Hi,
The smiles atom order is saved in a private property
'_smilesAtomOutputOrder', see discussion on Github:
https://github.com/rdkit/rdkit/issues/794
The order of atoms in PDB is the same as in RDKit's Mol object, thus it's
fairly easy to find such mapping.
----
Pozdrawiam, | Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl
2018-05-10 11:39 GMT+02:00 carlo del moro <delmoro.ca...@gmail.com>:
> Thanks to all for the replies,
>
> I put an example for better explain my problem.
> starting from a PDB representing HPE, I use RDKIT/obabel for calculate the
> relative SMILES. Next, using a RDKIT's function I fragment the smiles in
> substructure like this "CC(=O)O"; now I need to remap this substructure on
> the starting tridimensional structureand in order to get the atom
> coordinate. The task will be pretty easy if the numeration of the SMILES
> atom representation is the same of the starting PDB file. You know any
> methods to unify this two numeration? or to map the SMILES atom sequence on
> the PDB's one?
> This is the PDB for HPE.
>
>
> HETATM 4176 N HPE B 2 5.227 20.107 15.512 1.00 17.92
> N
> HETATM 4177 CA HPE B 2 4.065 20.646 16.205 1.00 16.87
> C
> HETATM 4178 C HPE B 2 2.784 20.702 15.373 1.00 18.59
> C
> HETATM 4179 O HPE B 2 2.806 21.092 14.215 1.00 17.45
> O
> HETATM 4180 CB HPE B 2 4.377 22.085 16.699 1.00 17.52
> C
> HETATM 4181 CG HPE B 2 5.532 22.067 17.720 1.00 14.97
> C
> HETATM 4182 CD HPE B 2 5.886 23.416 18.279 1.00 17.87
> C
> HETATM 4183 CE1 HPE B 2 6.717 24.309 17.627 1.00 17.26
> C
> HETATM 4184 CE2 HPE B 2 5.385 23.752 19.520 1.00 19.20
> C
> HETATM 4185 CZ1 HPE B 2 7.025 25.546 18.162 1.00 17.16
> C
> HETATM 4186 CZ2 HPE B 2 5.698 24.993 20.061 1.00 22.45
> C
> HETATM 4187 CH HPE B 2 6.517 25.906 19.409 1.00 19.18
> C
>
> Thanks to all.
>
> Carlo
>
> On Wed, May 9, 2018 at 8:37 PM, Dimitri Maziuk <dmaz...@bmrb.wisc.edu>
> wrote:
>
>> On 05/09/2018 10:27 AM, carlo del moro wrote:
>> > Dear All,
>> >
>> > we would like to know if it is possible to map the atom's ID of a SMILES
>> > represented substructure to the atom sequence of a ligand contained in a
>> > pdb file. This in order to get the spatial coordinates related to such
>> > substructure.
>>
>> http://alatis.nmrfam.wisc.edu/ will generate unique stable IDs from a 3D
>> structure, and output the old->new ID map. It'll take a PDB, you'll
>> have to convert your SMILES into a 3D .mol. ALATIS atom IDs should be
>> the same in the two maps, *provided both inputs describe the exact same
>> ligand*.
>>
>> (It's the *substructure* bit that I'm not entirely sure about.)
>> --
>> Dimitri Maziuk
>> Programmer/sysadmin
>> BioMagResBank, UW-Madison -- http://www.bmrb.wisc.edu
>>
>>
>> ------------------------------------------------------------
>> ------------------
>> 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
>
>
------------------------------------------------------------------------------
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
