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//
// Copyright (C) 2018-2022 Boran Adas and other RDKit contributors
//
// @@ 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 <GraphMol/Fingerprints/RDKitFPGenerator.h>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/Fingerprints/FingerprintGenerator.h>
#include <RDGeneral/hash/hash.hpp>
#include <cstdint>
#include <GraphMol/QueryOps.h>
#include <DataStructs/ExplicitBitVect.h>
#include <DataStructs/BitOps.h>
#include <GraphMol/Subgraphs/Subgraphs.h>
#include <GraphMol/Subgraphs/SubgraphUtils.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/random.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <climits>
#include <RDGeneral/hash/hash.hpp>
#include <RDGeneral/types.h>
#include <algorithm>
#include <boost/dynamic_bitset.hpp>
#include <GraphMol/Fingerprints/FingerprintUtil.h>
namespace RDKit {
namespace RDKitFP {
std::vector<std::uint32_t> *RDKitFPAtomInvGenerator::getAtomInvariants(
const ROMol &mol) const {
auto *result = new std::vector<std::uint32_t>();
result->reserve(mol.getNumAtoms());
for (ROMol::ConstAtomIterator atomIt = mol.beginAtoms();
atomIt != mol.endAtoms(); ++atomIt) {
unsigned int aHash = ((*atomIt)->getAtomicNum() % 128) << 1 |
static_cast<unsigned int>((*atomIt)->getIsAromatic());
result->push_back(aHash);
}
return result;
}
std::string RDKitFPAtomInvGenerator::infoString() const {
return "RDKitFPAtomInvGenerator";
}
RDKitFPAtomInvGenerator *RDKitFPAtomInvGenerator::clone() const {
return new RDKitFPAtomInvGenerator();
}
template <typename OutputType>
OutputType RDKitFPEnvGenerator<OutputType>::getResultSize() const {
return std::numeric_limits<OutputType>::max();
}
std::string RDKitFPArguments::infoString() const {
return "RDKitFPArguments minPath=" + std::to_string(d_minPath) +
" maxPath=" + std::to_string(d_maxPath) +
" useHs=" + std::to_string(df_useHs) +
" branchedPaths=" + std::to_string(df_branchedPaths) +
" useBondOrder=" + std::to_string(df_useBondOrder);
}
RDKitFPArguments::RDKitFPArguments(unsigned int minPath, unsigned int maxPath,
bool useHs, bool branchedPaths,
bool useBondOrder, bool countSimulation,
const std::vector<std::uint32_t> countBounds,
std::uint32_t fpSize,
std::uint32_t numBitsPerFeature)
: FingerprintArguments(countSimulation, countBounds, fpSize,
numBitsPerFeature),
d_minPath(minPath),
d_maxPath(maxPath),
df_useHs(useHs),
df_branchedPaths(branchedPaths),
df_useBondOrder(useBondOrder) {
PRECONDITION(minPath != 0, "minPath==0");
PRECONDITION(maxPath >= minPath, "maxPath<minPath");
}
template <typename OutputType>
void RDKitFPAtomEnv<OutputType>::updateAdditionalOutput(
AdditionalOutput *additionalOutput, size_t bitId) const {
PRECONDITION(additionalOutput, "bad output pointer");
if (additionalOutput->bitPaths) {
(*additionalOutput->bitPaths)[bitId].push_back(d_bondPath);
}
if (additionalOutput->atomToBits || additionalOutput->atomCounts) {
for (size_t i = 0; i < d_atomsInPath.size(); ++i) {
if (d_atomsInPath[i]) {
if (additionalOutput->atomToBits) {
auto &alist = additionalOutput->atomToBits->at(i);
if (std::find(alist.begin(), alist.end(), bitId) == alist.end()) {
alist.push_back(bitId);
}
}
if (additionalOutput->atomCounts) {
additionalOutput->atomCounts->at(i)++;
}
}
}
}
}
template <typename OutputType>
OutputType RDKitFPAtomEnv<OutputType>::getBitId(
FingerprintArguments *, // arguments
const std::vector<std::uint32_t> *, // atomInvariants
const std::vector<std::uint32_t> *, // bondInvariants
AdditionalOutput *, // additional Output
const bool, // hashResults
const std::uint64_t // fpSize
) const {
return d_bitId;
}
template <typename OutputType>
std::string RDKitFPEnvGenerator<OutputType>::infoString() const {
return "RDKitFPEnvGenerator";
}
template <typename OutputType>
std::vector<AtomEnvironment<OutputType> *>
RDKitFPEnvGenerator<OutputType>::getEnvironments(
const ROMol &mol, FingerprintArguments *arguments,
const std::vector<std::uint32_t> *fromAtoms,
const std::vector<std::uint32_t> *, // ignoreAtoms
const int, // confId
const AdditionalOutput *, // additionalOutput
const std::vector<std::uint32_t> *atomInvariants,
