Re: [Rdkit-discuss] Differences in chirality with BRICS fragmentation

2018-02-07 Thread Greg Landrum
On Wed, Feb 7, 2018 at 4:36 PM, Stephen Pickett wrote: > > > Thanks for taking a look. > > If you want to keep an eye on what's going on, here's the bug: https://github.com/rdkit/rdkit/issues/1734 > FYI, I hope to include a section about how we are using this

Re: [Rdkit-discuss] Differences in chirality with BRICS fragmentation

2018-02-07 Thread Stephen Pickett
rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Differences in chirality with BRICS fragmentation EXTERNAL It's no fair reviving old items on difficult topics like stereochemistry! ;-) This is due to a bug in BRICS.BreakBRICSBonds(): stereochemistry isn't handled correctly.

Re: [Rdkit-discuss] Differences in chirality with BRICS fragmentation

2018-02-07 Thread Greg Landrum
CN[C@@H](C)c1c1OC') > > >>> frags=Chem.GetMolFrags(BRICS.BreakBRICSBonds(mol),asMols=True) > > >>> bm=list(BRICS.BRICSBuild(frags)) > > >>> [Chem.MolToSmiles(m,1) for m in bm] > > […., 'CN[C@@H](C)c1c1OC', ….] > > > > Regards > &

Re: [Rdkit-discuss] Differences in chirality with BRICS fragmentation

2018-01-10 Thread Stephen Pickett
'CN[C@@H](C)c1c1OC') >>> frags=Chem.GetMolFrags(BRICS.BreakBRICSBonds(mol),asMols=True) >>> bm=list(BRICS.BRICSBuild(frags)) >>> [Chem.MolToSmiles(m,1) for m in bm] […., 'CN[C@@H](C)c1c1OC', ….] Regards Stephen From: Stephen Pickett Sent: 16 May 2017 09:01 To: Greg Landrum <

Re: [Rdkit-discuss] Differences in chirality with BRICS fragmentation

2017-05-16 Thread Stephen Pickett
Thanks Greg I’m hoping we can get to 17-03 Stephen From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: 16 May 2017 06:22 To: Stephen Pickett Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Differences in chirality with BRICS fragmentation EXTERNAL Hi Stephen, You're

Re: [Rdkit-discuss] Differences in chirality with BRICS fragmentation

2017-05-15 Thread Greg Landrum
Hi Stephen, You're perfectly correct, what you're seeing there is a bug. However you're using a two-year old version of the RDKit and a number of bugs in this area have been fixed in the intervening time. Still, since there's potentially a lot going on here, and I'm always nervous about