Major modifications are performed to enzy_htp/preparation/protonate.py.
The function protonate_ligand_with_pybel can 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_output can now raise a ValueError if 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-install script 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 to base environment.
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.