Add proteinbox workflow - #15

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MSiggel wants to merge 26 commits into

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feature/protein-box

Commits on Jun 12, 2026

feat: add slurm cluster autodiscovery (#11)
gregorweiss
authored
dbe43e9

Commits on Jun 18, 2026

feat: add Parsl-based parallel build orchestration (#17)
maxscheurer
authored
03fa949

Commits on Aug 12, 2026

feat: add Parsl-based GROMACS simulation orchestration
gregorweiss
authored
b4989f0

Commits on Sep 3, 2026

Add proteinbox models: ProteinSpecies, ProteinBoxComposition, Pdb2gmxConfig

MSiggel
and
claude
committed
7e3ef27
Add setup/protein.py: pdb2gmx wrapper, PDB cleaning, topology utilities

MSiggel
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claude
committed
f4904d7
Add relax_with_protein_restraints() to openmm_utils.py

MSiggel
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claude
committed
0671729
Add build_proteinbox() and wire up dispatch in workflows.py

MSiggel
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claude
committed
295d7e2
Add proteinbox MDP run schedule files (CHARMM36m settings)

MSiggel
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claude
committed
9c3209f
Track proteinbox MDP files (force-add past .gitignore *.mdp rule)

MSiggel
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claude
committed
9ce204b
Add proteinbox tests and example YAML

MSiggel
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claude
committed
6b07575
Fix review findings: Path import, cwd paths, metadata, protonation

MSiggel
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claude
committed
e325743
Add force field check, fix grompp cleanup, fix file handle leak

MSiggel
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claude
committed
a305c25
Add force field registry with auto-download and fix charge parsing

MSiggel
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claude
committed
0436d51
Add [gromacs] config section for gmx path and force field management

MSiggel
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claude
committed
59150e5
Align proteinbox gromacs configuration
MSiggel
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6aead54
Fix proteinbox lint formatting
MSiggel
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7cff1bc
Mock gmx binary in proteinbox unit test
MSiggel
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2180342
Address review: clearer proteinbox config key names
MSiggel
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3124f7d
Fix proteinbox correctness issues from review
MSiggel
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3665bc7
Bundle force field into proteinbox topology and reject LJ-PME variant
MSiggel
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5ddf2f9
Support multi-chain proteins with explicit chain declaration
MSiggel
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11643e3
Return None from ProteinSpecies.charge instead of raising
MSiggel
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1d83335
Support proteinbox in CSV pipeline and clean build intermediates
MSiggel
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f0176f6
Fix proteinbox CSV->YAML serialization and add CSV example
MSiggel
committed
f92895a
Harden proteinbox residue and force-field handling
MSiggel
committed
c563d9a
Lock pdbfixer dependency for proteinbox
MSiggel
committed
2450d80