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rdkit/Code/GraphMol/Fingerprints/testFingerprintGenerators.cpp

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//
// Copyright (C) 2018 Boran Adas, Google Summer of Code
//
// @@ 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 <GraphMol/Fingerprints/AtomPairs.h>
#include <GraphMol/Fingerprints/MorganFingerprints.h>
#include <GraphMol/Fingerprints/Fingerprints.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Fingerprints/AtomPairGenerator.h>
#include <GraphMol/Fingerprints/MorganGenerator.h>
#include <GraphMol/Fingerprints/RDKitFPGenerator.h>
#include <GraphMol/Fingerprints/TopologicalTorsionGenerator.h>
#include <GraphMol/Fingerprints/FingerprintGenerator.h>
#include <GraphMol/FileParsers/MolSupplier.h>
#include <GraphMol/FileParsers/FileParsers.h>
using namespace RDKit;
std::string smis[] = {
"C[C@@H]1CCC[C@H](C)[C@H]1C",
"N[C@@]1(C[C@H]([18F])C1)C(=O)O",
"CC(C)CCCC[C@@H]1C[C@H](/C=C/[C@]2(C)CC[C@H](O)CC2)[C@@H](O)[C@H]1O",
"COC(=O)/C=C/C(C)=C/C=C/C(C)=C/C=C/C=C(C)/C=C/C=C(\\C)/C=C/C(=O)[O-]",
"[O:1]=[C:2]([CH2:3][C:4]1=[CH:5][CH:6]=[CH:7][CH:8]=[CH:9]1)[NH2:10]",
"Cl[C@H]1[C@@H](Cl)[C@H](Cl)[C@@H](Cl)[C@H](Cl)[C@@H]1Cl",
"O=S(=O)(NC[C@H]1CC[C@H](CNCc2ccc3ccccc3c2)CC1)c1ccc2ccccc2c1",
"CCn1c2ccc3cc2c2cc(ccc21)C(=O)c1ccc(cc1)Cn1cc[n+](c1)Cc1ccc(cc1)-c1cccc(-"
"c2ccc(cc2)C[n+]2ccn(c2)Cc2ccc(cc2)C3=O)c1C(=O)O.[Br-].[Br-]",
"CCCCCCC1C23C4=c5c6c7c8c9c%10c%11c%12c%13c%14c%15c%16c%17c%18c%19c%20c%21c%"
"22c%23c(c5c5c6c6c8c%11c8c%11c%12c%15c%12c(c%20%16)c%21c%15c%23c5c(c68)c%"
"15c%12%11)C2(C[N+]1(C)C)C%22C%19c1c-%18c2c5c(c13)C4C7C9=C5C1(C2C%17%14)C("
"CCCCCC)[N+](C)(C)CC%10%131.[I-].[I-]",
"C12C3C4C5C6C7C8C1C1C9C5C5C%10C2C2C%11C%12C%13C3C3C7C%10C7C4C%11C1C3C(C5C8%"
"12)C(C62)C7C9%13"};
void testAtomPairFP() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test atom-pair fp generator" << std::endl;
ROMol *mol;
SparseIntVect<std::uint32_t> *fp;
std::uint32_t c1, c2, c3;
FingerprintGenerator<std::uint32_t> *atomPairGenerator =
AtomPair::getAtomPairGenerator<std::uint32_t>();
mol = SmilesToMol("CCC");
fp = atomPairGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal() == 3);
TEST_ASSERT(fp->getNonzeroElements().size() == 2);
c1 = AtomPair::getAtomCode(mol->getAtomWithIdx(0), 0, false);
c2 = AtomPair::getAtomCode(mol->getAtomWithIdx(1), 0, false);
c3 = AtomPair::getAtomCode(mol->getAtomWithIdx(2), 0, false);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c2, 1, false)) == 2);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c3, 2, false)) == 1);
delete mol;
delete fp;
mol = SmilesToMol("CC=O.Cl");
fp = atomPairGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal() == 3);
TEST_ASSERT(fp->getNonzeroElements().size() == 3);
c1 = AtomPair::getAtomCode(mol->getAtomWithIdx(0), 0, false);
c2 = AtomPair::getAtomCode(mol->getAtomWithIdx(1), 0, false);
c3 = AtomPair::getAtomCode(mol->getAtomWithIdx(2), 0, false);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c2, 1, false)) == 1);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c3, 2, false)) == 1);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c2, c3, 1, false)) == 1);
delete mol;
delete fp;
delete atomPairGenerator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testAtomPairArgs() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< "Test atom-pair fp generator with different arguments" << std::endl;
ROMol *mol;
SparseIntVect<std::uint32_t> *fp;
std::uint32_t c1, c2, c3;
FingerprintGenerator<std::uint32_t> *atomPairGenerator =
AtomPair::getAtomPairGenerator<std::uint32_t>(2);
mol = SmilesToMol("CCC");
fp = atomPairGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal() == 1);
TEST_ASSERT(fp->getNonzeroElements().size() == 1);
c1 = AtomPair::getAtomCode(mol->getAtomWithIdx(0), 0, false);
c2 = AtomPair::getAtomCode(mol->getAtomWithIdx(1), 0, false);
c3 = AtomPair::getAtomCode(mol->getAtomWithIdx(2), 0, false);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c2, 1, false)) == 0);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c3, 2, false)) == 1);
delete fp;
delete atomPairGenerator;
atomPairGenerator = AtomPair::getAtomPairGenerator<std::uint32_t>(1, 1);
fp = atomPairGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal() == 2);
TEST_ASSERT(fp->getNonzeroElements().size() == 1);
c1 = AtomPair::getAtomCode(mol->getAtomWithIdx(0), 0, false);
c2 = AtomPair::getAtomCode(mol->getAtomWithIdx(1), 0, false);
c3 = AtomPair::getAtomCode(mol->getAtomWithIdx(2), 0, false);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c2, 1, false)) == 2);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c3, 2, false)) == 0);
delete fp;
delete atomPairGenerator;
atomPairGenerator =
AtomPair::getAtomPairGenerator<std::uint32_t>(1, 30, true);
fp = atomPairGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal() == 3);
TEST_ASSERT(fp->getNonzeroElements().size() == 2);
c1 = AtomPair::getAtomCode(mol->getAtomWithIdx(0), 0, true);
c2 = AtomPair::getAtomCode(mol->getAtomWithIdx(1), 0, true);
c3 = AtomPair::getAtomCode(mol->getAtomWithIdx(2), 0, true);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c2, 1, true)) == 2);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c3, 2, true)) == 1);
delete fp;
delete atomPairGenerator;
atomPairGenerator = AtomPair::getAtomPairGenerator<std::uint32_t>(
1, 30, false, true, nullptr, false);
fp = atomPairGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal() == 3);
TEST_ASSERT(fp->getNonzeroElements().size() == 2);
c1 = AtomPair::getAtomCode(mol->getAtomWithIdx(0), 0, false);
c2 = AtomPair::getAtomCode(mol->getAtomWithIdx(1), 0, false);
c3 = AtomPair::getAtomCode(mol->getAtomWithIdx(2), 0, false);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c2, 1, false)) == 2);
TEST_ASSERT(fp->getVal(AtomPair::getAtomPairCode(c1, c3, 2, false)) == 1);
delete mol;
delete fp;
delete atomPairGenerator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testAtomPairOld() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test compatibility between atom pair "
"implementation for FingerprintGenerator"
" and old atom pairs implementation"
<< std::endl;
{
ROMol *mol;
SparseIntVect<std::int32_t> *fp1, *fp2;
SparseIntVect<std::uint32_t> *fpu;
FingerprintGenerator<std::uint32_t> *atomPairGenerator =
AtomPair::getAtomPairGenerator<std::uint32_t>();
BOOST_FOREACH (std::string sm, smis) {
mol = SmilesToMol(sm);
fp1 = AtomPairs::getAtomPairFingerprint(*mol);
fpu = atomPairGenerator->getSparseCountFingerprint(*mol);
fp2 = new SparseIntVect<std::int32_t>(fpu->size());
std::map<std::uint32_t, int> nz = fpu->getNonzeroElements();
for (std::map<std::uint32_t, int>::iterator it = nz.begin();
it != nz.end(); it++) {
fp2->setVal(static_cast<std::int32_t>(it->first), it->second);
}
TEST_ASSERT(DiceSimilarity(*fp1, *fp2) == 1.0);
TEST_ASSERT(*fp1 == *fp2);
delete mol;
delete fp1;
delete fp2;
delete fpu;
}
delete atomPairGenerator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
}
// todo this test needs to be updated since the fingerprint size logic is
// changed, count simulation no longer makes fingerprints larger
void testAtomPairNonSparseBitvector() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test consistency between different output types "
"for folded atom pair fingerprint"
<< std::endl;
{
ROMol *mol;
SparseIntVect<std::uint32_t> *fp1;
ExplicitBitVect *fp2;
FingerprintGenerator<std::uint32_t> *atomPairGenerator =
AtomPair::getAtomPairGenerator<std::uint32_t>();
