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martinate.sh requires python 2 while martinize2 requires python 3 #28

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OLaprevote opened this issue May 30, 2021 · 0 comments
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@OLaprevote
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OLaprevote commented May 30, 2021

martinate.sh contains some python lines using print statements, which is not compatible with python 3 and WILL make martinate.sh crash if using python 3. Meanwhile, vermouth package for getting martinize2 and working with martini3 forcefield is only supported by python >= 3.6 (see its setup.cfg).

This makes the example lines given in Martini3 paper impossible to run when downloading current gromit (e.g. martinate.sh -f 2oar.pdb -fetch opm --insane-d=5 --insane-l=DPPC --insane-sol=W -martinize /path/to/martinize2).

Replacing all spaces by parenthesis in all python print statements of .sh scripts, and using 2to3 -w forcefield to automatically update python scripts from python 2 to pyhon 3 makes the trick. (See Pull request #25.)

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