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CartesianProduct.h
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//
// Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
// All rights reserved.
//
// Redistribution and use in source and binary forms, with or without
// modification, are permitted provided that the following conditions are
// met:
//
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above
// copyright notice, this list of conditions and the following
// disclaimer in the documentation and/or other materials provided
// with the distribution.
// * Neither the name of Novartis Institutes for BioMedical Research Inc.
// nor the names of its contributors may be used to endorse or promote
// products derived from this software without specific prior written
// permission.
//
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
// "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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//
#include <RDGeneral/export.h>
#ifndef CARTESIANPRODUCT_H
#define CARTESIANPRODUCT_H
#include "EnumerationStrategyBase.h"
namespace RDKit {
//! This is a class for enumerating reagents using Cartesian Products of
/// reagents.
/*!
CartesianProductStrategy produces a standard walk through all possible
reagent combinations:
(0,0,0), (1,0,0), (2,0,0) ...
basic usage:
\verbatim
std::vector<MOL_SPTR_VECT> bbs;
bbs.push_back( bbs_for_reactants_1 );
bbs.push_back( bbs_for_reactants_2 );
RGRUOPS num_bbs;
num_bbs.push_back(bbs[0].size());
num_bbs.push_back(bbs[1].size());
CartesianProductStrategy rgroups(num_bbs);
for(size_t i=0; i<num_samples && rgroups; ++i) {
MOL_SPTR_VECT rvect = getReactantsFromRGroups(bbs, rgroups.next());
std::vector<MOL_SPTR_VECT> lprops = rxn.RunReactants(rvect);
...
}
\endverbatim
See EnumerationStrategyBase for more details and usage.
*/
class RDKIT_CHEMREACTIONS_EXPORT CartesianProductStrategy
: public EnumerationStrategyBase {
size_t m_numPermutationsProcessed{};
public:
CartesianProductStrategy() : EnumerationStrategyBase() {}
using EnumerationStrategyBase::initialize;
void initializeStrategy(const ChemicalReaction &,
const EnumerationTypes::BBS &) override {
m_numPermutationsProcessed = 0;
}
const char *type() const override { return "CartesianProductStrategy"; }
//! The current permutation {r1, r2, ...}
const EnumerationTypes::RGROUPS &next() override {
if (m_numPermutationsProcessed) {
increment();
} else {
++m_numPermutationsProcessed;
}
return m_permutation;
}
boost::uint64_t getPermutationIdx() const override {
return m_numPermutationsProcessed;
}
operator bool() const override { return hasNext(); }
EnumerationStrategyBase *copy() const override {
return new CartesianProductStrategy(*this);
}
private:
void increment() {
next(0);
++m_numPermutationsProcessed;
}
bool hasNext() const {
// Fix me -> use multiprecision int here???
return m_numPermutations == EnumerationStrategyBase::EnumerationOverflow ||
m_numPermutationsProcessed < rdcast<size_t>(m_numPermutations);
}
void next(size_t rowToIncrement) {
if (!hasNext()) {
return;
}
m_permutation[rowToIncrement] += 1;
size_t max_index_of_row = m_permutationSizes[rowToIncrement] - 1;
if (m_permutation[rowToIncrement] > max_index_of_row) {
m_permutation[rowToIncrement] = 0;
next(rowToIncrement + 1);
}
}
private:
#ifdef RDK_USE_BOOST_SERIALIZATION
friend class boost::serialization::access;
template <class Archive>
void serialize(Archive &ar, const unsigned int /*version*/) {
ar &boost::serialization::base_object<EnumerationStrategyBase>(*this);
ar & m_numPermutationsProcessed;
}
#endif
};
} // namespace RDKit
#ifdef RDK_USE_BOOST_SERIALIZATION
BOOST_CLASS_VERSION(RDKit::CartesianProductStrategy, 1)
#endif
#endif
EnumerationStrategyBase.h
RDKit::CartesianProductStrategy
Definition CartesianProduct.h:71
RDKit::CartesianProductStrategy::getPermutationIdx
boost::uint64_t getPermutationIdx() const override
Returns how many permutations have been processed by this strategy.
Definition CartesianProduct.h:97
RDKit::CartesianProductStrategy::copy
EnumerationStrategyBase * copy() const override
copy the enumeration strategy complete with current state
Definition CartesianProduct.h:103
RDKit::CartesianProductStrategy::type
const char * type() const override
Definition CartesianProduct.h:84
RDKit::CartesianProductStrategy::next
const EnumerationTypes::RGROUPS & next() override
The current permutation {r1, r2, ...}.
Definition CartesianProduct.h:87
RDKit::CartesianProductStrategy::initializeStrategy
void initializeStrategy(const ChemicalReaction &, const EnumerationTypes::BBS &) override
Definition CartesianProduct.h:79
RDKit::CartesianProductStrategy::CartesianProductStrategy
CartesianProductStrategy()
Definition CartesianProduct.h:75
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition Reaction.h:121
RDKit::EnumerationStrategyBase::initialize
void initialize(const ChemicalReaction &reaction, const EnumerationTypes::BBS &building_blocks)
Definition EnumerationStrategyBase.h:145
RDKit::EnumerationStrategyBase::m_permutation
EnumerationTypes::RGROUPS m_permutation
Definition EnumerationStrategyBase.h:125
RDKit::EnumerationStrategyBase::EnumerationStrategyBase
EnumerationStrategyBase()
Definition EnumerationStrategyBase.h:134
export.h
RDKIT_CHEMREACTIONS_EXPORT
#define RDKIT_CHEMREACTIONS_EXPORT
Definition export.h:57
RDKit::EnumerationTypes::RGROUPS
std::vector< boost::uint64_t > RGROUPS
Definition EnumerateTypes.h:56
RDKit::EnumerationTypes::BBS
std::vector< MOL_SPTR_VECT > BBS
Definition EnumerateTypes.h:42
RDKit::MolStandardize::Operations::serialize
RDKIT_MOLSTANDARDIZE_EXPORT void serialize(RWMOL_SPTR_PAIR output, PipelineResult &result, const PipelineOptions &options)
RDKit
Std stuff.
Definition Abbreviations.h:19