Re: [Rdkit-discuss] cite?

2014-04-16 Thread Greg Landrum
On Wed, Apr 16, 2014 at 8:16 AM, paul.czodrow...@merckgroup.com wrote: I have used this citation: RDKit, Open-Source Cheminformatics. http://www.rdkit.org. There has not (yet) been an RDKit paper published, so there's no official citation. Paul's suggestion above is what I would also use.

Re: [Rdkit-discuss] MMFF94 atom typing OHs connected to aromatic heterocycles.

2014-04-16 Thread Toby Wright
Thanks very much Paulo. Yours, Toby -- InhibOx Ltd On 15 April 2014 00:25, Paolo Tosco paolo.to...@unito.it wrote: Dear Toby, I checked the MMFF literature and indeed that hydrogen must be type 29; I just submitted a pull request with the bug fix. Apparently the test case that you

Re: [Rdkit-discuss] cite?

2014-04-16 Thread Dimitri Maziuk
On 4/16/2014 1:55 AM, Greg Landrum wrote: On Wed, Apr 16, 2014 at 8:16 AM, paul.czodrow...@merckgroup.com mailto:paul.czodrow...@merckgroup.com wrote: I have used this citation: RDKit, Open-Source Cheminformatics. http://www.rdkit.org. There has not (yet) been an RDKit paper

[Rdkit-discuss] Opposite of GetSubstructureMatches()

2014-04-16 Thread JP
Hi there RDKitters, This is probably an easy one, but I cannot find anything in the docs or the mailing list. I have a tuple of atom Ids (e.g. 21,22,24,26,27) and a mol and I would like to extract the substructure (molecule) which matches those indices. Note that in my case this will be a

Re: [Rdkit-discuss] Opposite of GetSubstructureMatches()

2014-04-16 Thread Christos Kannas
Hi JP, I think smol = Chem.PathToSubmol(mol, path), where path is a list of indices, will do what you want. Best, Christos Christos Kannas Researcher Ph.D Student Mob (UK): +44 (0) 7447700937 Mob (Cyprus): +357 99530608 [image: View Christos Kannas's profile on