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//
// 2019, Daniel Probst, Reymond Group @ University of Bern
//
// @@ 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 <algorithm>
#include <iostream>
#include <limits>
#include <numeric>
#include <stdexcept>
#include <cstdint>
#include <cmath>
#include <set>
#include <RDGeneral/BoostStartInclude.h>
#include <boost/random/uniform_int_distribution.hpp>
#include <RDGeneral/BoostEndInclude.h>
#include <RDGeneral/types.h>
#include <GraphMol/MolOps.h>
#include <GraphMol/Subgraphs/Subgraphs.h>
#include <GraphMol/Subgraphs/SubgraphUtils.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/SmilesParse/SmilesWrite.h>
#include "MHFP.h"
namespace RDKit {
namespace MHFPFingerprints {
MHFPEncoder::MHFPEncoder(unsigned int n_permutations, unsigned int seed)
: n_permutations_(n_permutations),
seed_(seed),
perms_a_(n_permutations, 0),
perms_b_(n_permutations, 0) {
boost::mt19937 rand;
rand.seed(seed_);
boost::random::uniform_int_distribution<boost::mt19937::result_type> dist_a(
1, max_hash_);
boost::random::uniform_int_distribution<boost::mt19937::result_type> dist_b(
0, max_hash_);
for (unsigned int i = 0; i < n_permutations_; i++) {
uint32_t a = dist_a(rand);
uint32_t b = dist_b(rand);
while (std::find(perms_a_.begin(), perms_a_.end(), a) != perms_a_.end()) {
a = dist_a(rand);
}
while (std::find(perms_b_.begin(), perms_b_.end(), b) != perms_b_.end()) {
b = dist_a(rand);
}
perms_a_[i] = a;
perms_b_[i] = b;
}
}
std::vector<uint32_t> MHFPEncoder::FromStringArray(
const std::vector<std::string> &vec) {
std::vector<uint32_t> mh(n_permutations_, max_hash_);
for (uint32_t i = 0; i < vec.size(); i++) {
auto hashi = FNV::hash(vec[i]);
for (size_t j = 0; j < n_permutations_; j++) {
uint32_t tmp =
(FastMod((perms_a_[j] * hashi + perms_b_[j]), prime_)) & max_hash_;
mh[j] = std::min(tmp, mh[j]);
}
}
return mh;
}
std::vector<uint32_t> MHFPEncoder::FromArray(const std::vector<uint32_t> &vec) {
std::vector<uint32_t> mh(n_permutations_, max_hash_);
for (uint32_t i = 0; i < vec.size(); i++) {
for (size_t j = 0; j < n_permutations_; j++) {
uint32_t tmp =
(FastMod((perms_a_[j] * vec[i] + perms_b_[j]), prime_)) & max_hash_;
mh[j] = std::min(tmp, mh[j]);
}
}
return mh;
}
std::vector<std::string> MHFPEncoder::CreateShingling(
const ROMol &mol, unsigned char radius, bool rings, bool isomeric,
bool kekulize, unsigned char min_radius) {
RWMol tmol(mol);
if (kekulize) {
MolOps::Kekulize(tmol);
}
std::vector<std::string> shingling;
if (rings) {
const VECT_INT_VECT bonds_vect = tmol.getRingInfo()->bondRings();
for (size_t i = 0; i < bonds_vect.size(); i++) {
std::unique_ptr<ROMol> m(Subgraphs::pathToSubmol(tmol, bonds_vect[i]));
shingling.emplace_back(MolToSmiles(*m));
}
}
unsigned char min_radius_internal = min_radius;
if (!min_radius) {
for (auto atom : tmol.atoms()) {
bool do_kekule = false;
const RDKit::Bond *bond_in = nullptr;
bool all_hs_explicit = false;
bool isomeric_smiles = true;
shingling.emplace_back(SmilesWrite::GetAtomSmiles(
atom, do_kekule, bond_in, all_hs_explicit, isomeric_smiles));
}
min_radius_internal++;
}
for (uint32_t index = 0; index < tmol.getNumAtoms(); ++index) {
for (unsigned char r = min_radius_internal; r < radius + 1; ++r) {
const PATH_TYPE path = findAtomEnvironmentOfRadiusN(tmol, r, index);
INT_MAP_INT amap;
bool use_query = false;
std::unique_ptr<ROMol> submol(
Subgraphs::pathToSubmol(tmol, path, use_query, amap));
