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RandomSample.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
// LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
// A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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//
#include <RDGeneral/export.h>
#ifndef RGROUP_RANDOM_SAMPLE_H
#define RGROUP_RANDOM_SAMPLE_H
#include "EnumerationStrategyBase.h"
#include <boost/random.hpp>
#include <boost/random/uniform_int_distribution.hpp>
#include <sstream>
namespace RDKit {
//! This is a class for fully randomly sampling reagents.
/// Note that this enumerator never halts.
/*!
basic usage:
\verbatim
std::vector<MOL_SPTR_VECT> bbs;
bbs.push_back( bbs_for_reactants_1 );
bbs.push_back( bbs_for_reactants_2 );
RandomSampleStrategy rgroups;
rgroups.initialize(rxn, 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 RandomSampleStrategy
: public EnumerationStrategyBase {
boost::uint64_t m_numPermutationsProcessed{};
boost::minstd_rand m_rng;
std::vector<boost::random::uniform_int_distribution<>> m_distributions;
public:
RandomSampleStrategy()
: EnumerationStrategyBase(),
m_rng(),
m_distributions() {
for (size_t i = 0; i < m_permutation.size(); ++i) {
m_distributions.emplace_back(0, m_permutation[i] - 1);
}
}
using EnumerationStrategyBase::initialize;
void initializeStrategy(const ChemicalReaction &,
const EnumerationTypes::BBS &) override {
m_distributions.clear();
for (size_t i = 0; i < m_permutationSizes.size(); ++i) {
m_distributions.emplace_back(0, m_permutationSizes[i] - 1);
}
m_numPermutationsProcessed = 0;
}
const char *type() const override { return "RandomSampleStrategy"; }
//! The current permutation {r1, r2, ...}
const EnumerationTypes::RGROUPS &next() override {
for (size_t i = 0; i < m_permutation.size(); ++i) {
m_permutation[i] = m_distributions[i](m_rng);
}
++m_numPermutationsProcessed;
return m_permutation;
}
boost::uint64_t getPermutationIdx() const override {
return m_numPermutationsProcessed;
}
operator bool() const override { return true; }
EnumerationStrategyBase *copy() const override {
return new RandomSampleStrategy(*this);
}
private:
#ifdef RDK_USE_BOOST_SERIALIZATION
friend class boost::serialization::access;
template <class Archive>
void save(Archive &ar, const unsigned int /*version*/) const {
// invoke serialization of the base class
ar << boost::serialization::base_object<const EnumerationStrategyBase>(
*this);
ar << m_numPermutationsProcessed;
std::stringstream random;
random << m_rng;
std::string s = random.str();
ar << s;
}
template <class Archive>
void load(Archive &ar, const unsigned int /*version*/) {
// invoke serialization of the base class
ar >> boost::serialization::base_object<EnumerationStrategyBase>(*this);
ar >> m_numPermutationsProcessed;
std::string s;
ar >> s;
std::stringstream random(s);
random >> m_rng;
// reset the uniform distributions
m_distributions.clear();
for (size_t i = 0; i < m_permutationSizes.size(); ++i) {
m_distributions.emplace_back(0, m_permutationSizes[i] - 1);
}
}
template <class Archive>
void serialize(Archive &ar, const unsigned int file_version) {
boost::serialization::split_member(ar, *this, file_version);
}
#endif
};
} // namespace RDKit
#ifdef RDK_USE_BOOST_SERIALIZATION
BOOST_CLASS_VERSION(RDKit::RandomSampleStrategy, 1)
#endif
#endif
EnumerationStrategyBase.h
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition Reaction.h:121
RDKit::EnumerationStrategyBase
Definition EnumerationStrategyBase.h:123
RDKit::RandomSampleStrategy
Definition RandomSample.h:66
RDKit::RandomSampleStrategy::copy
EnumerationStrategyBase * copy() const override
copy the enumeration strategy complete with current state
Definition RandomSample.h:113
RDKit::RandomSampleStrategy::next
const EnumerationTypes::RGROUPS & next() override
The current permutation {r1, r2, ...}.
Definition RandomSample.h:97
RDKit::RandomSampleStrategy::getPermutationIdx
boost::uint64_t getPermutationIdx() const override
Returns how many permutations have been processed by this strategy.
Definition RandomSample.h:107
RDKit::RandomSampleStrategy::RandomSampleStrategy
RandomSampleStrategy()
Definition RandomSample.h:72
RDKit::RandomSampleStrategy::type
const char * type() const override
Definition RandomSample.h:94
RDKit::RandomSampleStrategy::initializeStrategy
void initializeStrategy(const ChemicalReaction &, const EnumerationTypes::BBS &) override
Definition RandomSample.h:84
export.h
RDKIT_CHEMREACTIONS_EXPORT
#define RDKIT_CHEMREACTIONS_EXPORT
Definition export.h:49
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
Std stuff.
Definition Abbreviations.h:19