[Openchemistry-developers] GSoC Inquiry

[Karol Langner]

Hi Trevor,

Good to hear from you. CC'ing two lists that will also be interested in
this thread.

1. I'm sure there's interest in non-QM programs, the main question is
whether cclib is the best vehicle for such parsers (cclib targets
electronic structure data primarily). That's something to discuss, but even
if that would be better suited for a new project, we could re-use some of
the code between projects. Also, have you checked out if those formats are
supported by Open Babel? If it's just structure, adding a parser for these
formats to that project would be faster.

2. I think there's interest in biological assays, but again I'm not sure
that fits into the scope of cclib. There are probably projects out there
better suited for that.

3. Definitely, did you have any specific analyses in mind? Based on
reactants, or something like reaction path calculations?

Finally, I would point out you can propose a project of your own. Any of
three things you mentioned would be well received by Open Chemistry, which
is the umbrella project under cclib participates in GSOC. Check out the
full list of ideas at http://wiki.openchemistry.org/GSoC_Ideas_2018

On Mon, Feb 5, 2018 at 2:31 PM, Trevor Tanner <u0597274 at utah.edu> wrote:

> Dear Dr. Langner,
>
> As a huge cclib fan, I have been excited to read about its ideas for this
> year's GSoC.  I was just hoping to get some clarification on the different
> projects.
>
> 1. For "implementing new parsers", would cclib have any interest in
> supporting chemical data from non-QM computational chemistry programs?  For
> example, programs like SIRIUS 3 and MS-FINDER have separate schemes for
> predicting potential structures from tandem mass spectrometry experiments.
> Additionally, databases like Metacyc that contain computationally-predicted
> metabolites from bacterial genomes store chemical structures in their own,
> otherwise hard-to-access formats.
>
> 2. For "discovering computational chemistry content online", would there
> be interest in biological assays and a lightweight machine learning
> component?  For example, many PubChem assays are simple binary
> classifications that can be predicted using fast decision trees and
> fingerprints.
>
> 3. For "advanced analysis of quantum chemistry data", would there be any
> interest in basic analysis of simple chemical reactions?  For example, it
> could be useful to easily batch screen compounds with a pre-defined
> reaction for their product favorability.
>
> Thank you for your time.  I look forward to hearing back from you.
>
> Thanks again,
> Trevor Tanner
> (801) 742-5366
>
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