std::vector<std::uint32_t> defaultCountBounds = {1, 2, 4, 8};
mol = SmilesToMol("CCC");
fp1 = atomPairGenerator->getCountFingerprint(*mol);
fp2 = atomPairGenerator->getFingerprint(*mol);
std::map<std::uint32_t, int> nz = fp1->getNonzeroElements();
for (const auto &it : nz) {
for (unsigned int i = 0; i < defaultCountBounds.size(); ++i) {
bool isSet = static_cast<bool>(
fp2->getBit(it.first * defaultCountBounds.size() + i));
TEST_ASSERT(isSet ==
(it.second >= static_cast<long>(defaultCountBounds[i])));
}
}
delete mol;
delete fp1;
delete fp2;
mol = SmilesToMol("CC=O.Cl");
fp1 = atomPairGenerator->getCountFingerprint(*mol);
fp2 = atomPairGenerator->getFingerprint(*mol);
nz = fp1->getNonzeroElements();
for (const auto &it : nz) {
for (unsigned int i = 0; i < defaultCountBounds.size(); ++i) {
bool isSet = static_cast<bool>(
fp2->getBit(it.first * defaultCountBounds.size() + i));
TEST_ASSERT(isSet ==
(it.second >= static_cast<long>(defaultCountBounds[i])));
}
}
delete mol;
delete fp1;
delete fp2;
delete atomPairGenerator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
}
void testAtomPairOutput() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test atom-pair additional output" << std::endl;
ROMol *mol;
SparseIntVect<std::uint32_t> *fp;
std::uint32_t c1, c2, c3;
AdditionalOutput additionalOutput = {nullptr, nullptr, nullptr, nullptr};
std::vector<std::uint64_t> v;
FingerprintGenerator<std::uint32_t> *atomPairGenerator =
AtomPair::getAtomPairGenerator<std::uint32_t>();
mol = SmilesToMol("CCC");
additionalOutput.atomToBits =
new std::vector<std::vector<std::uint64_t>>(mol->getNumAtoms());
fp = atomPairGenerator->getSparseCountFingerprint(*mol, nullptr, nullptr, -1,
&additionalOutput);
c1 = AtomPair::getAtomCode(mol->getAtomWithIdx(0), 0, false);
c2 = AtomPair::getAtomCode(mol->getAtomWithIdx(1), 0, false);
c3 = AtomPair::getAtomCode(mol->getAtomWithIdx(2), 0, false);
v = additionalOutput.atomToBits->at(0);
TEST_ASSERT(std::find(v.begin(), v.end(),
(AtomPair::getAtomPairCode(c1, c2, 1, false))) !=
v.end());
TEST_ASSERT(std::find(v.begin(), v.end(),
(AtomPair::getAtomPairCode(c1, c3, 2, false))) !=
v.end());
v = additionalOutput.atomToBits->at(1);
TEST_ASSERT(std::find(v.begin(), v.end(),
(AtomPair::getAtomPairCode(c1, c2, 1, false))) !=
v.end());
TEST_ASSERT(std::find(v.begin(), v.end(),
(AtomPair::getAtomPairCode(c2, c3, 1, false))) !=
v.end());
v = additionalOutput.atomToBits->at(2);
TEST_ASSERT(std::find(v.begin(), v.end(),
(AtomPair::getAtomPairCode(c1, c3, 2, false))) !=
v.end());
TEST_ASSERT(std::find(v.begin(), v.end(),
(AtomPair::getAtomPairCode(c2, c3, 1, false))) !=
v.end());
delete mol;
delete fp;
delete additionalOutput.atomToBits;
delete atomPairGenerator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
// Old version test name testHashedAtomPairs
void testFoldedAtomPairs() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Folded Atom Pairs." << std::endl;
{
FingerprintGenerator<std::uint32_t> *generator =
AtomPair::getAtomPairGenerator<std::uint32_t>(1, 30, false, true,
nullptr, true, 1024);
ROMol *mol;
mol = SmilesToMol("c1ccccc1");
SparseIntVect<std::uint32_t> *fp1;
fp1 = generator->getCountFingerprint(*mol);
SparseIntVect<std::uint32_t> *fp2;
fp2 = generator->getCountFingerprint(*mol);
TEST_ASSERT(DiceSimilarity(*fp1, *fp2) == 1.0);
TEST_ASSERT(*fp1 == *fp2);
delete mol;
delete fp2;
mol = SmilesToMol("c1ccccn1");
fp2 = generator->getCountFingerprint(*mol);
RANGE_CHECK(0.0, DiceSimilarity(*fp1, *fp2), 1.0);
delete mol;
delete fp1;
delete fp2;
delete generator;
}
{
FingerprintGenerator<std::uint32_t> *generator1 =
AtomPair::getAtomPairGenerator<std::uint32_t>();
FingerprintGenerator<std::uint32_t> *generator2 =
AtomPair::getAtomPairGenerator<std::uint32_t>(1, 2);
FingerprintGenerator<std::uint32_t> *generator3 =
AtomPair::getAtomPairGenerator<std::uint32_t>(1, 3);
ROMol *mol;
mol = SmilesToMol("c1ccccc1");
SparseIntVect<std::uint32_t> *fp1;
fp1 = generator1->getCountFingerprint(*mol);
SparseIntVect<std::uint32_t> *fp2;
fp2 = generator3->getCountFingerprint(*mol);
TEST_ASSERT(DiceSimilarity(*fp1, *fp2) == 1.0);
TEST_ASSERT(*fp1 == *fp2);
delete fp2;
fp2 = generator2->getCountFingerprint(*mol);
RANGE_CHECK(0.0, DiceSimilarity(*fp1, *fp2), 1.0);
delete mol;
delete fp1;
delete fp2;
delete generator1;
delete generator2;
delete generator3;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testRootedAtomPairs() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Rooted Atom Pairs." << std::endl;
FingerprintGenerator<std::uint32_t> *generator =
AtomPair::getAtomPairGenerator<std::uint32_t>();
ROMol *mol;
SparseIntVect<std::uint32_t> *fp1, *fp2;
std::vector<std::uint32_t> roots;
mol = SmilesToMol("OCCCCC");
fp1 = generator->getSparseCountFingerprint(*mol);
SparseIntVect<std::uint32_t>::StorageType nz1 = fp1->getNonzeroElements();
TEST_ASSERT(nz1.size() > 0);
roots.push_back(0);
fp2 = generator->getSparseCountFingerprint(*mol, &roots);
SparseIntVect<std::uint32_t>::StorageType nz2 = fp2->getNonzeroElements();
TEST_ASSERT(nz2.size() > 0);
TEST_ASSERT(nz2.size() < nz1.size());
for (SparseIntVect<std::uint32_t>::StorageType::const_iterator bIt =
nz2.begin();
bIt != nz2.end(); ++bIt) {
TEST_ASSERT(bIt->second <= fp2->getVal(bIt->first));
}
delete mol;
delete fp1;
delete fp2;
delete generator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIgnoreAtomPairs() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test ignoring atoms in Atom Pairs."
<< std::endl;
FingerprintGenerator<std::uint32_t> *generator =
AtomPair::getAtomPairGenerator<std::uint32_t>(1, 5, false, true, nullptr,
true, 4096);
{
ROMol *mol;
SparseIntVect<std::uint32_t> *fp1, *fp2;
std::vector<std::uint32_t> roots;
mol = SmilesToMol("OCCCCC");
fp1 = generator->getSparseCountFingerprint(*mol);
SparseIntVect<std::uint32_t>::StorageType nz1 = fp1->getNonzeroElements();
TEST_ASSERT(nz1.size() > 0);
roots.push_back(0);
fp2 = generator->getSparseCountFingerprint(*mol, nullptr, &roots);
SparseIntVect<std::uint32_t>::StorageType nz2 = fp2->getNonzeroElements();
TEST_ASSERT(nz2.size() == nz1.size() - 5);
for (SparseIntVect<std::uint32_t>::StorageType::const_iterator bIt =
nz2.begin();
bIt != nz2.end(); ++bIt) {
TEST_ASSERT(bIt->second <= fp2->getVal(bIt->first));
}
delete mol;
delete fp1;
delete fp2;
}
{
ROMol *mol;
SparseIntVect<std::uint32_t> *fp2;
std::vector<std::uint32_t> roots;
mol = SmilesToMol("OCCCCC");
roots.push_back(0);
fp2 = generator->getSparseCountFingerprint(*mol, &roots, &roots);
SparseIntVect<std::uint32_t>::StorageType nz2 = fp2->getNonzeroElements();
TEST_ASSERT(nz2.size() == 0);
delete mol;
delete fp2;
}
{
ROMol *mol;
SparseIntVect<std::uint32_t> *fp1, *fp2;
std::vector<std::uint32_t> roots;
mol = SmilesToMol("OCCCCC");
fp1 = generator->getCountFingerprint(*mol);
SparseIntVect<std::uint32_t>::StorageType nz1 = fp1->getNonzeroElements();
TEST_ASSERT(nz1.size() > 0);
roots.push_back(0);
fp2 = generator->getCountFingerprint(*mol, nullptr, &roots);
SparseIntVect<std::uint32_t>::StorageType nz2 = fp2->getNonzeroElements();
TEST_ASSERT(nz2.size() < nz1.size());
for (SparseIntVect<std::uint32_t>::StorageType::const_iterator bIt =
nz2.begin();
bIt != nz2.end(); ++bIt) {
TEST_ASSERT(bIt->second <= fp2->getVal(bIt->first));
}
delete mol;
delete fp1;
delete fp2;
}
delete generator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testChiralPairs() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Atom Pairs including info about chirality."
