Re: [cclib-devel] [Openchemistry-developers] GSoC Inquiry

[Trevor T. <u05...@ut...>]

Hi Dr. Tenderholt,

Thank you for the kind e-mail!  I really appreciate the advice and will
definitely look into the MSDK and RDkit projects.

Thanks again,
Trevor

On Tue, Feb 6, 2018 at 8:25 AM, Adam Tenderholt <ate...@gm...>
wrote:

> 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 <kar...@gm...>
> 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 <u05...@ut...> 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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>