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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 <GraphMol/RDKitBase.h>
#include <GraphMol/Fingerprints/FingerprintGenerator.h>
#include <GraphMol/Fingerprints/AtomPairGenerator.h>
#include <GraphMol/Fingerprints/FingerprintUtil.h>
#include <RDGeneral/hash/hash.hpp>
namespace RDKit {
namespace AtomPair {
using namespace AtomPairs;
AtomPairAtomInvGenerator::AtomPairAtomInvGenerator(
bool includeChirality, bool topologicalTorsionCorrection)
: df_includeChirality(includeChirality),
df_topologicalTorsionCorrection(topologicalTorsionCorrection) {}
std::vector<std::uint32_t> *AtomPairAtomInvGenerator::getAtomInvariants(
const ROMol &mol) const {
auto *atomInvariants = new std::vector<std::uint32_t>(mol.getNumAtoms());
for (ROMol::ConstAtomIterator atomItI = mol.beginAtoms();
atomItI != mol.endAtoms(); ++atomItI) {
(*atomInvariants)[(*atomItI)->getIdx()] =
getAtomCode(*atomItI, 0, df_includeChirality) -
(df_topologicalTorsionCorrection ? 2 : 0);
}
return atomInvariants;
}
std::string AtomPairAtomInvGenerator::infoString() const {
return "AtomPairInvariantGenerator topologicalTorsionCorrection=" +
std::to_string(df_topologicalTorsionCorrection);
}
AtomPairAtomInvGenerator *AtomPairAtomInvGenerator::clone() const {
return new AtomPairAtomInvGenerator(df_includeChirality,
df_topologicalTorsionCorrection);
}
template <typename OutputType>
OutputType AtomPairEnvGenerator<OutputType>::getResultSize() const {
OutputType result = 1;
return (result << (numAtomPairFingerprintBits +
2 * (this->dp_fingerprintArguments->df_includeChirality
? numChiralBits
: 0)));
}
AtomPairArguments::AtomPairArguments(
const bool countSimulation, const bool includeChirality, const bool use2D,
const unsigned int minDistance, const unsigned int maxDistance,
const std::vector<std::uint32_t> countBounds, const std::uint32_t fpSize)
: FingerprintArguments(countSimulation, countBounds, fpSize, 1,
includeChirality),
df_use2D(use2D),
d_minDistance(minDistance),
d_maxDistance(maxDistance) {
PRECONDITION(minDistance <= maxDistance, "bad distances provided");
}
std::string AtomPairArguments::infoString() const {
return "AtomPairArguments use2D=" + std::to_string(df_use2D) +
" minDistance=" + std::to_string(d_minDistance) +
" maxDistance=" + std::to_string(d_maxDistance);
}
template <typename OutputType>
void AtomPairAtomEnv<OutputType>::updateAdditionalOutput(
AdditionalOutput *additionalOutput, size_t bitId) const {
PRECONDITION(additionalOutput, "bad output pointer");
if (additionalOutput->bitInfoMap) {
(*additionalOutput->bitInfoMap)[bitId].emplace_back(d_atomIdFirst,
d_atomIdSecond);
}
if (additionalOutput->atomToBits) {
additionalOutput->atomToBits->at(d_atomIdFirst).push_back(bitId);
additionalOutput->atomToBits->at(d_atomIdSecond).push_back(bitId);
}
if (additionalOutput->atomCounts) {
additionalOutput->atomCounts->at(d_atomIdFirst)++;
additionalOutput->atomCounts->at(d_atomIdSecond)++;
}
}
template <typename OutputType>
OutputType AtomPairAtomEnv<OutputType>::getBitId(
FingerprintArguments *arguments,
const std::vector<std::uint32_t> *atomInvariants,
const std::vector<std::uint32_t> *, // bondInvariants
AdditionalOutput *, // additionalOutput,
const bool hashResults,
const std::uint64_t // fpSize
) const {
PRECONDITION((atomInvariants->size() >= d_atomIdFirst) &&
(atomInvariants->size() >= d_atomIdSecond),
"bad atom invariants size");
auto *atomPairArguments = dynamic_cast<AtomPairArguments *>(arguments);
std::uint32_t codeSizeLimit =
(1 << (codeSize +
(atomPairArguments->df_includeChirality ? numChiralBits : 0))) -
1;
std::uint32_t atomCodeFirst =
(*atomInvariants)[d_atomIdFirst] % codeSizeLimit;
std::uint32_t atomCodeSecond =
(*atomInvariants)[d_atomIdSecond] % codeSizeLimit;
std::uint32_t bitId = 0;
if (hashResults) {
gboost::hash_combine(bitId, std::min(atomCodeFirst, atomCodeSecond));
gboost::hash_combine(bitId, d_distance);
gboost::hash_combine(bitId, std::max(atomCodeFirst, atomCodeSecond));
} else {
bitId = getAtomPairCode(atomCodeFirst, atomCodeSecond, d_distance,
atomPairArguments->df_includeChirality);
}
return bitId;
}
template <typename OutputType>
AtomPairAtomEnv<OutputType>::AtomPairAtomEnv(const unsigned int atomIdFirst,
const unsigned int atomIdSecond,
const unsigned int distance)
: d_atomIdFirst(atomIdFirst),
d_atomIdSecond(atomIdSecond),
