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
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
|
//
// Copyright (C) 2021 Greg Landrum
//
// @@ 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 "catch.hpp"
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Descriptors/MolDescriptors.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/Descriptors/ConnectivityDescriptors.h>
#include <GraphMol/Descriptors/PMI.h>
using namespace RDKit;
TEST_CASE("Kier kappa2", "[2D]") {
SECTION("values from https://doi.org/10.1002/qsar.19860050103") {
std::vector<std::pair<std::string, double>> data = {
// Table 5 from the paper
{"c1ccccc15.Cl5", 1.987},
{"c1ccccc15.F5", 1.735},
{"c1ccccc15.[N+]5(=O)O", 2.259},
{"c1ccccc15.C5(=O)C", 2.444},
#if 0
// expected values from paper (differences are due to hybridization mismatches)
{"c1ccccc15.N5(C)C", 2.646},
{"c1ccccc15.C5(=O)N", 2.416},
{"c1ccccc15.C5(=O)O", 2.416},
{"c1ccccc15.S5(=O)(=O)C", 2.617},
{"c1ccccc15.O5", 1.756},
#else
{"c1ccccc15.N5(C)C", 2.53},
{"c1ccccc15.C5(=O)N", 2.31},
{"c1ccccc15.C5(=O)O", 2.31},
{"c1ccccc15.S5(=O)(=O)C", 2.42},
{"c1ccccc15.O5", 1.65},
#endif
};
for (const auto &pr : data) {
std::unique_ptr<ROMol> m(SmilesToMol(pr.first));
REQUIRE(m);
auto k2 = Descriptors::calcKappa2(*m);
CHECK(k2 == Approx(pr.second).epsilon(0.01));
}
}
}
TEST_CASE("Kier Phi", "[2D]") {
SECTION("regression-test values from the paper") {
std::vector<std::pair<std::string, double>> data = {
// Table 1 from the paper
{"CCCCCC", 5.00},
{"CCCCCCC", 6.00},
{"CCCCCCCC", 7.00},
{"CCC(C)CC", 3.20},
{"CC(C)C(C)C", 2.22},
{"CC(C)(C)CC", 1.63},
{"C1CCCC1", 0.92},
{"C1CCCCC1", 1.54},
{"C1CCCCCC1", 2.25},
{"CCCCC=C", 4.53},
{"C=CCCC=C", 4.07},
{"C#CCCCC", 4.21},
{"c1ccccc1", 0.91},
// additional from Table 2
{"C=CCC=CC", 4.09},
{"CC=CC=CC", 4.09},
{"C1=CCCCC1", 1.31},
{"C1=CC=CCC1", 1.1},
{"C1=CCC=CC1", 1.1},
// additional from Table 3
{"CCCCCCCCCC", 9.00},
{"CC(C)CCCCC", 5.14},
{"CCC(C)CCCC", 5.14},
{"CC(C)CCCC", 4.17},
{"CCC(C)CCC", 4.17},
{"CCC(CC)CCC", 5.14},
{"CCC(CC)CC", 4.17},
{"CC(C)(C)CCC", 2.34},
{"CC(C)C(C)CC", 3.06},
{"CCC(C)(C)CC", 2.34},
{"CC(C)(C)C(C)C", 1.85},
// additional from table 4
{"CCOCC", 3.93},
{"CCC(=O)CC", 2.73},
{"CCc1ccc(CC)cc1", 2.49},
{"CCC(O)CC", 3.14},
{"CCCC(Cl)(Cl)CCC", 4.69},
{"CCC(F)C(F)CC", 3.75},
#if 0
// expected values from paper (differences are due to hybridization mismatches)
{"CCOC(=O)CC", 3.61},
{"CCC(=O)Nc1ccc(CC)cc1", 3.65},
#else
{"CCOC(=O)CC", 3.38},
{"CCC(=O)Nc1ccc(CC)cc1", 3.50},
#endif
};
for (const auto &pr : data) {
std::unique_ptr<ROMol> m(SmilesToMol(pr.first));
REQUIRE(m);
auto val = Descriptors::calcPhi(*m);
CHECK(val == Approx(pr.second).epsilon(0.01));
}
}
}
TEST_CASE("atom counts", "[2D]") {
{
SmilesParserParams ps;
ps.sanitize = true;
ps.removeHs = false;
std::unique_ptr<ROMol> m(SmilesToMol("CC[H]", ps));
REQUIRE(m);
CHECK(Descriptors::calcNumHeavyAtoms(*m) == 2);
CHECK(Descriptors::calcNumAtoms(*m) == 8);
}
}
#ifdef RDK_BUILD_DESCRIPTORS3D
TEST_CASE(
"Github #4167: SpherocityIndex() not being recalculated for different "
"conformers",
"[3D]") {
std::string pathName = getenv("RDBASE");
std::string sdfName =
pathName + "/Code/GraphMol/Descriptors/test_data/github4167.sdf";
bool sanitize = true;
bool removeHs = false;
RDKit::SDMolSupplier reader(sdfName, sanitize, removeHs);
