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
|
// Created by Guillaume GODIN
// Copyright (C) 2012-2016 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 <RDGeneral/test.h>
#include <RDGeneral/Invariant.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/RDLog.h>
#include <vector>
#include <algorithm>
#include <fstream>
#include <GraphMol/Descriptors/MORSE.h>
void testMORSE() {
std::cout << "=>start test MORSE\n";
std::string pathName = getenv("RDBASE");
std::string sdfName =
pathName + "/Code/GraphMol/Descriptors/test_data/PBF_egfr.sdf";
RDKit::SDMolSupplier reader(sdfName, true, false);
std::string fName =
pathName + "/Code/GraphMol/Descriptors/test_data/MORSE.out";
std::ifstream instrm(fName.c_str());
std::string line;
std::vector<std::vector<std::string>> data;
while (std::getline(instrm, line)) {
std::string phrase;
std::vector<std::string> row;
std::stringstream ss(line);
while (std::getline(ss, phrase, '\t')) {
row.push_back(phrase);
}
data.push_back(row);
}
std::cout << "=>read file\n";
int nDone = 0;
while (!reader.atEnd()) {
RDKit::ROMol *m = reader.next();
TEST_ASSERT(m);
std::string nm;
m->getProp("_Name", nm);
std::vector<double> dmorse;
RDKit::Descriptors::MORSE(*m, dmorse, -1);
std::vector<std::string> myrow = data[nDone];
std::string inm = myrow[0];
TEST_ASSERT(inm == nm);
for (size_t i = 0; i < dmorse.size(); i++) {
double ref = atof(myrow[i + 1].c_str());
if (fabs(ref) > 0.01) {
if (fabs((ref - dmorse[i]) / ref) > 1) {
std::cout << "value mismatch: pos" << i << " " << inm << " " << ref
<< " " << dmorse[i] << std::endl;
}
}
if (fabs(ref) < 0.01) {
if (fabs(ref - dmorse[i]) > 0.02) {
std::cout << "value mismatch: pos" << i << " " << inm << " " << ref
<< " " << dmorse[i] << std::endl;
}
}
if (ref > 1 && fabs(ref - dmorse[i]) / ref > 0.02) {
std::cout << "value mismatch: pos" << i << " " << inm << " " << ref
<< " " << dmorse[i] << std::endl;
}
// we're testing reasonably sized values and want to be sure that we're
// within 2% of the reference.
TEST_ASSERT(ref < 1 || fabs(ref - dmorse[i]) / ref < 0.02);
}
delete m;
++nDone;
}
BOOST_LOG(rdErrorLog) << "test on : " << nDone << " molecules done"
<< std::endl;
}
int main() {
RDLog::InitLogs();
testMORSE();
}
|
