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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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Adding loop remodelling to enzy_htp #181

Closed chrisjurich closed 1 month ago

chrisjurich commented 1 month ago

The ability to add missing loops is implemented in the enzy_htp.preparation.add_missing_residues() function. There is also the addition of a convenience function called enzy_htp.preparation.identify_missing_residues() which identifies which residues are missing for a given enzyme based on the PDB code alone. Missing loops can be filled with either the modeller or Rosetta molecular modelling packages, although Rosetta is used by default and preferred for a number of convenience/scope issues.

chrisjurich commented 1 month ago

I have updated the code to resolve various issues. The new code in RosettaInterface is somewhat unorganized. This is partially planned, as I have some code that will make it much easier to use RosettaScripts that will be added in a future (probably next) PR. There was also some discussion about making a new function in enzy_htp.structure.structure_operation that will do more complicated updating of Structure()'s, trying to avoid making new objects when possible. This will be added in a future PR and is made into an issue here https://github.com/ChemBioHTP/EnzyHTP/issues/183

shaoqx commented 1 month ago

Good to go! Merged!