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test.py
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test.py
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import unittest, os
from molecular_rectifier import Rectifier
from rdkit import Chem, Geometry, RDLogger
from rdkit.Chem import AllChem
RDLogger.DisableLog('rdApp.*')
import requests
from urllib.parse import quote
def name2mol(name) -> Chem.Mol:
"""
Using Cactus get a molecule from a name
"""
response: requests.Response = requests.get(
f'https://cactus.nci.nih.gov/chemical/structure/{quote(name)}/smiles')
response.raise_for_status()
smiles: str = response.text
mol: Chem.Mol = Chem.MolFromSmiles(smiles)
mol.SetProp('_Name', name)
AllChem.EmbedMolecule(mol)
return mol
class RectifierTester(unittest.TestCase):
# name: [before, after]
chemdex = {'phenylnaphthalene': ('c1ccc2ccccc2c1(c3ccccc3)', 'c1ccc(-c2cccc3ccccc23)cc1'),
'benzoazetine': ('C12CCCCC1CC2', 'C1CCC2CCCC2C1'),
#'conjoined': ('C1C2CCC2C1', 'C1CCCCC1'), # bridged hexane
'allene': ('C=C=C', 'C=CC'),
'benzocyclopronane': ('C12CCCCC1C2', 'C1CCC2CCCC2C1'),
'benzoindolium': ('c12cccc(nc3)c1c3ccc2', 'C1=Nc2cccc3cccc1c23'),
# 'norbornane': ('C1CC2CCC1C2', 'C1CC2CCC1C2'),
'tetralin': ('c1ccc2c(c1)CCCC2', 'c1ccc2c(c1)CCCC2'),
'mixed_ring': ('c1cccc2c1CCCC2', 'c1ccc2c(c1)CCCC2'),
'mixe_ring2': ('C1CCCc2c1cccc2', 'c1ccc2c(c1)CCCC2'),
'acenaphthylene': ('c1cc2c3c1cccc3ccc2', 'C1=Cc2cccc3cccc1c23'),
'pentalene': ('C1=CC2=CC=CC2=C1', 'C1=CC2=CC=CC2=C1'),
}
def test_cyclopentadiene(self):
"""
A pyrrole is altered to have a carbon as opposed to a nitrogen
"""
# aromatic cyclopent-ine -> cyclopentadiene
name = 'cyclopentadiene'
mol = Chem.MolFromSmiles('[nH]1cccc1')
mol.SetProp('_Name', name)
AllChem.EmbedMolecule(mol)
mod = Chem.RWMol(mol)
mod.GetAtomWithIdx(0).SetAtomicNum(6)
mol = mod.GetMol()
recto = Rectifier(mol, atoms_in_bridge_cutoff=3).fix()
gotten = Chem.MolToSmiles(AllChem.RemoveHs(recto.mol))
after = 'C1=CCC=C1'
#self.assertEqual(after, gotten, f'{name} failed {gotten} (expected {after})')
# it no longer gives cyclopentadiene, but a pyrrole
def test_bad_ring(self):
name = 'bad ring'
after = 'c1ccc2c(c1)CCCC2'
mol = Chem.MolFromSmiles(after)
mol.SetProp('_Name', name)
mol.GetBondBetweenAtoms(0, 1).SetBondType(Chem.BondType.SINGLE)
AllChem.EmbedMolecule(mol)
before = Chem.MolToSmiles(mol)
recto = Rectifier(mol).fix()
gotten = Chem.MolToSmiles(AllChem.RemoveHs(recto.mol))
self.assertEqual(gotten, after, f'{name} failed {gotten} (expected {after})')
def test_bad_ring2(self):
name = 'bad ring2'
before = 'c1ccc2c(c1)CCCC2'
after = 'c1ccc2ccccc2c1'
mol = Chem.MolFromSmiles(before)
mol.SetProp('_Name', name)
mol.GetBondBetweenAtoms(0, 1).SetBondType(Chem.BondType.SINGLE)
mol.GetBondBetweenAtoms(6, 7).SetBondType(Chem.BondType.AROMATIC)
before = Chem.MolToSmiles(mol)
AllChem.EmbedMolecule(mol)
recto = Rectifier(mol).fix()
gotten = Chem.MolToSmiles(AllChem.RemoveHs(recto.mol))
self.assertEqual(after, gotten, f'{name} failed {gotten} (expected {after})')
def test_emergency_overclose(self):
mol: Chem.Mol = Chem.MolFromSmiles('CC(C)(C)')
conf = Chem.Conformer()
for i in range(4):
conf.SetAtomPosition(i, Geometry.Point3D(i/4, 0, 0))
mol.AddConformer(conf)
recto = Rectifier(mol).fix()
