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498 lines
18 KiB
C++
498 lines
18 KiB
C++
//
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// Copyright (C) 2007-2013 Greg Landrum
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//
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// @@ All Rights Reserved @@
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// This file is part of the RDKit.
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// The contents are covered by the terms of the BSD license
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// which is included in the file license.txt, found at the root
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// of the RDKit source tree.
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//
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#include <GraphMol/RDKitBase.h>
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#include <GraphMol/Fingerprints/AtomPairs.h>
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#include <GraphMol/Subgraphs/Subgraphs.h>
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#include <DataStructs/SparseIntVect.h>
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#include <RDGeneral/hash/hash.hpp>
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#include <cstdint>
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#include <boost/dynamic_bitset.hpp>
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#include <boost/foreach.hpp>
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#include <GraphMol/Fingerprints/FingerprintUtil.h>
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namespace RDKit {
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namespace AtomPairs {
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template <typename T1, typename T2>
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void updateElement(SparseIntVect<T1> &v, T2 elem) {
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v.setVal(elem, v.getVal(elem) + 1);
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}
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template <typename T1>
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void updateElement(ExplicitBitVect &v, T1 elem) {
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v.setBit(elem % v.getNumBits());
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}
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template <typename T>
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void setAtomPairBit(std::uint32_t i, std::uint32_t j,
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std::uint32_t nAtoms,
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const std::vector<std::uint32_t> &atomCodes,
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const double *dm, T *bv, unsigned int minLength,
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unsigned int maxLength, bool includeChirality) {
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unsigned int dist = static_cast<unsigned int>(floor(dm[i * nAtoms + j]));
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if (dist >= minLength && dist <= maxLength) {
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std::uint32_t bitId =
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getAtomPairCode(atomCodes[i], atomCodes[j], dist, includeChirality);
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updateElement(*bv, static_cast<std::uint32_t>(bitId));
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}
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}
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SparseIntVect<std::int32_t> *getAtomPairFingerprint(
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const ROMol &mol, const std::vector<std::uint32_t> *fromAtoms,
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const std::vector<std::uint32_t> *ignoreAtoms,
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const std::vector<std::uint32_t> *atomInvariants, bool includeChirality,
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bool use2D, int confId) {
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return getAtomPairFingerprint(mol, 1, maxPathLen - 1, fromAtoms, ignoreAtoms,
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atomInvariants, includeChirality, use2D,
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confId);
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};
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SparseIntVect<std::int32_t> *getAtomPairFingerprint(
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const ROMol &mol, unsigned int minLength, unsigned int maxLength,
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const std::vector<std::uint32_t> *fromAtoms,
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const std::vector<std::uint32_t> *ignoreAtoms,
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const std::vector<std::uint32_t> *atomInvariants, bool includeChirality,
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bool use2D, int confId) {
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PRECONDITION(minLength <= maxLength, "bad lengths provided");
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PRECONDITION(!atomInvariants || atomInvariants->size() >= mol.getNumAtoms(),
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"bad atomInvariants size");
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const ROMol *lmol = &mol;
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std::unique_ptr<ROMol> tmol;
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if (includeChirality && !mol.hasProp(common_properties::_StereochemDone)) {
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tmol = std::unique_ptr<ROMol>(new ROMol(mol));
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MolOps::assignStereochemistry(*tmol);
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lmol = tmol.get();
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}
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auto *res = new SparseIntVect<std::int32_t>(
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1 << (numAtomPairFingerprintBits + 2 * (includeChirality ? 2 : 0)));
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const double *dm;
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if (use2D) {
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dm = MolOps::getDistanceMat(*lmol);
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} else {
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dm = MolOps::get3DDistanceMat(*lmol, confId);
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}
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const unsigned int nAtoms = lmol->getNumAtoms();
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std::vector<std::uint32_t> atomCodes;
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for (ROMol::ConstAtomIterator atomItI = lmol->beginAtoms();
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atomItI != lmol->endAtoms(); ++atomItI) {
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if (!atomInvariants) {
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atomCodes.push_back(getAtomCode(*atomItI, 0, includeChirality));
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} else {
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atomCodes.push_back((*atomInvariants)[(*atomItI)->getIdx()] %
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((1 << codeSize) - 1));
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}
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}
