Integrate pdbprep into codebase#592

Draft

DaniBodor wants to merge 14 commits intodevfrom

509_integrate_pdbprep_dbodor

Commits on Mar 13, 2024

minor formatting improvements
Dani Bodor
committed

Commits on Mar 19, 2024

add dependencies to env files
Dani Bodor
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style: update ruff settings for TODOs
Dani Bodor
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mimic do_pdbtools from pdbprep
Dani Bodor
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start testing pdbtools
Dani Bodor
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create function to run PRAS
Dani Bodor
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add pdb2pqr functionality
Dani Bodor
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rename file
Dani Bodor
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temporarily add test notebooks
Dani Bodor
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add detect protonation functions
Dani Bodor
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add `add_hydrogens` functions
Dani Bodor
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add PRAS to preprocess file
Dani Bodor
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move pdb2pqr function into detect protonation module
Dani Bodor
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rename hydrogenation
Dani Bodor
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