import toml
# The dictionary below has hard-coded values for each metadata fields. 
# You will need to write code to extract/gather these values from your specific data/notes.
# The script will print a .toml string that can be submitted to MDRepo.

example_data = {
    "initial": {
        "short_description": "A single sentence description of the simulation (text)",
        "description": "A description of the simulation (text)",
        "date": "The date this metadata file was generated (date in the format YYYY-MM-DD)",
        "lead_contributor_orcid": "The ORCID of the contributor responsible for uploading the simulation (ORCID in the format xxxx-xxxx-xxxx-xxxx)",
        "external_link": "A URL to an external data source for the simulation (URL)",
        "commands": "The commands used to produce the simulation (text)"
    },
    "software": {
        "name": "Software name (text)",
        "version": "Software version (text)"
    },
    "required_files": {
        "trajectory_file_name": "Trajectory files contain atomic coordinates of sequential snapshots of the simulation system. Examples of extensions of trajectory files generated by different popular MD simulation packages are: Gromacs - .xtc/.trr, AMBER - .netcdf/.crd, CHARMM - .dcd, NAMD - .dcd. (text)",
        "structure_file_name": "A structure file contains the atomic coordinates of one snapshot of the simulation system. The most popular format is a PDB file. Examples of extensions of structure files, other than PDB formated, generated by different popular MD simulation packages are: Gromacs - .gro, CHARMM - .cor. (text)",
        "topology_file_name": "The topology file contains the parameters for how the atoms in the molecule interact with each other through bonded and non-bonded interactions, as well as any added constraints or exclusions. Examples of extensions of topology files generated by different popular MD simulation packages are: Gromacs - .top/.tpr, AMBER - parm*.dat, CHARMM - .psf, NAMD - .psf. (text)"
    },
    "additional_files": [
        {
            "additional_file_type": "Additional file type (choices: Input, Structure, Trajectory, Topology, Periodic boundary condition, Restart, Logs, Checkpoint, Parameters, User defined file, Miscellaneous, Upload metadata) (text)",
            "additional_file_name": "Additional simulation files to be uploaded (text)",
            "additional_file_description": "Comments or description of the file (text)",
            "pk": "key (text)"
        }
    ],
    "replicates": {
        "replicate": "The replicate index for this simulation (number)",
        "total_replicates": "Total number of replicates produced in this series (number)"
    },
    "water": {
        "is_present": "Was water present in the simulation (true / false)",
        "model": "Water model used for the simulation (text)",
        "density": "Water density used for the simulation (decimal)",
        "water_density_units": "Water density units (choices: g/m^3) (text)"
    },
    "proteins": [
        {
            "molecule_id_type": "Molecule ID type (choices: Uniprot, PDB, No ID) (text)",
            "molecule_id": "Molecule ID for the simulation (text)",
            "pk": "key (text)"
        }
    ],
    "ligands": [
        {
            "name": "Name of the ligand (text)",
            "smiles": "SMILES string for the ligand (text)",
            "pk": "key (text)"
        }
    ],
    "solvents": [
        {
            "name": "Solvent name (text)",
            "ion_concentration": "Solvent concentration (decimal)",
            "solvent_concentration_units": "Solvent concentration units (choices: mol/L) (text)",
            "pk": "key (text)"
        }
    ],
    "forcefield": {
        "forcefield": "Type of force field used to produce the simulation (text)",
        "forcefield_comments": "Comments relating to the force field used (text)"
    },
    "temperature": {
        "temperature": "The temperature of the simulation (K) (allowed values from 273 K to 5000 K) (number)"
    },
    "protonation_method": {
        "protonation_method": "The method used for adding the protonation state (text)"
    },
    "timestep_information": {
        "integration_time_step": "The integration time step (in fs) used for the simulation (decimal)"
    },
    "papers": [
        {
            "title": "Paper title (text)",
            "authors": "Paper authors (text)",
            "journal": "Paper journal (text)",
            "year": "Paper published year (number)",
            "volume": "Paper volume (number)",
            "number": "Paper number (text)",
            "pages": "Paper pages (text)",
            "doi": "Paper DOI (text)",
            "pk": "key (text)"
        }
    ],
    "contributors": [
        {
            "name": "Name of the contributor (text)",
            "orcid": "ORCID of the contributor (ORCID in the format xxxx-xxxx-xxxx-xxxx)",
            "email": "Email of the contributor (email)",
            "institution": "Institution of the contributor (text)",
            "pk": "key (text)"
        }
    ]
}

if __name__ == "__main__":
    print(toml.dumps(example_data))