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ChemBioHTP / EnzyHTP

EnzyHTP is a python library that automates the complete life-cycle of enzyme modeling
https://enzyhtp-doc.readthedocs.io
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PyBel inconsistant output #99

Closed shaoqx closed 1 year ago

shaoqx commented 1 year ago

Most of the time using the PyBel (Openbabel 3.1.0) api in enzy_htp to protonate ligand will give a file with "HETATM" lines. (e.g.: test/preparation/test_protonate.py::test_pybel_protonate_pdb_ligand_4CO) But in the case of 4NEG, PyBel gives "ATOM" lines while parsing the ligand HEZ. (e.g.: test/preparation/test_protonate.py::test_fix_pybel_output) There is no obvious reason PyBel treats these 2 ligand files differently.

This causes a bug that _fix_pybel_output cant read the protonated ligand from PyBel in the current version of enzy_htp.

shaoqx commented 1 year ago

This bug now fixes in 49a4f94000dbdb5bc51b290af3901d0e673a800a. Will update to develop_refactor in next PR from QZ