Re: [Rdkit-discuss] Canonicalisation with reaction labels

2016-12-17 Thread Andrew Dalke
On Dec 16, 2016, at 3:27 PM, Andrew Dalke wrote: > 2013 RDKit didn't preserve the atom order between labeled and unlabeled atoms. ... > I no longer have an older version of RDKit installed. My memory is wrong. I have rebuilt a version from 2013 and been unable to find a failure case. That is,

Re: [Rdkit-discuss] Canonicalisation with reaction labels

2016-12-16 Thread Syed Asad Rahman
ge.net > Subject: Re: [Rdkit-discuss] Canonicalisation with reaction labels > > EXTERNAL > > Hi Stephen, > > The new canonicalization algorithm intentionally takes the atom-mapping > information into account. The logic is that the entire SMILES provided should > be canonic

Re: [Rdkit-discuss] Canonicalisation with reaction labels

2016-12-16 Thread Greg Landrum
Hi Stephen, The new canonicalization algorithm intentionally takes the atom-mapping information into account. The logic is that the entire SMILES provided should be canonical, so if the SMILES includes atom maps, those atom maps should be considered while canonicalizing. If you have a molecule

Re: [Rdkit-discuss] Canonicalisation with reaction labels

2016-12-16 Thread Andrew Dalke
On Dec 16, 2016, at 1:55 PM, Stephen Pickett wrote: > 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 =

[Rdkit-discuss] Canonicalisation with reaction labels

2016-12-16 Thread Stephen Pickett
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