If I've understood your question correctly... RDKit uses atom mapping and
it would be straight forwards to write a command line script. Hydrogens can
be treated explicitly.
http://www.rdkit.org/docs/GettingStartedInPython.html#chemical-reactions
rxn =
AllChem.ReactionFromSmarts('[C:1]=[C:2].[C:3]=[*:4][*:5]=[C:6]>>[C:1]1[C:2][C:3][*:4]=[*:5][C:6]1')>>>
ps = rxn.RunReactants((Chem.MolFromSmiles('OC=C'),
Chem.MolFromSmiles('C=CC(N)=C')))>>>
Chem.MolToSmiles(ps[0][0])'NC1=CCCC(O)C1'
On Tue, Jun 10, 2014 at 11:14 PM, Rudesh.AZ <rudesh.toofa...@arzeda.com>
wrote:
> Hi,
>
> Does Openbabel have the capability to map the atoms in a reaction SMILES
> string? If not, do you know of any other programs that could do this ,
> preferably on the command line.
>
> example:
> CC(Cl)=O.CO>>COC(C)=O
> becomes
>
> [CH3:1][C:2]([Cl:3])=[O:4].[CH3:5][OH:6]>>[CH3:5][O:6][C:2]([CH3:1])=[O:4]
>
> More useful would be the ability to map explicit hydrogens too.
>
>
> Many thanks,
>
> Rudesh
>
>
>
> --
> View this message in context:
> http://forums.openbabel.org/Atom-mapping-for-Reaction-SMILES-tp4657517.html
> Sent from the General discussion mailing list archive at Nabble.com.
>
>
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