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for (ROMol::ConstAtomIterator atomItI = lmol->beginAtoms();
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atomItI != lmol->endAtoms(); ++atomItI) {
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unsigned int i = (*atomItI)->getIdx();
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if (ignoreAtoms && std::find(ignoreAtoms->begin(), ignoreAtoms->end(), i) !=
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ignoreAtoms->end()) {
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continue;
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}
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if (!fromAtoms) {
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for (ROMol::ConstAtomIterator atomItJ = atomItI + 1;
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atomItJ != lmol->endAtoms(); ++atomItJ) {
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unsigned int j = (*atomItJ)->getIdx();
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if (ignoreAtoms && std::find(ignoreAtoms->begin(), ignoreAtoms->end(),
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j) != ignoreAtoms->end()) {
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continue;
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}
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setAtomPairBit(i, j, nAtoms, atomCodes, dm, res, minLength, maxLength,
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includeChirality);
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}
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} else {
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BOOST_FOREACH (std::uint32_t j, *fromAtoms) {
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if (j != i) {
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if (ignoreAtoms && std::find(ignoreAtoms->begin(), ignoreAtoms->end(),
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j) != ignoreAtoms->end()) {
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continue;
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}
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setAtomPairBit(i, j, nAtoms, atomCodes, dm, res, minLength, maxLength,
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includeChirality);
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}
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}
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}
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}
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return res;
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}
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SparseIntVect<std::int32_t> *getHashedAtomPairFingerprint(
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const ROMol &mol, unsigned int nBits, unsigned int minLength,
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unsigned int maxLength, const std::vector<std::uint32_t> *fromAtoms,
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const std::vector<std::uint32_t> *ignoreAtoms,
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const std::vector<std::uint32_t> *atomInvariants, bool includeChirality,
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bool use2D, int confId) {
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PRECONDITION(minLength <= maxLength, "bad lengths provided");
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PRECONDITION(!atomInvariants || atomInvariants->size() >= mol.getNumAtoms(),
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"bad atomInvariants size");
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const ROMol *lmol = &mol;
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std::unique_ptr<ROMol> tmol;
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if (includeChirality && !mol.hasProp(common_properties::_StereochemDone)) {
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tmol = std::unique_ptr<ROMol>(new ROMol(mol));
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MolOps::assignStereochemistry(*tmol);
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lmol = tmol.get();
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}
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auto *res = new SparseIntVect<std::int32_t>(nBits);
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const double *dm;
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try {
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if (use2D) {
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dm = MolOps::getDistanceMat(*lmol);
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} else {
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dm = MolOps::get3DDistanceMat(*lmol, confId);
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}
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} catch (const ConformerException &) {
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delete res;
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throw;
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}
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const unsigned int nAtoms = lmol->getNumAtoms();
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std::vector<std::uint32_t> atomCodes;
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atomCodes.reserve(nAtoms);
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for (ROMol::ConstAtomIterator atomItI = lmol->beginAtoms();
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atomItI != lmol->endAtoms(); ++atomItI) {
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if (!atomInvariants) {
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atomCodes.push_back(getAtomCode(*atomItI, 0, includeChirality));
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} else {
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atomCodes.push_back((*atomInvariants)[(*atomItI)->getIdx()]);
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}
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}
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for (ROMol::ConstAtomIterator atomItI = lmol->beginAtoms();
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atomItI != lmol->endAtoms(); ++atomItI) {
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unsigned int i = (*atomItI)->getIdx();
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if (ignoreAtoms && std::find(ignoreAtoms->begin(), ignoreAtoms->end(), i) !=
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ignoreAtoms->end()) {
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continue;
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}
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if (!fromAtoms) {
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for (ROMol::ConstAtomIterator atomItJ = atomItI + 1;
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atomItJ != lmol->endAtoms(); ++atomItJ) {
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unsigned int j = (*atomItJ)->getIdx();
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if (ignoreAtoms && std::find(ignoreAtoms->begin(), ignoreAtoms->end(),
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j) != ignoreAtoms->end()) {
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continue;
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}
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unsigned int dist =
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static_cast<unsigned int>(floor(dm[i * nAtoms + j]));
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if (dist >= minLength && dist <= maxLength) {
