[Openchemistry-developers] Computational Chemistry Web Repository discussion

[Nitish Garg]

Hi all,

When dockerizing my application, I was initially installing cclib using
apt-get. But then, *import cclib.io <http://cclib.io>* was failing
(although *import cclib.parser* works fine). Things work fine when I setup
cclib from source itself.
So I want to confirm if cclib.io is not included in the apt-get package.
Also, is there any other way I can install complete cclib in docker image
without keeping the source code? I believe it is not pip installable
currently.

Regards
Nitish Garg

On Thu, Apr 13, 2017 at 4:59 AM, Nitish Garg <nitish.garg.6174 at gmail.com>
wrote:

> Hi all,
>
> This mail is in continuation to the discussion over my GSOC proposal for
> the "Computational Chemistry Web Repository" project.
> (The groundwork for this project can be found at :
> https://github.com/nitish6174/cclib-web)
>
> Please note the issue in MOPAC parser as mentioned at bottom of mail.
>
> The schema looks like a good start. Where are you getting the IUPAC names?
>> If you haven't found an online resource or library that automatically
>> determines them, I don't know how often they'd be used. Out of the hundreds
>> of calculations I've ever run, I never figured out the IUPAC name for any.
>
>
> I am focusing on detecting the InChI (or InChIKey) of the molecule as from
> that, a lot of information can be found about that molecule (Using
> PubChemPy to get compund from InChI/InChIKey
> <http://pubchempy.readthedocs.io/en/latest/api.html#pubchempy.get_compounds>
> ).
> As many log files may not contain enough data to generate InChI, we can
> resort to manual input of InChI or common name for molecule (Using
> PubChemPy to find compund from common name
> <http://pubchempy.readthedocs.io/en/latest/api.html#pubchempy.get_compounds>
> ).
> The found PubChemPy compund can be used to get IUPAC name and other
> details. Anyway, won't talk much about IUPAC from now on as its not
> important. Also, I guess showing molecule specific properties is not that
> important for this project.
>
> I think you should assume that any attribute may potentially be different
>> for each log file. For your 'atommasses' example, one could be interested
>> in frequency calculations (IR or Raman) that are part of a study using
>> isotopic shifts (e.g. 1H -> 2H or 16O -> 18O) so there could be two
>> calculations that are essentially identical except for atommasses (and the
>> corresponding changes to the vib* attributes).
>
>
> Yes, I believe almost all the result fields might differ with each log
> file. Actually instead of 'atommasses', I should have taken atom numbers as
> example that if I have 10 log files for H2O, atom numbers should be stored
> just once and not 10 times. Will fix that.
>
> We'd appreciate if you could let us know which files are having problems,
>> especially if they are from the cclib or cclib-data repos. Make sure you're
>> using an up-to-date version of cclib, and if so, please create an Issue for
>> cclib.
>
>
> The ccread() function failed on these 2 files : "MOPAC/h2o-force.out" and
> "regression/Gaussian/Gaussian09/coeffs.log"
> This is because MOPAC parser has a typo `line.split[2]` in line 194. Also,
> `math` module is missing.
> I had fixed these in my fork and was about to submit a PR but saw that
> this issue is already opened (#346) but not yet resolved (the referenced PR
> (#347) on that issue has a Travis build fail). I have made a PR #365 which
> might fix this issue but if #347 can be corrected, my PR will be redundant.
> I hope the "coeffs.log" was meant for run_regressions test and not to be
> parsed.
>
> Regards
> Nitish Garg
> GitHub : https://github.com/nitish6174
>
>
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