"""
SimulationData moleculeIds
"""


class MoleculeIds:
    """
    Helper class to extract molecule IDs of "special" molecules. All values
    returned are strings.
    """

    def __init__(self, raw_data, sim_data):
        self._buildMoleculeIds()

    def _buildMoleculeIds(self):
        molecule_ids = {
            "full_RNAP": "APORNAP-CPLX[c]",
            "s30_full_complex": "CPLX0-3953[c]",
            "s50_full_complex": "CPLX0-3962[c]",
            "DnaA": "PD03831[c]",
            "DnaA_ATP_complex": "MONOMER0-160[c]",
            "LPS": "CPD0-939[c]",
            "murein": "CPD-12261[p]",
            "glycogen": "glycogen-monomer[c]",
            "ppGpp": "GUANOSINE-5DP-3DP[c]",
            "oriC_site": "G0-10506",
            "terC_site": "TERC",
            "RelA": "RELA-MONOMER[c]",
            "SpoT": "SPOT-MONOMER[c]",
            "water": "WATER[c]",
            "proton": "PROTON[c]",
            "ppi": "PPI[c]",
            "full_chromosome": "CHROM_FULL[c]",
        }

        self.__dict__.update(molecule_ids)