<< std::endl;
FingerprintGenerator<std::uint32_t> *generator =
AtomPair::getAtomPairGenerator<std::uint32_t>(1, 5, false, true, nullptr,
true, 4096);
FingerprintGenerator<std::uint32_t> *generatorChirality =
AtomPair::getAtomPairGenerator<std::uint32_t>(1, 5, true, true, nullptr,
true, 4096);
ROMol *m1, *m2, *m3;
m1 = SmilesToMol("CC[CH](F)Cl");
TEST_ASSERT(m1);
m2 = SmilesToMol("CC[C@H](F)Cl");
TEST_ASSERT(m1);
m3 = SmilesToMol("CC[C@@H](F)Cl");
TEST_ASSERT(m1);
{
SparseIntVect<std::uint32_t> *fp1, *fp2, *fp3;
fp1 = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp1->getTotalVal() == 10);
TEST_ASSERT(fp1->getNonzeroElements().size() == 10);
fp2 = generator->getSparseCountFingerprint(*m2);
TEST_ASSERT(fp2->getTotalVal() == 10);
TEST_ASSERT(fp2->getNonzeroElements().size() == 10);
fp3 = generator->getSparseCountFingerprint(*m3);
TEST_ASSERT(fp3->getTotalVal() == 10);
TEST_ASSERT(fp3->getNonzeroElements().size() == 10);
TEST_ASSERT((*fp1) == (*fp2));
TEST_ASSERT((*fp1) == (*fp3));
TEST_ASSERT((*fp2) == (*fp3));
delete fp1;
delete fp2;
delete fp3;
fp1 = generatorChirality->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp1->getTotalVal() == 10);
TEST_ASSERT(fp1->getNonzeroElements().size() == 10);
fp2 = generatorChirality->getSparseCountFingerprint(*m2);
TEST_ASSERT(fp2->getTotalVal() == 10);
TEST_ASSERT(fp2->getNonzeroElements().size() == 10);
fp3 = generatorChirality->getSparseCountFingerprint(*m3);
TEST_ASSERT(fp3->getTotalVal() == 10);
TEST_ASSERT(fp3->getNonzeroElements().size() == 10);
TEST_ASSERT((*fp1) != (*fp2));
TEST_ASSERT((*fp1) != (*fp3));
TEST_ASSERT((*fp2) != (*fp3));
delete fp1;
delete fp2;
delete fp3;
}
{
SparseIntVect<std::uint32_t> *fp1, *fp2, *fp3;
fp1 = generator->getCountFingerprint(*m1);
TEST_ASSERT(fp1->getTotalVal() == 10);
TEST_ASSERT(fp1->getNonzeroElements().size() == 10);
fp2 = generator->getCountFingerprint(*m2);
TEST_ASSERT(fp2->getTotalVal() == 10);
TEST_ASSERT(fp2->getNonzeroElements().size() == 10);
fp3 = generator->getCountFingerprint(*m3);
TEST_ASSERT(fp3->getTotalVal() == 10);
TEST_ASSERT(fp3->getNonzeroElements().size() == 10);
TEST_ASSERT((*fp1) == (*fp2));
TEST_ASSERT((*fp1) == (*fp3));
TEST_ASSERT((*fp2) == (*fp3));
delete fp1;
delete fp2;
delete fp3;
fp1 = generatorChirality->getCountFingerprint(*m1);
TEST_ASSERT(fp1->getTotalVal() == 10);
TEST_ASSERT(fp1->getNonzeroElements().size() == 10);
fp2 = generatorChirality->getCountFingerprint(*m2);
TEST_ASSERT(fp2->getTotalVal() == 10);
TEST_ASSERT(fp2->getNonzeroElements().size() == 10);
fp3 = generatorChirality->getCountFingerprint(*m3);
TEST_ASSERT(fp3->getTotalVal() == 10);
TEST_ASSERT(fp3->getNonzeroElements().size() == 10);
TEST_ASSERT((*fp1) != (*fp2));
TEST_ASSERT((*fp1) != (*fp3));
TEST_ASSERT((*fp2) != (*fp3));
delete fp1;
delete fp2;
delete fp3;
}
delete m1;
delete m2;
delete m3;
delete generator;
delete generatorChirality;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMorganFPOld() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test morgan fp generator" << std::endl;
ROMol *mol;
SparseIntVect<std::uint32_t> *fp, *fpOld;
int radius = 3;
FingerprintGenerator<std::uint32_t> *morganGenerator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(radius);
BOOST_FOREACH (std::string sm, smis) {
mol = SmilesToMol(sm);
fp = morganGenerator->getSparseCountFingerprint(*mol);
fpOld = MorganFingerprints::getFingerprint(*mol, radius);
TEST_ASSERT(DiceSimilarity(*fp, *fpOld) == 1.0);
TEST_ASSERT(*fp == *fpOld);
delete mol;
delete fp;
delete fpOld;
}
delete morganGenerator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMorganFP() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Morgan Fingerprints." << std::endl;
{
ROMol *mol;
SparseIntVect<std::uint32_t> *fp;
FingerprintGenerator<std::uint32_t> *morganGenerator;
mol = SmilesToMol("CCCCC");
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(0);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 2);
delete fp;
fp = morganGenerator->getCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 2);
delete fp;
delete morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(1);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 5);
delete fp;
fp = morganGenerator->getCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 5);
delete fp;
delete morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(2);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 7);
delete fp;
delete morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(3);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 7);
delete fp;
delete morganGenerator;
delete mol;
}
{
ROMol *mol;
SparseIntVect<std::uint32_t> *fp;
FingerprintGenerator<std::uint32_t> *morganGenerator;
mol = SmilesToMol("O=C(O)CC1CC1");
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(0);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 6);
delete fp;
delete morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(1);
fp = MorganFingerprints::getFingerprint(*mol, 1);
TEST_ASSERT(fp->getNonzeroElements().size() == 12);
delete fp;
delete morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(2);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 16);
delete fp;
delete morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(3);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 17);
delete fp;
delete morganGenerator;
delete mol;
}
{
// test that the results aren't order dependent, i.e. that we're
// "canonicalizing" the fps correctly
ROMol *mol, *mol2;
SparseIntVect<std::uint32_t> *fp, *fp2;
FingerprintGenerator<std::uint32_t> *morganGenerator;
mol = SmilesToMol("O=C(O)CC1CC1");
mol2 = SmilesToMol("OC(=O)CC1CC1");
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(0);
fp = morganGenerator->getSparseCountFingerprint(*mol);
fp2 = morganGenerator->getSparseCountFingerprint(*mol2);
TEST_ASSERT(fp->getNonzeroElements().size() == 6);
TEST_ASSERT(fp2->getNonzeroElements().size() == 6);
TEST_ASSERT(*fp == *fp2);
delete fp;
delete fp2;
delete morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(1);
fp = morganGenerator->getSparseCountFingerprint(*mol);
fp2 = morganGenerator->getSparseCountFingerprint(*mol2);
TEST_ASSERT(fp->getNonzeroElements().size() == 12);
TEST_ASSERT(fp2->getNonzeroElements().size() == 12);
TEST_ASSERT(*fp == *fp2);
delete fp;
delete fp2;
delete morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(2);
fp = morganGenerator->getSparseCountFingerprint(*mol);
fp2 = morganGenerator->getSparseCountFingerprint(*mol2);
TEST_ASSERT(fp->getNonzeroElements().size() == 16);
TEST_ASSERT(fp2->getNonzeroElements().size() == 16);
TEST_ASSERT(*fp == *fp2);
delete fp;
delete fp2;
delete morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(3);
fp = morganGenerator->getSparseCountFingerprint(*mol);
fp2 = morganGenerator->getSparseCountFingerprint(*mol2);
TEST_ASSERT(fp->getNonzeroElements().size() == 17);
TEST_ASSERT(fp2->getNonzeroElements().size() == 17);
TEST_ASSERT(*fp == *fp2);
delete fp;
delete fp2;
delete morganGenerator;
delete mol;
delete mol2;
}
{
// symmetry test:
ROMol *mol;
SparseIntVect<std::uint32_t> *fp;
FingerprintGenerator<std::uint32_t> *morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(2);
mol = SmilesToMol("OCCCCO");
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 7);
SparseIntVect<std::uint32_t>::StorageType::const_iterator iter;
for (iter = fp->getNonzeroElements().begin();
iter != fp->getNonzeroElements().end(); ++iter) {
TEST_ASSERT(iter->second == 2 || iter->second == 4);
}
delete fp;
delete mol;
delete morganGenerator;
}
{
// chirality test:
ROMol *mol;
SparseIntVect<std::uint32_t> *fp;
FingerprintGenerator<std::uint32_t> *morganGenerator;
mol = SmilesToMol("CC(F)(Cl)C(F)(Cl)C");
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(0);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 4);
delete fp;
delete morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(1);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 8);
delete mol;
delete fp;
delete morganGenerator;
mol = SmilesToMol("CC(F)(Cl)[C@](F)(Cl)C");
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(0);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 4);
delete fp;
delete morganGenerator;
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(1);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 8);
delete fp;
delete morganGenerator;
morganGenerator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(0, true, true);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 4);
delete fp;
delete morganGenerator;
morganGenerator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(1, true, true);
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 9);
delete fp;
delete morganGenerator;
delete mol;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMorganFPFromAtoms() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Test Morgan Fingerprints using fromAtoms argument." << std::endl;
FingerprintGenerator<std::uint32_t> *radius0Generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(0);
FingerprintGenerator<std::uint32_t> *radius1Generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(1);
FingerprintGenerator<std::uint32_t> *radius2Generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(2);
FingerprintGenerator<std::uint32_t> *radius3Generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(3);
{
ROMol *mol;
SparseIntVect<std::uint32_t> *fp;
std::vector<std::uint32_t> atoms;
atoms.push_back(0);
mol = SmilesToMol("CCCCC");
fp = radius0Generator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 2);
delete fp;
fp = radius0Generator->getSparseCountFingerprint(*mol, &atoms);
TEST_ASSERT(fp->getNonzeroElements().size() == 1);
delete fp;
fp = radius1Generator->getSparseCountFingerprint(*mol, &atoms);
TEST_ASSERT(fp->getNonzeroElements().size() == 2);
delete fp;
// tests issue 3415636
fp = radius2Generator->getSparseCountFingerprint(*mol, &atoms);
TEST_ASSERT(fp->getNonzeroElements().size() == 3);
delete fp;
delete mol;
}
{
ROMol *mol;
SparseIntVect<std::uint32_t> *fp;
std::vector<std::uint32_t> atoms;
mol = SmilesToMol("CCCCC");
fp = radius0Generator->getSparseCountFingerprint(*mol, &atoms);
TEST_ASSERT(fp->getNonzeroElements().size() == 0);
delete fp;
fp = radius1Generator->getSparseCountFingerprint(*mol, &atoms);
TEST_ASSERT(fp->getNonzeroElements().size() == 0);
delete fp;
delete mol;
}
{
ROMol *mol;
SparseIntVect<std::uint32_t> *fp;
std::vector<std::uint32_t> atoms;
atoms.push_back(0);
mol = SmilesToMol("C(CC)CO");
fp = radius0Generator->getSparseCountFingerprint(*mol, &atoms);
TEST_ASSERT(fp->getNonzeroElements().size() == 1);
delete fp;
fp = radius1Generator->getSparseCountFingerprint(*mol, &atoms);
TEST_ASSERT(fp->getNonzeroElements().size() == 2);
delete fp;
fp = radius2Generator->getSparseCountFingerprint(*mol, &atoms);
TEST_ASSERT(fp->getNonzeroElements().size() == 3);
delete fp;
// tests issue 3415636
fp = radius3Generator->getSparseCountFingerprint(*mol, &atoms);
TEST_ASSERT(fp->getNonzeroElements().size() == 3);
delete fp;
delete mol;
}
delete radius0Generator;
delete radius1Generator;
delete radius2Generator;
delete radius3Generator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMorganFPBitVect() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Morgan Fingerprints as bit vects."
