Re: [Rdkit-discuss] reading multiple conformers from file

On 15 August 2017 at 12:05, Greg Landrum wrote: > Nope, just the discussion that you see there. > Doing the work stalled on people (well, at least me) not having time to > actually do it. :-( > > I still think it would be interesting, but it seems unlikely that it will >

Re: [Rdkit-discuss] reading multiple conformers from file

Nope, just the discussion that you see there. Doing the work stalled on people (well, at least me) not having time to actually do it. :-( I still think it would be interesting, but it seems unlikely that it will get done unless someone else can make the time. -greg On Mon, Aug 14, 2017 at 6:25

Re: [Rdkit-discuss] reading multiple conformers from file

Hello, I was just wondering, has there been any progress on the multi-conformer sdf file reader since last year? best Thomas On 27 October 2016 at 05:20, Greg Landrum wrote: > Hi Thomas, > > You're right, reading multiple conformations out of an SDF does seem like >

Re: [Rdkit-discuss] reading multiple conformers from file

Ok, let's start talking about this here: https://github.com/rdkit/rdkit/issues/1137 -greg On Mon, Oct 31, 2016 at 1:11 PM, Markus Sitzmann wrote: > +1 for a json format ... hmm, how about a general json-based molecular > structure format ... let us call it "cson"

Re: [Rdkit-discuss] reading multiple conformers from file

+1 for a json format ... hmm, how about a general json-based molecular structure format ... let us call it "cson" (that is an homage to Google gson and Chemical Markup Language CML :-) Markus On Mon, Oct 31, 2016 at 11:18 AM, Brian Cole wrote: > I would 2nd the suggestion of

Re: [Rdkit-discuss] reading multiple conformers from file

Rdkit already has a way to serialize conformers, the binary pickle format! Perhaps we should make a file extension for multiple molecules. Say ".rdk" and call it a day. Like inchi the source code is the reference :) Brian Kelley > On Oct 27, 2016, at 2:05 AM, Greg Landrum

Re: [Rdkit-discuss] reading multiple conformers from file

It would seem that a major issue with RDKit's multiconformer file is the inability to associate structure-level and atom-level properties with conformations. t's not quite orthogonal to the question of how to read, say, a multiconformer SD file into RDKit's multiconformer format, because the

Re: [Rdkit-discuss] reading multiple conformers from file

Hello Greg, Is the canonical SMILES string always unique for every isomer and tautomerization state of a molecule? If yes, then I have already written a function to load multiple molecules and their conformers, which I can share it here. best Thomas PS: thanks to David for pointing this out.

Re: [Rdkit-discuss] reading multiple conformers from file

The RDKit has support for the TPL format, an old BioCad/MSI/Accelrys format. It's easy to imagine something better, but this is at least already there and there could be other software that speaks it: https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/FileParsers/test_data/cmpd2.tpl I'd

Re: [Rdkit-discuss] reading multiple conformers from file

Hi Thomas, You're right, reading multiple conformations out of an SDF does seem like one of those common operations. Unfortunately the RDKit does not currently support it in an easy way. A python implementation of this would be a good topic for Friday's UGM hackathon, we can see if anyone finds

[Rdkit-discuss] reading multiple conformers from file

Hello everyone, I am a new user of RDkit and I was looking in the documentation for an easy way to load multiple conformers from a structure file like .sdf. The code must 1) distinguish between different protonation states of the same molecule, 2) create a new Mol() object for each protonation