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// Created by Guillaume GODIN
// Copyright (C) 2012-2017 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 <chrono> // for high_resolution_clock
#include <GraphMol/Descriptors/EEM.h>
void testEEM1() {
std::cout << "=>start test EEM\n";
std::string pathName = getenv("RDBASE");
std::string sdfName =
pathName + "/Code/GraphMol/Descriptors/test_data/setEEM1.sdf";
auto start = std::chrono::high_resolution_clock::now();
RDKit::SDMolSupplier reader(sdfName, true, false);
std::string fName =
pathName + "/Code/GraphMol/Descriptors/test_data/eem1.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, ',')) {
row.push_back(phrase);
}
data.push_back(row);
}
int nDone = 0;
int errorMols = 0;
while (!reader.atEnd()) {
RDKit::ROMol *m = reader.next();
TEST_ASSERT(m);
std::string nm;
m->getProp("_Name", nm);
int errorAtoms = 0;
std::vector<std::string> myrow = data[nDone];
std::string inm = myrow[0];
TEST_ASSERT(inm == nm);
int confId = -1;
std::vector<double> charges;
RDKit::Descriptors::EEM(*m, charges, confId);
int numAtoms = m->getNumAtoms();
for (int i = 0; i < numAtoms; i++) {
double ref = atof(myrow[i + 2].c_str());
if (fabs(ref - charges[i]) >= 0.01) {
std::cout << inm << ","
<< "ref: " << ref << " ,val: " << charges[i]
<< "Symbol: " << m->getAtomWithIdx(i)->getSymbol() << "\n";
++errorAtoms;
}
// TEST_ASSERT(fabs(ref - charges[i]) < 0.01);
}
// if (nDone>1) {break;}
if (nDone % 100 == 0) {
std::cout << nDone << "\n";
}
if (errorAtoms > 0) {
std::cout << nDone << " " << inm << " " << errorAtoms << "\n";
++errorMols;
}
TEST_ASSERT(errorAtoms == 0);
delete m;
// break;
++nDone;
}
auto finish = std::chrono::high_resolution_clock::now();
std::chrono::duration<double> elapsed = finish - start;
std::cout << "Elapsed time: " << elapsed.count() << " s\n";
std::cout << "Errors:" << errorMols << "\n";
TEST_ASSERT(errorMols == 0);
BOOST_LOG(rdErrorLog) << "test on : " << nDone << " molecules done"
<< std::endl;
}
void testEEM2() {
std::cout << "=>start test EEM\n";
std::string pathName = getenv("RDBASE");
std::string sdfName =
pathName + "/Code/GraphMol/Descriptors/test_data/setEEM2.sdf";
auto start = std::chrono::high_resolution_clock::now();
RDKit::SDMolSupplier reader(sdfName, true, false);
std::string fName =
pathName + "/Code/GraphMol/Descriptors/test_data/eem2.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, ',')) {
row.push_back(phrase);
}
data.push_back(row);
}
int nDone = 0;
int errorMols = 0;
while (!reader.atEnd()) {
RDKit::ROMol *m = reader.next();
TEST_ASSERT(m);
std::string nm;
m->getProp("_Name", nm);
int errorAtoms = 0;
std::vector<std::string> myrow = data[nDone];
std::string inm = myrow[0];
TEST_ASSERT(inm == nm);
int confId = -1;
std::vector<double> charges;
RDKit::Descriptors::EEM(*m, charges, confId);
int numAtoms = m->getNumAtoms();
for (int i = 0; i < numAtoms; i++) {
double ref = atof(myrow[i + 2].c_str());
if (fabs(ref - charges[i]) >= 0.01) {
std::cout << inm << ","
<< "ref: " << ref << " ,val: " << charges[i]
<< "Symbol: " << m->getAtomWithIdx(i)->getSymbol() << "\n";
++errorAtoms;
}
TEST_ASSERT(fabs(ref - charges[i]) < 0.01);
}
if (nDone % 100 == 0) {
std::cout << nDone << "\n";
}
if (errorAtoms > 0) {
std::cout << "id" << nDone << ", name:" << inm << "\n";
++errorMols;
std::cout << RDKit::MolToSmiles(*m) << "\n";
}
delete m;
++nDone;
}
auto finish = std::chrono::high_resolution_clock::now();
std::chrono::duration<double> elapsed = finish - start;
std::cout << "Elapsed time: " << elapsed.count() << " s\n";
std::cout << "Errors Mols:" << errorMols << "\n";
BOOST_LOG(rdErrorLog) << "test on : " << nDone << " molecules done"
<< std::endl;
}
int main() {
RDLog::InitLogs();
testEEM1();
}
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