<< std::endl;
{
ROMol *mol;
ExplicitBitVect *fp;
FingerprintGenerator<std::uint32_t> *radius0Generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(0, false);
FingerprintGenerator<std::uint32_t> *radius1Generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(1, false);
FingerprintGenerator<std::uint32_t> *radius2Generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(2, false);
FingerprintGenerator<std::uint32_t> *radius3Generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(3, false);
mol = SmilesToMol("CCCCC");
fp = radius0Generator->getFingerprint(*mol);
TEST_ASSERT(fp->getNumOnBits() == 2);
delete fp;
fp = radius1Generator->getFingerprint(*mol);
TEST_ASSERT(fp->getNumOnBits() == 5);
delete fp;
fp = radius2Generator->getFingerprint(*mol);
TEST_ASSERT(fp->getNumOnBits() == 7);
delete fp;
fp = radius3Generator->getFingerprint(*mol);
TEST_ASSERT(fp->getNumOnBits() == 7);
delete fp;
delete mol;
delete radius0Generator;
delete radius1Generator;
delete radius2Generator;
delete radius3Generator;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMorganFPFeatureInvs() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Test Morgan Fingerprints with feature invariants." << std::endl;
{
ROMol *mol;
mol = SmilesToMol("Cc1ccccc1");
TEST_ASSERT(mol);
MorganFingerprint::MorganFeatureAtomInvGenerator *invGen =
new MorganFingerprint::MorganFeatureAtomInvGenerator();
std::vector<std::uint32_t> *invars = invGen->getAtomInvariants(*mol);
TEST_ASSERT((*invars)[0] == 0);
TEST_ASSERT((*invars)[1] != 0);
TEST_ASSERT((*invars)[1] == (*invars)[2]);
TEST_ASSERT((*invars)[1] == (*invars)[3]);
TEST_ASSERT((*invars)[1] == (*invars)[4]);
TEST_ASSERT((*invars)[1] == (*invars)[5]);
TEST_ASSERT((*invars)[1] == (*invars)[6]);
delete mol;
delete invGen;
delete invars;
}
{
ROMol *mol;
mol = SmilesToMol("FCCCl");
TEST_ASSERT(mol);
MorganFingerprint::MorganFeatureAtomInvGenerator *invGen =
new MorganFingerprint::MorganFeatureAtomInvGenerator();
std::vector<std::uint32_t> *invars = invGen->getAtomInvariants(*mol);
TEST_ASSERT((*invars)[1] == (*invars)[2]);
TEST_ASSERT((*invars)[1] == 0);
TEST_ASSERT((*invars)[0] == (*invars)[3]);
TEST_ASSERT((*invars)[0] != 0);
delete mol;
delete invGen;
delete invars;
}
{
ROMol *mol;
mol = SmilesToMol("Cc1ncccc1O");
TEST_ASSERT(mol);
std::vector<const ROMol *> patterns(2);
RWMol *p;
p = SmartsToMol("[A]");
patterns[0] = static_cast<const ROMol *>(p);
p = SmartsToMol("[a]");
patterns[1] = static_cast<const ROMol *>(p);
MorganFingerprint::MorganFeatureAtomInvGenerator *invGen =
new MorganFingerprint::MorganFeatureAtomInvGenerator(&patterns);
std::vector<std::uint32_t> *invars = invGen->getAtomInvariants(*mol);
TEST_ASSERT((*invars)[0] != 0);
TEST_ASSERT((*invars)[1] != 0);
TEST_ASSERT((*invars)[0] != (*invars)[1]);
TEST_ASSERT((*invars)[1] == (*invars)[2]);
TEST_ASSERT((*invars)[0] == (*invars)[7]);
delete mol;
delete invGen;
delete invars;
delete patterns[0];
delete patterns[1];
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testMorganFPOptions() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test additional Morgan fingerprints options."
<< std::endl;
{
ROMol *m1, *m2;
ExplicitBitVect *fp1, *fp2;
FingerprintGenerator<std::uint32_t> *generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(2);
FingerprintGenerator<std::uint32_t> *generatorNoBoundType =
MorganFingerprint::getMorganGenerator<std::uint32_t>(2, true, false,
false);
std::vector<std::uint32_t> invars(3);
invars[0] = 1;
invars[1] = 1;
invars[2] = 1;
m1 = SmilesToMol("CCC");
TEST_ASSERT(m1);
m2 = SmilesToMol("CC=C");
TEST_ASSERT(m2);
fp1 =
generator->getFingerprint(*m1, nullptr, nullptr, -1, nullptr, &invars);
invars[0] = 1;
invars[1] = 1;
invars[2] = 1;
fp2 =
generator->getFingerprint(*m2, nullptr, nullptr, -1, nullptr, &invars);
TEST_ASSERT((*fp1) != (*fp2));
delete fp1;
delete fp2;
invars[0] = 1;
invars[1] = 1;
invars[2] = 1;
fp1 = generatorNoBoundType->getFingerprint(*m1, nullptr, nullptr, -1,
nullptr, &invars);
invars[0] = 1;
invars[1] = 1;
invars[2] = 1;
fp2 = generatorNoBoundType->getFingerprint(*m2, nullptr, nullptr, -1,
nullptr, &invars);
TEST_ASSERT((*fp1) == (*fp2));
delete fp1;
delete fp2;
delete m1;
delete m2;
delete generator;
delete generatorNoBoundType;
}
{
ROMol *m1, *m2, *m3;
ExplicitBitVect *fp1, *fp2, *fp3;
FingerprintGenerator<std::uint32_t> *generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(2);
FingerprintGenerator<std::uint32_t> *generatorChirality =
MorganFingerprint::getMorganGenerator<std::uint32_t>(2, true, true);
m1 = SmilesToMol("C[C@H](F)Cl");
TEST_ASSERT(m1);
m2 = SmilesToMol("C[C@@H](F)Cl");
TEST_ASSERT(m2);
m3 = SmilesToMol("CC(F)Cl");
TEST_ASSERT(m3);
fp1 = generator->getFingerprint(*m1);
fp2 = generator->getFingerprint(*m2);
fp3 = generator->getFingerprint(*m3);
TEST_ASSERT((*fp1) == (*fp2));
TEST_ASSERT((*fp1) == (*fp3));
TEST_ASSERT((*fp2) == (*fp3));
delete fp1;
delete fp2;
delete fp3;
fp1 = generatorChirality->getFingerprint(*m1);
fp2 = generatorChirality->getFingerprint(*m2);
fp3 = generatorChirality->getFingerprint(*m3);
TEST_ASSERT((*fp1) != (*fp2));
TEST_ASSERT((*fp1) != (*fp3));
TEST_ASSERT((*fp2) != (*fp3));
delete fp1;
delete fp2;
delete fp3;
delete m1;
delete m2;
delete m3;
delete generator;
delete generatorChirality;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGitHubIssue695() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test GitHub Issue 695: Include cis/trans "
"stereochemistry when useChirality=true with the "
"morgan fingerprints"
<< std::endl;
FingerprintGenerator<std::uint32_t> *generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(1);
FingerprintGenerator<std::uint32_t> *generatorChirality =
MorganFingerprint::getMorganGenerator<std::uint32_t>(1, true, true);
{
ROMol *m1 = SmilesToMol("CC=CC");
TEST_ASSERT(m1);
SparseIntVect<std::uint32_t> *fp;
SparseIntVect<std::uint32_t>::StorageType::const_iterator iter;
fp = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNonzeroElements().size() == 4);
iter = fp->getNonzeroElements().find(736731344);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246703798);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246728737);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(3545353036);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
delete fp;
fp = generatorChirality->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNonzeroElements().size() == 4);
iter = fp->getNonzeroElements().find(736731344);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246703798);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246728737);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(3545353036);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
delete fp;
delete m1;
}
{
ROMol *m1 = SmilesToMol("C/C=C/C");
TEST_ASSERT(m1);
SparseIntVect<std::uint32_t> *fp;
SparseIntVect<std::uint32_t>::StorageType::const_iterator iter;
fp = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNonzeroElements().size() == 4);
iter = fp->getNonzeroElements().find(736731344);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246703798);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246728737);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(3545353036);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
delete fp;
fp = generatorChirality->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNonzeroElements().size() == 4);
iter = fp->getNonzeroElements().find(736735794);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246703798);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246728737);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(3545353036);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
delete fp;
delete m1;
}
{
ROMol *m1 = SmilesToMol("C/C=C\\C");
TEST_ASSERT(m1);
SparseIntVect<std::uint32_t> *fp;
SparseIntVect<std::uint32_t>::StorageType::const_iterator iter;
fp = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNonzeroElements().size() == 4);
iter = fp->getNonzeroElements().find(736731344);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246703798);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246728737);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(3545353036);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
