[chimerax-users] Using ChimeraX as a Python Library

Tue Jul 6 18:43:51 PDT 2021

Tom, Eric, Greg-

Thank you so much for your responses.  This is extremely helpful. I have a
few options now, and I'm definitely unblocked. I'm especially interested in
trying to use a ChimeraX server-- I can see that being really helpful to
reduce the memory footprint of docker images.

My first step will be to just use subprocess to directly call the chimerax
executable.  That will certainly get the job done.  My next step would be
to try using chimerax as the python interpreter. From there, I'll take
stock and see what's important to look at next.

Thanks so much again for your help!

On Tue, Jul 6, 2021 at 3:15 PM Tom Goddard <goddard at sonic.net> wrote:

> Here's a bit more info on installing a PyPi package in ChimeraX on Windows
>
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-June/002304.html
>
> And if you are still interested in compiling ChimeraX there is info about
> that  in the programming manual
>
> https://www.cgl.ucsf.edu/chimerax/docs/devel/building.html
>
>   Tom
>
>
> On Jul 6, 2021, at 12:21 PM, Tom Goddard <goddard at sonic.net> wrote:
>
> If you want to install additional PyPi packages into the ChimeraX Python
> use
>
> chimerax -m pip install <NameOfPyPiPackage>
>
> as discussed in this message
>
> https://www.rbvi.ucsf.edu/pipermail/chimerax-users/2021-March/002000.html
>
> If you don't have permission to modify ChimeraX where you might need to
> use the --user option to pip install.  On windows you probably need to use
> the chimerax-console.exe executable.
>
> Tom
>
> On Jul 6, 2021, at 11:29 AM, James Loy via ChimeraX-users <
> chimerax-users at cgl.ucsf.edu> wrote:
>
> Tom, Eric--
>
> Thanks for the responses!
>
> We'd certainly like to read the cif files, but in addition, we'd like to
> add hydrogens to the protein as well. For an MVP, I was just going to have
> some script that calls the chimerax CLI.  Something like this (in python):
>
> for code in pdb_codes:
>     subprocess.run(f"chimerax --nogui --cmd 'load {code}.cif; addh; save
> {code}.addh.cif; exit'"
>
> This will likely be okay. But, if I am able to call a python script using
> chimera basically as the interpreter then that might work better. My only
> question would be how could I utilize other third party libraries? Say, if
> I were to use chimerax as the interpreter for the entire cif processing
> pipeline, then I would need to utilize a few outside modules.
>
> Thanks again for your help-- I really appreciate it!
> -James
>
> On Tue, Jul 6, 2021 at 1:07 PM Eric Pettersen <pett at cgl.ucsf.edu> wrote:
>
>> If the *only* thing you need ChimeraX for is to read/parse mmCIF files,
>> we do package that part as a separate library: GitHub - RBVI/readcif: A
>> fast C++ CIF and mmCIF parser <https://github.com/RBVI/readcif>
>>
>> --Eric
>>
>> Eric Pettersen
>> UCSF Computer Graphics Lab
>>
>>
>> On Jul 6, 2021, at 11:01 AM, Tom Goddard via ChimeraX-users <
>> chimerax-users at cgl.ucsf.edu> wrote:
>>
>> Hi James,
>>
>>   The ChimeraX Python modules have not been packaged to be used outside
>> the ChimeraX application.  I have tried making a chimerax module that can
>> be installed in any Python (with the right version for binary
>> compatibility) where all its Python capabilities can be used without
>> needing the application user interface.  But we have not distributed that,
>> it has lots of problems.  We have put it into two grant proposals to get
>> funding for it but one proposal was not funded and the other we are still
>> waiting to hear about.
>>
>>   In theory it shouldn't be hard to reuse specific parts of ChimeraX, for
>> instance reading mmCIF files.  That is in the mmcif ChimeraX Python module.
>>
>> https://github.com/RBVI/ChimeraX/tree/develop/src/bundles/mmcif
>>
>> But that needs various other ChimeraX modules (atomstruct, element,
>> pyinstance, pdbconnect, readcif, logger, arrays) listed in the mmcif
>> bundle_info.xml file
>>
>>
>> https://github.com/RBVI/ChimeraX/blob/develop/src/bundles/mmcif/bundle_info.xml
>>
>> and those in turn require some other ChimeraX Python modules.  ChimeraX
>> contains hundreds of Python modules, so how will you figure out which ones
>> you need?  The easy solution is to take them all.  But there are more
>> problems, because the ChimeraX application initializes many of the modules,
>> for instance, letting the atomic data structures module know where the
>> residue template files are located.  So you also need to figure that out.
>> These many obstacles are why we proposed funding to make the code more
>> usable without running the ChimeraX application -- it will be a good bit of
>> work.
>>
>>   So the standard solution is instead to just run your processing scripts
>> with the ChimeraX application from the command-line
>>
>> chimerax --nogui myscript.py
>>
>>   For compiling ChimeraX you must be using old ChimeraX source code (your
>> example is fetching Python 3.7 but ChimeraX has used Python 3.8 for the
>> last 9 months).  The current ChimeraX build does not fetch third party
>> libraries with rsync, it uses https and curl and does not need a password.
>> So use the current ChimeraX source from github and  you should not have
>> that problem.
>>
>> https://github.com/RBVI/ChimeraX
>>
>>   Tom
>>
>>
>>
>> On Jul 3, 2021, at 5:51 AM, James Loy via ChimeraX-users <
>> chimerax-users at cgl.ucsf.edu> wrote:
>>
>> Hello!
>>
>> Thank you for creating such an amazing piece of software!
>>
>> I'm trying to use portions of ChimeraX for part of a CIF file processing
>> pipeline. In order to automate the process, I'm building a docker image
>> that has ChimeraX installed. Ideally, we would like to use the pieces of
>> ChimeraX we need by importing the relevant python modules. Is this
>> possible? If so, must I build ChimeraX from source?
>>
>> Additionally, I have tried several times to build v1.1.1 from source and
>> I have not been able to. I am always prompted for a password when trying to
>> rsync the dependencies:
>> /bin/sh -c 'rsync -a $1 .' -- plato.cgl.ucsf.edu
>> :/usr/local/projects/chimerax/www/data/prereqs/python/Python-3.7.8.tar.xz
>> user at plato.cgl.ucsf.edu's password:
>> In order to build from source, do I need to register somewhere to get
>> credentials?
>>
>> Just to be clear, this CIF file processing pipeline is for academic (UT
>> Austin) use, not commercial.
>>
>> Thanks in advance!
>> James
>> --
>> James Loy, Ph. D.
>> 614.915.9792
>> LinkedIn <https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/>
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>>
>
> --
> James Loy, Ph. D.
> 614.915.9792
> LinkedIn <https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/>
> _______________________________________________
> ChimeraX-users mailing list
> ChimeraX-users at cgl.ucsf.edu
> Manage subscription:
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>
>
>
>

-- 
James Loy, Ph. D.
614.915.9792
LinkedIn <https://www.linkedin.com/in/james-m-loy-ph-d-ba2256a/>
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