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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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Fix the messed up atom order from PyMol #118

Open shaoqx opened 1 year ago

shaoqx commented 1 year ago 
          `retain_order` seems not necessary. It will make the saved PDB looks weird. You can try look into the saved PDB.

_Originally posted by @shaoqx in https://github.com/ChemBioHTP/EnzyHTP/pull/116#discussion_r1259127656_

shaoqx commented 1 year ago

It causes error in the multichain system. We should not use retain_order and create a function to restore the order.

shaoqx commented 1 year ago

A good design would be having an align_atom_order(stru, ref_stru) function in structure_operation.general as this function stands for aligning atom orders/indexes of Structure()s in general. Because in this issue, the method of fixing is independent of pymol knowledge. And we call it afterexport_enzy_htp_stru() in api.py