Re: [Rdkit-discuss] RDkit Ruby binding /gem

2016-07-01 Thread Yannick .Djoumbou
Thank Greg, Good point. Regards, On Thu, Jun 30, 2016 at 11:58 AM, Greg Landrum wrote: > > > On Thu, Jun 30, 2016 at 7:19 PM, Yannick .Djoumbou > wrote: > >> >> Thanks for the suggestion. I will try that. >> I really think a native ruby gem would be really awesome, especially for >> all those

Re: [Rdkit-discuss] EmbedMultipleConfs problem

2016-07-01 Thread Paolo Tosco
Dear Richard, the reason why that SMILES fails to generate 3D conformations is that the stereochemistry on the bridged ring system cannot be satisfied, as the bridge would have to cross the ring, which is not possible. The stereocentres on the bridgehead carbons cannot be both R, as required b

Re: [Rdkit-discuss] Again on getting rid of ring-atoms in MCS smarts/smiles

2016-07-01 Thread Luca Fenu - Network
I kept working on the issue I posted about before, and here’s the issue I believe may be at the bottom of what I am seeing – code snippets should be executable: # the two molecules whose MCS I’m computing: [cid:image004.png@01D1D3BF.6BEA3360] from rdkit import Chem def ring_labels (a): # similar

[Rdkit-discuss] EmbedMultipleConfs problem

2016-07-01 Thread Richard Cooper
Hi RDKitters, Asking for a friend. The example below using the given molecule and EmbedMultipleConfs returns an empty list without throwing anything or producing any warnings. I've got quite a few smiles that fail in the same manner, but can't see any obvious pattern. It might be related to chira