#include <EnumerateBase.h>

Inheritance diagram for RDKit::EnumerateLibraryBase:

Public Member Functions
	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< MOL_SPTR_VECT >	next ()=0
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 void	toStream (std::ostream &ss) const =0
	serializes (pickles) to a stream
virtual std::string	Serialize () const
	returns a string with a serialized (pickled) representation
virtual void	initFromStream (std::istream &ss)=0
	initializes from a stream pickle
virtual void	initFromString (const std::string &text)
	initializes from a string pickle

Protected Attributes
ChemicalReaction	m_rxn
boost::shared_ptr< EnumerationStrategyBase >	m_enumerator
boost::shared_ptr< EnumerationStrategyBase >	m_initialEnumerator

Detailed Description

Base class for enumerating chemical reactions from collections of building blocks and reagents.

basic usage:

EnumerateLibraryBase &enumerator;
while (enumerator) {
  MOL_SPTR_VECT res = enumerator.next();
  // do something with enumeration products here
}

See Reaction.h for more details on how ChemicalReactions are used.

Definition at line 63 of file EnumerateBase.h.

Constructor & Destructor Documentation

◆ EnumerateLibraryBase() [1/3]

RDKit::EnumerateLibraryBase::EnumerateLibraryBase ( )

inline

default constructor

Definition at line 71 of file EnumerateBase.h.

References m_enumerator, m_initialEnumerator, and m_rxn.

Referenced by RDKit::EnumerateLibrary::EnumerateLibrary(), RDKit::EnumerateLibrary::EnumerateLibrary(), and EnumerateLibraryBase().

◆ EnumerateLibraryBase() [2/3]

RDKit::EnumerateLibraryBase::EnumerateLibraryBase	(	const ChemicalReaction &	rxn,
		EnumerationStrategyBase *	enumerator = nullptr )

inline

construct with a chemical reaction and an enumeration strategy

Definition at line 74 of file EnumerateBase.h.

References m_enumerator, m_initialEnumerator, and m_rxn.

◆ EnumerateLibraryBase() [3/3]

RDKit::EnumerateLibraryBase::EnumerateLibraryBase ( const EnumerateLibraryBase & rhs )

inline

Copy constructor.

Definition at line 83 of file EnumerateBase.h.

References EnumerateLibraryBase(), m_enumerator, m_initialEnumerator, and m_rxn.

◆ ~EnumerateLibraryBase()

virtual RDKit::EnumerateLibraryBase::~EnumerateLibraryBase ( )

inlinevirtual

Definition at line 88 of file EnumerateBase.h.

Member Function Documentation

◆ getEnumerator()

const EnumerationStrategyBase & RDKit::EnumerateLibraryBase::getEnumerator ( )

inline

return the current enumeration strategy

Definition at line 107 of file EnumerateBase.h.

References m_enumerator, and PRECONDITION.

◆ getPosition()

const EnumerationTypes::RGROUPS & RDKit::EnumerateLibraryBase::getPosition ( ) const

Get the current position into the reagent vectors Use getState/setState to save/restart the enumeration from this position.

◆ getReaction()

const ChemicalReaction & RDKit::EnumerateLibraryBase::getReaction ( ) const

inline

returns the underlying chemical reaction

Definition at line 104 of file EnumerateBase.h.

References m_rxn.

◆ getState()

std::string RDKit::EnumerateLibraryBase::getState ( ) const

Get the current state of the enumerator This is the position of the enumerator and the enumerators state that can be used to restart enumerating from this position.

◆ initFromStream()

virtual void RDKit::EnumerateLibraryBase::initFromStream ( std::istream & ss )

pure virtual

initializes from a stream pickle

Implemented in RDKit::EnumerateLibrary.

Referenced by initFromString().

◆ initFromString()

virtual void RDKit::EnumerateLibraryBase::initFromString ( const std::string & text )

inlinevirtual

initializes from a string pickle

Definition at line 157 of file EnumerateBase.h.

References initFromStream().

Referenced by RDKit::EnumerateLibrary::EnumerateLibrary().

◆ next()

virtual std::vector< MOL_SPTR_VECT > RDKit::EnumerateLibraryBase::next ( )

pure virtual

get the next set of products (See run_Reactants) for details This returns a vector of a vector of molecules. Each result vector corresponds for a product template. i.e. res = library.next(); res[0] are the results for library.getReaction().getProdcts()[0]

Implemented in RDKit::EnumerateLibrary.

◆ nextSmiles()

virtual std::vector< std::vector< std::string > > RDKit::EnumerateLibraryBase::nextSmiles ( )

virtual

get the next set of products as smiles This returns a vector of a vector strings. Each result vector corresponds for a product template.

◆ operator bool()

virtual RDKit::EnumerateLibraryBase::operator bool ( ) const

inlinevirtual

Are there any enumerations left?

Definition at line 91 of file EnumerateBase.h.

References m_enumerator, and PRECONDITION.

◆ reset()

void RDKit::EnumerateLibraryBase::reset ( )

inline

reset the enumeration to the beginning.

Definition at line 97 of file EnumerateBase.h.

References m_enumerator, and m_initialEnumerator.

◆ resetState()

void RDKit::EnumerateLibraryBase::resetState ( )

Reset the enumerator to the beginning.

◆ Serialize()

virtual std::string RDKit::EnumerateLibraryBase::Serialize ( ) const

inlinevirtual

returns a string with a serialized (pickled) representation

Definition at line 147 of file EnumerateBase.h.

References toStream().

◆ setState()

void RDKit::EnumerateLibraryBase::setState ( const std::string & )

Set the current state of the enumerator Restart the enumerator from this position.

◆ toStream()

virtual void RDKit::EnumerateLibraryBase::toStream ( std::ostream & ss ) const

pure virtual

serializes (pickles) to a stream

Implemented in RDKit::EnumerateLibrary.

Referenced by Serialize().

Member Data Documentation

◆ m_enumerator

boost::shared_ptr<EnumerationStrategyBase> RDKit::EnumerateLibraryBase::m_enumerator

protected

Definition at line 66 of file EnumerateBase.h.

Referenced by EnumerateLibraryBase(), EnumerateLibraryBase(), EnumerateLibraryBase(), getEnumerator(), operator bool(), and reset().

◆ m_initialEnumerator

boost::shared_ptr<EnumerationStrategyBase> RDKit::EnumerateLibraryBase::m_initialEnumerator

protected

Definition at line 67 of file EnumerateBase.h.

Referenced by EnumerateLibraryBase(), EnumerateLibraryBase(), EnumerateLibraryBase(), and reset().

◆ m_rxn

ChemicalReaction RDKit::EnumerateLibraryBase::m_rxn

protected

Definition at line 65 of file EnumerateBase.h.

Referenced by EnumerateLibraryBase(), EnumerateLibraryBase(), EnumerateLibraryBase(), and getReaction().

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

EnumerateBase.h

Public Member Functions

Protected Attributes

Detailed Description

Constructor & Destructor Documentation

◆ EnumerateLibraryBase() [1/3]

◆ EnumerateLibraryBase() [2/3]

◆ EnumerateLibraryBase() [3/3]

◆ ~EnumerateLibraryBase()

Member Function Documentation

◆ getEnumerator()

◆ getPosition()

◆ getReaction()

◆ getState()

◆ initFromStream()

◆ initFromString()

◆ next()

◆ nextSmiles()

◆ operator bool()

◆ reset()

◆ resetState()

◆ Serialize()

◆ setState()

◆ toStream()

Member Data Documentation

◆ m_enumerator

◆ m_initialEnumerator

◆ m_rxn