delete fp;
fp = generatorChirality->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp);
TEST_ASSERT(fp->getNonzeroElements().size() == 4);
iter = fp->getNonzeroElements().find(736735858);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246703798);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(2246728737);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
iter = fp->getNonzeroElements().find(3545353036);
TEST_ASSERT(iter != fp->getNonzeroElements().end() && iter->second == 2);
delete fp;
delete m1;
}
delete generator;
delete generatorChirality;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGitHubIssue874() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Single atoms setting radius 1 bits in Morgan fingerprints "
<< std::endl;
{
std::string smiles = "Cl";
ROMol *m1 = SmilesToMol(smiles);
TEST_ASSERT(m1);
TEST_ASSERT(m1->getNumAtoms() == 1);
FingerprintGenerator<std::uint32_t> *radius0Generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(0);
FingerprintGenerator<std::uint32_t> *radius1Generator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(1);
SparseIntVect<std::uint32_t> *fp;
fp = radius0Generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp->getNonzeroElements().size() == 1);
delete fp;
fp = radius1Generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp->getNonzeroElements().size() == 1);
delete fp;
delete m1;
delete radius0Generator;
delete radius1Generator;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testInvariantGenerators() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test different invariant generator combinations"
<< std::endl;
ROMol *mol;
SparseIntVect<std::uint32_t> *fp;
int radius = 3;
AtomInvariantsGenerator *atomInvariantsGenerator =
new MorganFingerprint::MorganAtomInvGenerator();
BondInvariantsGenerator *bondInvariantsGenerator =
new MorganFingerprint::MorganBondInvGenerator();
FingerprintGenerator<std::uint32_t> *morganGenerator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(
radius, true, false, true, false, atomInvariantsGenerator,
bondInvariantsGenerator);
mol = SmilesToMol("CCCCC");
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 7);
delete mol;
delete fp;
delete morganGenerator;
delete atomInvariantsGenerator;
delete bondInvariantsGenerator;
atomInvariantsGenerator = new MorganFingerprint::MorganAtomInvGenerator();
bondInvariantsGenerator = new MorganFingerprint::MorganBondInvGenerator();
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(
radius, true, false, true, false, atomInvariantsGenerator,
bondInvariantsGenerator);
mol = SmilesToMol("CCCCC");
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 7);
delete mol;
delete fp;
delete morganGenerator;
delete atomInvariantsGenerator;
delete bondInvariantsGenerator;
atomInvariantsGenerator =
new MorganFingerprint::MorganFeatureAtomInvGenerator();
bondInvariantsGenerator = new MorganFingerprint::MorganBondInvGenerator();
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(
radius, true, false, true, false, atomInvariantsGenerator,
bondInvariantsGenerator);
mol = SmilesToMol("CCCCC");
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 5);
delete mol;
delete fp;
delete morganGenerator;
delete atomInvariantsGenerator;
delete bondInvariantsGenerator;
atomInvariantsGenerator = new AtomPair::AtomPairAtomInvGenerator();
bondInvariantsGenerator = new MorganFingerprint::MorganBondInvGenerator();
morganGenerator = MorganFingerprint::getMorganGenerator<std::uint32_t>(
radius, true, false, true, false, atomInvariantsGenerator,
bondInvariantsGenerator);
mol = SmilesToMol("CCCCC");
fp = morganGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 7);
delete mol;
delete fp;
delete morganGenerator;
delete atomInvariantsGenerator;
delete bondInvariantsGenerator;
atomInvariantsGenerator = new MorganFingerprint::MorganAtomInvGenerator();
bondInvariantsGenerator = nullptr;
FingerprintGenerator<std::uint32_t> *atomPairGenerator =
AtomPair::getAtomPairGenerator<std::uint32_t>(1, radius, false, true,
atomInvariantsGenerator,
bondInvariantsGenerator);
mol = SmilesToMol("CCC");
fp = atomPairGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 2);
delete mol;
delete fp;
delete atomPairGenerator;
delete atomInvariantsGenerator;
delete bondInvariantsGenerator;
atomInvariantsGenerator =
new MorganFingerprint::MorganFeatureAtomInvGenerator();
bondInvariantsGenerator = nullptr;
atomPairGenerator = AtomPair::getAtomPairGenerator<std::uint32_t>(
1, radius, false, true, atomInvariantsGenerator, bondInvariantsGenerator);
mol = SmilesToMol("CCC");
fp = atomPairGenerator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getNonzeroElements().size() == 2);
delete mol;
delete fp;
delete atomPairGenerator;
delete atomInvariantsGenerator;
delete bondInvariantsGenerator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testCustomInvariants() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test invariant overriding" << std::endl;
ROMol *mol;
SparseIntVect<std::uint32_t> *fp1, *fp2;
int radius = 3;
AtomInvariantsGenerator *atomInvariantsGenerator =
new AtomPair::AtomPairAtomInvGenerator();
FingerprintGenerator<std::uint32_t> *morganGenerator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(
radius, true, false, true, false, atomInvariantsGenerator);
FingerprintGenerator<std::uint32_t> *defaultMorganGenerator =
MorganFingerprint::getMorganGenerator<std::uint32_t>(radius);
mol = SmilesToMol("CCCCC");
std::vector<std::uint32_t> *customInvariants =
atomInvariantsGenerator->getAtomInvariants(*mol);
fp1 = morganGenerator->getSparseCountFingerprint(*mol);
fp2 = defaultMorganGenerator->getSparseCountFingerprint(
*mol, nullptr, nullptr, -1, nullptr, customInvariants);
TEST_ASSERT(DiceSimilarity(*fp1, *fp2) == 1.0);
TEST_ASSERT(*fp1 == *fp2);
delete mol;
delete fp1;
delete fp2;
delete morganGenerator;
delete defaultMorganGenerator;
delete atomInvariantsGenerator;
delete customInvariants;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testRDKitFP() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test RDKit fp generator" << std::endl;
ROMol *mol;
SparseIntVect<std::uint64_t> *fp, *fpTemp, *fpOld;
// I won't lie: having to do this makes my head hurt, but fixing it to create
// a ctor that takes a Parameters object is more effort than I can devote at
// the moment
unsigned int minPath = 1;
unsigned int maxPath = 7;
bool useHs = true;
bool branchedPaths = true;
bool useBondOrder = true;
AtomInvariantsGenerator *atomInvariantsGenerator = nullptr;
bool countSimulation = false;
const std::vector<std::uint32_t> countBounds = {1, 2, 4, 8};
std::uint32_t fpSize = 2048;
std::uint32_t numBitsPerFeature = 1;
std::unique_ptr<FingerprintGenerator<std::uint64_t>> fpGenerator(
RDKitFP::getRDKitFPGenerator<std::uint64_t>(
minPath, maxPath, useHs, branchedPaths, useBondOrder,
atomInvariantsGenerator, countSimulation, countBounds, fpSize,
numBitsPerFeature));
BOOST_FOREACH (std::string sm, smis) {
mol = SmilesToMol(sm);
fp = fpGenerator->getSparseCountFingerprint(*mol);
fpTemp = getUnfoldedRDKFingerprintMol(*mol);
// Old and new versions produce different length results, but data should be
// the same
std::map<std::uint64_t, int> nz = fpTemp->getNonzeroElements();
fpOld = new SparseIntVect<std::uint64_t>(fp->getLength());
for (auto it = nz.begin(); it != nz.end(); it++) {
fpOld->setVal(it->first, it->second);
}
TEST_ASSERT(DiceSimilarity(*fp, *fpOld) == 1.0);
TEST_ASSERT(*fp == *fpOld);
delete mol;
delete fp;
delete fpOld;
delete fpTemp;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testRDKFPUnfolded() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test unfolded version of RDKFP " << std::endl;
{
FingerprintGenerator<std::uint64_t> *generator =
RDKitFP::getRDKitFPGenerator<std::uint64_t>();
ROMol *m1 = SmilesToMol("c1ccccc1N");
TEST_ASSERT(m1);
SparseIntVect<std::uint64_t> *fp1;
SparseIntVect<std::uint64_t>::StorageType::const_iterator iter;
fp1 = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp1);
