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<mailto: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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