claude mcp add "biomolecule-modeling" --scope user -- \
  uvx --from git+https://github.com/YOUR_USERNAME/biomolecule-modeling-mcp biomodeling

query_pdb_structure          # inspect chains, sequences, gaps, structural breaks
  └─ split_pdb               # separate protein / nucleic acid / ligands
       └─ fix_pdb_structure  # clean structure (PDBFixer): residues, hydrogens, heavy atoms
            └─ assemble_pdb_structures  # recombine components after separate fixing
                 └─ relax_pdb_structure # energy minimise ± short restrained MD (OpenMM)

conda install -c conda-forge openmm pdbfixer

git clone https://github.com/YOUR_USERNAME/biomolecule-modeling-mcp
cd biomolecule-modeling-mcp
uv sync

claude mcp add "biomolecule-modeling" --scope user -- \
  /path/to/uv run --directory /path/to/biomolecule-modeling-mcp python main.py

uv run utils/pdb_query.py structure.pdb        # inspect structure
uv run utils/pdb_fix.py input.pdb              # fix structure
uv run utils/openmm_relax.py input.pdb         # minimise structure

query_pdb_structure(
    pdb_file="1UBQ.pdb",
    notes="Initial inspection before cleaning. Need to identify chain types, "
          "any non-standard residues, and structural gaps."
)

chains:
  A — protein, 76 residues (MET1–GLY76), no numbering gaps, no structural breaks
heterogens: HOH (58 water molecules)
non_standard_residues: []
missing_residues: []

fix_pdb_structure(
    input_pdb="1UBQ.pdb",
    output_pdb="1UBQ_fixed.pdb",
    remove_heterogens=True,      # removes the 58 water molecules
    add_hydrogens=True,
    ph=7.0,
    fix_missing_residues=False,  # no gaps — nothing to fix
    notes="Removing waters, adding hydrogens at pH 7.0. No non-standard residues "
          "or gaps detected so no other fixing steps needed."
)

output_pdb: 1UBQ_fixed.pdb
n_residues: 76
n_atoms: 1231
heterogens_removed: 58
nonstandard_residues: []
missing_atoms_added: 0
hydrogens_added: true

relax_pdb_structure(
    input_pdb="1UBQ_fixed.pdb",
    output_pdb="1UBQ_relaxed.pdb",
    preset="amber14_implicit",
    run_md=False,
    notes="Minimisation-only run. Structure is clean and small (76 residues); "
          "a full MD run is not needed for clash removal."
)

output_pdb: 1UBQ_relaxed.pdb
preset_used: amber14_implicit
n_atoms: 1231
energy_initial_kJ_mol: -18423.4
energy_final_kJ_mol:   -24817.9

query_pdb_structure(
    pdb_file="./structures/complex.pdb",
    notes="Inspecting the multi-chain complex before chain selection and cleaning."
)

chains:
  A — protein, 312 residues (SER5–LEU316), 2 numbering gaps (at 47–51, 203–208)
  B — protein, 289 residues (MET1–LYS289), no gaps
  C — protein, 145 residues (ALA1–GLU145), no gaps
  D — nucleic (DNA), 24 residues
heterogens: MG (3 ions), HOH (412 waters), ATP (1 molecule)
non_standard_residues: [MSE → MET in chain A (4 occurrences)]

fix_pdb_structure(
    input_pdb="./structures/complex.pdb",
    output_pdb="./structures/complex_AB_fixed.pdb",
    chains_to_keep=["A", "B"],
    replace_nonstandard_residues=True,   # converts MSE → MET
    remove_heterogens=True,              # removes ATP, Mg²⁺, waters
    add_missing_heavy_atoms=True,
    add_hydrogens=True,
    ph=7.0,
    fix_missing_residues=False,          # gaps are 4–5 residues; skipping loop modelling
    notes="Keeping chains A and B only per user request. Converting 4 × MSE → MET "
          "in chain A. Removing ATP, Mg ions, and waters — these cannot be "
          "parameterised with standard AMBER presets. Not fixing the two loops "
          "in chain A (gaps of 4–5 residues) to avoid poor loop geometry."
)

output_pdb: complex_AB_fixed.pdb
n_residues: 601   (312 + 289)
n_atoms: 9847
chains_kept: [A, B]
nonstandard_residues: [MSE→MET ×4 in chain A]
heterogens_removed: 416   (ATP ×1, MG ×3, HOH ×412)
missing_atoms_added: 12
hydrogens_added: true

relax_pdb_structure(
    input_pdb="./structures/complex_AB_fixed.pdb",
    output_pdb="./structures/complex_AB_relaxed.pdb",
    preset="amber14_implicit",
    run_md=True,
    restrain_backbone=True,
    restraint_k=1000.0,
    production_steps=25000,
    notes="Running short restrained MD (25 000 steps ≈ 100 ps) to relax side chains "
          "around the 12 newly added heavy atoms and the two gap termini in chain A. "
          "Backbone restrained at 1000 kJ/mol/nm² to preserve experimental fold."
)

output_pdb: complex_AB_relaxed.pdb
preset_used: amber14_implicit
n_atoms: 9847
energy_initial_kJ_mol: -71203.1
energy_post_min_kJ_mol: -89441.6
energy_post_md_kJ_mol:  -94308.2
energy_final_kJ_mol:    -95112.4

biomolecule-modeling-mcp/
├── main.py                  # MCP server entry point; all @mcp.tool() definitions
├── pyproject.toml           # dependencies + CLI entry point (biomodeling)
├── utils/
│   ├── pdb_query.py         # Structure inspection (BioPython)
│   ├── pdb_fix.py           # PDBFixer wrapper
│   ├── pdb_splitter.py      # Split multi-component PDB by chain type
│   ├── pdb_assemble.py      # Merge PDB files
│   └── openmm_relax.py      # OpenMM energy minimisation + restrained MD
└── data/                    # Example / test PDB files