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
|
//
// Copyright (C) 2022-2023 Greg Landrum and other RDKit contributors
//
// @@ 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 <catch2/catch_all.hpp>
#include "AlignMolecules.h"
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/ROMol.h>
#include <GraphMol/Conformer.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/MolTransforms/MolTransforms.h>
using namespace RDKit;
TEST_CASE("symmetric functional groups") {
SECTION("basics") {
auto m1 =
"CCC(=O)[O-] "
"|(-1.11,0.08,-0.29;0.08,-0.18,0.58;1.34,0.03,-0.16;1.74,1.22,-0.32;2.06,-1.04,-0.66)|"_smiles;
REQUIRE(m1);
// swap the bond orders to the Os
RWMol m2(*m1);
m2.getAtomWithIdx(3)->setFormalCharge(-1);
m2.getAtomWithIdx(4)->setFormalCharge(0);
m2.getBondBetweenAtoms(2, 3)->setBondType(Bond::BondType::SINGLE);
m2.getBondBetweenAtoms(2, 4)->setBondType(Bond::BondType::DOUBLE);
{
auto rmsd = MolAlign::getBestRMS(m2, *m1);
CHECK(rmsd == Catch::Approx(0.0).margin(1e-3));
}
{
// previous behavior
int probeId = -1;
int refId = -1;
std::vector<MatchVectType> mp;
int maxMatches = 1e6;
bool symmetrize = false;
auto rmsd = MolAlign::getBestRMS(m2, *m1, probeId, refId, mp, maxMatches,
symmetrize);
CHECK(rmsd == Catch::Approx(0.747).margin(1e-3));
}
}
SECTION("terminal sulfate1") {
auto m1 =
"CS(=O)(=O)[O-] |(-0.93,-0.06,-0.04;0.82,0.07,0.13;1.27,-0.04,1.54;1.21,1.40,-0.48;1.53,-1.11,-0.82)|"_smiles;
REQUIRE(m1);
// swap the bond orders to the Os
RWMol m2(*m1);
m2.getAtomWithIdx(2)->setFormalCharge(-1);
m2.getAtomWithIdx(4)->setFormalCharge(0);
m2.getBondBetweenAtoms(1, 2)->setBondType(Bond::BondType::SINGLE);
m2.getBondBetweenAtoms(1, 4)->setBondType(Bond::BondType::DOUBLE);
{
auto rmsd = MolAlign::getBestRMS(m2, *m1);
CHECK(rmsd == Catch::Approx(0.0).margin(1e-3));
}
{
// previous behavior
int probeId = -1;
int refId = -1;
std::vector<MatchVectType> mp;
int maxMatches = 1e6;
bool symmetrize = false;
auto rmsd = MolAlign::getBestRMS(m2, *m1, probeId, refId, mp, maxMatches,
symmetrize);
CHECK(rmsd == Catch::Approx(0.097).margin(1e-3));
}
}
SECTION("terminal sulfate2") {
auto m1 =
"CS(=O)(=O)[O-] |(-0.93,-0.06,-0.04;0.82,0.07,0.13;1.27,-0.04,1.54;1.21,1.40,-0.48;1.53,-1.11,-0.82)|"_smiles;
REQUIRE(m1);
// swap the bond orders to the Os
RWMol m2(*m1);
m2.getAtomWithIdx(3)->setFormalCharge(-1);
m2.getAtomWithIdx(4)->setFormalCharge(0);
m2.getBondBetweenAtoms(1, 3)->setBondType(Bond::BondType::SINGLE);
m2.getBondBetweenAtoms(1, 4)->setBondType(Bond::BondType::DOUBLE);
{
auto rmsd = MolAlign::getBestRMS(m2, *m1);
CHECK(rmsd == Catch::Approx(0.0).margin(1e-3));
}
{
// previous behavior
int probeId = -1;
int refId = -1;
std::vector<MatchVectType> mp;
int maxMatches = 1e6;
bool symmetrize = false;
auto rmsd = MolAlign::getBestRMS(m2, *m1, probeId, refId, mp, maxMatches,
symmetrize);
CHECK(rmsd == Catch::Approx(0.097).margin(1e-3));
}
}
}
#ifdef RDK_BUILD_THREADSAFE_SSS
TEST_CASE("multithreaded getBestRMS") {
SECTION("basics") {
// has 288 self matches
auto m1 =
"FC(F)(F)C(F)(F)C(F)(F)C(F)(F)F |(-1.17097,1.42189,1.14513;-1.54917,0.262724,0.549205;-1.70317,-0.764739,1.49745;-2.82875,0.445186,-0.0104401;-0.695326,-0.20819,-0.58675;-1.32875,-1.40402,-1.02194;-0.794122,0.733556,-1.61075;0.695194,-0.600926,-0.295382;1.26585,-1.00432,-1.52316;0.671971,-1.69988,0.563393;1.62838,0.438987,0.231506;1.1944,0.938004,1.42313;1.6862,1.50141,-0.682411;2.92826,-0.0596757,0.321018)|"_smiles;
