Hi All,

 

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:

 

foreach file in the list:

    open PDB file

    construct output filename from input filename

    calculate & and write out hydrogen bonds using hbonds command

    close file

end foreach

 

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?

 

Thank you,

Svetlana