const std::vector<std::uint32_t> *, // bondInvariants
const bool // hashResults
) const {
PRECONDITION(!atomInvariants || atomInvariants->size() >= mol.getNumAtoms(),
"bad atomInvariants size");
auto *fpArguments = dynamic_cast<RDKitFPArguments *>(arguments);
std::vector<AtomEnvironment<OutputType> *> result;
// get all paths
INT_PATH_LIST_MAP allPaths;
RDKitFPUtils::enumerateAllPaths(
mol, allPaths, fromAtoms, fpArguments->df_branchedPaths,
fpArguments->df_useHs, fpArguments->d_minPath, fpArguments->d_maxPath);
// identify query bonds
std::vector<short> isQueryBond(mol.getNumBonds(), 0);
std::vector<const Bond *> bondCache;
RDKitFPUtils::identifyQueryBonds(mol, bondCache, isQueryBond);
boost::dynamic_bitset<> atomsInPath(mol.getNumAtoms());
for (INT_PATH_LIST_MAP_CI paths = allPaths.begin(); paths != allPaths.end();
paths++) {
for (const auto &path : paths->second) {
// the bond hashes of the path
std::vector<std::uint32_t> bondHashes = RDKitFPUtils::generateBondHashes(
mol, atomsInPath, bondCache, isQueryBond, path,
fpArguments->df_useBondOrder, atomInvariants);
if (!bondHashes.size()) {
continue;
}
// hash the path to generate a seed:
unsigned long seed;
if (path.size() > 1) {
std::sort(bondHashes.begin(), bondHashes.end());
// finally, we will add the number of distinct atoms in the path at the
// end
// of the vect. This allows us to distinguish C1CC1 from CC(C)C
bondHashes.push_back(static_cast<std::uint32_t>(atomsInPath.count()));
seed = gboost::hash_range(bondHashes.begin(), bondHashes.end());
} else {
seed = bondHashes[0];
}
result.push_back(new RDKitFPAtomEnv<OutputType>(
static_cast<OutputType>(seed), atomsInPath, path));
}
}
return result;
}
template <typename OutputType>
FingerprintGenerator<OutputType> *getRDKitFPGenerator(
const RDKitFPArguments &args,
AtomInvariantsGenerator *atomInvariantsGenerator, bool ownsAtomInvGen) {
auto *envGenerator = new RDKitFPEnvGenerator<OutputType>();
bool ownsAtomInvGenerator = ownsAtomInvGen;
if (!atomInvariantsGenerator) {
atomInvariantsGenerator = new RDKitFPAtomInvGenerator();
ownsAtomInvGenerator = true;
}
return new FingerprintGenerator<OutputType>(
envGenerator, new RDKitFPArguments(args), atomInvariantsGenerator,
nullptr, ownsAtomInvGenerator, false);
}
template <typename OutputType>
FingerprintGenerator<OutputType> *getRDKitFPGenerator(
unsigned int minPath, unsigned int maxPath, bool useHs, bool branchedPaths,
bool useBondOrder, AtomInvariantsGenerator *atomInvariantsGenerator,
bool countSimulation, const std::vector<std::uint32_t> countBounds,
std::uint32_t fpSize, std::uint32_t numBitsPerFeature,
bool ownsAtomInvGen) {
RDKitFPArguments arguments(minPath, maxPath, useHs, branchedPaths,
useBondOrder, countSimulation, countBounds, fpSize,
numBitsPerFeature);
return getRDKitFPGenerator<OutputType>(arguments, atomInvariantsGenerator,
ownsAtomInvGen);
}
template RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator<std::uint32_t> *
getRDKitFPGenerator(unsigned int minPath, unsigned int maxPath, bool useHs,
bool branchedPaths, bool useBondOrder,
AtomInvariantsGenerator *atomInvariantsGenerator,
bool countSimulation,
const std::vector<std::uint32_t> countBounds,
std::uint32_t fpSize, std::uint32_t numBitsPerFeature,
bool ownsAtomInvGen);
template RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator<std::uint64_t> *
getRDKitFPGenerator(unsigned int minPath, unsigned int maxPath, bool useHs,
bool branchedPaths, bool useBondOrder,
AtomInvariantsGenerator *atomInvariantsGenerator,
bool countSimulation,
const std::vector<std::uint32_t> countBounds,
std::uint32_t fpSize, std::uint32_t numBitsPerFeature,
bool ownsAtomInvGen);
template RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator<std::uint32_t> *
getRDKitFPGenerator(const RDKitFPArguments &, AtomInvariantsGenerator *, bool);
template RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator<std::uint64_t> *
getRDKitFPGenerator(const RDKitFPArguments &, AtomInvariantsGenerator *, bool);
} // namespace RDKitFP
} // namespace RDKit
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