Thanks Paolo, That would be a really nice contribution to the RDKit Cookbook. hint hint. :-)
-greg On Fri, Oct 5, 2018 at 12:20 AM Paolo Tosco <[email protected]> wrote: > 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]> > 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]> 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]> 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 >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >>> >>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> >>> Virus-free. >>> www.avast.com >>> <https://www.avast.com/sig-email?utm_medium=email&utm_source=link&utm_campaign=sig-email&utm_content=webmail> >>> _______________________________________________ >>> Rdkit-discuss mailing list >>> [email protected] >>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >>> >> > > > > _______________________________________________ > Rdkit-discuss mailing > [email protected]https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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