REQUIRE(m1);
auto m2 =
"FC(F)(F)C(F)(F)C(F)(F)C(F)(F)F |(-1.4374,1.69863,0.0454955;-1.63421,0.384221,0.267923;-1.76372,0.215075,1.6529;-2.89568,0.031803,-0.240695;-0.665291,-0.57679,-0.303489;-1.12767,-1.85176,0.0867448;-0.706055,-0.620221,-1.69542;0.736642,-0.522726,0.120365;0.785974,-0.733214,1.50576;1.36074,-1.67057,-0.401737;1.57617,0.630117,-0.22085;1.06853,1.80237,0.30467;1.8928,0.75494,-1.55471;2.80916,0.458118,0.433039)|"_smiles;
REQUIRE(m2);
auto probeId = 0;
auto refId = 0;
std::vector<MatchVectType> mp;
int maxMatches = 1e6;
bool symmetrize = true;
RDNumeric::DoubleVector *weights = nullptr;
int numThreads = 1;
auto ref = MolAlign::getBestRMS(*m2, *m1, probeId, refId, mp, maxMatches,
symmetrize, weights, numThreads);
numThreads = 4;
auto mt_val = MolAlign::getBestRMS(*m2, *m1, probeId, refId, mp, maxMatches,
symmetrize, weights, numThreads);
CHECK(ref == Catch::Approx(mt_val).epsilon(0.00001));
}
SECTION("more symmetry") {
std::string rdbase = getenv("RDBASE");
std::string fname1 =
rdbase + "/Code/GraphMol/MolAlign/test_data/symmetric.mol";
std::unique_ptr<ROMol> m1{MolFileToMol(fname1)};
REQUIRE(m1);
auto probeId = 0;
auto refId = 0;
std::vector<MatchVectType> mp;
int maxMatches = 1e6;
bool symmetrize = true;
RDNumeric::DoubleVector *weights = nullptr;
{
int numThreads = 1;
auto start = std::chrono::high_resolution_clock::now();
auto ref = MolAlign::getBestRMS(*m1, *m1, probeId, refId, mp, maxMatches,
symmetrize, weights, numThreads);
auto finish = std::chrono::high_resolution_clock::now();
std::cerr << (finish - start).count() << std::endl;
CHECK(ref == Catch::Approx(0.0).epsilon(0.00001));
}
{
int numThreads = 4;
auto start = std::chrono::high_resolution_clock::now();
auto ref = MolAlign::getBestRMS(*m1, *m1, probeId, refId, mp, maxMatches,
symmetrize, weights, numThreads);
auto finish = std::chrono::high_resolution_clock::now();
std::cerr << (finish - start).count() << std::endl;
CHECK(ref == Catch::Approx(0.0).epsilon(0.00001));
}
}
}
#endif
TEST_CASE("getAllConformerBestRMS") {
std::string rdbase = getenv("RDBASE");
std::string fname1 =
rdbase + "/Code/GraphMol/MolAlign/test_data/symmetric.confs.sdf";
SDMolSupplier suppl(fname1);
std::unique_ptr<ROMol> mol{suppl[0]};
REQUIRE(mol);
for (auto i = 1u; i < suppl.length(); ++i) {
std::unique_ptr<ROMol> nm{suppl[i]};
REQUIRE(nm);
mol->addConformer(new Conformer(nm->getConformer()), true);
}
// CHECK(mol->getNumConformers() == 10);
SECTION("basics") {
auto nconfs = mol->getNumConformers();
std::vector<double> rmsds;
{
auto start = std::chrono::high_resolution_clock::now();
rmsds = MolAlign::getAllConformerBestRMS(*mol);
CHECK(rmsds.size() == (nconfs * (nconfs - 1)) / 2);
auto finish = std::chrono::high_resolution_clock::now();
std::cerr << (finish - start).count() << std::endl;
ROMol refMol(*mol);
ROMol prbMol(*mol);
auto refVal = MolAlign::getBestRMS(refMol, prbMol, 1, 0);
CHECK(rmsds[0] == Catch::Approx(refVal).epsilon(0.00001));
}
std::vector<double> mtrmsds;
{
auto start = std::chrono::high_resolution_clock::now();
int numThreads = 4;
mtrmsds = MolAlign::getAllConformerBestRMS(*mol, numThreads);
CHECK(mtrmsds.size() == (nconfs * (nconfs - 1)) / 2);
auto finish = std::chrono::high_resolution_clock::now();
std::cerr << (finish - start).count() << std::endl;
}
for (auto i = 0u; i < rmsds.size(); ++i) {
CHECK(rmsds[i] == Catch::Approx(mtrmsds[i]).epsilon(0.00001));
}
}
}
|
