File size: 3,589 Bytes
e73ce34 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 | from __future__ import annotations
import pytest
from rdkit import Chem
from app.exception_handlers import InvalidInputException
from app.modules.toolkits.openbabel_wrapper import get_ob_canonical_SMILES
from app.modules.toolkits.openbabel_wrapper import get_ob_InChI
from app.modules.toolkits.openbabel_wrapper import get_ob_mol
from app.modules.toolkits.rdkit_wrapper import check_RO5_violations
from app.modules.toolkits.rdkit_wrapper import get_3d_conformers
from app.modules.toolkits.rdkit_wrapper import has_stereo_defined
from app.modules.toolkits.rdkit_wrapper import is_valid_molecule
@pytest.fixture
def invalid_smiles():
return "invalid"
def test_invalid_canonical_smiles(invalid_smiles):
with pytest.raises(InvalidInputException):
get_ob_canonical_SMILES(invalid_smiles)
def test_invalid_inchi(invalid_smiles):
with pytest.raises(InvalidInputException):
get_ob_InChI(invalid_smiles)
def test_invalid_smiles_3d():
smiles = "CCC[R]"
with pytest.raises(InvalidInputException):
get_ob_mol(smiles, threeD=True)
def test_invalid_2d(invalid_smiles):
with pytest.raises(InvalidInputException):
get_ob_mol(invalid_smiles)
def test_mol_weight_violation():
smiles = "FC=1C(F)=C(F)C(=C(F)C1F)CON=CC=C(C)C(Br)CC(Br)C(=C)C"
mol = Chem.MolFromSmiles(smiles)
violations = check_RO5_violations(mol)
assert violations == 2
def test_num_h_acceptors_violation():
smiles = "C(=O)(O)C(=O)OC(=O)OC(=O)OC(=O)OC(=O)OC(=O)OC(=O)OC(=O)OC(=O)OC(=O)O"
mol = Chem.MolFromSmiles(smiles)
violations = check_RO5_violations(mol)
assert violations == 1
def test_num_h_donors_violation():
smiles = "NCCCNCCCCNCCCNCNCCCNCCCCNCCCNC"
mol = Chem.MolFromSmiles(smiles)
violations = check_RO5_violations(mol)
assert violations == 1
def test_exception_handling():
smiles = "C1#CC#C1"
mol = Chem.MolFromSmiles(smiles)
result = get_3d_conformers(mol)
assert result is not None
def test_valid_smiles():
smiles = "C1=CC=CC=C1"
result = is_valid_molecule(smiles)
assert result == "smiles"
def test_valid_molblock():
molblock = """
RDKit 2D
6 6 0 0 0 0 0 0 0 0999 V2000
0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1261 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8522 0.7071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8522 1.4142 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1261 2.1213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4000 2.1213 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 1 1 0
M END
"""
result = is_valid_molecule(molblock)
assert result == "mol"
def test_invalid_molblock():
molblock = """
RDKit 2D
M END
"""
result = is_valid_molecule(molblock)
assert result is False
def test_invalid_input(invalid_smiles):
result = is_valid_molecule(invalid_smiles)
assert result is False
def test_no_stereochemistry():
smiles = "C1=CC=CC=C1"
mol = Chem.MolFromSmiles(smiles)
assert has_stereo_defined(mol) is False
def test_chiral_center():
smiles = "C[C@H](Cl)Br"
mol = Chem.MolFromSmiles(smiles)
assert has_stereo_defined(mol) is True
def test_tetrahedral_stereochemistry():
smiles = "C[C@@H]1CCCC[C@H]1Br"
mol = Chem.MolFromSmiles(smiles)
assert has_stereo_defined(mol) is True
def test_invalid_molecule():
mol = None
assert has_stereo_defined(mol) is False
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