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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([*:1])cc1')
self.assertEqual(Chem.MolToSmiles(fs[1],True),'C[*:2]')
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(cc1)[*:1]')
self.assertEqual(frags[1][1],'C[*:1].c1ccc(cc1)O[*:1]')
self.assertEqual(frags[2][0],'O([*:1])[*:2]')
self.assertEqual(frags[2][1],'C[*:2].c1ccc([*:1])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(cc1)[*:1]')
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)
if __name__=="__main__":
unittest.main()
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