Dear Michal,
On Thu, Nov 7, 2013 at 12:46 PM, Michal Krompiec
<michal.kromp...@gmail.com>wrote:
> Hello again,
> I browsed through the sources and I found the answer to my question:
> the atom at index 0 from the replacement is used for the new bond. It
> would be nice to be able to specify the index of this bonding atom as
> a parameter in AllChem.ReplaceSubstructs.
>
> Is it possible to reorder atoms in a molecule (i.e. to have a chosen
> atom at index 0)?
>
Indeed there is, the functionality was added at the last minute to the
2013.09 release.
Here's how you use it:
In [2]: m = Chem.MolFromSmiles('NCO')
In [3]: print Chem.MolToMolBlock(m)
RDKit
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 1 0
M END
In [4]: m2 = Chem.RenumberAtoms(m,(1,2,0))
In [5]: print Chem.MolToMolBlock(m2)
RDKit
3 2 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 0.0000 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3 1 1 0
1 2 1 0
M END
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