"""
SimulationData moleculeIds
"""
[docs]
class MoleculeIds(object):
"""
Helper class to extract molecule IDs of "special" molecules. All values
returned are strings.
"""
def __init__(self, raw_data, sim_data):
self._buildMoleculeIds()
[docs]
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)