mordred-descriptor/mordred

from multiprocessing import freeze_support

from rdkit import Chem

from mordred import Chi, ABCIndex, RingCount, Calculator, is_missing, descriptors

if __name__ == "__main__":
    freeze_support()

    benzene = Chem.MolFromSmiles("c1ccccc1")

    # Create empty Calculator instance
    calc1 = Calculator()

    # Register descriptor instance
    calc1.register(Chi.Chi(type="path_cluster", order=4))

    # Register descriptor class using preset
    calc1.register(RingCount.RingCount)

    # Register all descriptors in module
    calc1.register(ABCIndex)

    # Calculate descriptors
    result = calc1(benzene)

    print(result)
    # >>> [0.0, 1, 0, 0, 0, 1, (snip)

    # Calculator constructor can register descriptors
    calc2 = Calculator(Chi.Chi)

    # Descriptors module contains all descriptors
    calc3 = Calculator(descriptors)

    # User can access all descriptor instances by descriptors property
    print(calc3.descriptors)
    # >>> (mordred.EccentricConnectivityIndex.EccentricConnectivityIndex(), (snip)

    # Calculate descriptors
    result = calc3(benzene)

    # get first missing value
    na1 = next(r for r in result if is_missing(r))

    # get reason
    print(na1.error)
    # >>> missing 3D coordinate

    # Delete all missing value
    result = result.drop_missing()

    # convert to dict
    print(result.asdict())