test_isomers.py

import pytest
import time

from rdkit import Chem

import datamol as dm


def test_enumerate_tautomers():
    mol = dm.to_mol("OC1=CC2CCCCC2[N:1]=C1")

    mols = dm.enumerate_tautomers(mol, n_variants=10)

    assert {dm.to_smiles(m) for m in mols} == {"O=C1C=[N:1]C2CCCCC2C1", "OC1=CC2CCCCC2[N:1]=C1"}


def test_enumerate_stereo():
    mol = dm.to_mol("OC1=CC2CCCCC2[N:1]=C1")

    mols = dm.enumerate_stereoisomers(mol, n_variants=10)

    assert {dm.to_smiles(m) for m in mols} == {
        "OC1=C[C@@H]2CCCC[C@@H]2[N:1]=C1",
        "OC1=C[C@@H]2CCCC[C@H]2[N:1]=C1",
        "OC1=C[C@H]2CCCC[C@@H]2[N:1]=C1",
        "OC1=C[C@H]2CCCC[C@H]2[N:1]=C1",
    }


def test_enumerate_stereo_undefined_failure():
    mol = dm.to_mol(
        "N=1C(NC2CC2)=C3C(=NC1)N(/C=C/C=4C=C(C=CC4C)C(=O)NC=5C=C(C=C(C5)N6CCN(CC6)C)C(F)(F)F)C=N3"
    )
    with pytest.raises(RuntimeError):
        dm.enumerate_stereoisomers(mol, clean_it=True)

    mols = dm.enumerate_stereoisomers(mol, clean_it=False)
    assert len(mols) == 2  # only one double bond


def test_enumerate_stereo_timeout():
    mol = dm.to_mol(
        "CC1=C2C(C(=O)C3(C(CC4C(C3C(C(C2(C)C)(CC1OC(=O)C(C(C5=CC=CC=C5)NC(=O)C6=CC=CC=C6)O)O)OC(=O)C7=CC=CC=C7)(CO4)OC(=O)C)O)C)OC(=O)C"
    )

    # NOTE(hadim): it's impossible to predict anything given a timeout for different
    # machines so we here we just check the code can run without errors
    dm.enumerate_stereoisomers(mol, n_variants=10, timeout_seconds=1)


def test_enumerate_structural():
    mol = dm.to_mol("CCCCC")  # pentane has only three structural isomers
    mols_iso = dm.enumerate_structisomers(
        mol,
        n_variants=5,
        allow_cycle=False,
        depth=2,
        allow_double_bond=False,
        allow_triple_bond=False,
    )
    mols_cyclo_iso = dm.enumerate_structisomers(mol, n_variants=5, depth=2, allow_cycle=True)

    assert {dm.to_smiles(m) for m in mols_iso} == {"CCC(C)C", "CC(C)(C)C"}
    # expect 3 molecules with cycles
    assert sum([Chem.rdMolDescriptors.CalcNumRings(x) == 1 for x in mols_cyclo_iso]) == 3  # type: ignore

    # mols_cyclo_iso_double = dm.enumerate_structisomers(
    #     mol, n_variants=10, allow_cycle=True, allow_double_bond=True
    # )
    # should have mol with double link
    # assert sum(["=" in dm.to_smiles(x) for x in mols_cyclo_iso_double]) > 0


@pytest.mark.skip_platform("win")
def test_enumerate_structural_timeout():
    mol = dm.to_mol("CCCCC")

    # NOTE(hadim): it's impossible to predict anything given a timeout for different
    # machines so we here we just check the code can run without errors
    dm.enumerate_structisomers(mol, n_variants=10, timeout_seconds=1)


def test_canonical_tautomer():
    smiles = "Oc1c(cccc3)c3nc2ccncc12"
    mol = dm.to_mol(smiles)

    canonical_mol = dm.canonical_tautomer(mol)

    assert dm.to_smiles(canonical_mol) == "O=c1c2ccccc2[nH]c2ccncc12"
    assert dm.to_inchikey(canonical_mol) == dm.to_inchikey(mol)


def test_remove_stereochemistry():
    mol = dm.to_mol("C[C@H]1CCC[C@@H](C)[C@@H]1Cl")
    mol_no_stereo = dm.remove_stereochemistry(mol)
    assert dm.to_smiles(mol_no_stereo) == "CC1CCCC(C)C1Cl"