Hi Guillaume et al.,
First of all, I’d like to recommend “Molecular Descriptors for Cheminformatics”
(http://eu.wiley.com/WileyCDA/WileyTitle/productCd-3527318526.html) as a
slightly more up to date version of the Handbook of Molecular Descriptors, and
a truly excellent resource in this area.
Secondly, I’m not sure that I-State = E-State is correct. I think I-State (or
Intrinsic-State) indices are local vertex invariants defined as a function of
principle quantum number, and simple and valence vertex degree. The E-State
(or Electrotopological-State) indices are a result of propagating these I-State
indices of atoms though the molecular graph (again producing local vertex
invariants). The exact formulae for both may be found in the original
publication:
Hall, L.H. and Kier, L.B., J. Chem. Inf. Comput. Sci., 1995, 35 (6), pp
1039–1045
http://pubs.acs.org/doi/abs/10.1021/ci00028a014
DOI: 10.1021/ci00028a014
If you are replicating some of the descriptors in DRAGON, I think they stopped
using E-state indices as an atom weighting scheme a while ago, and started
using I-State. The reason for that, I don’t know.
Just a heads up, I have been working on implementing a subset of the DRAGON
molecular descriptors as part of my “scikit-chem” project (which uses rdkit to
provide a scikit-learn like interface for some common cheminformatics tasks)
for use in my PhD. This includes MoRSE, RDF, WHIM, autocorrelation, GETAWAY,
matrix features, topological and constitutional indices and more. The code is
unfortunately currently a complete mess so I am too ashamed to push it publicly
to github at the moment, but I’ve implemented a large subset of these already.
I am currently running short on time to finish my PhD, otherwise I would offer
to help with the RDKit implementation (I don’t think it would easy be to port
my implementations directly).
Thanks,
Rich
--
Richard Lewis
PhD Candidate
Centre for Molecular Informatics
University of Cambridge
http://www.ch.cam.ac.uk/group/bender/person/rl403
<http://www.ch.cam.ac.uk/group/bender/person/rl403>
> On 15 Oct 2016, at 07:41, Guillaume GODIN <guillaume.go...@firmenich.com>
> wrote:
>
> Thanks Greg & Marco,
>
> so after reading a little around the Dictionary + 3D descriptors pdf...
> I-State are in fact "E-state" and are available in rdkit in python
> (https://github.com/rdkit/rdkit/tree/master/rdkit/Chem/EState
> <https://github.com/rdkit/rdkit/tree/master/rdkit/Chem/EState>) as
> fingerprint per atom.
>
> I will look at it.
>
> Best regards,
>
> Dr. Guillaume GODIN
> Principal Scientist
> Chemoinformatic & Datamining
> Innovation
> CORPORATE R&D DIVISION
> DIRECT LINE +41 (0)22 780 3645
> MOBILE +41 (0)79 536 1039
> Firmenich SA
> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>
> De : Greg Landrum <greg.land...@gmail.com>
> Envoyé : samedi 15 octobre 2016 06:00
> À : Guillaume GODIN; rdkit-discuss@lists.sourceforge.net
> Objet : Re: [Rdkit-discuss] where to find I-State of atoms
>
> Guillaume,
>
> I've been using this chapter from the Handbook of Chemoinformatics for the 3D
> descriptors:
> http://michem.disat.unimib.it/chm/download/materiale/geometrical_descriptors.pdf
>
> <http://michem.disat.unimib.it/chm/download/materiale/geometrical_descriptors.pdf>
>
> Section 2.6 has a discussion of the MoRSE descriptor, along with a definition
> of the I values.
>
> Is there sufficient info there for you?
>
> -greg
>
>
> On Fri, Oct 14, 2016 at 8:41 PM, Giuseppe Marco Randazzo
> <gmranda...@gmail.com <mailto:gmranda...@gmail.com>> wrote:
> This book >>> http://onlinelibrary.wiley.com/book/10.1002/9783527613106
> <http://onlinelibrary.wiley.com/book/10.1002/9783527613106> <<< that look
> like a bible.
>
> Best regards,
>
> GMR
>
>
>
>
>
>> On 14 Oct 2016, at 19:28, Guillaume GODIN <guillaume.go...@firmenich.com
>> <mailto:guillaume.go...@firmenich.com>> wrote:
>>
>> Dear All,
>>
>> I'm looking for the definition & values of the atomic "I-State" used in
>> Dragon for RDF, MORSE descriptors.
>>
>> Do you have a source for those physical descriptors ?
>>
>> best regards,
>>
>> Dr. Guillaume GODIN
>> Principal Scientist
>> Chemoinformatic & Datamining
>> Innovation
>> CORPORATE R&D DIVISION
>> DIRECT LINE +41 (0)22 780 3645 <tel:%2B41%20%280%2922%20780%203645>
>> MOBILE +41 (0)79 536 1039 <tel:%2B41%20%280%2979%20536%201039>
>> Firmenich SA
>> RUE DES JEUNES 1 | CASE POSTALE 239 | CH-1211 GENEVE 8
>>
>>
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