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//
// 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 <sstream>
#include <GraphMol/Descriptors/RDF.h>
void testRDF() {
std::cout << "=>start test rdf\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/RDF.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> drdf;
RDKit::Descriptors::RDF(*m, drdf, -1);
std::vector<std::string> myrow = data[nDone];
std::string inm = myrow[0];
TEST_ASSERT(inm == nm);
for (size_t i = 0; i < drdf.size(); i++) {
double ref = atof(myrow[i + 1].c_str());
if (fabs(ref) > 1) {
if (fabs((ref - drdf[i]) / ref) > 0.02) {
std::cerr << "value mismatch: pos" << i << " " << inm
<< " dragon: " << ref << " rdkit: " << drdf[i] << std::endl;
}
}
if (fabs(ref) <= 1) {
if (fabs((ref - drdf[i])) > 0.02) {
std::cerr << "value mismatch: pos" << i << " " << inm
<< " dragon: " << ref << " rdkit: " << drdf[i] << std::endl;
}
}
// FIX: this tolerance seems too high
if (ref > 0.5 && fabs(ref - drdf[i]) / ref >= 0.02) {
std::cerr << "value mismatch: pos" << i << " " << inm
<< " dragon: " << ref << " rdkit: " << drdf[i] << " "
<< fabs(ref - drdf[i]) / ref << std::endl;
}
TEST_ASSERT(ref < 0.5 || fabs(ref - drdf[i]) / ref < 0.02);
}
delete m;
++nDone;
}
BOOST_LOG(rdErrorLog) << "test on : " << nDone << " molecules done"
<< std::endl;
}
int main() {
RDLog::InitLogs();
testRDF();
}
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