Yes I have time to Check again and look like it's the intrinsec state. I've
started to write the rdf and morse diretly in rdkit + and test case.
You can look at my fork. But the I don't have an implementation of I-state for
the moment.
You are welcome to help. Specialy for the whim , gateway and other staff not
already available.
Br
Guillaume
Envoyé de mon iPhone
Le 15 oct. 2016 à 14:11, Rich Lewis <rl...@cam.ac.uk<mailto:rl...@cam.ac.uk>> a
écrit :
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
On 15 Oct 2016, at 07:41, Guillaume GODIN
<guillaume.go...@firmenich.com<mailto: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) 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<mailto:greg.land...@gmail.com>>
Envoyé : samedi 15 octobre 2016 06:00
À : Guillaume GODIN;
rdkit-discuss@lists.sourceforge.net<mailto: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
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 <<<
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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