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Rosettasurface in Pyrosetta 4

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Rosettasurface in Pyrosetta 4


    I would like to dock a small protein on a metal surface. It may be similar simulations which has done by Jeff Gray's group. But I found the code in surface_docking was written for pyrosetta 2 based on python 2.x . I have tried to transform the script to python3.. However, unknown errors appeared all the time.

    Can anyone tell me how to use these code in Pyrosetta4 (python3) or provide any detailed tutorial for surface_docking in Pyrosetta4? 

Thanks very much!


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Mon, 2021-11-22 23:35

Generally the biggest and most tricky to solve difference is the imports. Unfortunately, to not have overly long variables, most scripts abuse the star import and as a result one cannot tell where anything came from. But generally one can see the traceback of a function not found and search the documentation for that and get its full path. The major issue is from the fact that stuff in `pyrosetta.rosetta.core` was in a different module `rosetta`. So in a pinch you could make the namespace pollution from the star import worse, by doing `from pyrosetta import *`, `from pyrosetta.rosetta import *` and , `from pyrosetta.rosetta.core import *`.

Then for the generic issues like print as a statement etc. the python tool 2to3 will likely fix them —bar for the usual things like file -> io.IOBase and cmp in operations (?) etc.

Mon, 2021-11-29 09:13