self.assertEqual(AllChem.RemoveHs(recto.mol).GetNumAtoms(), 1)
def test_sub_downgrade(self):
# none of these should be touched
xanthine = Chem.MolFromSmiles('c1[nH]c2c(n1)nc(nc2O)O')
caffeine = Chem.MolFromSmiles('CN1C=NC2=C1C(=O)N(C(=O)N2C)C')
naphthalene = Chem.MolFromSmiles('c1c2ccccc2ccc1')
naphthoquinone = Chem.MolFromSmiles('O=C1c2ccccc2C(=O)cc1')
anthracene = Chem.MolFromSmiles('c1ccc2cc3ccccc3cc2c1')
primulin = Chem.MolFromSmiles(
'COc1cc(cc(c1O)OC)c2c(cc3c(cc(cc3[o+]2)O)O)O[C@H]4[C@@H]([C@H]([C@H]([C@H](O4)CO)O)O)O')
for mol in (xanthine, caffeine, naphthalene, naphthoquinone, anthracene, primulin):
self.assertTrue(Rectifier(mol).fix().mol.HasSubstructMatch(mol),
'failed to fix molecule')
# this will
phenol = Chem.MolFromSmiles('Oc1ccccc1')
phenmonoone = Chem.Mol(phenol) # not a real thing...
phenmonoone.GetBondWithIdx(0).SetBondType(Chem.BondType.DOUBLE)
self.assertTrue(Rectifier(phenmonoone).fix().mol.HasSubstructMatch(phenol),
'failed to fix substituent!')
def test_real_merger(self):
molblock = '''spiro-ditoluene
RDKit 2D
13 14 0 0 0 0 0 0 0 0999 V2000
1.5000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-5.9196 -0.8437 0.0724 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.8002 0.1514 1.1984 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.4463 -0.5624 0.0483 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.6193 -0.9951 -1.1259 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1462 -0.7139 -1.1501 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3270 0.4327 1.1743 C 0 0 0 0 0 0 0 0 0 0 0 0
3 8 4 0
3 4 4 0
4 5 4 0
4 1 1 0
5 6 4 0
6 7 4 0
7 8 4 0
9 13 4 0
9 10 4 0
10 11 4 0
10 2 1 0
11 12 4 0
6 12 4 0
6 13 4 0
M END'''
mol = Chem.MolFromMolBlock(molblock, sanitize=False, removeHs=False)
recto = Rectifier(mol)
recto.fix()
self.assertEqual('CC1CCC2(CCCC(C)C2)CC1', Chem.MolToSmiles(AllChem.RemoveHs(recto.mol)))
def test_unproto_indole(self):
correct = Chem.MolFromSmiles('c1ccc2[nH]ccc2c1')
mol = Chem.MolFromSmiles('c1ccc2nccc2c1', sanitize=False)
recto = Rectifier(mol)
self.assertIn(4, recto._get_nitrogens(Chem.DetectChemistryProblems(mol)[0].GetAtomIndices()))
# recto.log.setLevel(logging.DEBUG)
# recto.log.handlers[0].setLevel(logging.DEBUG)
recto.fix()
self.assertEqual(Chem.MolToInchi(correct), Chem.MolToInchi(recto.mol))
def test_methylpyridine(self):
# N-methylpyridine
correct = Chem.MolFromSmiles('c1cc[n+](C)cc1')
mol = Chem.MolFromSmiles('c1ccn(C)cc1', sanitize=False)
recto = Rectifier(mol)
recto.valence_correction = 'charge' # element
recto.fix()
self.assertEqual(Chem.MolToInchi(correct), Chem.MolToInchi(recto.mol))
correct = Chem.MolFromSmiles('c1ccc(C)cc1')
recto = Rectifier(mol)
recto.valence_correction = 'element'
recto.fix()
self.assertEqual(Chem.MolToInchi(correct), Chem.MolToInchi(recto.mol))
from functools import partial
def test_factory(name):
def test(self):
before, after = self.chemdex[name]
mol = Chem.MolFromSmiles(before)
mol.SetProp('_Name', name)
AllChem.EmbedMolecule(mol)
recto = Rectifier(mol).fix()
gotten = Chem.MolToSmiles(AllChem.RemoveHs(recto.mol))
self.assertEqual(after, gotten, f'{name} failed {gotten} (expected {after}) from {before}')
return test
for name in RectifierTester.chemdex:
setattr(RectifierTester,
f'test_{name}',
test_factory(name))