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SubstructureCache.h
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//
// Copyright (C) 2014 Novartis Institutes for BioMedical Research
//
// @@ 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 <RDGeneral/export.h>
#pragma once
#include <list>
#include <vector>
#include <string>
#include <stdexcept>
#include "../RDKitBase.h"
#include "Graph.h"
#include "Seed.h"
#include "DebugTrace.h" // algorithm filter definitions
namespace RDKit {
namespace FMCS {
class RDKIT_FMCS_EXPORT SubstructureCache {
public:
#pragma pack(push, 1)
struct KeyNumericMetrics {
typedef unsigned long long TValue;
TValue Value{0};
public:
KeyNumericMetrics() {}
};
#pragma pack(pop)
struct HashKey {
KeyNumericMetrics NumericMetrics;
public:
void computeKey(const Seed &seed,
const std::vector<unsigned int> &queryAtomLabels,
const std::vector<unsigned int> &queryBondLabels) {
computeMorganCodeHash(seed, queryAtomLabels, queryBondLabels);
}
private:
void computeMorganCodeHash(
const Seed &seed, const std::vector<unsigned int> &queryAtomLabels,
const std::vector<unsigned int> &queryBondLabels) {
size_t nv = seed.getNumAtoms();
size_t ne = seed.getNumBonds();
std::vector<unsigned long> currCodes(nv);
std::vector<unsigned long> prevCodes(nv);
size_t nIterations = seed.getNumBonds();
if (nIterations > 5) {
nIterations = 5;
}
for (unsigned int seedAtomIdx = 0; seedAtomIdx < seed.getNumAtoms();
++seedAtomIdx) {
currCodes[seedAtomIdx] = queryAtomLabels.at(
seed.MoleculeFragment.Atoms.at(seedAtomIdx)->getIdx());
}
for (size_t iter = 0; iter < nIterations; ++iter) {
for (size_t i = 0; i < nv; ++i) {
prevCodes[i] = currCodes[i];
}
for (size_t seedBondIdx = 0; seedBondIdx < ne; ++seedBondIdx) {
const Bond *bond = seed.MoleculeFragment.Bonds[seedBondIdx];
unsigned int order = queryBondLabels.at(
seed.MoleculeFragment.Bonds.at(seedBondIdx)->getIdx());
unsigned int atom1 = seed.MoleculeFragment.SeedAtomIdxMap
.find(bond->getBeginAtomIdx())
->second;
unsigned int atom2 =
seed.MoleculeFragment.SeedAtomIdxMap.find(bond->getEndAtomIdx())
->second;
unsigned int v1 = prevCodes[atom1];
unsigned int v2 = prevCodes[atom2];
currCodes[atom1] += v2 * v2 + (v2 + 23) * (order + 1721);
currCodes[atom2] += v1 * v1 + (v1 + 23) * (order + 1721);
}
}
KeyNumericMetrics::TValue result = 0;
for (unsigned int seedAtomIdx = 0; seedAtomIdx < nv; ++seedAtomIdx) {
unsigned long code = currCodes[seedAtomIdx];
result += code * (code + 6849) + 29;
}
NumericMetrics.Value = result;
}
// not implemented yet:
/*
void computeFingerprint(const Seed& seed)
{
unsigned int radius = seed.getNumBonds();
if (radius > 5)
radius = 5;
ExplicitBitVect *mf =
RDKit::MorganFingerprints::getFingerprintAsBitVect(seed.GraphTopology,
radius); //SLOW !!!
// ...
delete mf;
NumericMetrics.Field.hasFingerprint = 1;
}
*/
};
typedef HashKey TKey;
typedef std::list<FMCS::Graph> TIndexEntry; // hash-key is not unique key
private:
std::vector<TIndexEntry> ValueStorage;
std::map<KeyNumericMetrics::TValue, size_t> NumericIndex; // TIndexEntry
public:
// returns computed key, and pointer to index entry with a set of subgraphs
// corresponding to the key if found.
