that's.... a bit of a hack.
On Thu, Oct 4, 2018 at 1:37 PM Patrick Walters <[email protected]
<mailto:[email protected]>> wrote:
I just wrote a blog post on this topic.
https://practicalcheminformatics.blogspot.com/2018/09/assigning-bond-orders-to-pdb-ligands.html
On Thu, Oct 4, 2018 at 3:35 PM MARIA BRANDL via Rdkit-discuss
<[email protected]
<mailto:[email protected]>> wrote:
Hello Eric,
RDKit can assign bond orders from a smiles string to a PDB
coordinate file.
See chapter on 3D functionality in
https://www.rdkit.org/docs/Cookbook.html.
I assume that the coordinates need to have connectivity (but
not bond order) information,
which should not be too hard to compute as long as your
coordinates are not too distorted.
Hope this helps,
Best wishes
Maria Brandl
On Thursday, 4 October 2018, 15:49:10 BST, Eric Jonas
<[email protected] <mailto:[email protected]>> wrote:
Hello! I have a large database of molecules where I have, for
each molecule:
1. A geometry (element, x, y, z)
2. a SMILES string
and I would like to get the associated Chem.Mol structure. Of
course, there's no guarantee that the ordering of the atoms in
the Mol will match up with the order in my geometry list. I'm
trying to figure out the right way of turning this geometry
into a valid conformation for my Mol. Is there any reliable
way of doing this? I know that going strictly from
geometry->Mol can be challenging (OBabel has some reasonable
support, as does the python library xyz2mol ) but those tools
seem to depend largely on bond-length heuristics, and it seems
if I have the SMILES string it should be possible to do a
better job.
Thanks,
...Eric
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