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from rdkit import RDConfig
import unittest
from rdkit import Chem
from rdkit.Chem import rdMMPA
def natoms(tpl):
return tuple(x.GetNumAtoms() if x is not None else 0 for x in tpl)
class TestCase(unittest.TestCase):
def setUp(self):
pass
def test1(self):
m = Chem.MolFromSmiles('c1ccccc1OC')
frags = rdMMPA.FragmentMol(m)
self.assertEqual(len(frags), 3)
for frag in frags:
self.assertEqual(len(frag), 2)
frags = sorted(frags, key=natoms)
self.assertEqual(frags[0][0], None)
self.assertEqual(frags[1][0], None)
self.assertNotEqual(frags[2][0], None)
self.assertNotEqual(frags[0][1], None)
self.assertNotEqual(frags[1][1], None)
self.assertNotEqual(frags[2][1], None)
self.assertEqual(frags[0][1].GetNumAtoms(), m.GetNumAtoms() + 2)
self.assertEqual(frags[1][1].GetNumAtoms(), m.GetNumAtoms() + 2)
fs = Chem.GetMolFrags(frags[0][1], asMols=True)
self.assertEqual(len(fs), 2)
self.assertEqual(Chem.MolToSmiles(fs[0], True), 'c1ccc([*:1])cc1')
self.assertEqual(Chem.MolToSmiles(fs[1], True), 'CO[*:1]')
fs = Chem.GetMolFrags(frags[1][1], asMols=True)
self.assertEqual(len(fs), 2)
self.assertEqual(Chem.MolToSmiles(fs[0], True), 'c1ccc(O[*:1])cc1')
self.assertEqual(Chem.MolToSmiles(fs[1], True), 'C[*:1]')
fs = Chem.GetMolFrags(frags[2][0], asMols=True)
self.assertEqual(len(fs), 1)
self.assertEqual(Chem.MolToSmiles(fs[0], True), 'O([*:1])[*:2]')
fs = Chem.GetMolFrags(frags[2][1], asMols=True)
self.assertEqual(len(fs), 2)
self.assertEqual(Chem.MolToSmiles(fs[0], True), 'c1ccc([*:2])cc1')
self.assertEqual(Chem.MolToSmiles(fs[1], True), 'C[*:1]')
def test2(self):
m = Chem.MolFromSmiles('c1ccccc1OC')
frags = rdMMPA.FragmentMol(m, resultsAsMols=False)
self.assertEqual(len(frags), 3)
for frag in frags:
self.assertEqual(len(frag), 2)
frags = sorted(frags)
self.assertEqual(frags[0][0], '')
self.assertEqual(frags[1][0], '')
self.assertNotEqual(frags[2][0], '')
self.assertNotEqual(frags[0][1], '')
self.assertNotEqual(frags[1][1], '')
self.assertNotEqual(frags[2][1], '')
self.assertEqual(frags[0][1], 'CO[*:1].c1ccc([*:1])cc1')
self.assertEqual(frags[1][1], 'C[*:1].c1ccc(O[*:1])cc1')
self.assertEqual(frags[2][0], 'O([*:1])[*:2]')
self.assertEqual(frags[2][1], 'C[*:1].c1ccc([*:2])cc1')
def test3(self):
m = Chem.MolFromSmiles('c1ccccc1OC')
frags = rdMMPA.FragmentMol(m, resultsAsMols=False, pattern='cO')
self.assertEqual(len(frags), 1)
for frag in frags:
self.assertEqual(len(frag), 2)
frags = sorted(frags)
self.assertEqual(frags[0][0], '')
self.assertNotEqual(frags[0][1], '')
self.assertEqual(frags[0][1], 'CO[*:1].c1ccc([*:1])cc1')
def test4(self):
m = Chem.MolFromSmiles('Cc1ccccc1NC(=O)C(C)[NH+]1CCCC1') # ZINC00000051
frags = rdMMPA.FragmentMol(m, resultsAsMols=False)
#for frag in sorted(frags):
# print(frag)
cores = set(x[0] for x in frags)
self.assertTrue('C([*:1])([*:2])[*:3]' in cores)
