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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/FileParsers/FileParsers.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include <RDGeneral/RDLog.h>
#include <vector>
#include <algorithm>
#include <fstream>
#include <sstream>
#include <GraphMol/Descriptors/WHIM.h>
void testWHIM2() {
std::cout << "=>start test chlorobenzene whim from rdkit\n";
std::string pathName = getenv("RDBASE");
std::string sdfName =
pathName + "/Code/GraphMol/Descriptors/test_data/chlorobenzene.sdf";
RDKit::SDMolSupplier reader(sdfName, true, false);
int nDone = 0;
while (!reader.atEnd()) {
++nDone;
RDKit::ROMol *m = reader.next();
TEST_ASSERT(m);
std::string nm;
m->getProp("_Name", nm);
std::vector<double> dwhim;
RDKit::Descriptors::WHIM(*m, dwhim, -1, 0.01);
for (int j = 0; j < 114; j++) {
std::cout << dwhim[j] << ",";
}
std::cout << "\n";
delete m;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testWHIM3() {
std::cout << "=>start test chlorobenzene whim original\n";
std::string pathName = getenv("RDBASE");
std::string sdfName =
pathName + "/Code/GraphMol/Descriptors/test_data/chlorobenzene2.sdf";
RDKit::SDMolSupplier reader(sdfName, true, false);
int nDone = 0;
while (!reader.atEnd()) {
++nDone;
RDKit::ROMol *m = reader.next();
TEST_ASSERT(m);
std::string nm;
m->getProp("_Name", nm);
std::vector<double> dwhim;
RDKit::Descriptors::WHIM(*m, dwhim, -1, 0.01);
for (int j = 0; j < 114; j++) {
std::cout << dwhim[j] << ",";
}
std::cout << "\n";
delete m;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testWHIM1() {
std::cout << "=>start test rdf\n";
std::string pathName = getenv("RDBASE");
std::string sdfName =
pathName + "/Code/GraphMol/Descriptors/test_data/1mol.sdf";
RDKit::SDMolSupplier reader(sdfName, true, false);
int nDone = 0;
while (!reader.atEnd()) {
++nDone;
RDKit::ROMol *m = reader.next();
TEST_ASSERT(m);
std::string nm;
m->getProp("_Name", nm);
std::vector<double> dwhim;
// for (int i=1;i<11;i++) {
// std::cout << "i:" << 0.005*i << "\n";
RDKit::Descriptors::WHIM(*m, dwhim, -1, 0.01);
for (int j = 0; j < 114; j++) {
std::cout << dwhim[j] << ",";
}
std::cout << "\n";
//}
std::cout << "=>read molecule: " << nDone << std::endl;
delete m;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testWHIM() {
std::cout << "=>start test WHIM\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/whim.new.out";
std::ifstream instrm(fName.c_str());
// std::string ofName =
// pathName + "/Code/GraphMol/Descriptors/test_data/whim.new.out";
// std::ofstream outstrm(ofName.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> dwhim;
RDKit::Descriptors::WHIM(*m, dwhim, -1, 0.01);
std::vector<std::string> myrow = data[nDone];
std::string inm = myrow[0];
TEST_ASSERT(inm == nm);
// outstrm << nm;
for (int i = 0; i < 114; i++) {
double ref = atof(myrow[i + 1].c_str());
if (fabs(ref - dwhim[i]) >= 0.01) {
std::cerr << "value mismatch: pos" << i << " " << inm << " " << ref
<< " " << dwhim[i] << std::endl;
}
// outstrm << "\t" << dwhim[i];
// TEST_ASSERT((ref < 1e-3 && dwhim[i] < 1e-3) ||
// fabs(ref - dwhim[i]) / ref < 0.01);
TEST_ASSERT(fabs(ref - dwhim[i]) < 0.01);
}
// outstrm << std::endl;
delete m;
++nDone;
}
BOOST_LOG(rdErrorLog) << "test on : " << nDone << " molecules done"
<< std::endl;
}
int main() {
RDLog::InitLogs();
testWHIM();
// testWHIM3();
// testWHIM();
}
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