Re: [Rdkit-discuss] atom mapping in reaction searches

ss@lists.sourceforge.net> Betreff: Re: [Rdkit-discuss] atom mapping in reaction searches 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

Re: [Rdkit-discuss] atom mapping in reaction searches

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

Re: [Rdkit-discuss] atom mapping in reaction searches

n 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" <s_wandern...@gmx.de> > *An:* rdkit-discuss@

Re: [Rdkit-discuss] Atom mapping

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

Re: [Rdkit-discuss] Atom mapping

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,

Re: [Rdkit-discuss] Atom mapping

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

Re: [Rdkit-discuss] atom mapping in reaction searches

ern...@gmx.de> An: rdkit-discuss@lists.sourceforge.net Betreff: [Rdkit-discuss] atom mapping in reaction searches Hey guys,   I'm still working on my search engine for reactions and I'm a bit puzzled as to what RDKit does with atom mapping information. I'm still working with the PostgreSQL cartridg

Re: [Rdkit-discuss] Atom mapping

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 >

Re: [Rdkit-discuss] Atom mapping

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

[Rdkit-discuss] Atom mapping

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. Best regards Carlo

[Rdkit-discuss] atom mapping in reaction searches

Hey guys,   I'm still working on my search engine for reactions and I'm a bit puzzled as to what RDKit does with atom mapping information. I'm still working with the PostgreSQL cartridge version 0.73.0, which should correspond to the release 2017.9.3.   I'm starting off with this example

Re: [Rdkit-discuss] atom mapping using GetSubstructMatch

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

[Rdkit-discuss] atom mapping using GetSubstructMatch

I am trying to map atoms in one molecule to those of another using GetSubstructMatch, but have a problem with molecule pairs like the two below The problem is that GetSubstructMatch ignored the H on the n, so that the protonated “n" in mol1 is mapped to the deprotonated “n” in mol2, and vice

Re: [Rdkit-discuss] Atom mapping

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

[Rdkit-discuss] Atom mapping

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 First with Constructive Count Vector method by Crabtree and Mehta (https://dl.acm.org/citation.cfm?id=1498697) Has anyone implemented anything similar in with RDKit?