[Rdkit-discuss] USR/USRCAT implementation in RDKit

Dear all, A c++ implementation and Python wrappers of the ultrafast shape recognition (USR) descriptor (Ballester and Richards, J. Comput. Chem. (2007), 28, 1711) and the USR CREDO atom types (USRCAT) descriptor (Schreyer and Blundell, J. Cheminf. (2012), 4, 27) are now available for the RDKit.

Re: [Rdkit-discuss] name generator

Thanks Greg, I agree, it certainly works for molecules, however I am testing whether cactus is able to provide names to molecular fragments as well. Things like methyl phosphinite (COP) are named after that. See: http://cactus.nci.nih.gov/chemical/structure/COP/iupac_name Do you have any hints

Re: [Rdkit-discuss] how to make Compute2DCoords respecting coords from molfile

Hi Michal, On Wed, Aug 28, 2013 at 1:16 PM, Michał Nowotka mmm...@gmail.com wrote: Imagine this scenario: I read random molfile and I want to produce an image of it: 1. If the molfile already contains coordinates, use them 2. If the molfile coordinates are all zeros, compute them I

Re: [Rdkit-discuss] how to make Compute2DCoords respecting coords from molfile

Thanks Greg, can you explain what is GetConformer? In [3]: m = Chem.MolFromSmiles('Cc1c1') In [4]: CoordsAreAllZero(m) --- ValueErrorTraceback (most recent call last)

Re: [Rdkit-discuss] name generator

Hi Sergio,there may be random entries in the Resolver database behindhttp://cactus.nci.nih.gov/chemical/structure but definitelynothing systematic.MarkusOn Wed, 28 Aug 2013 07:54:26 -0400, Sergio Martinez Cuesta sermar...@gmail.com wrote:Thanks Greg,I agree, it certainly works for molecules,