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std::uint32_t bit = 0;
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gboost::hash_combine(bit, std::min(atomCodes[i], atomCodes[j]));
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gboost::hash_combine(bit, dist);
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gboost::hash_combine(bit, std::max(atomCodes[i], atomCodes[j]));
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updateElement(*res, static_cast<std::int32_t>(bit % nBits));
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}
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}
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} else {
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BOOST_FOREACH (std::uint32_t j, *fromAtoms) {
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if (j != i) {
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if (ignoreAtoms && std::find(ignoreAtoms->begin(), ignoreAtoms->end(),
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j) != ignoreAtoms->end()) {
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continue;
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}
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unsigned int dist =
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static_cast<unsigned int>(floor(dm[i * nAtoms + j]));
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if (dist >= minLength && dist <= maxLength) {
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std::uint32_t bit = 0;
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gboost::hash_combine(bit, std::min(atomCodes[i], atomCodes[j]));
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gboost::hash_combine(bit, dist);
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gboost::hash_combine(bit, std::max(atomCodes[i], atomCodes[j]));
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updateElement(*res, static_cast<std::int32_t>(bit % nBits));
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}
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}
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}
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}
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}
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return res;
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}
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ExplicitBitVect *getHashedAtomPairFingerprintAsBitVect(
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const ROMol &mol, unsigned int nBits, unsigned int minLength,
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unsigned int maxLength, const std::vector<std::uint32_t> *fromAtoms,
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const std::vector<std::uint32_t> *ignoreAtoms,
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const std::vector<std::uint32_t> *atomInvariants,
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unsigned int nBitsPerEntry, bool includeChirality, bool use2D, int confId) {
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PRECONDITION(minLength <= maxLength, "bad lengths provided");
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PRECONDITION(!atomInvariants || atomInvariants->size() >= mol.getNumAtoms(),
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"bad atomInvariants size");
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static int bounds[4] = {1, 2, 4, 8};
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unsigned int blockLength = nBits / nBitsPerEntry;
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SparseIntVect<std::int32_t> *sres = getHashedAtomPairFingerprint(
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mol, blockLength, minLength, maxLength, fromAtoms, ignoreAtoms,
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atomInvariants, includeChirality, use2D, confId);
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auto *res = new ExplicitBitVect(nBits);
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if (nBitsPerEntry != 4) {
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BOOST_FOREACH (SparseIntVect<boost::int64_t>::StorageType::value_type val,
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sres->getNonzeroElements()) {
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for (unsigned int i = 0; i < nBitsPerEntry; ++i) {
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if (val.second > static_cast<int>(i))
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res->setBit(val.first * nBitsPerEntry + i);
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}
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}
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} else {
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BOOST_FOREACH (SparseIntVect<boost::int64_t>::StorageType::value_type val,
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sres->getNonzeroElements()) {
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for (unsigned int i = 0; i < nBitsPerEntry; ++i) {
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if (val.second >= bounds[i]) {
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res->setBit(val.first * nBitsPerEntry + i);
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}
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}
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}
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}
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delete sres;
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return res;
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}
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SparseIntVect<boost::int64_t> *getTopologicalTorsionFingerprint(
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const ROMol &mol, unsigned int targetSize,
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const std::vector<std::uint32_t> *fromAtoms,
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const std::vector<std::uint32_t> *ignoreAtoms,
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const std::vector<std::uint32_t> *atomInvariants, bool includeChirality) {
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PRECONDITION(!atomInvariants || atomInvariants->size() >= mol.getNumAtoms(),
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"bad atomInvariants size");
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const ROMol *lmol = &mol;
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std::unique_ptr<ROMol> tmol;
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if (includeChirality && !mol.hasProp(common_properties::_StereochemDone)) {
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tmol = std::unique_ptr<ROMol>(new ROMol(mol));
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MolOps::assignStereochemistry(*tmol);
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lmol = tmol.get();
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}
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boost::uint64_t sz = 1;
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sz = (sz << (targetSize *
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(codeSize + (includeChirality ? numChiralBits : 0))));
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// NOTE: this -1 is incorrect but it's needed for backwards compatibility.
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// hopefully we'll never have a case with a torsion that hits this.
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//
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// mmm, bug compatible.
