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// Created by Guillaume GODIN
// Copyright (C) 2012-2020 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/GraphMol.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/MolWriters.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <RDGeneral/RDLog.h>
#include <vector>
#include <algorithm>
#include <fstream>
#include <sstream>
#include <chrono> // for high_resolution_clock
#include <GraphMol/Descriptors/AtomFeat.h>
using namespace RDKit;
void test1() {
auto m = "CO"_smiles;
TEST_ASSERT(m);
std::vector<double> res;
int atomid = 0;
RDKit::Descriptors::AtomFeatVect(*m, res, atomid);
std::vector<double> exp{ 0. , 1. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 0. ,
0. , 0. , 1. , 0. , 0. , 0. , 0. , 0. , 0. , 0. , 1. , 0. , 0. ,
0. , 0. , 0. , 1. , 0. , 0. , 0. , 0. , 1. , 0. , 0. , 0. , 0. ,
0. , 0. , 0. , 0. , 0. , 0. , 0. , 1. , 0. , 0.5};
// 49 features
TEST_ASSERT(res.size() == 49);
for (std::size_t i = 0; i < res.size(); i++) {
TEST_ASSERT(fabs(res[i] - exp[i]) < 0.001);
// std::cout << res[i] << "," ;
}
}
void test2() {
auto m = "C1CC=C1[NH3+]"_smiles;
TEST_ASSERT(m);
std::vector<double> res;
std::vector<double> molatf{ 0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0.2,
0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0.2,
0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,0,0,1,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,1,0,0,0,0.2,
0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,1,0,0,0,0,0.2,
0,0,1,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,0,1,0,0.2};
for (unsigned int j = 0; j < m->getNumAtoms(); j++) {
RDKit::Descriptors::AtomFeatVect(*m, res, j);
// 49 features
TEST_ASSERT(res.size() == 49);
for (std::size_t i = 0; i < res.size(); i++) {
TEST_ASSERT(fabs(res[i] - molatf[i + j * 49]) < 0.001);
}
res.clear();
res.resize(49);
}
}
void test3() {
auto m = "O[C@H](F)[C@H](F)O"_smiles;
TEST_ASSERT(m);
std::vector<double> molatf{ 0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667,
0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667,
0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0.166667,
0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667,
0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0.166667,
0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667};
std::vector<double> res;
for (unsigned int j = 0; j < m->getNumAtoms(); j++) {
RDKit::Descriptors::AtomFeatVect(*m, res, j);
// 49 features
TEST_ASSERT(res.size() == 49);
for (std::size_t i = 0; i < res.size(); i++) {
TEST_ASSERT(fabs(res[i] - molatf[i + j * 49]) < 0.001);
}
res.clear();
res.resize(49);
}
}
void test4() {
auto m = "O[C@H](F)[C@H](F)O"_smiles;
TEST_ASSERT(m);
std::vector<double> res;
std::vector<double> molatf{ 0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667,0,0,0,
0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667,0,1,0,
0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0.166667,0,0,0,
0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667,0,1,0,
0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0.166667,0,0,0,
0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667,0,0,0};
for (unsigned int j = 0; j < m->getNumAtoms(); j++) {
RDKit::Descriptors::AtomFeatVect(*m, res, j, true);
// 52 features
TEST_ASSERT(res.size() == 52);
for (std::size_t i = 0; i < res.size(); i++) {
TEST_ASSERT(fabs(res[i] - molatf[i + j * 52]) < 0.001);
}
res.clear();
res.resize(52);
}
}
void test5() {
auto m = "O[C@@H](F)[C@@H](F)O"_smiles;
TEST_ASSERT(m);
std::vector<double> res;
std::vector<double> molatf{ 0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667,0,0,0,
0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667,1,0,0,
0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0.166667,0,0,0,
0,1,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667,1,0,0,
0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,1,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,1,0,0,0,0,0.166667,0,0,0,
0,0,0,1,0,0,0,0,0,0,0,0,0,0,0,1,0,0,0,0,0,0,0,1,0,0,0,1,0,0,0,0,0,0,1,0,0,0,0,0,0,0,0,0,1,0,0,0,0.166667,0,0,0};
for (unsigned int j = 0; j < m->getNumAtoms(); j++) {
RDKit::Descriptors::AtomFeatVect(*m, res, j, true);
// 52 features
TEST_ASSERT(res.size() == 52);
for (std::size_t i = 0; i < res.size(); i++) {
TEST_ASSERT(fabs(res[i] - molatf[i + j * 52]) < 0.001);
}
res.clear();
res.resize(52);
}
}
int main() {
RDLog::InitLogs();
test1();
test2();
test3();
test4();
test5();
}
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