MACROS/functional_group.py at main · streamflowmaster/MACROS · GitHub

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from rdkit import Chem
from rdkit import RDLogger

functional_groups = {
    'Acid anhydride': Chem.MolFromSmarts('[CX3](=[OX1])[OX2][CX3](=[OX1])'),
    'Acyl halide': Chem.MolFromSmarts('[CX3](=[OX1])[F,Cl,Br,I]'),
    'Alcohol': Chem.MolFromSmarts('[#6][OX2H]'),
    'Aldehyde': Chem.MolFromSmarts('[CX3H1](=O)[#6,H]'),
    'Alkane': Chem.MolFromSmarts('[CX4;H3,H2]'),
    'Alkene': Chem.MolFromSmarts('[CX3]=[CX3]'),
    'Alkyne': Chem.MolFromSmarts('[CX2]#[CX2]'),
    'Amide': Chem.MolFromSmarts('[NX3][CX3](=[OX1])[#6]'),
    'Amine': Chem.MolFromSmarts('[NX3;H2,H1,H0;!$(NC=O)]'),
    'Arene': Chem.MolFromSmarts('[cX3]1[cX3][cX3][cX3][cX3][cX3]1'),
    'Azo compound': Chem.MolFromSmarts('[#6][NX2]=[NX2][#6]'),
    'Carbamate': Chem.MolFromSmarts('[NX3][CX3](=[OX1])[OX2H0]'),
    'Carboxylic acid': Chem.MolFromSmarts('[CX3](=O)[OX2H]'),
    'Enamine': Chem.MolFromSmarts('[NX3][CX3]=[CX3]'),
    'Enol': Chem.MolFromSmarts('[OX2H][#6X3]=[#6]'),
    'Ester': Chem.MolFromSmarts('[#6][CX3](=O)[OX2H0][#6]'),
    'Ether': Chem.MolFromSmarts('[OD2]([#6])[#6]'),
    'Haloalkane': Chem.MolFromSmarts('[#6][F,Cl,Br,I]'),
    'Hydrazine': Chem.MolFromSmarts('[NX3][NX3]'),
    'Hydrazone': Chem.MolFromSmarts('[NX3][NX2]=[#6]'),
    'Imide': Chem.MolFromSmarts('[CX3](=[OX1])[NX3][CX3](=[OX1])'),
    'Imine': Chem.MolFromSmarts('[$([CX3]([#6])[#6]),$([CX3H][#6])]=[$([NX2][#6]),$([NX2H])]'),
    'Isocyanate': Chem.MolFromSmarts('[NX2]=[C]=[O]'),
    'Isothiocyanate': Chem.MolFromSmarts('[NX2]=[C]=[S]'),
    'Ketone': Chem.MolFromSmarts('[#6][CX3](=O)[#6]'),
    'Nitrile': Chem.MolFromSmarts('[NX1]#[CX2]'),
    'Phenol': Chem.MolFromSmarts('[OX2H][cX3]:[c]'),
    'Phosphine': Chem.MolFromSmarts('[PX3]'),
    'Sulfide': Chem.MolFromSmarts('[#16X2H0]'),
    'Sulfonamide': Chem.MolFromSmarts('[#16X4]([NX3])(=[OX1])(=[OX1])[#6]'),
    'Sulfonate': Chem.MolFromSmarts('[#16X4](=[OX1])(=[OX1])([#6])[OX2H0]'),
    'Sulfone': Chem.MolFromSmarts('[#16X4](=[OX1])(=[OX1])([#6])[#6]'),
    'Sulfonic acid': Chem.MolFromSmarts('[#16X4](=[OX1])(=[OX1])([#6])[OX2H]'),
    'Sulfoxide': Chem.MolFromSmarts('[#16X3]=[OX1]'),
    'Thial': Chem.MolFromSmarts('[CX3H1](=S)[#6,H]'),
    'Thioamide': Chem.MolFromSmarts('[NX3][CX3]=[SX1]'),
    'Thiol': Chem.MolFromSmarts('[#16X2H]')
}

def match_group(mol: Chem.Mol, func_group) -> int:
    if type(func_group) == Chem.Mol:
        n = len(mol.GetSubstructMatches(func_group))
    else:
        n = func_group(mol)
    return 0 if n == 0 else 1

def get_functional_groups(smiles: str) -> dict:
    RDLogger.DisableLog('rdApp.*')
    smiles = smiles.strip().replace(' ', '')
    mol = Chem.MolFromSmiles(smiles)
    if mol is None:
        return None
    func_groups = list()
    for func_group_name, smarts in functional_groups.items():
        func_groups.append(match_group(mol, smarts))

    return func_groups


#  data.smiles.map(get_functional_groups)