std::unique_ptr<ROMol> m1(reader.next());
std::unique_ptr<ROMol> m2(reader.next());
REQUIRE(m1);
REQUIRE(m2);
m1->addConformer(new RDKit::Conformer(m2->getConformer()), true);
REQUIRE(m1->getNumConformers() == 2);
{
int confId = 0;
auto v1_0 = RDKit::Descriptors::spherocityIndex(*m1, confId, true);
auto v2 = RDKit::Descriptors::spherocityIndex(*m2, confId, true);
confId = 1;
auto v1_1 = RDKit::Descriptors::spherocityIndex(*m1, confId, true);
CHECK(v1_0 != v1_1);
CHECK(v1_1 == v2);
}
{
std::vector<double (*)(const ROMol &, int, bool, bool)> funcs{
RDKit::Descriptors::NPR1,
RDKit::Descriptors::NPR2,
RDKit::Descriptors::PMI1,
RDKit::Descriptors::PMI2,
RDKit::Descriptors::PMI3,
RDKit::Descriptors::radiusOfGyration,
RDKit::Descriptors::inertialShapeFactor,
RDKit::Descriptors::eccentricity,
RDKit::Descriptors::asphericity};
for (const auto func : funcs) {
bool useAtomMasses = true;
bool force = true;
int confId = 0;
auto v1_0 = func(*m1, confId, useAtomMasses, force);
auto v2 = func(*m2, confId, useAtomMasses, force);
confId = 1;
auto v1_1 = func(*m1, confId, useAtomMasses, force);
CHECK(v1_0 != v1_1);
CHECK(v1_1 == v2);
}
}
// { // surrogate for NPR1, NPR2, PMI1, PM2,
// int confId = 0;
// auto v1_0 = RDKit::Descriptors::spherocityIndex(*m1, confId, true);
// auto v2 = RDKit::Descriptors::spherocityIndex(*m2, confId, true);
// confId = 1;
// auto v1_1 = RDKit::Descriptors::spherocityIndex(*m1, confId, true);
// CHECK(v1_0 != v1_1);
// CHECK(v1_1 == v2);
// }
}
#endif
TEST_CASE(
"Github #5104: NumRotatableBonds() incorrect for partially sanitized "
"molecule") {
SECTION("basics") {
auto m1 = "c1ccccc1c1ccc(CCC)cc1"_smiles;
CHECK(Descriptors::calcNumRotatableBonds(
*m1, Descriptors::NumRotatableBondsOptions::NonStrict) == 3);
CHECK(Descriptors::calcNumRotatableBonds(
*m1, Descriptors::NumRotatableBondsOptions::Strict) == 3);
CHECK(Descriptors::calcNumRotatableBonds(
*m1, Descriptors::NumRotatableBondsOptions::StrictLinkages) == 2);
m1->getBondBetweenAtoms(5, 6)->setBondType(Bond::BondType::AROMATIC);
CHECK(Descriptors::calcNumRotatableBonds(
*m1, Descriptors::NumRotatableBondsOptions::NonStrict) == 3);
CHECK(Descriptors::calcNumRotatableBonds(
*m1, Descriptors::NumRotatableBondsOptions::Strict) == 3);
CHECK(Descriptors::calcNumRotatableBonds(
*m1, Descriptors::NumRotatableBondsOptions::StrictLinkages) == 2);
}
SECTION("as reported") {
SmilesParserParams ps;
ps.sanitize = false;
std::unique_ptr<RWMol> m1(SmilesToMol("c1ccccc1c1ccc(CCC)cc1", ps));
REQUIRE(m1);
unsigned int whatFailed;
MolOps::sanitizeMol(*m1, whatFailed,
MolOps::SanitizeFlags::SANITIZE_ALL ^
MolOps::SanitizeFlags::SANITIZE_KEKULIZE);
CHECK(Descriptors::calcNumRotatableBonds(
*m1, Descriptors::NumRotatableBondsOptions::NonStrict) == 3);
CHECK(Descriptors::calcNumRotatableBonds(
*m1, Descriptors::NumRotatableBondsOptions::Strict) == 3);
CHECK(Descriptors::calcNumRotatableBonds(
*m1, Descriptors::NumRotatableBondsOptions::StrictLinkages) == 2);
}
SECTION("linkages") {
auto m1 = "c1cc[nH]c1c1[nH]c(CCC)cc1"_smiles;
CHECK(Descriptors::calcNumRotatableBonds(
*m1, Descriptors::NumRotatableBondsOptions::StrictLinkages) == 3);
m1->getBondBetweenAtoms(4, 5)->setBondType(Bond::BondType::AROMATIC);
CHECK(Descriptors::calcNumRotatableBonds(
*m1, Descriptors::NumRotatableBondsOptions::StrictLinkages) == 3);
}
}
|
