bio_logic.py

# lookup sidechain parents


def bondLookUp(atom, amac):
    if atom in {"O", "OXT"}:
        parent = ["C", C]
    elif atom in {"CB", "HA", "HA2", "HA3"}:
        parent = ["CA", C]
    elif (atom == "SG" or "HB" in atom or "OG" in atom or "CG" in atom):
        parent = ["CB", C]
    elif atom in {"H", "H1", "H2", "H3"}:
        parent = ["N", N]
    elif atom == "HG1":
        parent = ["OG1", O]
    elif atom in {"HG23", "HG22", "HG21"}:
        parent = ["CG2", C]

    elif ("CD" in atom or "ND" in atom or atom in {"SD", "HG2", "HG3", "OD1", "OD2", "HG12", "HG13", "HG13"):
        parent = ["CG1", C] if amac in {"ILE", "VAL"} else ["CG", C]

    elif atom in {"CE2", "CE3", "NE2", "HD2"}:
        if amac=="GLN": parent = ["CD",C]
        elif amac in {"ARG", "LYS", "PRO"}: parent = ["CD",C]
        elif amac=="ASP": parent = ["OD2", O]
        else: parent = ["CD2",C]

    elif atom in {"CE1", "HD11", "HD12", "HD13", "HD1", "NE1"}:
        parent = ["ND1", N] if (amac == "HIS") else ["CD1", C]

    elif atom in {"NE", "HD3", "CE", "OE1", "OE2"}:
        parent = ["SD", S] if(amac == "MET") else ["CD", C]

    elif atom in {"CZ", "HE", "HE1"}:
        if (amac=="ARG"):    parent = ["NE", N]
        elif (amac=="TRP"):    parent = ["NE1", N]
        elif (amac=="MET"):    parent = ["CE", C]
        elif amac in {"PHE", "HIS", "TYR"}: parent = ["CE1", C]

    elif atom in {"NH1", "NH2", "HZ", "OH"}:
        parent = ["CZ", C]
    elif atom in {"HH11", "HH12", "1HH1", "1HH2"}:
        parent = ["NH1", N]
    elif atom in {"HH21", "HH22", "2HH2", "1HH2"}:
        parent = ["NH2", N]
    elif atom in {"HD21", "HD22", "HD23"}:
        parent = ["CD2", C] if amac == "LEU" else ["ND2", N]
    elif atom in {"HE3", "NZ"}:
        parent = ["CE3", C] if amac == "TRP" else ["CE", C]

    elif atom in {"HZ1", "HZ2", "HZ3"}:
        if (amac=="TRP" and atom=="HZ2"): parent = ["CZ2", S]
        elif (amac=="TRP" and atom=="HZ3"): parent = ["CZ3", S]
        else: parent = ["NZ",N]

    elif (atom=="HG"):
        if (amac=="LEU"): parent = ["CG", C]
        if (amac=="CYS"): parent = ["SG", S]   # elif instead?
        else: parent = ["OG", O]

    elif atom in {"HE2", "CZ2", "HE21", "HE22"}:
        if amac in {"HIS", "GLN"}: parent = ["NE2", N]
        elif amac in {"PHE", "TYR", "TRP"}: parent = ["CE2", C]
        elif (amac=="GLU"): parent = ["OE2",O]
        elif amac in {"MET", "LYS"}: parent = ["CE",C]

    elif(atom=="HH"):    parent = ["OH", O]
    elif(atom=="CZ3"):    parent = ["CE3", C]
    elif(atom=="CH2"):    parent = ["CZ2", C]
    elif(atom=="HH2"):    parent = ["CH2", C]
    return parent