// then caller must find exactly matched subgraph in the result set with own
// search algorithm,
// including a resolving of collisions of hash key
TIndexEntry *find(const Seed &seed,
const std::vector<unsigned int> &queryAtomLabels,
const std::vector<unsigned int> &queryBondLabels,
TKey &key) { // compute key and find entry
key.computeKey(seed, queryAtomLabels, queryBondLabels);
const auto entryit = NumericIndex.find(key.NumericMetrics.Value);
if (NumericIndex.end() != entryit) {
return &ValueStorage[entryit->second];
}
return nullptr; // not found
}
// if find() did not found any entry for this key of seed a new entry will be
// created
void add(const Seed &seed, TKey &key,
TIndexEntry *entry) { // "compute" value and store it in NEW entry
// if not found
if (!entry) {
try {
ValueStorage.emplace_back();
} catch (...) {
return; // not enough memory room to add the item, but it's just a
// cache
}
entry = &ValueStorage.back();
}
entry->push_back(seed.Topology);
if (!NumericIndex
.insert(std::make_pair(key.NumericMetrics.Value,
ValueStorage.size() - 1))
.second) {
return; // not enough memory room to add the item, but it is just cache
}
}
size_t keyssize() const { // for statistics only
return ValueStorage.size();
}
size_t fullsize() const { // for statistics only
return std::accumulate(
ValueStorage.begin(), ValueStorage.end(), 0,
[](const auto &acc, const auto &v) { return acc + v.size(); });
}
};
} // namespace FMCS
} // namespace RDKit
DebugTrace.h
Graph.h
RDKitBase.h
pulls in the core RDKit functionality
Seed.h
RDKit::FMCS::Seed
Definition Seed.h:61
RDKit::FMCS::SubstructureCache
Definition SubstructureCache.h:23
RDKit::FMCS::SubstructureCache::TKey
HashKey TKey
Definition SubstructureCache.h:113
RDKit::FMCS::SubstructureCache::TIndexEntry
std::list< FMCS::Graph > TIndexEntry
Definition SubstructureCache.h:114
RDKit::FMCS::SubstructureCache::find
TIndexEntry * find(const Seed &seed, const std::vector< unsigned int > &queryAtomLabels, const std::vector< unsigned int > &queryBondLabels, TKey &key)
Definition SubstructureCache.h:124
RDKit::FMCS::SubstructureCache::fullsize
size_t fullsize() const
Definition SubstructureCache.h:164
RDKit::FMCS::SubstructureCache::keyssize
size_t keyssize() const
Definition SubstructureCache.h:160
RDKit::FMCS::SubstructureCache::add
void add(const Seed &seed, TKey &key, TIndexEntry *entry)
Definition SubstructureCache.h:138
export.h
RDKIT_FMCS_EXPORT
#define RDKIT_FMCS_EXPORT
Definition export.h:169
RDKit::FMCS
Definition Composition2N.h:13
RDKit
Std stuff.
Definition Abbreviations.h:19
RDKit::FMCS::SubstructureCache::HashKey
Definition SubstructureCache.h:35
RDKit::FMCS::SubstructureCache::HashKey::computeKey
void computeKey(const Seed &seed, const std::vector< unsigned int > &queryAtomLabels, const std::vector< unsigned int > &queryBondLabels)
Definition SubstructureCache.h:39
RDKit::FMCS::SubstructureCache::HashKey::NumericMetrics
KeyNumericMetrics NumericMetrics
Definition SubstructureCache.h:36
RDKit::FMCS::SubstructureCache::KeyNumericMetrics
Definition SubstructureCache.h:26
RDKit::FMCS::SubstructureCache::KeyNumericMetrics::Value
TValue Value
Definition SubstructureCache.h:28
RDKit::FMCS::SubstructureCache::KeyNumericMetrics::KeyNumericMetrics
KeyNumericMetrics()
Definition SubstructureCache.h:31
RDKit::FMCS::SubstructureCache::KeyNumericMetrics::TValue
unsigned long long TValue
Definition SubstructureCache.h:27