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

[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