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
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
|
//
// Copyright (C) 2018 Susan H. Leung
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/test.h>
#include <GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogParams.h>
#include <GraphMol/MolStandardize/FragmentCatalog/FragmentCatalogUtils.h>
#include <GraphMol/MolStandardize/Fragment.h>
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/FileParseException.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/MolStandardize/MolStandardize.h>
#include <iostream>
#include <fstream>
using namespace RDKit;
using namespace MolStandardize;
void test2() {
BOOST_LOG(rdInfoLog) << "-----------------------\n test2" << std::endl;
std::string smi1, smi2, smi3, smi4, smi5, smi6, smi8, smi9, smi10, smi11,
smi12;
// testing parsing of fragment catalog
// std::string rdbase = getenv("RDBASE");
// std::string fgrpFile = rdbase +
// "/Code/GraphMol/MolStandardize/FragmentCatalog/"
// "data/fragmentPatterns.txt";
// auto* fparams = new FragmentCatalogParams(fgrpFile);
// unsigned int numfg = fparams->getNumFuncGroups();
// TEST_ASSERT(fparams->getNumFuncGroups() == 61);
//
// FragmentCatalog fcat(fparams);
FragmentRemover fragremover;
// single salt removal
smi1 = "CN(C)C.Cl";
std::shared_ptr<ROMol> m1(SmilesToMol(smi1));
std::shared_ptr<ROMol> remove(fragremover.remove(*m1));
TEST_ASSERT(MolToSmiles(*remove) == "CN(C)C");
// double salt removal
smi2 = "CN(C)C.Cl.Cl.Br";
std::shared_ptr<ROMol> m2(SmilesToMol(smi2));
std::shared_ptr<ROMol> remove2(fragremover.remove(*m2));
TEST_ASSERT(MolToSmiles(*remove2) == "CN(C)C");
// FragmentPatterns should match entire fragments only,
// matches within larger fragments should be left
smi3 = "CN(Br)Cl";
std::shared_ptr<ROMol> m3(SmilesToMol(smi3));
std::shared_ptr<ROMol> remove3(fragremover.remove(*m3));
TEST_ASSERT(MolToSmiles(*remove3) == "CN(Cl)Br");
// FragmentPatterns should match entire fragments only,
// matches within larger fragments should be left
smi4 = "CN(Br)Cl.Cl";
std::shared_ptr<ROMol> m4(SmilesToMol(smi4));
std::shared_ptr<ROMol> remove4(fragremover.remove(*m4));
TEST_ASSERT(MolToSmiles(*remove4) == "CN(Cl)Br");
// charged salts
smi5 = "C[NH+](C)(C).[Cl-]";
std::shared_ptr<ROMol> m5(SmilesToMol(smi5));
std::shared_ptr<ROMol> remove5(fragremover.remove(*m5));
TEST_ASSERT(MolToSmiles(*remove5) == "C[NH+](C)C");
// Last match should be left.
smi6 = "CC(=O)O.[Na]";
std::shared_ptr<ROMol> m6(SmilesToMol(smi6));
std::shared_ptr<ROMol> remove6(fragremover.remove(*m6));
TEST_ASSERT(MolToSmiles(*remove6) == "CC(=O)O");
// Last match should be removed.
FragmentRemover fr_noleavelast(defaultCleanupParameters.fragmentFile, false);
std::shared_ptr<ROMol> remove7(fr_noleavelast.remove(*m6));
TEST_ASSERT(MolToSmiles(*remove7) == "");
// Multiple identical last fragments should all be left.
smi8 = "Cl.Cl";
std::shared_ptr<ROMol> m8(SmilesToMol(smi8));
std::shared_ptr<ROMol> remove8(fragremover.remove(*m8));
TEST_ASSERT(MolToSmiles(*remove8) == "Cl.Cl");
// Last match should be left.
smi9 = "[Na+].OC(=O)Cc1ccc(CN)cc1.OS(=O)(=O)C(F)(F)F";
std::shared_ptr<ROMol> m9(SmilesToMol(smi9));
std::shared_ptr<ROMol> remove9(fragremover.remove(*m9));
TEST_ASSERT(MolToSmiles(*remove9) == "NCc1ccc(CC(=O)O)cc1");
// 1,4-Dioxane should be removed..
smi10 = "c1ccccc1O.O1CCOCC1";
std::shared_ptr<ROMol> m10(SmilesToMol(smi10));
std::shared_ptr<ROMol> remove10(fragremover.remove(*m10));
TEST_ASSERT(MolToSmiles(*remove10) == "Oc1ccccc1");
// Benzene should be removed.
smi11 = "c1ccccc1.CCCBr";
std::shared_ptr<ROMol> m11(SmilesToMol(smi11));
std::shared_ptr<ROMol> remove11(fragremover.remove(*m11));
TEST_ASSERT(MolToSmiles(*remove11) == "CCCBr");
// Various fragments should be removed.
