[Rdkit-discuss] couldn't import Chem from rdkit

2017-11-30 Thread Sundar
__future__ import print_function In [2]: from rdkit import Chem --- ImportError Traceback (most recent call last) in () > 1 from rdkit import Chem /Scr/scr-test-sundar/Scr-sundar/sundar/Progr

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Sundar
Hi Jason, Thanks for the info. That's exactly what I want. I want to download the compound in any format (smiles/mol/sdf) for which I only have the Substance ID. Sundar On Fri, Dec 1, 2017 at 8:06 PM, Jason Biggs <jasondbi...@gmail.com> wrote: > Sundar, > What you do will depen

Re: [Rdkit-discuss] Sanitizing SD file

2017-12-16 Thread Sundar
, Sundar On Thu, Dec 14, 2017 at 1:14 AM, Greg Landrum <greg.land...@gmail.com> wrote: > > > On Thu, Dec 14, 2017 at 6:35 AM, Francois BERENGER < > beren...@bioreg.kyushu-u.ac.jp> wrote: > >> On 12/14/2017 02:10 PM, Greg Landrum wrote: >> > >> >

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Sundar
eon...@gmail.com> wrote: > In what way? Given a single PubChem compound or substance ID you just want > to pull the smiles or molfile into RDKit? > > Tim > On 01/12/17 17:26, Sundar wrote: > > Hi RDkit users, > > I was wondering if RDkit has a means of downloading comp

[Rdkit-discuss] Sanitizing SD file

2017-12-13 Thread Sundar
atom. How do I sanitize it to fix these errors without losing its charge and 3D coordinates? Or how to disregard all these errors and get all the molecules read with nothing missing? Thanks, Sundar -- Check out the vibrant

[Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Sundar
Hi RDkit users, I was wondering if RDkit has a means of downloading compounds from Pubchem. Also let me other ways that helps here. Thanks, Jubi -- Check out the vibrant tech community on one of the world's most engaging

Re: [Rdkit-discuss] RDkit and Pubchem

2017-12-01 Thread Sundar
; > https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/ > 2244/SDF?record_type=3d > > setting up a python function to query this shouldn't be difficult. > > Jason Biggs > > > On Fri, Dec 1, 2017 at 12:51 PM, Sundar <jubilantsun...@gmail.com> wrote: > >&

[Rdkit-discuss] Diversity picker

2018-01-03 Thread Sundar
Hi RDKit users, Is it possible to pick a subset of (diverse) compounds that have less than a particular Tanimoto coefficient (for eg. 0.7) from a larger set using RDKit. The current version of the Diverse Picker picks a diverse set based on a "number of compounds" instead of Tanimoto score.

[Rdkit-discuss] reducing space in image rendered using Draw.MolsToGridImage

2018-11-26 Thread Sundar
How to reduce the space between each row of images while using Draw.MolsToGridImage to render an image? Currently the default space is unnecessarily big. -- Thanks, Sundar ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https