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*
>
> ------------------------------
>
> This e-mail was sent by GlaxoSmithKline Services Unlimited
> (registered in England and Wales No. 1047315), which is a
> member of the GlaxoSmithKline group of companies. The
> registered address of GlaxoSmithKline Services Unlimited
> is 980 Great West Road, Brentford, Middlesex TW8 9GS.
>
> *GSK monitors email communications sent to and from GSK in order to
> protect GSK, our employees, customers, suppliers and business partners,
> from cyber threats and loss of GSK Information. GSK monitoring is conducted
> with appropriate confidentiality controls and in accordance with local laws
> and after appropriate consultation.*
>
> ------------------------------------------------------------
> ------------------
> Check out the vibrant tech community on one of the world's most
> engaging tech sites, SlashDot.org! http://sdm.link/slashdot
> _______________________________________________
> Rdkit-discuss mailing list
> Rdkit-discuss@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>
>
------------------------------------------------------------------------------
Check out the vibrant tech community on one of the world's most
engaging tech sites, SlashDot.org! http://sdm.link/slashdot
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
