Re: [Rdkit-discuss] rearomatize only benzene rigns after kekulize + clearAromaticFlags

Ok guys, I came up with a possible solution for the N,C 6 rings aromatic rearomatisation after kekulize. I still need to find a ways to do it also for guanidinium salts. ? def TestL_n(L,n,aro): suppl = Chem.SDMolSupplier('/Users/mbp/Downloads/molecules-20-18279-s001/Compounds List for

Re: [Rdkit-discuss] (no subject)

Hello: Greg and Curt your comments are very much appreciated. Thanks for getting back to me! Best, Markus On Wed, Sep 21, 2016 at 8:31 PM, Greg Landrum wrote: > Hi Markus, > > Curt's instincts are dead on: the problem here is the rings. > > I'll show the fix and then

Re: [Rdkit-discuss] error while calculating rms and shape tanimoto

Hi >>Files 1.pdb and 2.pdb do not contain CONECT records (so missing bond orders?). I removed CONECT records from Files a.pdb and b.pdb. still code is running fine >>File 1.pdb contains an atom with name BR43. Maybe the PDB parser can't parse that (seems valid to me, FWTW). Also

Re: [Rdkit-discuss] error while calculating rms and shape tanimoto

Files 1.pdb and 2.pdb do not contain CONECT records (so missing bond orders?). File 1.pdb contains an atom with name BR43. Maybe the PDB parser can't parse that (seems valid to me, FWTW). Paul On 22/09/16 11:15, Amit singh wrote: Hi Files a.pdb and b.pdb are from RDKit test data (working

Re: [Rdkit-discuss] error while calculating rms and shape tanimoto

Hi Files a.pdb and b.pdb are from RDKit test data (working fine) Files 1.pdb and 2.pdb (other than test data, which are giving error) On Thu, Sep 22, 2016 at 3:03 PM, Greg Landrum wrote: > HI Amit, > > > On Thu, Sep 22, 2016 at 9:23 AM, Amit singh

Re: [Rdkit-discuss] error while calculating rms and shape tanimoto

HI Amit, On Thu, Sep 22, 2016 at 9:23 AM, Amit singh wrote: > > I am a new entry in this discussion forum and also for RDKit > Welcome! > I am trying to calculate shape tanimoto and rms between two molecules > (PDB files) from 3D functionality of RDKit. > Code is

Re: [Rdkit-discuss] rearomatize only benzene rigns after kekulize + clearAromaticFlags

On Wed, Sep 21, 2016 at 4:31 PM, Guillaume GODIN < guillaume.go...@firmenich.com> wrote: > After testing the code, It works perfectly, thanks! > Well, there's at least that. ;-) > Unfortunatly, I discovered that it's still not compatible with the > aromaticity method used in the article i

[Rdkit-discuss] error while calculating rms and shape tanimoto

Dear All I am a new entry in this discussion forum and also for RDKit I am trying to calculate shape tanimoto and rms between two molecules (PDB files) from 3D functionality of RDKit. Code is working fine for the pdb files given in test data. But gives error whenever I uses other pdb files