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> > <#m_-1427665032406965802_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> > _______________________________________________ > Rdkit-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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