TEST_ASSERT(fp1->getNonzeroElements().size() == 38);
iter = fp1->getNonzeroElements().find(374073638);
TEST_ASSERT(iter != fp1->getNonzeroElements().end() && iter->second == 6);
iter = fp1->getNonzeroElements().find(464351883);
TEST_ASSERT(iter != fp1->getNonzeroElements().end() && iter->second == 2);
iter = fp1->getNonzeroElements().find(1949583554);
TEST_ASSERT(iter != fp1->getNonzeroElements().end() && iter->second == 6);
iter = fp1->getNonzeroElements().find(4105342207);
TEST_ASSERT(iter != fp1->getNonzeroElements().end() && iter->second == 1);
iter = fp1->getNonzeroElements().find(794080973);
TEST_ASSERT(iter != fp1->getNonzeroElements().end() && iter->second == 1);
iter = fp1->getNonzeroElements().find(3826517238);
TEST_ASSERT(iter != fp1->getNonzeroElements().end() && iter->second == 2);
delete m1;
delete fp1;
delete generator;
}
{
FingerprintGenerator<std::uint64_t> *generator =
RDKitFP::getRDKitFPGenerator<std::uint64_t>();
ROMol *m1 = SmilesToMol("Cl");
TEST_ASSERT(m1);
SparseIntVect<std::uint64_t> *fp1;
SparseIntVect<std::uint64_t>::StorageType::const_iterator iter;
fp1 = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp1);
TEST_ASSERT(fp1->getNonzeroElements().size() == 0);
delete m1;
delete fp1;
delete generator;
}
// additional outputs are not fully functional yet
/*{
FingerprintGenerator<std::uint64_t> *generator =
RDKitFP::getRDKitFPGenerator<std::uint64_t>();
ROMol *m1 = SmilesToMol("CCCO");
TEST_ASSERT(m1);
SparseIntVect<std::uint64_t> *fp1;
SparseIntVect<std::uint64_t>::StorageType::const_iterator iter;
std::map<std::uint64_t, std::vector<std::vector<int>>> bitInfo;
std::map<std::uint64_t, std::vector<std::vector<int>>>::const_iterator
iter2;
fp1 = getUnfoldedRDKFingerprintMol(*m1, 1, 7, true, true, true, nullptr,
nullptr, nullptr, &bitInfo);
TEST_ASSERT(fp1);
TEST_ASSERT(fp1->getNonzeroElements().size() == 5);
iter = fp1->getNonzeroElements().find(1524090560);
TEST_ASSERT(iter != fp1->getNonzeroElements().end() && iter->second == 1);
iter = fp1->getNonzeroElements().find(1940446997);
TEST_ASSERT(iter != fp1->getNonzeroElements().end() && iter->second == 1);
iter = fp1->getNonzeroElements().find(3977409745);
TEST_ASSERT(iter != fp1->getNonzeroElements().end() && iter->second == 1);
iter = fp1->getNonzeroElements().find(4274652475);
TEST_ASSERT(iter != fp1->getNonzeroElements().end() && iter->second == 1);
iter = fp1->getNonzeroElements().find(4275705116);
TEST_ASSERT(iter != fp1->getNonzeroElements().end() && iter->second == 2);
iter2 = bitInfo.find(4275705116);
TEST_ASSERT(iter2 != bitInfo.end() && iter2->second[0][0] == 0);
TEST_ASSERT(iter2 != bitInfo.end() && iter2->second.size() == 2 &&
iter2->second[1][0] == 1);
iter2 = bitInfo.find(4274652475);
TEST_ASSERT(iter2 != bitInfo.end() && iter2->second[0][0] == 2);
iter2 = bitInfo.find(3977409745);
TEST_ASSERT(iter2 != bitInfo.end() && iter2->second[0].size() == 3 &&
iter2->second[0][0] == 0);
TEST_ASSERT(iter2 != bitInfo.end() && iter2->second[0].size() == 3 &&
iter2->second[0][1] == 1);
TEST_ASSERT(iter2 != bitInfo.end() && iter2->second[0].size() == 3 &&
iter2->second[0][2] == 2);
iter2 = bitInfo.find(1524090560);
TEST_ASSERT(iter2 != bitInfo.end() && iter2->second[0].size() == 2 &&
iter2->second[0][0] == 1);
TEST_ASSERT(iter2 != bitInfo.end() && iter2->second[0].size() == 2 &&
iter2->second[0][1] == 2);
delete m1;
}*/
}
void testTopologicalTorsionFPOld() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test topological torsion fp generator" << std::endl;
ROMol *mol;
SparseIntVect<std::int64_t> *fpSigned;
SparseIntVect<std::uint64_t> *fp, *fpOld;
FingerprintGenerator<std::uint64_t> *fpGenerator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
BOOST_FOREACH (std::string sm, smis) {
mol = SmilesToMol(sm);
fp = fpGenerator->getSparseCountFingerprint(*mol);
fpSigned = AtomPairs::getTopologicalTorsionFingerprint(*mol);
fpOld = new SparseIntVect<std::uint64_t>(fp->getLength());
std::map<std::int64_t, int> nz = fpSigned->getNonzeroElements();
for (std::map<std::int64_t, int>::iterator it = nz.begin(); it != nz.end();
it++) {
fpOld->setVal(static_cast<std::uint64_t>(it->first), it->second);
}
TEST_ASSERT(DiceSimilarity(*fp, *fpOld) == 1.0);
TEST_ASSERT(*fp == *fpOld);
delete mol;
delete fp;
delete fpOld;
delete fpSigned;
}
delete fpGenerator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testTorsions() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Topological Torsions." << std::endl;
ROMol *mol;
SparseIntVect<std::uint64_t> *fp;
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
mol = SmilesToMol("CCCC");
fp = generator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal() == 1);
TEST_ASSERT(fp->getNonzeroElements().size() == 1);
delete mol;
delete fp;
mol = SmilesToMol("CCCCO.Cl");
fp = generator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal() == 2);
TEST_ASSERT(fp->getNonzeroElements().size() == 2);
delete fp;
delete generator;
generator = TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>(
false, 3);
fp = generator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal() == 3);
TEST_ASSERT(fp->getNonzeroElements().size() == 3);
delete mol;
delete fp;
delete generator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
// previous version test name: testHashedTorsions
void testFoldedTorsions() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Folded torsions." << std::endl;
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
ROMol *mol;
mol = SmilesToMol("c1ccccc1");
SparseIntVect<std::uint32_t> *fp1;
fp1 = generator->getCountFingerprint(*mol);
SparseIntVect<std::uint32_t> *fp2;
fp2 = generator->getCountFingerprint(*mol);
TEST_ASSERT(DiceSimilarity(*fp1, *fp2) == 1.0);
TEST_ASSERT(*fp1 == *fp2);
delete mol;
delete fp2;
mol = SmilesToMol("c1ccccn1");
fp2 = generator->getCountFingerprint(*mol);
RANGE_CHECK(0.0, DiceSimilarity(*fp1, *fp2), 1.0);
delete mol;
delete fp1;
delete fp2;
delete generator;
}
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>(false,
6);
ROMol *mol;
mol = SmilesToMol("c1ccccc1");
SparseIntVect<std::uint32_t> *fp1;
fp1 = generator->getCountFingerprint(*mol);
SparseIntVect<std::uint32_t> *fp2;
fp2 = generator->getCountFingerprint(*mol);
TEST_ASSERT(DiceSimilarity(*fp1, *fp2) == 1.0);
TEST_ASSERT(*fp1 == *fp2);
delete mol;
delete fp2;
mol = SmilesToMol("c1ccccn1");
fp2 = generator->getCountFingerprint(*mol);
RANGE_CHECK(0.0, DiceSimilarity(*fp1, *fp2), 1.0);
delete mol;
delete fp1;
delete fp2;
delete generator;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testBulkTorsions() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Bulk Topological Torsions." << std::endl;
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
std::string fName = getenv("RDBASE");
fName += "/Projects/DbCLI/testData/pubchem.200.sdf";
SDMolSupplier suppl(fName);
while (!suppl.atEnd()) {
ROMol *mol = suppl.next();
SparseIntVect<std::uint64_t> *fp;
fp = generator->getSparseCountFingerprint(*mol);
TEST_ASSERT(fp->getTotalVal() > 1);
delete mol;
delete fp;
}
delete generator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testRootedTorsions() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test Rooted Topological Torsions." << std::endl;
ROMol *mol;
SparseIntVect<std::uint64_t> *fp1, *fp2;
std::vector<std::uint32_t> roots;
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
mol = SmilesToMol("OCCCC");
roots.push_back(0);
fp1 = generator->getSparseCountFingerprint(*mol);
SparseIntVect<std::uint64_t>::StorageType nz1 = fp1->getNonzeroElements();
TEST_ASSERT(nz1.size() > 0);
fp2 = generator->getSparseCountFingerprint(*mol, &roots);
SparseIntVect<std::uint64_t>::StorageType nz2 = fp2->getNonzeroElements();
TEST_ASSERT(nz2.size() > 0);
TEST_ASSERT(nz2.size() < nz1.size());
for (SparseIntVect<std::uint64_t>::StorageType::const_iterator bIt =
nz2.begin();
bIt != nz2.end(); ++bIt) {
TEST_ASSERT(bIt->second <= fp2->getVal(bIt->first));
}
delete mol;
delete fp1;
delete fp2;
delete generator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIgnoreTorsions() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test ignoring atoms in Topological Torsions."
