[chimerax-users] Using ChimeraX as a Python Library

[Greg Couch]

FYI, readcif doesn't build the molecular data structures, it just parses 
(mm)CIF files quickly.  That is, it's the foundation that you would need 
to build a mmCIF reader.

     -- Greg

On 7/6/2021 11:07 AM, Eric Pettersen via ChimeraX-users 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 <mailto: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 
>> <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 
>> <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 <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 <mailto: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 
>>> <http://plato.cgl.ucsf.edu>:/usr/local/projects/chimerax/www/data/prereqs/python/Python-3.7.8.tar.xz
>>> user at plato.cgl.ucsf.edu <mailto: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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>>
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