Re: [Rdkit-devel] Pharm2D -- 4-point pharmacophores

[Greg L. <gre...@gm...>]

Hi Ondrej,

There's an illustration of the representation here:
http://rdkit.org/docs/RDKit_Book.html#representation-of-pharmacophore-fingerprints
Some discussion in the code of the terminology used:
https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Pharm2D/Generate.py#L11
and an illustration of the way the distances are defined:
https://github.com/rdkit/rdkit/blob/master/Docs/Code/Chem/Pharm2D.triangles.jpg

It's been a while since I really looked at that code, but I don'd think
there's really any reason why support for more than 3 features couldn't be
enabled.

-greg


On Tue, Feb 9, 2016 at 10:02 PM, Ondrej Micka <mit...@gm...> wrote:

> Hello,
> I'd like to implement four-point (or generally N-point) pharmacophores
> into rdkit's  Pharm2D module. It seems that same parts of the module can
> support more-than-three-point pharmacophores without any modification,
> while some other can't. Is there any more thorough documentation than
> the one generated by epydoc which could help me uderstand how the
> generation of 2D pharmacophore fingerprints works?
> Thanks,
> Ondrej
>
>
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