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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/TopologicalTorsionGenerator.h>
#include <GraphMol/Fingerprints/FingerprintUtil.h>
#include <GraphMol/Fingerprints/AtomPairGenerator.h>
namespace RDKit {
namespace TopologicalTorsion {
using namespace AtomPairs;
TopologicalTorsionArguments::TopologicalTorsionArguments(
const bool includeChirality, const uint32_t torsionAtomCount,
const bool countSimulation, const std::vector<std::uint32_t> countBounds,
const std::uint32_t fpSize)
: FingerprintArguments(countSimulation, countBounds, fpSize, 1,
includeChirality),
d_torsionAtomCount(torsionAtomCount) {};
template <typename OutputType>
OutputType TopologicalTorsionEnvGenerator<OutputType>::getResultSize() const {
OutputType result = 1;
return (result << ((
dynamic_cast<const TopologicalTorsionArguments *>(
this->dp_fingerprintArguments)
->d_torsionAtomCount *
(codeSize + (dynamic_cast<const TopologicalTorsionArguments *>(
this->dp_fingerprintArguments)
->df_includeChirality
? numChiralBits
: 0)))));
};
std::string TopologicalTorsionArguments::infoString() const {
return "TopologicalTorsionArguments torsionAtomCount=" +
std::to_string(d_torsionAtomCount) +
" onlyShortestPaths=" + std::to_string(df_onlyShortestPaths);
};
template <typename OutputType>
void TopologicalTorsionAtomEnv<OutputType>::updateAdditionalOutput(
AdditionalOutput *additionalOutput, size_t bitId) const {
PRECONDITION(additionalOutput, "bad output pointer");
if (additionalOutput->atomToBits || additionalOutput->atomCounts) {
for (auto aid : d_atomPath) {
if (additionalOutput->atomToBits) {
additionalOutput->atomToBits->at(aid).push_back(bitId);
}
if (additionalOutput->atomCounts) {
additionalOutput->atomCounts->at(aid)++;
}
}
}
if (additionalOutput->bitPaths) {
(*additionalOutput->bitPaths)[bitId].push_back(d_atomPath);
}
}
template <typename OutputType>
OutputType TopologicalTorsionAtomEnv<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 {
return d_bitId;
};
template <typename OutputType>
std::vector<AtomEnvironment<OutputType> *>
TopologicalTorsionEnvGenerator<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 {
auto *topologicalTorsionArguments =
dynamic_cast<TopologicalTorsionArguments *>(arguments);
std::vector<AtomEnvironment<OutputType> *> result;
boost::dynamic_bitset<> *fromAtomsBV = nullptr;
if (fromAtoms) {
fromAtomsBV = new boost::dynamic_bitset<>(mol.getNumAtoms());
for (auto fAt : *fromAtoms) {
fromAtomsBV->set(fAt);
}
}
boost::dynamic_bitset<> *ignoreAtomsBV = nullptr;
if (ignoreAtoms) {
ignoreAtomsBV = new boost::dynamic_bitset<>(mol.getNumAtoms());
for (auto fAt : *ignoreAtoms) {
ignoreAtomsBV->set(fAt);
}
}
boost::dynamic_bitset<> pAtoms(mol.getNumAtoms());
bool useBonds = false;
bool useHs = false;
int rootedAtAtom = -1;
PATH_LIST paths = findAllPathsOfLengthN(
mol, topologicalTorsionArguments->d_torsionAtomCount, useBonds, useHs,
rootedAtAtom, topologicalTorsionArguments->df_onlyShortestPaths);
for (PATH_LIST::const_iterator pathIt = paths.begin(); pathIt != paths.end();
++pathIt) {
bool keepIt = true;
if (fromAtomsBV) {
keepIt = false;
}
std::vector<std::uint32_t> pathCodes;
const PATH_TYPE &path = *pathIt;
if (fromAtomsBV) {
if (fromAtomsBV->test(static_cast<std::uint32_t>(path.front())) ||
fromAtomsBV->test(static_cast<std::uint32_t>(path.back()))) {
keepIt = true;
}
}
if (keepIt && ignoreAtomsBV) {
for (int pElem : path) {
if (ignoreAtomsBV->test(pElem)) {
keepIt = false;
break;
}
}
}
if (keepIt) {
pAtoms.reset();
for (auto pIt = path.begin(); pIt < path.end(); ++pIt) {
// look for a cycle that doesn't start at the first atom
// we can't effectively canonicalize these at the moment
// (was github #811)
if (pIt != path.begin() && *pIt != *(path.begin()) && pAtoms[*pIt]) {
pathCodes.clear();
break;
}
pAtoms.set(*pIt);
unsigned int code = (*atomInvariants)[*pIt] % ((1 << codeSize) - 1) + 1;
// subtract off the branching number:
if (pIt != path.begin() && pIt + 1 != path.end()) {
--code;
}
pathCodes.push_back(code);
}
if (pathCodes.size()) {
OutputType code;
if (hashResults) {
code = getTopologicalTorsionHash(pathCodes);
} else {
code = getTopologicalTorsionCode(
pathCodes, topologicalTorsionArguments->df_includeChirality);
}
result.push_back(new TopologicalTorsionAtomEnv<OutputType>(code, path));
}
}
}
delete fromAtomsBV;
delete ignoreAtomsBV;
return result;
};
template <typename OutputType>
std::string TopologicalTorsionEnvGenerator<OutputType>::infoString() const {
return "TopologicalTorsionEnvGenerator";
};
template <typename OutputType>
FingerprintGenerator<OutputType> *getTopologicalTorsionGenerator(
const TopologicalTorsionArguments &args,
AtomInvariantsGenerator *atomInvariantsGenerator,
const bool ownsAtomInvGen) {
auto *envGenerator = new TopologicalTorsionEnvGenerator<OutputType>();
bool ownsAtomInvGenerator = ownsAtomInvGen;
if (!atomInvariantsGenerator) {
atomInvariantsGenerator =
new AtomPair::AtomPairAtomInvGenerator(args.df_includeChirality, true);
ownsAtomInvGenerator = true;
}
return new FingerprintGenerator<OutputType>(
envGenerator, new TopologicalTorsionArguments(args),
atomInvariantsGenerator, nullptr, ownsAtomInvGenerator, false);
};
template <typename OutputType>
FingerprintGenerator<OutputType> *getTopologicalTorsionGenerator(
bool includeChirality, uint32_t torsionAtomCount,
AtomInvariantsGenerator *atomInvariantsGenerator, bool countSimulation,
std::uint32_t fpSize, std::vector<std::uint32_t> countBounds,
bool ownsAtomInvGen) {
TopologicalTorsionArguments arguments(includeChirality, torsionAtomCount,
countSimulation, countBounds, fpSize);
return getTopologicalTorsionGenerator<OutputType>(
arguments, atomInvariantsGenerator, ownsAtomInvGen);
};
// Topological torsion fingerprint does not support 32 bit output yet
template RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator<std::uint64_t> *
getTopologicalTorsionGenerator(bool includeChirality, uint32_t torsionAtomCount,
AtomInvariantsGenerator *atomInvariantsGenerator,
bool countSimulation, std::uint32_t fpSize,
std::vector<std::uint32_t> countBounds,
bool ownsAtomInvGen);
template RDKIT_FINGERPRINTS_EXPORT FingerprintGenerator<std::uint64_t> *
getTopologicalTorsionGenerator(const TopologicalTorsionArguments &,
AtomInvariantsGenerator *, const bool);
} // namespace TopologicalTorsion
} // namespace RDKit
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