# FIX: this needs to be investigated, it's not currently passing
#self.assertTrue('O=C(N[*:3])C([*:1])[*:2]' in cores)
self.assertEqual(len(frags), 18)
for frag in frags:
self.assertEqual(len(frag), 2)
def test5(self):
m = Chem.MolFromSmiles(
"CC[C@H](C)[C@@H](C(=O)N[C@H]1CSSC[C@H]2C(=O)NCC(=O)N3CCC[C@H]3C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CSSC[C@@H](C(=O)N[C@H](C(=O)N4CCC[C@H]4C(=O)N[C@H](C(=O)N2)C)CC(=O)N)NC1=O)C(=O)N)CO)Cc5ccc(cc5)O)CCCC[NH3+])N") # ALPHA-CONOTOXIN SI
frags = rdMMPA.FragmentMol(m, resultsAsMols=False)
self.assertFalse(len(frags))
frags = rdMMPA.FragmentMol(m, maxCuts=2, maxCutBonds=21, resultsAsMols=False)
self.assertEqual(len(frags), 231)
def test6(self):
m = Chem.MolFromSmiles(
"CC[C@H](C)[C@@H](C(=O)N[C@H]1CSSC[C@H]2C(=O)NCC(=O)N3CCC[C@H]3C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CSSC[C@@H](C(=O)N[C@H](C(=O)N4CCC[C@H]4C(=O)N[C@H](C(=O)N2)C)CC(=O)N)NC1=O)C(=O)N)CO)Cc5ccc(cc5)O)CCCC[NH3+])N") # ALPHA-CONOTOXIN SI
frags = rdMMPA.FragmentMol(m, resultsAsMols=False)
self.assertFalse(len(frags))
frags1 = rdMMPA.FragmentMol(m, minCuts=1, maxCuts=1, maxCutBonds=21,
resultsAsMols=False)
frags2 = rdMMPA.FragmentMol(m, minCuts=2, maxCuts=2, maxCutBonds=21,
resultsAsMols=False)
frags = rdMMPA.FragmentMol(m, maxCuts=2, maxCutBonds=21, resultsAsMols=False)
self.assertEqual(set(frags1+frags2), set(frags))
self.assertEqual(set(frags1).intersection(set(frags2)), set())
def test7(self):
m = Chem.MolFromSmiles("Oc1ccccc1N")
frags1 = rdMMPA.FragmentMol(m, minCuts=1, maxCuts=1, maxCutBonds=21,
resultsAsMols=False)
frags2 = rdMMPA.FragmentMol(m, minCuts=2, maxCuts=2, maxCutBonds=21,
resultsAsMols=False)
frags = rdMMPA.FragmentMol(m, maxCuts=2, maxCutBonds=21, resultsAsMols=False)
self.assertEqual(set(frags1+frags2), set(frags))
def test8(self):
m = Chem.MolFromSmiles('Cc1ccccc1NC(=O)C(C)[NH+]1CCCC1') # ZINC00000051
sm = Chem.MolFromSmarts("[#6+0;!$(*=,#[!#6])]!@!=!#[*]")
matching_atoms = m.GetSubstructMatches(sm)
bonds = []
for a,b in matching_atoms:
bond = m.GetBondBetweenAtoms(a,b)
bonds.append(bond.GetIdx())
frags = rdMMPA.FragmentMol(m, resultsAsMols=False)
frags2 = rdMMPA.FragmentMol(m, bonds, resultsAsMols=False)
frags3 = rdMMPA.FragmentMol(m, tuple(bonds), resultsAsMols=False)
self.assertEqual(frags, frags2)
self.assertEqual(frags2, frags3)
def test9(self):
m = Chem.MolFromSmiles("Oc1ccccc1N")
try:
frags1 = rdMMPA.FragmentMol(m, minCuts=1, maxCuts=0, maxCutBonds=21,
resultsAsMols=False)
self.assertTrue(False) # should not get here
except ValueError as e:
self.assertEqual(str(e), "supplied maxCuts is less than minCuts")
try:
frags1 = rdMMPA.FragmentMol(m, minCuts=0, maxCuts=0, maxCutBonds=21,
resultsAsMols=False)
self.assertTrue(False) # should not get here
except ValueError as e:
self.assertEqual(str(e), "minCuts must be greater than 0")
if __name__ == "__main__":
unittest.main()
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