Shaoqz/refactor geometry 3 amber interface - Githubissues

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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Shaoqz/refactor geometry 3 amber interface #137

Closed shaoqx closed 8 months ago

shaoqx commented 8 months ago

3rd PR of amber_interface and geometry/sample refactoring:

Structure

Add structure/structure_operation/connectivity.py that initiate connectivity for structure (final part & test TODO)
Add PrepinParser for parsing .prepin files
Add StructureEnsemble class to carry conformational ensembles from MD or conformational sampling.
Add StructureConstraint class to carry constraint information for Structure

Test

Add a merged structure test set test/test_data/diversed_stru of PDBs with different levels of chemical diversity

Sampling

Add _interface/ncaa_library.py that manages a shared NCAA library for parameterization and connectivity etc.
Add AmberParameterizer and AmberParameter in _interface/amber_interface.py that handle the parameterization for MD
Add the outer framework for equi_md_sampling in geometry/sampling