hanks for pointing me to the correct syntax to do so.
Best regards
Sebastian
Gesendet: Montag, 14. Mai 2018 um 08:58 Uhr
Von: "Greg Landrum"
An: "Sebastian Wandernoth"
Cc: "RDKit Discuss"
Betreff: Re: [Rdkit-discuss] atom mapping in reaction searches
Hi S
Hi Sebastian,
The reason this had me confused is that information about atom mapping is
not taken into account when doing substructure search matching. This is
true both of molecules and reactions.
I also tried to reproduce your examples in Python and failed completely.
Your question about thresh
Hi Sebastian,
I'm a bit mystified by this and am going to have to dig around a bit to see
if I can figure out what's going on.
-greg
On Wed, May 9, 2018 at 9:59 PM Sebastian Wandernoth
wrote:
> Hey guys,
>
> any chance to get an answer on my issue? Even if the answer is that this
> feature is
On 10/05/2018 10:39, carlo del moro wrote:
I put an example for better explain my problem.
starting from a PDB representing HPE, I use RDKIT/obabel for calculate the
relative SMILES.
The three-letter-code (chemical component id) in a PDB file has meaning - it is a pointer to chemistry. The
c
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,
Ma
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
Hey guys,
any chance to get an answer on my issue? Even if the answer is that this feature is currently not included in RDKit, it would still be helpful :-)
Best regards
Sebastian
Gesendet: Dienstag, 24. April 2018 um 09:33 Uhr
Von: "Sebastian Wandernoth"
An: rdkit-discuss@lists.sour
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.
On 09/05/2018 16:27, carlo del moro wrote:
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.
Depending on how
Dear Jan,
this gist shows a way to do what you need:
https://gist.github.com/ptosco/9b4a637a2814426846fe181f15aa8cdc
Basically, you'll need to convert explicit Hs into real atoms. Please
note that indices in the tuple obtained in the match with hydrogens
still apply to the original molecules
Hi Jan,
I'm not aware of an implementation of atom mapping for reactions based on
the RDKit.
-greg
On Wed, Oct 4, 2017 at 9:03 AM, Jan Halborg Jensen
wrote:
> I just came across this paper http://pubs.acs.org/doi/
> abs/10.1021/acs.jctc.7b00764 which presents an variant of the Fewest
> Bonds
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