[Rdkit-discuss] Canonicalisation with reaction labels

Hi With a 2013 RDkit install we get consistent canonicalization between reaction labelled and unlabelled atoms. >>> mol = Chem.MolFromSmiles('C1CC([*])CCN1') >>> Chem.MolToSmiles(mol) '[*]C1CCNCC1' >>> mol = Chem.MolFromSmiles('C1CC([*:1])CCN1') >>> Chem.MolToSmiles(mol) '[*:1]C1CCNCC1' In 2015-

Re: [Rdkit-discuss] Canonicalisation with reaction labels

Thanks Greg, that’s clear. Stephen From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: 16 December 2016 14:33 To: Stephen Pickett Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] Canonicalisation with reaction labels EXTERNAL Hi Stephen, The new canonicalization

[Rdkit-discuss] Differences in chirality with BRICS fragmentation

Hi I have come across a difference in behaviour with the BRICS algorithms depending on how the molecule is fragmented when using non-canonical smiles input. RDKIT 2015_03, Python 2.7.10 BRICSDecompose gives back the starting chirality >>> smi='C1CCOC[C@H]1NC' >>> mol=Chem.MolFromSmiles(smi) >>

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

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&#x

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

uild the molecule ('CN[C@@H](C)c1c1OC'), BreakBRICSBonds works fine and I can regenerate the initial molecule with BRICSBuild. >>> mol=Chem.MolFromSmiles('CN[C@@H](C)c1c1OC') >>> frags=Chem.GetMolFrags(BRICS.BreakBRICSBonds(mol),asMols=True) >>> bm=list(BRICS

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

Hi Greg Thanks for taking a look. FYI, I hope to include a section about how we are using this algorithm at the UK QSAR meeting in Cardiff in April. Stephen From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: 07 February 2018 15:27 To: Stephen Pickett Cc: rdkit-discuss

[Rdkit-discuss] DeleteSubstructs issue

Hi There appears to be an issue with the DeleteSubstructs method when deleting groups from an aromatic N. The H-count is not reset properly leading to a kekulise error. The workaround is to Kekulise the molecule first. Of course, this would require more extensive SMARTS based substructures to u

Re: [Rdkit-discuss] use cases for weighted sampling of a compound library

The combi chem design literature has a lot on this topic. Designing the library to match a desired profile. Here is on to get started. https://pubs.acs.org/doi/full/10.1021/ci980332b Gillet et al. J. Chem. Inf. Comput. Sci. 1999, 39, 1, 169-177. In this case optimising the RMS to the desired pr