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Re: can python handle CHIME .spt files?

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  Re: can python handle CHIME .spt files? Davin Potts <python@discontinuity.net> - 2015-02-18 15:55 -0600

#85822 — Re: can python handle CHIME .spt files?

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Hi James —

I’m not entirely sure I understand what you’re wanting to do, but my ears perked up when you mentioned Jmol and Chime so I’ll try to offer some pointers:

* If you want to assess which .spt files are failing when trying to read them with Jmol, then yes, Python can be used to automate the feeding of files to Jmol and can capture whether the loading is successful or not.

* If you want a way to parse problematic .spt files that can no longer be read in using Jmol or MDL Chime, it is possible to create an .spt parser in Python capable of reading your files though my quick searches for an existing .spt parser library in Python came up empty.  If this is your goal (to read those problematic .spt files), have you considered using OpenBabel to read them and convert them to another mainstream chemical structure format (SDF, MOL, etc.), cleaned up and ready for reading by any of a variety of other tools?


You may already be aware but just in case it isn’t evident, Python itself does not ship with capabilities for reading/writing chemical structure formats but there are lots of chemistry tools built on top of Python that do.  You may well find it most productive to pick up one of those tools in lieu of Python itself.


Hope this helps,


Davin



> On Feb 18, 2015, at 2:56 PM, James Zimmerman <JKZMM@clemson.edu> wrote:
> 
> I have a lot of old files that were written in Chime, then made compatible with Jmol.  Now there are problems with that.  Will Python give me a way to be able to show the .spt files that  Chime could read?  I don’t want to start learning Python unless I know there is a way.
>  
>                 Thank you very much.
>  
> James Zimmerman
> Emeritus Professor of Biochemistry
> -- 
> https://mail.python.org/mailman/listinfo/python-list <https://mail.python.org/mailman/listinfo/python-list>

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