Enumerate.h
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#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{INT_MAX};
bool sanePartialProducts{false};
EnumerationParams() {}
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 &params = 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() override;
void toStream(std::ostream &ss) const override;
void initFromStream(std::istream &ss) override;
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();
} // namespace RDKit
#endif
EnumerateBase.h
RDKit::ChemicalReaction
This is a class for storing and applying general chemical reactions.
Definition: Reaction.h:121
RDKit::EnumerateLibraryBase
Definition: EnumerateBase.h:63
RDKit::EnumerateLibrary
This is a class for running reactions on sets of reagents.
Definition: Enumerate.h:112
RDKit::EnumerateLibrary::EnumerateLibrary
EnumerateLibrary(const std::string &s)
Definition: Enumerate.h:117
RDKit::EnumerateLibrary::next
std::vector< MOL_SPTR_VECT > next() override
Get the next product set.
RDKit::EnumerateLibrary::EnumerateLibrary
EnumerateLibrary()
Definition: Enumerate.h:116
RDKit::EnumerateLibrary::EnumerateLibrary
EnumerateLibrary(const EnumerateLibrary &rhs)
RDKit::EnumerateLibrary::toStream
void toStream(std::ostream &ss) const override
serializes (pickles) to a stream
RDKit::EnumerateLibrary::initFromStream
void initFromStream(std::istream &ss) override
initializes from a stream pickle
RDKit::EnumerateLibrary::EnumerateLibrary
EnumerateLibrary(const ChemicalReaction &rxn, const EnumerationTypes::BBS &reagents, const EnumerationParams &params=EnumerationParams())
RDKit::EnumerateLibrary::getReagents
const EnumerationTypes::BBS & getReagents() const
Return the reagents used in the library.
Definition: Enumerate.h:131
RDKit::EnumerateLibrary::EnumerateLibrary
EnumerateLibrary(const ChemicalReaction &rxn, const EnumerationTypes::BBS &reagents, const EnumerationStrategyBase &enumerator, const EnumerationParams &params=EnumerationParams())
RDKit::EnumerationStrategyBase
Definition: EnumerationStrategyBase.h:121
RDKit::MolPickler::molFromPickle
static void molFromPickle(const std::string &pickle, ROMol *mol, unsigned int propertyFlags)
constructs a molecule from a pickle stored in a string
RDKit::MolPickler::pickleMol
static void pickleMol(const ROMol *mol, std::ostream &ss)
pickles a molecule and sends the results to stream ss
export.h
RDKIT_CHEMREACTIONS_EXPORT
#define RDKIT_CHEMREACTIONS_EXPORT
Definition: export.h:49
RDKit::EnumerationStrategyPickler::pickle
RDKIT_CHEMREACTIONS_EXPORT void pickle(const boost::shared_ptr< EnumerationStrategyBase > &enumerator, std::ostream &ss)
pickles a EnumerationStrategy and adds the results to a stream ss
RDKit::EnumerationTypes::BBS
std::vector< MOL_SPTR_VECT > BBS
Definition: EnumerateTypes.h:42
RDKit
Std stuff.
Definition: Abbreviations.h:18
RDKit::removeNonmatchingReagents
RDKIT_CHEMREACTIONS_EXPORT EnumerationTypes::BBS removeNonmatchingReagents(const ChemicalReaction &rxn, EnumerationTypes::BBS bbs, const EnumerationParams &params=EnumerationParams())
RDKit::EnumerateLibraryCanSerialize
RDKIT_CHEMREACTIONS_EXPORT bool EnumerateLibraryCanSerialize()
RDKit::EnumerationParams
Definition: Enumerate.h:60
RDKit::EnumerationParams::EnumerationParams
EnumerationParams()
Definition: Enumerate.h:63
RDKit::EnumerationParams::EnumerationParams
EnumerationParams(const EnumerationParams &rhs)
Definition: Enumerate.h:65