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sz -= 1;
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auto *res = new SparseIntVect<boost::int64_t>(sz);
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std::vector<std::uint32_t> atomCodes;
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atomCodes.reserve(lmol->getNumAtoms());
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for (ROMol::ConstAtomIterator atomItI = lmol->beginAtoms();
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atomItI != lmol->endAtoms(); ++atomItI) {
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if (!atomInvariants) {
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atomCodes.push_back(getAtomCode(*atomItI, 0, includeChirality));
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} else {
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// need to add to the atomCode here because we subtract off up to 2 below
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// as part of the branch correction
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atomCodes.push_back(
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(*atomInvariants)[(*atomItI)->getIdx()] % ((1 << codeSize) - 1) + 2);
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}
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}
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boost::dynamic_bitset<> *fromAtomsBV = nullptr;
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if (fromAtoms) {
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fromAtomsBV = new boost::dynamic_bitset<>(lmol->getNumAtoms());
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BOOST_FOREACH (std::uint32_t fAt, *fromAtoms) { fromAtomsBV->set(fAt); }
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}
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boost::dynamic_bitset<> *ignoreAtomsBV = nullptr;
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if (ignoreAtoms) {
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ignoreAtomsBV = new boost::dynamic_bitset<>(mol.getNumAtoms());
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BOOST_FOREACH (std::uint32_t fAt, *ignoreAtoms) {
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ignoreAtomsBV->set(fAt);
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}
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}
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boost::dynamic_bitset<> pAtoms(lmol->getNumAtoms());
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PATH_LIST paths = findAllPathsOfLengthN(*lmol, targetSize, false);
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for (PATH_LIST::const_iterator pathIt = paths.begin(); pathIt != paths.end();
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++pathIt) {
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bool keepIt = true;
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if (fromAtomsBV) {
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keepIt = false;
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}
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std::vector<std::uint32_t> pathCodes;
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const PATH_TYPE &path = *pathIt;
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if (fromAtomsBV) {
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if (fromAtomsBV->test(static_cast<std::uint32_t>(path.front())) ||
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fromAtomsBV->test(static_cast<std::uint32_t>(path.back()))) {
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keepIt = true;
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}
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}
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if (keepIt && ignoreAtomsBV) {
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BOOST_FOREACH (int pElem, path) {
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if (ignoreAtomsBV->test(pElem)) {
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keepIt = false;
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break;
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}
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}
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}
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if (keepIt) {
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pAtoms.reset();
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for (auto pIt = path.begin(); pIt < path.end(); ++pIt) {
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// look for a cycle that doesn't start at the first atom
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// we can't effectively canonicalize these at the moment
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// (was github #811)
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if (pIt != path.begin() && *pIt != *(path.begin()) && pAtoms[*pIt]) {
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pathCodes.clear();
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break;
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}
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pAtoms.set(*pIt);
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unsigned int code = atomCodes[*pIt] - 1;
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// subtract off the branching number:
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if (pIt != path.begin() && pIt + 1 != path.end()) {
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--code;
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}
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pathCodes.push_back(code);
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}
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if (pathCodes.size()) {
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boost::int64_t code =
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getTopologicalTorsionCode(pathCodes, includeChirality);
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updateElement(*res, code);
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}
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}
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}
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delete fromAtomsBV;
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delete ignoreAtomsBV;
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return res;
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}
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namespace {
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template <typename T>
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void TorsionFpCalc(T *res, const ROMol &mol, unsigned int nBits,
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unsigned int targetSize,
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const std::vector<std::uint32_t> *fromAtoms,
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const std::vector<std::uint32_t> *ignoreAtoms,
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const std::vector<std::uint32_t> *atomInvariants,
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bool includeChirality) {
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PRECONDITION(!atomInvariants || atomInvariants->size() >= mol.getNumAtoms(),
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"bad atomInvariants size");
