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
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
|
# $Id$
#
# Copyright (C) 2003-2005 Rational Discovery LLC
# All Rights Reserved
#
""" This is a rough coverage test of the python wrapper
it's intended to be shallow, but broad
"""
import unittest, os
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit.RDLogger import logger
logger = logger()
from rdkit import Chem
from rdkit.Chem import FragmentCatalog
from rdkit import DataStructs
class TestCase(unittest.TestCase):
def setUp(self):
self.fName = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FragCatalog', 'test_data',
'funcGroups.txt')
self.smiName = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'FragCatalog', 'test_data',
'mols.smi')
def test0Params(self):
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
ctype = fparams.GetTypeString()
self.assertEqual(ctype, "Fragment Catalog Parameters")
self.assertEqual(fparams.GetLowerFragLength(), 1)
self.assertEqual(fparams.GetUpperFragLength(), 6)
ngps = fparams.GetNumFuncGroups()
self.assertEqual(ngps, 15)
for i in range(ngps):
mol = fparams.GetFuncGroup(i)
def test1Catalog(self):
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
fcat = FragmentCatalog.FragCatalog(fparams)
self.assertEqual(fcat.GetNumEntries(), 0)
self.assertEqual(fcat.GetFPLength(), 0)
nparams = fcat.GetCatalogParams()
self.assertEqual(nparams.GetLowerFragLength(), 1)
self.assertEqual(nparams.GetUpperFragLength(), 6)
def test2Generator(self):
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName, " ", 0, 1, 0)
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
self.assertEqual(fcat.GetNumEntries(), 21)
self.assertEqual(fcat.GetFPLength(), 21)
for id in range(fcat.GetNumEntries()):
self.assertEqual(fcat.GetEntryBitId(id), id)
self.assertEqual(fcat.GetEntryOrder(id), fcat.GetBitOrder(id))
self.assertEqual(fcat.GetEntryDescription(id), fcat.GetBitDescription(id))
self.assertEqual(tuple(fcat.GetEntryFuncGroupIds(id)), tuple(fcat.GetBitFuncGroupIds(id)))
def test3FPgenerator(self):
with open(self.smiName, 'r') as smiF:
smiLines = smiF.readlines()
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName, " ", 0, 1, 0)
smiles = []
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
smiles.append(Chem.MolToSmiles(mol))
self.assertEqual(fcat.GetNumEntries(), 21)
self.assertEqual(fcat.GetFPLength(), 21)
fpgen = FragmentCatalog.FragFPGenerator()
obits = [3, 2, 3, 3, 2, 3, 5, 5, 5, 4, 5, 6]
obls = [(0, 1, 2), (1, 3), (1, 4, 5), (1, 6, 7), (0, 8), (0, 6, 9), (0, 1, 2, 3, 10),
(0, 1, 2, 8, 11), (1, 3, 4, 5, 12), (1, 4, 5, 13), (1, 3, 6, 7, 14),
(0, 1, 6, 7, 9, 15)]
for i in range(len(smiles)):
smi = smiles[i]
mol = Chem.MolFromSmiles(smi)
fp = fpgen.GetFPForMol(mol, fcat)
if i < len(obits):
self.assertEqual(fp.GetNumOnBits(), obits[i])
obl = fp.GetOnBits()
if i < len(obls):
self.assertEqual(tuple(obl), obls[i])
def test4Serialize(self):
with open(self.smiName, 'r') as smiF:
smiLines = smiF.readlines()
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName, " ", 0, 1, 0)
smiles = []
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
smiles.append(Chem.MolToSmiles(mol))
self.assertEqual(fcat.GetNumEntries(), 21)
self.assertEqual(fcat.GetFPLength(), 21)
pkl = cPickle.dumps(fcat)
fcat2 = cPickle.loads(pkl)
self.assertEqual(fcat2.GetNumEntries(), 21)
self.assertEqual(fcat2.GetFPLength(), 21)
fpgen = FragmentCatalog.FragFPGenerator()
for i in range(len(smiles)):
smi = smiles[i]
mol = Chem.MolFromSmiles(smi)
fp1 = fpgen.GetFPForMol(mol, fcat)
fp2 = fpgen.GetFPForMol(mol, fcat2)
self.assertEqual(fp1.GetNumOnBits(), fp2.GetNumOnBits())
obl1 = fp1.GetOnBits()
obl2 = fp2.GetOnBits()
self.assertEqual(tuple(obl1), tuple(obl2))
def test5FPsize(self):
with open(self.smiName, 'r') as smiF:
smiLines = smiF.readlines()
fparams = FragmentCatalog.FragCatParams(6, 6, self.fName)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = [Chem.MolFromSmiles('C1CCCOC1O')]
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
self.assertEqual(fcat.GetFPLength(), 1)
for i in range(fcat.GetFPLength()):
self.assertEqual(fcat.GetBitOrder(i), 6)
self.assertEqual(fcat.GetBitDescription(i), "C1CC<-O>OCC1")
self.assertEqual(tuple(fcat.GetBitFuncGroupIds(i)), (1, ))
def test6DownEntries(self):
fparams = FragmentCatalog.FragCatParams(1, 6, self.fName, 1.0e-8)
fcat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
suppl = Chem.SmilesMolSupplier(self.smiName, " ", 0, 1, 0)
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, fcat)
self.assertEqual(fcat.GetNumEntries(), 21)
self.assertEqual(fcat.GetFPLength(), 21)
self.assertEqual(tuple(fcat.GetEntryDownIds(0)), (2, 8, 9, 16))
self.assertEqual(tuple(fcat.GetEntryDownIds(1)), (2, 3, 5, 7))
def test7Issue116(self):
smiList = ['Cc1ccccc1']
suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList), ',', 0, -1, 0)
fparams = FragmentCatalog.FragCatParams(2, 2, self.fName, 1.0e-8)
cat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, cat)
self.assertEqual(cat.GetFPLength(), 2)
self.assertEqual(cat.GetBitDescription(0), 'ccC')
fpgen = FragmentCatalog.FragFPGenerator()
mol = Chem.MolFromSmiles('Cc1ccccc1')
fp = fpgen.GetFPForMol(mol, cat)
self.assertEqual(fp[0], 1)
self.assertEqual(fp[1], 1)
mol = Chem.MolFromSmiles('c1ccccc1-c1ccccc1')
fp = fpgen.GetFPForMol(mol, cat)
self.assertEqual(fp[0], 0)
self.assertEqual(fp[1], 1)
def test8Issue118(self):
smiList = ['CCN(C(N)=O)N=O']
fName = os.path.join(RDConfig.RDDataDir, 'FunctionalGroups.txt')
suppl = Chem.SmilesMolSupplierFromText('\n'.join(smiList), ',', 0, -1, 0)
fparams = FragmentCatalog.FragCatParams(2, 4, fName, 1.0e-8)
cat = FragmentCatalog.FragCatalog(fparams)
fgen = FragmentCatalog.FragCatGenerator()
for mol in suppl:
nent = fgen.AddFragsFromMol(mol, cat)
self.assertEqual(cat.GetFPLength(), 1)
self.assertEqual(cat.GetBitDescription(0), 'CCN(<-C(=O)N>)<-N=O>')
if __name__ == '__main__':
unittest.main()
|
