[Openchemistry-developers] GSoC Inquiry

[Adam Tenderholt]

Hi Trevor,

Your proposals sound like things that could be proposed to the MSDK and/or
RDkit projects, both of which are part of OpenChemistry. You should reach
out to those projects/mentors if you haven't done so already.

Best regards,

Adam


On Mon, Feb 5, 2018 at 2:46 PM Karol Langner <karol.langner at gmail.com>
wrote:

> 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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