d_distance(distance) {}
template <typename OutputType>
std::vector<AtomEnvironment<OutputType> *>
AtomPairEnvGenerator<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 {
const unsigned int atomCount = mol.getNumAtoms();
PRECONDITION(!additionalOutput || !additionalOutput->atomToBits ||
additionalOutput->atomToBits->size() == atomCount,
"bad atomToBits size in AdditionalOutput");
auto *atomPairArguments = dynamic_cast<AtomPairArguments *>(arguments);
std::vector<AtomEnvironment<OutputType> *> result =
std::vector<AtomEnvironment<OutputType> *>();
const double *distanceMatrix;
if (atomPairArguments->df_use2D) {
distanceMatrix = MolOps::getDistanceMat(mol);
} else {
distanceMatrix = MolOps::get3DDistanceMat(mol, confId);
}
for (ROMol::ConstAtomIterator atomItI = mol.beginAtoms();
atomItI != mol.endAtoms(); ++atomItI) {
unsigned int i = (*atomItI)->getIdx();
if (ignoreAtoms && std::find(ignoreAtoms->begin(), ignoreAtoms->end(), i) !=
ignoreAtoms->end()) {
continue;
}
for (ROMol::ConstAtomIterator atomItJ = atomItI + 1;
atomItJ != mol.endAtoms(); ++atomItJ) {
unsigned int j = (*atomItJ)->getIdx();
if (ignoreAtoms && std::find(ignoreAtoms->begin(), ignoreAtoms->end(),
j) != ignoreAtoms->end()) {
continue;
}
if (fromAtoms &&
(std::find(fromAtoms->begin(), fromAtoms->end(), i) ==
fromAtoms->end()) &&
(std::find(fromAtoms->begin(), fromAtoms->end(), j) ==
fromAtoms->end())) {
continue;
}
auto distance =
static_cast<unsigned int>(floor(distanceMatrix[i * atomCount + j]));
if (distance >= atomPairArguments->d_minDistance &&
distance <= atomPairArguments->d_maxDistance) {
result.push_back(new AtomPairAtomEnv<OutputType>(i, j, distance));
}
}
}
return result;
}
template <typename OutputType>
std::string AtomPairEnvGenerator<OutputType>::infoString() const {
return "AtomPairEnvironmentGenerator";
}
template <typename OutputType>
FingerprintGenerator<OutputType> *getAtomPairGenerator(
const AtomPairArguments &args,
AtomInvariantsGenerator *atomInvariantsGenerator,
const bool ownsAtomInvGen) {
AtomEnvironmentGenerator<OutputType> *atomPairEnvGenerator =
new AtomPair::AtomPairEnvGenerator<OutputType>();
bool ownsAtomInvGenerator = ownsAtomInvGen;
if (!atomInvariantsGenerator) {
atomInvariantsGenerator =
new AtomPairAtomInvGenerator(args.df_includeChirality);
ownsAtomInvGenerator = true;
}
return new FingerprintGenerator<OutputType>(
atomPairEnvGenerator, new AtomPairArguments(args),
atomInvariantsGenerator, nullptr, ownsAtomInvGenerator, false);
}
template <typename OutputType>
FingerprintGenerator<OutputType> *getAtomPairGenerator(
const unsigned int minDistance, const unsigned int maxDistance,
const bool includeChirality, const bool use2D,
AtomInvariantsGenerator *atomInvariantsGenerator,
const bool useCountSimulation, const std::uint32_t fpSize,
const std::vector<std::uint32_t> countBounds, const bool ownsAtomInvGen) {
AtomPair::AtomPairArguments arguments(useCountSimulation, includeChirality,
use2D, minDistance, maxDistance,
countBounds, fpSize);
return getAtomPairGenerator<OutputType>(arguments, atomInvariantsGenerator,
ownsAtomInvGen);
}
template RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator<std::uint32_t> *
getAtomPairGenerator(const AtomPairArguments &, AtomInvariantsGenerator *,
const bool);
template RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator<std::uint64_t> *
getAtomPairGenerator(const AtomPairArguments &, AtomInvariantsGenerator *,
const bool);
template RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator<std::uint32_t> *
getAtomPairGenerator(const unsigned int minDistance,
const unsigned int maxDistance,
const bool includeChirality, const bool use2D,
AtomInvariantsGenerator *atomInvariantsGenerator,
const bool useCountSimulation, const std::uint32_t fpSize,
const std::vector<std::uint32_t> countBounds,
const bool ownsAtomInvGen);
template RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator<std::uint64_t> *
getAtomPairGenerator(const unsigned int minDistance,
const unsigned int maxDistance,
const bool includeChirality, const bool use2D,
AtomInvariantsGenerator *atomInvariantsGenerator,
const bool useCountSimulation, const std::uint32_t fpSize,
const std::vector<std::uint32_t> countBounds,
const bool ownsAtomInvGen);
} // namespace AtomPair
} // namespace RDKit
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