RDKit::EnumerateLibrary Class Reference

This is a class for running reactions on sets of reagents. More...

#include <Enumerate.h>

Inheritance diagram for RDKit::EnumerateLibrary:

Public Member Functions
	EnumerateLibrary ()
	EnumerateLibrary (const std::string &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)
const EnumerationTypes::BBS &	getReagents () const
	Return the reagents used in the library. This may be fewer reagents than.
std::vector< MOL_SPTR_VECT >	next () override
	Get the next product set.
void	toStream (std::ostream &ss) const override
	serializes (pickles) to a stream
void	initFromStream (std::istream &ss) override
	initializes from a stream pickle
Public Member Functions inherited from RDKit::EnumerateLibraryBase
	EnumerateLibraryBase ()
	default constructor
	EnumerateLibraryBase (const ChemicalReaction &rxn, EnumerationStrategyBase *enumerator=nullptr)
	construct with a chemical reaction and an enumeration strategy
	EnumerateLibraryBase (const EnumerateLibraryBase &rhs)
	Copy constructor.
virtual	~EnumerateLibraryBase ()
virtual	operator bool () const
	Are there any enumerations left?
void	reset ()
	reset the enumeration to the beginning.
const ChemicalReaction &	getReaction () const
	returns the underlying chemical reaction
const EnumerationStrategyBase &	getEnumerator ()
	return the current enumeration strategy
virtual std::vector< std::vector< std::string > >	nextSmiles ()
const EnumerationTypes::RGROUPS &	getPosition () const
std::string	getState () const
void	setState (const std::string &)
void	resetState ()
	Reset the enumerator to the beginning.
virtual std::string	Serialize () const
	returns a string with a serialized (pickled) representation
virtual void	initFromString (const std::string &text)
	initializes from a string pickle

Additional Inherited Members
Protected Attributes inherited from RDKit::EnumerateLibraryBase
ChemicalReaction	m_rxn
boost::shared_ptr< EnumerationStrategyBase >	m_enumerator
boost::shared_ptr< EnumerationStrategyBase >	m_initialEnumerator

Detailed Description

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:

 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();
   ...
 }

In general, reactions will enumerate to more products than desired, a standard use is:

 for(int i=0;i<num_samples && (bool)en; ++i) {
   std::vector<MOL_SPTR_VECT> products = en.next();
   ...
 }

Definition at line 111 of file Enumerate.h.

Constructor & Destructor Documentation

EnumerateLibrary() [1/5]

RDKit::EnumerateLibrary::EnumerateLibrary ( )

inline

Definition at line 116 of file Enumerate.h.

References RDKit::EnumerateLibraryBase::EnumerateLibraryBase().

Referenced by EnumerateLibrary().

EnumerateLibrary() [2/5]

RDKit::EnumerateLibrary::EnumerateLibrary ( const std::string & s )

inline

Definition at line 117 of file Enumerate.h.

References RDKit::EnumerateLibraryBase::EnumerateLibraryBase(), and RDKit::EnumerateLibraryBase::initFromString().

EnumerateLibrary() [3/5]

RDKit::EnumerateLibrary::EnumerateLibrary	(	const ChemicalReaction &	rxn,
		const EnumerationTypes::BBS &	reagents,
		const EnumerationParams &	params = EnumerationParams() )

EnumerateLibrary() [4/5]

RDKit::EnumerateLibrary::EnumerateLibrary	(	const ChemicalReaction &	rxn,
		const EnumerationTypes::BBS &	reagents,
		const EnumerationStrategyBase &	enumerator,
		const EnumerationParams &	params = EnumerationParams() )

EnumerateLibrary() [5/5]

RDKit::EnumerateLibrary::EnumerateLibrary

(

const EnumerateLibrary &

rhs

)

References EnumerateLibrary().

Member Function Documentation

getReagents()

const EnumerationTypes::BBS & RDKit::EnumerateLibrary::getReagents ( ) const

inline

Return the reagents used in the library. This may be fewer reagents than.

Definition at line 132 of file Enumerate.h.

initFromStream()

void RDKit::EnumerateLibrary::initFromStream ( std::istream & ss )

overridevirtual

initializes from a stream pickle

Implements RDKit::EnumerateLibraryBase.

References RDKit::MolPickler::pickleMol().

next()

std::vector< MOL_SPTR_VECT > RDKit::EnumerateLibrary::next ( )

overridevirtual

Get the next product set.

Implements RDKit::EnumerateLibraryBase.

toStream()

void RDKit::EnumerateLibrary::toStream ( std::ostream & ss ) const

overridevirtual

serializes (pickles) to a stream

Implements RDKit::EnumerateLibraryBase.

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The documentation for this class was generated from the following file:

• Enumerate.h