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 <wpwalt...@gmail.com> 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 < > rdkit-discuss@lists.sourceforge.net> 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 < >> jo...@ericjonas.com> 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 >> Rdkit-discuss@lists.sourceforge.net >> 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_7716656946544593368_m_-1427665032406965802_DAB4FAD8-2DD7-40BB-A1B8-4E2AA1F9FDF2> >> _______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >> >
_______________________________________________ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
