Add proteinbox workflow#15

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feature/protein-box

Commits on May 31, 2026

Add proteinbox models: ProteinSpecies, ProteinBoxComposition, Pdb2gmxConfig

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Add setup/protein.py: pdb2gmx wrapper, PDB cleaning, topology utilities

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Add relax_with_protein_restraints() to openmm_utils.py

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Add build_proteinbox() and wire up dispatch in workflows.py

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Add proteinbox MDP run schedule files (CHARMM36m settings)

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Track proteinbox MDP files (force-add past .gitignore *.mdp rule)

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Add proteinbox tests and example YAML

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Fix review findings: Path import, cwd paths, metadata, protonation

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Add force field check, fix grompp cleanup, fix file handle leak

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Add force field registry with auto-download and fix charge parsing

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Add [gromacs] config section for gmx path and force field management

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Align proteinbox gromacs configuration
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Fix proteinbox lint formatting
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Mock gmx binary in proteinbox unit test
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