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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
// OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
// SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
// LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
// DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
// THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
// (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
// OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.n
//
#include <RDGeneral/export.h>
#ifndef RDKIT_ENUMERATE_H
#define RDKIT_ENUMERATE_H
#include "EnumerateBase.h"
/*! \file Enumerate.h
\brief Contains the public API of the for the reaction enumeration engine
\b Note that this should be considered beta and that the API may change in
future releases.
*/
namespace RDKit {
//! This is a class for providing enumeration options that control
// how enumerations are performed.
/*!
Option
reagentMaxMatchCount [default INT_MAX]
This specifies how many times the reactant template can match a reagent.
sanePartialProducts [default false]
If true, forces all products of the reagent plus the product templates\n\
pass chemical sanitization. Note that if the product template itself\n\
does not pass sanitization, then none of the products will.
*/
struct RDKIT_CHEMREACTIONS_EXPORT EnumerationParams
{
int reagentMaxMatchCount;
bool sanePartialProducts;
EnumerationParams() :
reagentMaxMatchCount(INT_MAX), sanePartialProducts(false) {
}
EnumerationParams(const EnumerationParams &rhs) :
reagentMaxMatchCount(rhs.reagentMaxMatchCount),
sanePartialProducts(rhs.sanePartialProducts) {
}
};
//! Helper function, remove reagents that are incompatible
// with the reaction.
// rxn must be sanitized, initialized and preprocessed.
// this happens automatically in EnumerateLibrary
RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::BBS removeNonmatchingReagents(
const ChemicalReaction &rxn,
EnumerationTypes::BBS bbs,
const EnumerationParams ¶ms=EnumerationParams());
//! This is a class for running reactions on sets of reagents.
/*!
This class is a fully self contained reaction engine that can be
serialized and restarted. For example, a million products can
be generated, the engine can be saved for later and reloaded
to retrieve the next million products.
basic usage will be something like:
\verbatim
ChemicalReaction rxn = ...
BBS bbs(num_rgroups);
... somehow LoadRGroups(bbs[0]);
... somehow LoadRGroups(bbs[1]..);
...
EnumerateLibrary enumerator(en, bbs);
for(; (bool)en; ++i) {
// This is the same as rxn.run_Reactants( reagents );
std::vector<MOL_SPTR_VECT> products = en.next();
...
}
\endverbatim
In general, reactions will enumerate to more products than desired,
a standard use is:
\verbatim
for(int i=0;i<num_samples && (bool)en; ++i) {
std::vector<MOL_SPTR_VECT> products = en.next();
...
}
\endverbatim
*/
class RDKIT_CHEMREACTIONS_EXPORT EnumerateLibrary : public EnumerateLibraryBase {
EnumerationTypes::BBS m_bbs;
public:
EnumerateLibrary() : EnumerateLibraryBase(), m_bbs() {}
EnumerateLibrary(const std::string &s) : EnumerateLibraryBase(), m_bbs() {
initFromString(s);
}
EnumerateLibrary(const ChemicalReaction &rxn,
const EnumerationTypes::BBS &reagents,
const EnumerationParams & params = EnumerationParams());
EnumerateLibrary(const ChemicalReaction &rxn,
const EnumerationTypes::BBS &reagents,
const EnumerationStrategyBase &enumerator,
const EnumerationParams & params = EnumerationParams());
EnumerateLibrary(const EnumerateLibrary &rhs);
//! Return the reagents used in the library
const EnumerationTypes::BBS &getReagents() const { return m_bbs; }
//! Get the next product set
std::vector<MOL_SPTR_VECT> next();
void toStream(std::ostream &ss) const;
void initFromStream(std::istream &ss);
private:
#ifdef RDK_USE_BOOST_SERIALIZATION
friend class boost::serialization::access;
template <class Archive>
void save(Archive &ar, const unsigned int /*version*/) const {
ar &boost::serialization::base_object<EnumerateLibraryBase>(*this);
size_t sz = m_bbs.size();
ar &sz;
std::string pickle;
for (size_t i = 0; i < m_bbs.size(); ++i) {
sz = m_bbs[i].size();
ar &sz;
for (size_t j = 0; j < m_bbs[i].size(); ++j) {
MolPickler::pickleMol(*m_bbs[i][j], pickle);
ar &pickle;
}
}
}
template <class Archive>
void load(Archive &ar, const unsigned int /*version*/) {
ar &boost::serialization::base_object<EnumerateLibraryBase>(*this);
size_t sz;
ar &sz;
m_bbs.resize(sz);
for (size_t i = 0; i < m_bbs.size(); ++i) {
ar &sz;
m_bbs[i].resize(sz);
std::string pickle;
for (size_t j = 0; j < m_bbs[i].size(); ++j) {
ar &pickle;
RWMol *mol = new RWMol();
MolPickler::molFromPickle(pickle, *mol);
m_bbs[i][j].reset(mol);
}
}
}
BOOST_SERIALIZATION_SPLIT_MEMBER();
#endif
};
RDKIT_CHEMREACTIONS_EXPORT bool EnumerateLibraryCanSerialize();
}
#endif
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