This PR contains the refactoring of the rm_water() and get_protonation() function is original EnzyHTP. These two functions are now 2 individual submodules under enzy_htp/preparation: protonation.py and clean.py. Generic API applying changes to Structure() is designed as science APIs (under preparation) and general APIs (under structure_operation). APIs in general.py is waiting for further division into different files in the future.
The structure module is also cleaned and refactored along the way in those clean/protonation-related parts.
Fixed a major bug in structure_io class about chain id fix for HETATM chains.
shaoqx
commented
1 year ago
This PR contains the refactoring of the rm_water() and get_protonation() function is original EnzyHTP. These two functions are now 2 individual submodules under enzy_htp/preparation: protonation.py and clean.py. Generic API applying changes to Structure() is designed as science APIs (under preparation) and general APIs (under structure_operation). APIs in general.py is waiting for further division into different files in the future. The structure module is also cleaned and refactored along the way in those clean/protonation-related parts. Fixed a major bug in structure_io class about chain id fix for HETATM chains.