Adding json to mmcif files as part as deposition

[TJGorrie]

Requirements, a python3 environment with the adding_stats_to_mmcif python package (https://github.com/berrisfordjohn/adding_stats_to_mmcif) installed.

from adding_stats_to_mmcif.add_json_data_to_mmcif import *
import argparse

def addJson2mmcif(json_file, mmcif_file):
    gc = AddJsonDataToMmcif()
    data = gc.get_data(json_file)
    # Can either overwrite existing file, or write to a new one, not sure what would be the best to do...
    if data:
        ret = gc.add_to_cif(input_mmcif_file=mmcif_file, output_mmcif_file=mmcif_file, data_dictionary=data)

if __name__ ==  "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument("--json", help="input json file", required=True)
    parser.add_argument("--mmcif", help="input mmcif file", required=True)
    args = parser.parse_args()
    addJson2mmcif(json_file=args['json'], mmcif_file=args['mmcif'])

For DLS I suppose the script just needs to call the function and run it on each mmcif file providing an input crystallisation conditions from @Daren-fearon is located in an agreed place.

Example Json for testing:

 {
    "_entity_src_gen":{
        "pdbx_gene_src_ncbi_taxonomy_id": "562",
        "pdbx_gene_src_scientific_name": "Escherichia coli"
    },
    "_exptl_crystal":{
        "pdbx_crystal_image": "Y",
        "pdbx_crystal_image_format": "png",
        "pdbx_crystal_image_url": "https://htxlab.embl.fr/#/bridge/plates/CD030083/inspections/6#B9-1"
    },
    "_exptl_crystal_grow":{
        "crystal_id": "1",
        "method": "vapor diffusion",
        "apparatus": "CrystalDirect CD-2 Mitegen",
        "atmosphere": "room air",
        "pH": "6.1",
        "temp": "292",
        "time": "around 2 months"

    },
    "_pdbx_exptl_crystal_grow_comp": {
        "crystal_id": ["1", "1", "1"],
        "sol_id": ["reservoir", "reservoir", "reservoir"],
        "comp_id": ["1", "2", "3"],
        "comp_name": ["tri-sodium citrate", "isopropanol", "PEG 4000"],
        "conc": ["0.1", "20", "20"],
        "conc_units": ["molar", "percent_volume_by_volume", "percent_weight_by_volume"]
    },
    "_pdbx_exptl_crystal_grow_sol": {
        "crystal_id": ["1", "1"],
        "sol_id": ["macromolecule", "reservoir"],
        "volume": ["100", "100"],
        "volume_units": ["nl", "nl"]
    }
}