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const ROMol *lmol = &mol;
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std::unique_ptr<ROMol> tmol;
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if (includeChirality && !mol.hasProp(common_properties::_StereochemDone)) {
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tmol = std::unique_ptr<ROMol>(new ROMol(mol));
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MolOps::assignStereochemistry(*tmol);
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lmol = tmol.get();
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}
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std::vector<std::uint32_t> atomCodes;
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atomCodes.reserve(lmol->getNumAtoms());
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for (ROMol::ConstAtomIterator atomItI = lmol->beginAtoms();
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atomItI != lmol->endAtoms(); ++atomItI) {
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if (!atomInvariants) {
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atomCodes.push_back(getAtomCode(*atomItI, 0, includeChirality));
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} else {
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// need to add to the atomCode here because we subtract off up to 2 below
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// as part of the branch correction
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atomCodes.push_back(((*atomInvariants)[(*atomItI)->getIdx()] << 1) + 1);
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}
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}
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boost::dynamic_bitset<> *fromAtomsBV = nullptr;
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if (fromAtoms) {
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fromAtomsBV = new boost::dynamic_bitset<>(lmol->getNumAtoms());
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BOOST_FOREACH (std::uint32_t fAt, *fromAtoms) { fromAtomsBV->set(fAt); }
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}
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boost::dynamic_bitset<> *ignoreAtomsBV = nullptr;
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if (ignoreAtoms) {
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ignoreAtomsBV = new boost::dynamic_bitset<>(lmol->getNumAtoms());
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BOOST_FOREACH (std::uint32_t fAt, *ignoreAtoms) {
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ignoreAtomsBV->set(fAt);
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}
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}
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PATH_LIST paths = findAllPathsOfLengthN(*lmol, targetSize, false);
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for (PATH_LIST::const_iterator pathIt = paths.begin(); pathIt != paths.end();
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++pathIt) {
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bool keepIt = true;
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if (fromAtomsBV) {
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keepIt = false;
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}
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const PATH_TYPE &path = *pathIt;
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if (fromAtomsBV) {
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if (fromAtomsBV->test(static_cast<std::uint32_t>(path.front())) ||
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fromAtomsBV->test(static_cast<std::uint32_t>(path.back()))) {
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keepIt = true;
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}
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}
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if (keepIt && ignoreAtomsBV) {
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BOOST_FOREACH (int pElem, path) {
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if (ignoreAtomsBV->test(pElem)) {
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keepIt = false;
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break;
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}
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}
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}
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if (keepIt) {
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std::vector<std::uint32_t> pathCodes(targetSize);
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for (unsigned int i = 0; i < targetSize; ++i) {
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unsigned int code = atomCodes[path[i]] - 1;
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// subtract off the branching number:
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if (i > 0 && i < targetSize - 1) {
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--code;
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}
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pathCodes[i] = code;
|
|
}
|
|
size_t bit = getTopologicalTorsionHash(pathCodes);
|
|
updateElement(*res, bit % nBits);
|
|
}
|
|
}
|
|
delete fromAtomsBV;
|
|
delete ignoreAtomsBV;
|
|
}
|
|
} // namespace
|
|
SparseIntVect<boost::int64_t> *getHashedTopologicalTorsionFingerprint(
|
|
const ROMol &mol, unsigned int nBits, unsigned int targetSize,
|
|
const std::vector<std::uint32_t> *fromAtoms,
|
|
const std::vector<std::uint32_t> *ignoreAtoms,
|
|
const std::vector<std::uint32_t> *atomInvariants, bool includeChirality) {
|
|
PRECONDITION(!atomInvariants || atomInvariants->size() >= mol.getNumAtoms(),
|
|
"bad atomInvariants size");
|
|
auto *res = new SparseIntVect<boost::int64_t>(nBits);
|
|
TorsionFpCalc(res, mol, nBits, targetSize, fromAtoms, ignoreAtoms,
|
|
atomInvariants, includeChirality);
|
|
return res;
|
|
}
|
|
|
|
ExplicitBitVect *getHashedTopologicalTorsionFingerprintAsBitVect(
|
|
const ROMol &mol, unsigned int nBits, unsigned int targetSize,
|
|
const std::vector<std::uint32_t> *fromAtoms,
|
|
const std::vector<std::uint32_t> *ignoreAtoms,
|
|
const std::vector<std::uint32_t> *atomInvariants,
|
|
unsigned int nBitsPerEntry, bool includeChirality) {
|
|
PRECONDITION(!atomInvariants || atomInvariants->size() >= mol.getNumAtoms(),
|
|
"bad atomInvariants size");
|
|
static int bounds[4] = {1, 2, 4, 8};
|
|
unsigned int blockLength = nBits / nBitsPerEntry;
|
|
auto *sres = new SparseIntVect<boost::int64_t>(blockLength);
|
|
TorsionFpCalc(sres, mol, blockLength, targetSize, fromAtoms, ignoreAtoms,
|
|
atomInvariants, includeChirality);
|
|
auto *res = new ExplicitBitVect(nBits);
|
|
|
|
if (nBitsPerEntry != 4) {
|
|
BOOST_FOREACH (SparseIntVect<boost::int64_t>::StorageType::value_type val,
|
|
sres->getNonzeroElements()) {
|
|
for (unsigned int i = 0; i < nBitsPerEntry; ++i) {
|
|
if (val.second > static_cast<int>(i))
|
|
res->setBit(val.first * nBitsPerEntry + i);
|
|
}
|
|
}
|
|
} else {
|
|
BOOST_FOREACH (SparseIntVect<boost::int64_t>::StorageType::value_type val,
|
|
sres->getNonzeroElements()) {
|
|
for (unsigned int i = 0; i < nBitsPerEntry; ++i) {
|
|
if (val.second >= bounds[i]) {
|
|
res->setBit(val.first * nBitsPerEntry + i);
|
|
}
|
|
}
|
|
}
|
|
}
|
|
delete sres;
|
|
return res;
|
|
}
|
|
} // end of namespace AtomPairs
|
|
} // end of namespace RDKit
|