smi12 = "CC(NC1=CC=C(O)C=C1)=O.CCCCC.O.CCO.CCCO.C1CCCCC1.C1CCCCCC1";
std::shared_ptr<ROMol> m12(SmilesToMol(smi12));
std::shared_ptr<ROMol> remove12(fragremover.remove(*m12));
TEST_ASSERT(MolToSmiles(*remove12) == "CC(=O)Nc1ccc(O)cc1");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
}
void test_largest_fragment() {
BOOST_LOG(rdInfoLog) << "-----------------------\n test largest fragment"
<< std::endl;
std::string smi1, smi2, smi3, smi4, smi5, smi6, smi7, smi8, smi9, smi10;
LargestFragmentChooser lfragchooser;
LargestFragmentChooser lfrag_preferOrg(true);
MolStandardize::CleanupParameters params =
MolStandardize::CleanupParameters();
// Multiple organic fragments of different sizes.
smi2 = "O=C(O)c1ccccc1.O=C(O)c1ccccc1.O=C(O)c1ccccc1";
// std::shared_ptr<ROMol> m2( SmilesToMol(smi2) );
// boost::shared_ptr<ROMol> lfrag2 = lfragchooser.choose(*m2);
// std::cout << MolToSmiles(*lfrag2) << std::endl;
// TEST_ASSERT(MolToSmiles(*lfrag2) == "O=C(O)c1ccccc1");
std::shared_ptr<RWMol> m2(SmilesToMol(smi2));
std::shared_ptr<RWMol> res2(MolStandardize::fragmentParent(*m2, params));
TEST_ASSERT(MolToSmiles(*res2) == "O=C(O)c1ccccc1");
// No organic fragments
smi3 = "[N+](=O)([O-])[O-]";
std::shared_ptr<ROMol> m3(SmilesToMol(smi3));
std::shared_ptr<ROMol> lfrag3(lfragchooser.choose(*m3));
TEST_ASSERT(MolToSmiles(*lfrag3) == "O=[N+]([O-])[O-]");
// Larger inorganic should be chosen
smi4 = "[N+](=O)([O-])[O-].[CH3+]";
std::shared_ptr<ROMol> m4(SmilesToMol(smi4));
std::shared_ptr<ROMol> lfrag4(lfragchooser.choose(*m4));
TEST_ASSERT(MolToSmiles(*lfrag4) == "O=[N+]([O-])[O-]");
// Smaller organic fragment should be chosen over larger inorganic fragment.
smi5 = "[N+](=O)([O-])[O-].[CH3+]";
std::shared_ptr<ROMol> m5(SmilesToMol(smi5));
std::shared_ptr<ROMol> lfrag5(lfrag_preferOrg.choose(*m5));
TEST_ASSERT(MolToSmiles(*lfrag5) == "[CH3+]");
// Salt without charges.
smi1 = "[Na].O=C(O)c1ccccc1";
std::shared_ptr<RWMol> m1(SmilesToMol(smi1));
std::shared_ptr<RWMol> res1(MolStandardize::fragmentParent(*m1, params));
// TEST_ASSERT(MolToSmiles(*lfrag) == "CN(C)C");
smi6 = "[Na]OC(=O)c1ccccc1";
std::shared_ptr<RWMol> m6(SmilesToMol(smi6));
// MolStandardize::cleanup(*m6, params);
std::shared_ptr<RWMol> res6(MolStandardize::fragmentParent(*m6, params));
TEST_ASSERT(MolToSmiles(*res6) == "O=C([O-])c1ccccc1");
smi7 = "c1ccccc1C(=O)O[Ca]OC(=O)c1ccccc1";
std::shared_ptr<RWMol> m7(SmilesToMol(smi7));
std::shared_ptr<RWMol> res7(MolStandardize::fragmentParent(*m7, params));
TEST_ASSERT(MolToSmiles(*res7) == "O=C([O-])c1ccccc1");
smi8 = "[Pt](Cl)(Cl)(O)(O)(NC(C)C)NC(C)C";
std::shared_ptr<RWMol> m8(SmilesToMol(smi8));
std::shared_ptr<RWMol> res8(MolStandardize::fragmentParent(*m8, params));
TEST_ASSERT(MolToSmiles(*res8) == "CC(C)[NH-]");
// Mercury containing compound.
smi9 = "CC[Hg]SC1=C(C=CC=C1)C(=O)[O][Na]";
std::shared_ptr<RWMol> m9(SmilesToMol(smi9));
std::shared_ptr<RWMol> res9(MolStandardize::fragmentParent(*m9, params));
TEST_ASSERT(MolToSmiles(*res9) == "CC[Hg]Sc1ccccc1C(=O)[O-]");
// Covalent bond with metal.
smi10 = "[Ag]OC(=O)O[Ag]";
std::shared_ptr<RWMol> m10(SmilesToMol(smi10));
std::shared_ptr<RWMol> res10(MolStandardize::fragmentParent(*m10, params));
TEST_ASSERT(MolToSmiles(*res10) == "O=C([O-])[O-]");
BOOST_LOG(rdInfoLog) << "Finished" << std::endl;
// params->preferOrganic = true;
//
}
int main() {
test2();
test_largest_fragment();
return 0;
}
|
