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// 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/SmilesParse/SmilesParse.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <RDGeneral/RDLog.h>
#include <vector>
#include <algorithm>
#include <fstream>
#include <sstream>
#include <GraphMol/Descriptors/AUTOCORR2D.h>
using namespace RDKit;
void testautocorrelation() {
BOOST_LOG(rdErrorLog)
<< "----------------------------\nstart test autocorr2D\n";
std::string pathName = getenv("RDBASE");
std::string sdfName =
pathName + "/Code/GraphMol/Descriptors/test_data/PBF_egfr.sdf";
// std::string sdfName ="PBF_egfr.sdf";
RDKit::SDMolSupplier reader(sdfName, true, false);
std::string fName =
pathName + "/Code/GraphMol/Descriptors/test_data/auto2D.out";
// std::string fName = "auto2D.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);
}
int nDone = 0;
while (!reader.atEnd()) {
RDKit::ROMol *m = reader.next();
TEST_ASSERT(m);
std::string nm;
m->getProp("_Name", nm);
std::vector<double> res2d;
RDKit::Descriptors::AUTOCORR2D(*m, res2d);
std::vector<std::string> myrow = data[nDone];
std::string inm = myrow[0];
TEST_ASSERT(inm == nm);
for (int i = 0; i < 192; i++) {
double ref = atof(myrow[i + 1].c_str());
if (fabs(ref - res2d[i]) > 0.05) {
std::cout << "value mismatch: pos" << i << " " << inm << " " << ref
<< " " << res2d[i] << std::endl;
}
TEST_ASSERT(fabs(ref - res2d[i]) < 0.05);
}
res2d.clear();
res2d.resize(48);
delete m;
++nDone;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGithub3806() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Test Github #3806: NaNs from AUTOCORR2D descriptor" << std::endl;
{
auto m = "CC"_smiles;
std::vector<double> vs;
RDKit::Descriptors::AUTOCORR2D(*m, vs);
TEST_ASSERT(vs.size() == 192);
for (unsigned i = 0; i < vs.size(); ++i) {
TEST_ASSERT(!std::isnan(vs[i]));
}
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
int main() {
RDLog::InitLogs();
testautocorrelation();
testGithub3806();
}
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