<< std::endl;
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
{
ROMol *mol;
SparseIntVect<std::uint64_t> *fp1, *fp2;
std::vector<std::uint32_t> roots;
mol = SmilesToMol("OCCCC");
roots.push_back(0);
fp1 = generator->getSparseCountFingerprint(*mol);
SparseIntVect<std::uint64_t>::StorageType nz1 = fp1->getNonzeroElements();
TEST_ASSERT(nz1.size() == 2);
fp2 = generator->getSparseCountFingerprint(*mol, &roots);
SparseIntVect<std::uint64_t>::StorageType nz2 = fp2->getNonzeroElements();
TEST_ASSERT(nz2.size() == 1);
for (SparseIntVect<std::uint64_t>::StorageType::const_iterator bIt =
nz2.begin();
bIt != nz2.end(); ++bIt) {
TEST_ASSERT(bIt->second <= fp2->getVal(bIt->first));
}
delete mol;
delete fp1;
delete fp2;
}
{
ROMol *mol;
SparseIntVect<std::uint64_t> *fp2;
std::vector<std::uint32_t> roots;
mol = SmilesToMol("OCCCC");
roots.push_back(1);
fp2 = generator->getSparseCountFingerprint(*mol, nullptr, &roots);
SparseIntVect<std::uint64_t>::StorageType nz2 = fp2->getNonzeroElements();
TEST_ASSERT(nz2.size() == 0);
delete mol;
delete fp2;
}
{
ROMol *mol;
SparseIntVect<std::uint64_t> *fp2;
std::vector<std::uint32_t> roots;
mol = SmilesToMol("OCCCC");
roots.push_back(0);
fp2 = generator->getSparseCountFingerprint(*mol, &roots, &roots);
SparseIntVect<std::uint64_t>::StorageType nz2 = fp2->getNonzeroElements();
TEST_ASSERT(nz2.size() == 0);
delete mol;
delete fp2;
}
delete generator;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testPairsAndTorsionsOptions() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdInfoLog) << "testing atom pair and torsions options" << std::endl;
{
FingerprintGenerator<std::uint32_t> *generator =
AtomPair::getAtomPairGenerator<std::uint32_t>();
std::string smi = "C1=CC=CC=C1";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
smi = "C1=CC=CC=N1";
RWMol *m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
SparseIntVect<std::uint32_t> *fp1 =
generator->getSparseCountFingerprint(*m1);
SparseIntVect<std::uint32_t> *fp2 =
generator->getSparseCountFingerprint(*m2);
TEST_ASSERT(*fp1 != *fp2);
delete fp1;
delete fp2;
UINT_VECT invars(6, 1);
fp1 = generator->getSparseCountFingerprint(*m1, nullptr, nullptr, -1,
nullptr, &invars);
fp2 = generator->getSparseCountFingerprint(*m2, nullptr, nullptr, -1,
nullptr, &invars);
TEST_ASSERT(*fp1 == *fp2);
delete m1;
delete m2;
delete fp1;
delete fp2;
delete generator;
}
{
FingerprintGenerator<std::uint32_t> *generator =
AtomPair::getAtomPairGenerator<std::uint32_t>(1, 5, false, true,
nullptr, true, 1024);
std::string smi = "C1=CC=CC=C1";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
smi = "C1=CC=CC=N1";
RWMol *m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
SparseIntVect<std::uint32_t> *fp1, *fp2;
fp1 = generator->getCountFingerprint(*m1);
fp2 = generator->getCountFingerprint(*m2);
TEST_ASSERT(*fp1 != *fp2);
delete fp1;
delete fp2;
UINT_VECT invars(6, 1);
fp1 = generator->getCountFingerprint(*m1, nullptr, nullptr, -1, nullptr,
&invars);
fp2 = generator->getCountFingerprint(*m2, nullptr, nullptr, -1, nullptr,
&invars);
TEST_ASSERT(*fp1 == *fp2);
delete m1;
delete m2;
delete fp1;
delete fp2;
delete generator;
}
{
FingerprintGenerator<std::uint32_t> *generator =
AtomPair::getAtomPairGenerator<std::uint32_t>(1, 5, false, true,
nullptr, true, 1024);
std::string smi = "C1=CC=CC=C1";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
smi = "C1=CC=CC=N1";
RWMol *m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
ExplicitBitVect *fp1, *fp2;
fp1 = generator->getFingerprint(*m1);
fp2 = generator->getFingerprint(*m2);
TEST_ASSERT(*fp1 != *fp2);
delete fp1;
delete fp2;
UINT_VECT invars(6, 1);
fp1 =
generator->getFingerprint(*m1, nullptr, nullptr, -1, nullptr, &invars);
fp2 =
generator->getFingerprint(*m2, nullptr, nullptr, -1, nullptr, &invars);
TEST_ASSERT(*fp1 == *fp2);
delete m1;
delete m2;
delete fp1;
delete fp2;
delete generator;
}
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
std::string smi = "C1=CC=CC=C1";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
smi = "C1=CC=CC=N1";
RWMol *m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
SparseIntVect<std::uint64_t> *fp1, *fp2;
fp1 = generator->getSparseCountFingerprint(*m1);
fp2 = generator->getSparseCountFingerprint(*m2);
TEST_ASSERT(*fp1 != *fp2);
delete fp1;
delete fp2;
UINT_VECT invars(6, 1);
fp1 = generator->getSparseCountFingerprint(*m1, nullptr, nullptr, -1,
nullptr, &invars);
fp2 = generator->getSparseCountFingerprint(*m2, nullptr, nullptr, -1,
nullptr, &invars);
TEST_ASSERT(*fp1 == *fp2);
delete m1;
delete m2;
delete fp1;
delete fp2;
delete generator;
}
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
std::string smi = "C1=CC=CC=C1";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
smi = "C1=CC=CC=N1";
RWMol *m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
SparseIntVect<std::uint32_t> *fp1, *fp2;
fp1 = generator->getCountFingerprint(*m1);
fp2 = generator->getCountFingerprint(*m2);
TEST_ASSERT(*fp1 != *fp2);
delete fp1;
delete fp2;
UINT_VECT invars(6, 1);
fp1 = generator->getCountFingerprint(*m1, nullptr, nullptr, -1, nullptr,
&invars);
fp2 = generator->getCountFingerprint(*m2, nullptr, nullptr, -1, nullptr,
&invars);
TEST_ASSERT(*fp1 == *fp2);
delete m1;
delete m2;
delete fp1;
delete fp2;
delete generator;
}
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
std::string smi = "C1=CC=CC=C1";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
smi = "C1=CC=CC=N1";
RWMol *m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
ExplicitBitVect *fp1, *fp2;
fp1 = generator->getFingerprint(*m1);
fp2 = generator->getFingerprint(*m2);
TEST_ASSERT(*fp1 != *fp2);
delete fp1;
delete fp2;
UINT_VECT invars(6, 1);
fp1 =
generator->getFingerprint(*m1, nullptr, nullptr, -1, nullptr, &invars);
fp2 =
generator->getFingerprint(*m2, nullptr, nullptr, -1, nullptr, &invars);
TEST_ASSERT(*fp1 == *fp2);
delete m1;
delete m2;
delete fp1;
delete fp2;
delete generator;
}
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>(
false, 4, nullptr, true, {1, 2, 4, 8}, 1024);
std::string smi = "C1=CC=CC=C1";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
smi = "C1=CC=CC=N1";
RWMol *m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
SparseIntVect<std::uint32_t> *fp1 = generator->getCountFingerprint(*m1);
SparseIntVect<std::uint32_t> *fp2 = generator->getCountFingerprint(*m2);
TEST_ASSERT(*fp1 != *fp2);
delete fp1;
delete fp2;
UINT_VECT invars(6, 1);
fp1 = generator->getCountFingerprint(*m1, nullptr, nullptr, -1, nullptr,
&invars);
fp2 = generator->getCountFingerprint(*m2, nullptr, nullptr, -1, nullptr,
&invars);
TEST_ASSERT(*fp1 == *fp2);
delete m1;
delete m2;
delete fp1;
delete fp2;
delete generator;
}
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>(
false, 4, nullptr, true, {1, 2, 4, 8}, 1024);
std::string smi = "C1=CC=CC=C1";
RWMol *m1 = SmilesToMol(smi);
TEST_ASSERT(m1);
smi = "C1=CC=CC=N1";
RWMol *m2 = SmilesToMol(smi);
TEST_ASSERT(m2);
ExplicitBitVect *fp1 = generator->getFingerprint(*m1);
ExplicitBitVect *fp2 = generator->getFingerprint(*m2);
TEST_ASSERT(*fp1 != *fp2);
delete fp1;
delete fp2;
UINT_VECT invars(6, 1);
fp1 =
generator->getFingerprint(*m1, nullptr, nullptr, -1, nullptr, &invars);
fp2 =
generator->getFingerprint(*m2, nullptr, nullptr, -1, nullptr, &invars);
TEST_ASSERT(*fp1 == *fp2);
delete m1;
delete m2;
delete fp1;
delete fp2;
delete generator;
}
BOOST_LOG(rdInfoLog) << "done" << std::endl;
}
void testChiralTorsions() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Test Topological Torsions including info about chirality."
<< std::endl;
// Folded size 4096 is causing a collision for this test hence the unusual
// 4000 size
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>(
false, 4, nullptr, true, {1, 2, 4, 8}, 4096);
FingerprintGenerator<std::uint64_t> *generatorChirality =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>(
true, 4, nullptr, true, {1, 2, 4, 8}, 4096);
ROMol *m1, *m2, *m3;
m1 = SmilesToMol("CC[CH](F)Cl");
TEST_ASSERT(m1);
m2 = SmilesToMol("CC[C@H](F)Cl");
TEST_ASSERT(m1);
m3 = SmilesToMol("CC[C@@H](F)Cl");
TEST_ASSERT(m1);
{
SparseIntVect<std::uint64_t> *fp1, *fp2, *fp3;
fp1 = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp1->getTotalVal() == 2);
TEST_ASSERT(fp1->getNonzeroElements().size() == 2);
fp2 = generator->getSparseCountFingerprint(*m2);
TEST_ASSERT(fp2->getTotalVal() == 2);
TEST_ASSERT(fp2->getNonzeroElements().size() == 2);
fp3 = generator->getSparseCountFingerprint(*m3);
TEST_ASSERT(fp3->getTotalVal() == 2);
TEST_ASSERT(fp3->getNonzeroElements().size() == 2);
TEST_ASSERT((*fp1) == (*fp2));
TEST_ASSERT((*fp1) == (*fp3));
TEST_ASSERT((*fp2) == (*fp3));
delete fp1;
delete fp2;
delete fp3;
fp1 = generatorChirality->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp1->getTotalVal() == 2);
TEST_ASSERT(fp1->getNonzeroElements().size() == 2);
fp2 = generatorChirality->getSparseCountFingerprint(*m2);
TEST_ASSERT(fp2->getTotalVal() == 2);
TEST_ASSERT(fp2->getNonzeroElements().size() == 2);
fp3 = generatorChirality->getSparseCountFingerprint(*m3);
TEST_ASSERT(fp3->getTotalVal() == 2);
TEST_ASSERT(fp3->getNonzeroElements().size() == 2);
TEST_ASSERT((*fp1) != (*fp2));
TEST_ASSERT((*fp1) != (*fp3));
TEST_ASSERT((*fp2) != (*fp3));
delete fp1;
delete fp2;
delete fp3;
}
{
SparseIntVect<std::uint32_t> *fp1, *fp2, *fp3;
fp1 = generator->getCountFingerprint(*m1);
TEST_ASSERT(fp1->getTotalVal() == 2);
TEST_ASSERT(fp1->getNonzeroElements().size() == 2);
fp2 = generator->getCountFingerprint(*m2);
TEST_ASSERT(fp2->getTotalVal() == 2);
TEST_ASSERT(fp2->getNonzeroElements().size() == 2);
fp3 = generator->getCountFingerprint(*m3);
TEST_ASSERT(fp3->getTotalVal() == 2);
TEST_ASSERT(fp3->getNonzeroElements().size() == 2);
TEST_ASSERT((*fp1) == (*fp2));
TEST_ASSERT((*fp1) == (*fp3));
TEST_ASSERT((*fp2) == (*fp3));
delete fp1;
delete fp2;
delete fp3;
fp1 = generatorChirality->getCountFingerprint(*m1);
TEST_ASSERT(fp1->getTotalVal() == 2);
TEST_ASSERT(fp1->getNonzeroElements().size() == 2);
fp2 = generatorChirality->getCountFingerprint(*m2);
TEST_ASSERT(fp2->getTotalVal() == 2);
TEST_ASSERT(fp2->getNonzeroElements().size() == 2);
fp3 = generatorChirality->getCountFingerprint(*m3);
TEST_ASSERT(fp3->getTotalVal() == 2);
TEST_ASSERT(fp3->getNonzeroElements().size() == 2);
TEST_ASSERT((*fp1) != (*fp2));
TEST_ASSERT((*fp1) != (*fp3));
TEST_ASSERT((*fp2) != (*fp3));
delete fp1;
delete fp2;
delete fp3;
}
delete m1;
delete m2;
delete m3;
delete generator;
delete generatorChirality;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGitHubIssue25() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Test GitHub Issue 25: fingerprint backwards compatibility."
