Re: [Cdk-devel] Adding a descriptor to the CDK

[John M. <joh...@gm...>]

Hi Andrew,

It depends what you ultimate end game is... (i.e. why?) I would be very
hesitant to add complex *models* as *descriptors* which is what I think
you're suggesting. There are some already (e.g. IonisationPotential IP,
ALogP) but they're nothing but a headache, not very accurate, and buggy
(for example the IP changes based on the storage order of atoms in a
bond!). I tend to think the *descriptors* should be "primitive" properties
for example nitrogen/oxygen balance, linear paths, ring sizes, h
donor/acceptor, radial fingerprints, etc, etc. Users can then build their
*models* down stream based on these values (we even have the *cdk-model *module
for simple Baysian models).

You can implement and distribute *models *as *descritpros* outside of CDK
in a portable and pluggable manner (extending IMolecularDescriptor
<http://cdk.github.io/cdk/2.1/docs/api/index.html?org/openscience/cdk/qsar/IMolecularDescriptor.html>)
and if they prove to be accurate and useful then they could be merged into
the main CDK. We've recently be discussing the idea of Contrib location and
this use would fit nicely. Perhaps others disagree?

Best Wishes,
John

P.S. For your example the SubstructureFingerprint
<http://cdk.github.io/cdk/2.1/docs/api/index.html?org/openscience/cdk/fingerprint/SubstructureFingerprinter.html>
can
generate a binary descriptor based on pre-define functional groups (or you
can define your own).

On 18 January 2018 at 18:35, Andrew Lang <asi...@gm...> wrote:

> Hi Guys:
>
> My end goal is to add new descriptors to the CDK.
>
> I can:
>
> Generate a list of fragments using: http://vpsolovev.ru/programs/smf/
>
> and
>
> Use R to build a linear model
>
> What I'd like to know is:
>
> 1. Are these fragments the way to go (prefered method) when one wants to
> develop a new descriptor for the CDK.
>
> 2. How does one add a descriptor to the CDK given my programming skills
> are non-expert level.
>
> Thanks,
>
> Andy
>
> Andrew Lang
> Professor and Chair, Mathematics
> Oral Roberts University
>
>
>
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