Interesting question. Not sure if it's relevant but in ECBlast we do provide
Canonicalised reaction labels. I agree with Greg that AAM is important.
https://github.com/asad/ReactionDecoder
http://www.ebi.ac.uk/thornton-srv/software/rbl/
Regards,
Asad
Sent from my iPhone
> On 16 Dec 2016, at 14:42, Stephen Pickett <stephen.d.pick...@gsk.com> wrote:
>
> 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 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 with atom maps and you would like the canonical SMILES
> without the maps, you can do this (with the most recent version of the code):
>
> In [18]: mol = Chem.MolFromSmiles('C1CC([*:1])CCN1')
>
> In [19]: nmol = Chem.Mol(mol)
>
> In [20]: for at in nmol.GetAtoms(): at.SetAtomMapNum(0)
>
> In [21]: Chem.MolToSmiles(mol,True)
> Out[21]: 'C1CC([*:1])CCN1'
>
> In [22]: Chem.MolToSmiles(nmol,True)
> Out[22]: '[*]C1CCNCC1'
>
> A somewhat less clear (IMO) way of doing this that works in all versions is:
>
> In [27]: nmol = Chem.Mol(mol)
>
> In [28]: for at in nmol.GetAtoms(): at.ClearProp('molAtomMapNumber')
>
> In [29]: Chem.MolToSmiles(nmol,True)
> Out[29]: '[*]C1CCNCC1'
>
>
> I hope this helps,
> -greg
>
>
>
> On Fri, Dec 16, 2016 at 1:55 PM, Stephen Pickett <stephen.d.pick...@gsk.com>
> wrote:
> 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 2015-09 we are seeing differences.
> >>> mol = Chem.MolFromSmiles('C1CC([*])CCN1')
> >>> Chem.MolToSmiles(mol)
> '[*]C1CCNCC1'
> >>> mol = Chem.MolFromSmiles('C1CC([*:1])CCN1')
> >>> Chem.MolToSmiles(mol)
> 'C1CC([*:1])CCN1'
>
> I can understand why canonicalization can be different between versions but
> I’m not sure whether this change in behaviour is expected?
> I’m afraid that I don’t have ready access to a more recent install to test
> this out.
>
> Thanks
>
> Stephen
>
>
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