<< std::endl;
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
ROMol *m1 = SmilesToMol("CCCCO");
TEST_ASSERT(m1);
SparseIntVect<std::uint64_t> *fp1;
fp1 = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp1);
TEST_ASSERT(fp1->getTotalVal() == 2);
TEST_ASSERT(fp1->getNonzeroElements().size() == 2);
TEST_ASSERT((*fp1)[4437590048LL] == 1);
TEST_ASSERT((*fp1)[12893306913LL] == 1);
delete fp1;
delete m1;
delete generator;
}
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>(
false, 4, nullptr, true, {1, 2, 4, 8}, 1000);
ROMol *m1 = SmilesToMol("CCCCO");
TEST_ASSERT(m1);
SparseIntVect<std::uint32_t> *fp1;
fp1 = generator->getCountFingerprint(*m1);
TEST_ASSERT(fp1);
TEST_ASSERT(fp1->getTotalVal() == 2);
TEST_ASSERT(fp1->getNonzeroElements().size() == 2);
TEST_ASSERT((*fp1)[24] == 1);
TEST_ASSERT((*fp1)[288] == 1);
delete fp1;
delete m1;
delete generator;
}
{
FingerprintGenerator<std::uint32_t> *generator =
AtomPair::getAtomPairGenerator<std::uint32_t>();
ROMol *m1 = SmilesToMol("CCO");
TEST_ASSERT(m1);
SparseIntVect<std::uint32_t> *fp1;
fp1 = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp1);
TEST_ASSERT(fp1->getTotalVal() == 3);
TEST_ASSERT(fp1->getNonzeroElements().size() == 3);
TEST_ASSERT((*fp1)[558113] == 1);
TEST_ASSERT((*fp1)[1590306] == 1);
TEST_ASSERT((*fp1)[1590337] == 1);
delete fp1;
delete m1;
delete generator;
}
{
FingerprintGenerator<std::uint32_t> *generator =
AtomPair::getAtomPairGenerator<std::uint32_t>();
ROMol *m1 = SmilesToMol("CCO");
TEST_ASSERT(m1);
SparseIntVect<std::uint32_t> *fp1;
fp1 = generator->getCountFingerprint(*m1);
TEST_ASSERT(fp1);
TEST_ASSERT(fp1->getTotalVal() == 3);
TEST_ASSERT(fp1->getNonzeroElements().size() == 3);
TEST_ASSERT((*fp1)[1375] == 1);
TEST_ASSERT((*fp1)[1423] == 1);
TEST_ASSERT((*fp1)[1503] == 1);
delete fp1;
delete m1;
delete generator;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGitHubIssue334() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test GitHub Issue 334: explicit Hs in SMILES "
"modifies atom pair (and topological torsion) FP."
<< std::endl;
{
FingerprintGenerator<std::uint32_t> *generator =
AtomPair::getAtomPairGenerator<std::uint32_t>();
ROMol *m1 = SmilesToMol("N#C");
TEST_ASSERT(m1);
SparseIntVect<std::uint32_t> *fp1;
fp1 = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp1);
delete m1;
m1 = SmilesToMol("N#[CH]");
SparseIntVect<std::uint32_t> *fp2;
fp2 = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp2);
delete m1;
TEST_ASSERT(fp1->getTotalVal() == fp2->getTotalVal());
TEST_ASSERT(fp1->getNonzeroElements().size() ==
fp2->getNonzeroElements().size());
TEST_ASSERT(*fp1 == *fp2);
delete fp1;
delete fp2;
delete generator;
}
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
ROMol *m1 = SmilesToMol("N#C");
TEST_ASSERT(m1);
SparseIntVect<std::uint64_t> *fp1;
fp1 = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp1);
delete m1;
m1 = SmilesToMol("N#[CH]");
SparseIntVect<std::uint64_t> *fp2;
fp2 = generator->getSparseCountFingerprint(*m1);
TEST_ASSERT(fp2);
delete m1;
TEST_ASSERT(fp1->getTotalVal() == fp2->getTotalVal());
TEST_ASSERT(fp1->getNonzeroElements().size() ==
fp2->getNonzeroElements().size());
TEST_ASSERT(*fp1 == *fp2);
delete fp1;
delete fp2;
delete generator;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testGitHubIssue811() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << " Test GitHub Issue 811: rooted atom fingerprint "
"non identical for the same molecules #811"
<< std::endl;
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>(false,
7);
std::string dirName = getenv("RDBASE");
dirName += "/Code/GraphMol/Fingerprints/testData/";
ROMol *m1 = MolFileToMol(dirName + "github811a.mol");
TEST_ASSERT(m1);
ROMol *m2 = MolFileToMol(dirName + "github811b.mol");
TEST_ASSERT(m2);
SparseIntVect<std::uint64_t> *fp1, *fp2;
std::vector<std::uint32_t> roots;
roots.push_back(1);
fp1 = generator->getSparseCountFingerprint(*m1, &roots);
SparseIntVect<std::uint64_t>::StorageType nz1 = fp1->getNonzeroElements();
TEST_ASSERT(nz1.size() == 4);
fp2 = generator->getSparseCountFingerprint(*m1, &roots);
SparseIntVect<std::uint64_t>::StorageType nz2 = fp2->getNonzeroElements();
TEST_ASSERT(nz2.size() == 4);
TEST_ASSERT(*fp1 == *fp2);
delete fp1;
delete fp2;
delete m1;
delete m2;
delete generator;
}
{
FingerprintGenerator<std::uint64_t> *generator =
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>();
ROMol *m1 = SmilesToMol("C1CC1");
TEST_ASSERT(m1);
SparseIntVect<std::uint64_t> *fp1;
fp1 = generator->getSparseCountFingerprint(*m1);
SparseIntVect<std::uint64_t>::StorageType nz1 = fp1->getNonzeroElements();
TEST_ASSERT(nz1.size() == 1);
delete fp1;
delete m1;
delete generator;
}
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testBulkFP() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog)
<< " Test convenience and bulk fp calculation functions" << std::endl;
std::vector<std::pair<FingerprintGenerator<std::uint64_t> *, FPType>>
testPairs;
std::vector<const ROMol *> molVect;
BOOST_FOREACH (std::string sm, smis) { molVect.push_back(SmilesToMol(sm)); }
testPairs.push_back(std::pair<FingerprintGenerator<std::uint64_t> *, FPType>(
AtomPair::getAtomPairGenerator<std::uint64_t>(), FPType::AtomPairFP));
testPairs.push_back(std::pair<FingerprintGenerator<std::uint64_t> *, FPType>(
MorganFingerprint::getMorganGenerator<std::uint64_t>(2),
FPType::MorganFP));
testPairs.push_back(std::pair<FingerprintGenerator<std::uint64_t> *, FPType>(
RDKitFP::getRDKitFPGenerator<std::uint64_t>(), FPType::RDKitFP));
testPairs.push_back(std::pair<FingerprintGenerator<std::uint64_t> *, FPType>(
TopologicalTorsion::getTopologicalTorsionGenerator<std::uint64_t>(),
FPType::TopologicalTorsionFP));
BOOST_FOREACH (auto it, testPairs) {
std::vector<SparseIntVect<std::uint64_t> *> *results =
getSparseCountFPBulk(molVect, it.second);
std::vector<SparseIntVect<std::uint64_t> *> compareRes;
BOOST_FOREACH (auto m, molVect) {
compareRes.push_back(it.first->getSparseCountFingerprint(*m));
}
for (unsigned long i = 0; i < results->size(); ++i) {
TEST_ASSERT(*((*results)[i]) == *compareRes[i]);
delete (*results)[i];
delete compareRes[i];
}
delete results;
}
BOOST_FOREACH (auto &&m, molVect) { delete m; }
BOOST_FOREACH (auto &&t, testPairs) { delete t.first; }
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
int main(int argc, char *argv[]) {
(void)argc;
(void)argv;
RDLog::InitLogs();
#if 1
testAtomPairFP();
testAtomPairArgs();
testAtomPairOld();
// testAtomPairNonSparseBitvector();
testAtomPairOutput();
testFoldedAtomPairs();
testRootedAtomPairs();
testIgnoreAtomPairs();
testChiralPairs();
testMorganFP();
testMorganFPOld();
testMorganFPFromAtoms();
testMorganFPBitVect();
testMorganFPFeatureInvs();
testMorganFPOptions();
testGitHubIssue695();
testGitHubIssue874();
testInvariantGenerators();
testCustomInvariants();
testRDKitFP();
testRDKFPUnfolded();
testTopologicalTorsionFPOld();
testTorsions();
testFoldedTorsions();
testBulkTorsions();
testRootedTorsions();
testIgnoreTorsions();
testPairsAndTorsionsOptions();
testChiralTorsions();
#endif
testGitHubIssue25();
testGitHubIssue334();
testGitHubIssue811();
testBulkFP();
return 0;
}
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