if (amap.find(index) == amap.end()) {
continue;
}
std::string smiles =
MolToSmiles(*submol, isomeric, kekulize, amap[index]);
if (!smiles.empty()) {
shingling.emplace_back(smiles);
}
}
}
return shingling;
}
std::vector<std::string> MHFPEncoder::CreateShingling(
const std::string &smiles, unsigned char radius, bool rings, bool isomeric,
bool kekulize, unsigned char min_radius) {
std::unique_ptr<RWMol> m(SmilesToMol(smiles));
PRECONDITION(m, "could not parse smiles");
return CreateShingling(*m, radius, rings, isomeric, kekulize, min_radius);
}
std::vector<uint32_t> MHFPEncoder::Encode(ROMol &mol, unsigned char radius,
bool rings, bool isomeric,
bool kekulize,
unsigned char min_radius) {
return FromStringArray(
CreateShingling(mol, radius, rings, isomeric, kekulize, min_radius));
}
std::vector<std::vector<uint32_t>> MHFPEncoder::Encode(
std::vector<ROMol> &mols, unsigned char radius, bool rings, bool isomeric,
bool kekulize, unsigned char min_radius) {
size_t n = mols.size();
std::vector<std::vector<uint32_t>> results(n);
for (size_t i = 0; i < n; i++) {
results[i] = FromStringArray(CreateShingling(
mols[i], radius, rings, isomeric, kekulize, min_radius));
}
return results;
}
std::vector<uint32_t> MHFPEncoder::Encode(std::string &smiles,
unsigned char radius, bool rings,
bool isomeric, bool kekulize,
unsigned char min_radius) {
return FromStringArray(
CreateShingling(smiles, radius, rings, isomeric, kekulize, min_radius));
}
// Someone has to come up with a plural for smiles... smiless, smileses?
std::vector<std::vector<uint32_t>> MHFPEncoder::Encode(
std::vector<std::string> &smileses, unsigned char radius, bool rings,
bool isomeric, bool kekulize, unsigned char min_radius) {
size_t n = smileses.size();
std::vector<std::vector<uint32_t>> results(n);
for (size_t i = 0; i < n; i++) {
results[i] = FromStringArray(CreateShingling(
smileses[i], radius, rings, isomeric, kekulize, min_radius));
}
return results;
}
ExplicitBitVect MHFPEncoder::EncodeSECFP(ROMol &mol, unsigned char radius,
bool rings, bool isomeric,
bool kekulize,
unsigned char min_radius,
size_t length) {
return Fold(HashShingling(CreateShingling(mol, radius, rings, isomeric,
kekulize, min_radius)),
length);
}
std::vector<ExplicitBitVect> MHFPEncoder::EncodeSECFP(
std::vector<ROMol> &mols, unsigned char radius, bool rings, bool isomeric,
bool kekulize, unsigned char min_radius, size_t length) {
size_t n = mols.size();
std::vector<ExplicitBitVect> results(n);
for (size_t i = 0; i < n; i++) {
results[i] =
Fold(HashShingling(CreateShingling(mols[i], radius, rings, isomeric,
kekulize, min_radius)),
length);
}
return results;
}
ExplicitBitVect MHFPEncoder::EncodeSECFP(std::string &smiles,
unsigned char radius, bool rings,
bool isomeric, bool kekulize,
unsigned char min_radius,
size_t length) {
return Fold(HashShingling(CreateShingling(smiles, radius, rings, isomeric,
kekulize, min_radius)),
length);
}
std::vector<ExplicitBitVect> MHFPEncoder::EncodeSECFP(
std::vector<std::string> &smileses, unsigned char radius, bool rings,
bool isomeric, bool kekulize, unsigned char min_radius, size_t length) {
size_t n = smileses.size();
std::vector<ExplicitBitVect> results(n);
for (size_t i = 0; i < n; i++) {
results[i] =
Fold(HashShingling(CreateShingling(smileses[i], radius, rings, isomeric,
kekulize, min_radius)),
length);
}
return results;
}
} // namespace MHFPFingerprints
} // namespace RDKit
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