Greg,
Is it available in c++? Also, just to make sure - the argument is a list of
old positions for each new position?
Thanks,
Igor
On Thu, Nov 7, 2013 at 8:41 AM, Greg Landrum <greg.land...@gmail.com> wrote:
> 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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