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
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.
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
>
&
'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 <
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
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
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