Re: [Rdkit-discuss] Are atom and bond indexes deterministic?
It looks like it should be deterministic, in that it always loops through the existing non-hydrogen atoms in their internal order, adding H's to each in turn. https://github.com/rdkit/rdkit/blob/ffc123a6659705adae33a6f5bf3913d65aa7b54d/Code/GraphMol/AddHs.cpp Steve On Wed, 3 Oct 2018 at 21:23, Peter St. John wrote: > Ah, well I suppose the follow up question is then does 'AddHs' add > hydrogens in a deterministic fashion? > If I have a canonicalized SMILES and do > > mol = Chem.MolFromSmiles(SMILES) > molH = Chem.AddHs(mol) > > and then store information about the bonds in molH, should those be > relatively consistent if I run the same code later? > My limited experiments seem to indicate they are, but I'm not sure if that > persists across python sessions or different hardware. > > Thanks again! > -- Peter > > > On Wed, Oct 3, 2018 at 9:53 AM Dmitri Maziuk via Rdkit-discuss < > rdkit-discuss@lists.sourceforge.net> wrote: > >> On Wed, 3 Oct 2018 17:26:24 +0200 >> Greg Landrum wrote: >> >> > Yep good point. >> > Though you can opt to keep the Hs if you want, that is not the default >> > behavior. >> >> ;) I work for NMR people, we get very attached to our protons. >> >> Seriously though, I forget whether it was rdkit or openbabel, but back >> when I was testing them I managed to read L-alanine MOL in and get >> D-alanine InChI string out in one of them. >> -- >> Dmitri Maziuk >> >> >> ___ >> 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 > ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Are atom and bond indexes deterministic?
On 10/03/2018 03:23 PM, Peter St. John wrote: > Ah, well I suppose the follow up question is then does 'AddHs' add > hydrogens in a deterministic fashion? It should, what's not guaranteed is that it will be the right order. Obviously, if (using my previous example) L- and D-alanine is the "same molecule" for your purposes, then it doesn't matter. If it does mater, then alatis (the link I sent earlier) is the best option that I know of. -- Dimitri Maziuk Programmer/sysadmin BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu signature.asc Description: OpenPGP digital signature ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Are atom and bond indexes deterministic?
Yep good point. Though you can opt to keep the Hs if you want, that is not the default behavior. On Wed, 3 Oct 2018 at 17:07, Dmitri Maziuk via Rdkit-discuss < rdkit-discuss@lists.sourceforge.net> wrote: > On Wed, 3 Oct 2018 06:21:06 +0200 > Greg Landrum wrote: > > > The atom ordering in the RDKit molecule created from a SMILES or Mol > block > > will always be the same and will corresponds to the ordering of the atoms > > in the input > > ... provided your molecule has no protons and/or you don't removeH/addH in > the process. > > -- > Dmitri Maziuk > > > ___ > 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
Re: [Rdkit-discuss] Are atom and bond indexes deterministic?
On Wed, 3 Oct 2018 06:21:06 +0200 Greg Landrum wrote: > The atom ordering in the RDKit molecule created from a SMILES or Mol block > will always be the same and will corresponds to the ordering of the atoms > in the input ... provided your molecule has no protons and/or you don't removeH/addH in the process. -- Dmitri Maziuk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
