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<div>Hi All,</div>
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<div>Here's my problem: I need to calculate hydrogen bonds for several thousand PDB files. Chimera has nice hbonds command line command - sweet! Since Chimera was vanishing from Ubuntu, I had to switch to other available tools, i.e. Windows. After I got my
python up and running and communicating with Chimera modules. Here's my very simple pseudo-idea:</div>
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<div>foreach file in the list:</div>
<div> open PDB file</div>
<div> construct output filename from input filename</div>
<div> calculate & and write out hydrogen bonds using hbonds command</div>
<div> close file</div>
<div>end foreach</div>
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<div>Short and sweet. Except that one cannot use a command line command within python code. Command files don't work either because they do not understand python commands. Someone must have run into the same problem before me :-) Is there a way around this
problem?</div>
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<div>Thank you,</div>
<div>Svetlana</div>
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