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//
// 2019, Daniel Probst, Reymond Group @ University of Bern
//
// @@ 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/RDLog.h>
#include <GraphMol/RDKitBase.h>
#include <RDGeneral/test.h>
#include <RDGeneral/utils.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Fingerprints/MHFP.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/FileParsers.h>
#include <GraphMol/Fingerprints/MHFP.h>
using namespace RDKit;
void testMHFPInit() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test MHFP fingerprint encoder initialization"
<< std::endl;
std::string s = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C";
std::string t = "Cn1cnc2c1c(=O)[nH]c(=O)n2C";
ROMol *mol_s = SmilesToMol(s);
ROMol *mol_t = SmilesToMol(t);
MHFPFingerprints::MHFPEncoder enc(128, 42);
auto fp_s = enc.Encode(s);
auto fp_t = enc.Encode(t);
auto fp_mol_s = enc.Encode(*mol_s);
auto fp_mol_t = enc.Encode(*mol_t);
TEST_ASSERT(fp_s.size() == 128);
TEST_ASSERT(fp_s[0] == fp_mol_s[0]);
TEST_ASSERT(fp_t[127] == fp_mol_t[127]);
delete mol_s;
delete mol_t;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMHFPHashing() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test MHFP hashing of string and uint arrays"
<< std::endl;
MHFPFingerprints::MHFPEncoder enc(8);
std::vector<uint32_t> input_a = {1, 2, 4, 5, 6, 7, 8, 9};
std::vector<uint32_t> output_a = {188049437, 364485576, 737251017,
810894466, 300249621, 154369992,
2221926165, 283729444};
TEST_ASSERT(enc.FromArray(input_a) == output_a);
std::vector<std::string> input_b = {"a", "b", "c", "d", "e", "f"};
std::vector<uint32_t> output_b = {631555539, 835857365, 445245415, 4162827301,
955545975, 943207071, 712975995, 363547692};
TEST_ASSERT(enc.FromStringArray(input_b) == output_b);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMHFPShingling() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test MHFP shingling creation" << std::endl;
std::string s = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C";
std::string t = "Cn1cnc2c1c(=O)[nH]c(=O)n2C";
ROMol *mol_s = SmilesToMol(s);
MHFPFingerprints::MHFPEncoder enc;
auto fp_s = enc.Encode(s);
auto fp_t = enc.Encode(t);
auto sh_a = enc.CreateShingling(s);
auto sh_b = enc.CreateShingling(*mol_s);
TEST_ASSERT(sh_a.size() == 44);
TEST_ASSERT(sh_b.size() == 44);
TEST_ASSERT(enc.CreateShingling(s, 3, false).size() == 42);
TEST_ASSERT(enc.CreateShingling(s, 3, true, false, true, 0).size() == 58);
delete mol_s;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMHFPSECFP() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test SECFP fingerprint functionality" << std::endl;
std::string s = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C";
ROMol *mol_s = SmilesToMol(s);
MHFPFingerprints::MHFPEncoder enc;
auto fp_s = enc.EncodeSECFP(s, 3, true, false, true, 1, 16);
auto fp_mol_s = enc.EncodeSECFP(*mol_s, 3, true, false, true, 1, 16);
TEST_ASSERT(fp_s.size() == 16);
TEST_ASSERT(fp_s[10]);
TEST_ASSERT(fp_s[15]);
delete mol_s;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMHFPDistance() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test MHFP shingling creation" << std::endl;
std::string s = "CN1C=NC2=C1C(=O)N(C(=O)N2C)C";
std::string t = "Cn1cnc2c1c(=O)[nH]c(=O)n2C";
MHFPFingerprints::MHFPEncoder enc;
auto fp_s = enc.Encode(s);
auto fp_t = enc.Encode(t);
TEST_ASSERT(feq(MHFPFingerprints::MHFPEncoder::Distance(fp_s, fp_s), 0.0));
TEST_ASSERT(
feq(MHFPFingerprints::MHFPEncoder::Distance(fp_s, fp_t), 0.7109375));
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
int main(int argc, char *argv[]) {
(void)argc;
(void)argv;
RDLog::InitLogs();
testMHFPInit();
testMHFPShingling();
testMHFPHashing();
testMHFPSECFP();
return 0;
}
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