Fix issue #156: A bug in the preparation.protonate._fix_pybel_output and its potential cause #161
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…pybel, and raise ValueError if improper hydrogen atoms are detected in _fix_pybel_output.
SwordJack
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chrisjurich
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Pretty good overall start! I appreciate the attention to detail and think this is a great contribution to the workflow since there are many problems with pybel. I do think a lot of what you wrote is somewhat redundant since there are other functions that do what you want to do. I mostly noticed PDBParser() not being used as well as parsing values from a PDB file, which is usually achieved more easily with the PyMOLInterface
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Dear Colleagues,
The issue #156 is now fixed in this pull request.
Major modifications are performed to
enzy_htp/preparation/protonate.py.The function
protonate_ligand_with_pybelcan now detect the existence of hydrogen atom(s) and raise an info if Hydrogen atom(s) is detected, then remove hydrogen atoms.The function
_fix_pybel_outputcan now raise aValueErrorif there is any hydrogen atom in the middle, i.e., the hydrogen atom(s) should be absent or at the end of the file.Some updates to
dev-tools/conda-installscript are also performed to enable users to automatically install EnzyHTP solely or as a dependency, while a warning will be prompted if a user is to install it tobaseenvironment.Best,
Yinjie.