Re: [Rdkit-discuss] remove redundant bits from bitvector fingerprints

2014-06-13 Thread Stephen O'hagan
OK, thanks for this – I’ll have a go and see it works for me. Cheers, Steve. From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: 13 June 2014 13:23 To: Stephen O'hagan Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] remove redundant bits from bitvector fingerprints

Re: [Rdkit-discuss] remove redundant bits from bitvector fingerprints

2014-06-13 Thread Greg Landrum
gt; *From:* Greg Landrum [mailto:greg.land...@gmail.com] > *Sent:* 04 June 2014 04:40 > *To:* Stephen O'hagan > *Cc:* rdkit-discuss@lists.sourceforge.net > *Subject:* Re: [Rdkit-discuss] remove redundant bits from bitvector > fingerprints > > > > Hi Steve, > > >

Re: [Rdkit-discuss] remove redundant bits from bitvector fingerprints

2014-06-04 Thread Stephen O'hagan
...@gmail.com] Sent: 04 June 2014 04:40 To: Stephen O'hagan Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] remove redundant bits from bitvector fingerprints Hi Steve, On Tue, Jun 3, 2014 at 2:08 PM, Stephen O'hagan mailto:soha...@manchester.ac.uk>> wrote: I have a

Re: [Rdkit-discuss] remove redundant bits from bitvector fingerprints

2014-06-03 Thread Greg Landrum
Hi Steve, On Tue, Jun 3, 2014 at 2:08 PM, Stephen O'hagan wrote: > I have a fragment of code generating fingerprints for a long list of > molecules (length ~ 1000) > > > > for index in range(0,len(smi)): > > smiles=smi[index] > > mol=Chem.MolFromSmiles(smiles) > > AllChem.Embe

[Rdkit-discuss] remove redundant bits from bitvector fingerprints

2014-06-03 Thread Stephen O'hagan
I have a fragment of code generating fingerprints for a long list of molecules (length ~ 1000) for index in range(0,len(smi)): smiles=smi[index] mol=Chem.MolFromSmiles(smiles) AllChem.EmbedMolecule(mol) AllChem.UFFOptimizeMolecule(mol) dm = Chem.Get3DDistanceMatrix(mol) fp = Gene