def test_atom_constraint4(self):
testmol = Chem.MolFromSmiles('CC=C')
s = """
fragment a{
C labeled c1 {connected to >1 C with any bond}
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertListEqual(sorted(match_index), sorted(((1, ), )))
def test_atom_constraint5(self):
testmol = Chem.MolFromSmiles('CC=C')
s = """
fragment a{
C labeled c1 {!connected to >1 C with any bond}
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ((0, ), (2, )))
def test_atom_constraint2(self):
testmol = Chem.MolFromSmiles('CCC')
s = """
fragment a{
C labeled c1
C labeled c2 single bond to c1 {connected to =1 C}
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertListEqual(sorted(match_index), sorted(((1, 0), (1, 2))))
def test_atom_prefix2(self):
testmol = Chem.MolFromSmiles('Cc1ccccc1')
s = """
fragment a{
nonaromatic C labeled c1
aromatic C labeled c2 single bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertListEqual(sorted(match_index), sorted(((0, 1), )))
def test_other_bond7(self):
testmol = Chem.MolFromSmiles('CCC')
s = """
cyclic fragment a{
C labeled c1
C labeled c2 single bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ())
def test_non_ring_bond(self):
testmol = Chem.MolFromSmiles('CCC1CCC1')
s = """
fragment a{
C labeled c1
C labeled c2 nonring bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ((0, 1), (1, 0), (1, 2), (2, 1)))
def test_atom_prefix3(self):
testmol = Chem.MolFromSmiles('CC=C')
s = """
fragment a{
C labeled c1
allylic C labeled c2 single bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ((0, 1), ))
def test_atom_constraint6(self):
testmol = Chem.MolFromSmiles('CC1CCC1')
s = """
fragment a{
C labeled c1 {!in ring of size >0}
C labeled c2 single bond to c1 {in ring of size >0}
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ((0, 1), ))
def test_atom_constraint3(self):
testmol = Chem.MolFromSmiles('CC=C')
s = """
fragment a{
C labeled c1
C labeled c2 single bond to c1 {connected to =1 C with double bond}
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ((0, 1), ))
def test_other_bond3(self):
testmol = Chem.MolFromSmiles('C=CC')
s = """
olefinic fragment a{
C labeled c1
C labeled c2 single bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertListEqual(sorted(match_index), sorted(((1, 2), (2, 1))))
def test_other_bond10(self):
testmol = Chem.MolFromSmiles('CCS')
s = """
fragment a{
X labeled c1
& labeled c2 single bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ((1, 2), ))
def test_other_bond6(self):
testmol = Chem.MolFromSmiles('CCC')
s = """
linear fragment a{
C labeled c1
C labeled c2 single bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ((0, 1), (1, 0), (1, 2), (2, 1)))
def test_strong_bond(self):
testmol = Chem.MolFromSmiles('CC=CC#C')
s = """
fragment a{
C labeled c1
C labeled c2 strong bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ((1, 2), (2, 1), (3, 4), (4, 3)))
def test_ring_bond2(self):
testmol = Chem.MolFromSmiles('CCC1CCC1')
s = """
fragment a{
C labeled c1
C labeled c2 ring bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ((2, 3), (2, 5), (3, 2), (3, 4), (4, 3),
(4, 5), (5, 2), (5, 4)))
def test_other_bond9(self):
testmol = Chem.MolFromSmiles('CCO')
s = """
fragment a{
X labeled c1
X labeled c2 single bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertListEqual(sorted(match_index),
sorted(((0, 1), (1, 0), (1, 2), (2, 1))))
def test_other_bond8(self):
testmol = Chem.MolFromSmiles('C1CCC1C')
s = """
cyclic fragment a{
C labeled c1
C labeled c2 single bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ((0, 1), (0, 3), (1, 0), (1, 2), (2, 1),
(2, 3), (3, 0), (3, 2), (3, 4), (4, 3)))
def test_aromatic_bond(self):
testmol = Chem.MolFromSmiles('c1ccccc1')
s = """
fragment a{
C labeled c1
C labeled c2 aromatic bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index,
((0, 1), (0, 5), (1, 0), (1, 2), (2, 1), (2, 3),
(3, 2), (3, 4), (4, 3), (4, 5), (5, 0), (5, 4)))
def test_double_triple_bond(self):
testmol = Chem.MolFromSmiles('C=C-C#C')
s = """
fragment a{
C labeled c1
C labeled c2 double bond to c1
C labeled c3 single bond to c2
C labeled c4 triple bond to c3
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index, ((0, 1, 2, 3), ))
def test_any_bond1(self):
testmol = Chem.MolFromSmiles('CC=CC#C')
s = """
fragment a{
C labeled c1
C labeled c2 any bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertListEqual(
sorted(match_index),
sorted(((0, 1), (1, 0), (1, 2), (2, 1), (2, 3), (3, 2), (3, 4),
(4, 3))))
def test_symbol_atomsuffix(self):
testmol = Chem.MolFromSmiles('CCC')
s = """
fragment a{
$ labeled c1
$ labeled c2 single bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertEqual(match_index,
((0, 1), (0, 3), (0, 4), (0, 5), (1, 0), (1, 2),
(1, 6), (1, 7), (2, 1), (2, 8), (2, 9), (2, 10),
(3, 0), (4, 0), (5, 0), (6, 1), (7, 1), (8, 2),
(9, 2), (10, 2)))
def test_ring_bond1(self):
testmol = Chem.MolFromSmiles('CCC1CCC1')
s = """
fragment a{
C labeled c1
C labeled c2 ring bond to c1
C labeled c3 ring bond to c2
C labeled c4 ring bond to c3
ringbond c4 ring bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
self.assertListEqual(
sorted(match_index),
sorted(((2, 3, 4, 5), (2, 5, 4, 3), (3, 2, 5, 4), (3, 4, 5, 2),
(4, 3, 2, 5), (4, 5, 2, 3), (5, 2, 3, 4), (5, 4, 3, 2))))
Created on Tue Oct 23 11:22:49 2018
@author: gerha
"""
from pgradd.RINGParser.Reader import Read
from rdkit import Chem
## fragment prefix test
testmol = Chem.MolFromSmiles('C[CH2+]')
s = """
positive fragment a{
C labeled c1
C labeled c2 single bond to c1
}
"""
molquery = Read(s)
assert match_index == ((0, 1), (1, 0))
testmol = Chem.MolFromSmiles('C[CH2-]')
s = """
negative fragment a{
C labeled c1
C labeled c2 single bond to c1
}
"""
molquery = Read(s)
match_index = molquery.GetQueryMatches(testmol)
assert match_index == ((0, 1), (1, 0))
testmol = Chem.MolFromSmiles('[CH][CH][C+][C-][C][CH+][CH-][CH4+]')