RDKit::EnumerateLibraryBase Class Reference

#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.

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 RDKit::ChemicalReaction::initReactantMatchers().

EnumerateLibraryBase() [3/3]

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

inline

Copy constructor.

Definition at line 83 of file EnumerateBase.h.

~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 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.

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.

initFromString()

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

inlinevirtual

initializes from a string pickle

Definition at line 157 of file EnumerateBase.h.

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 PRECONDITION.

reset()

void RDKit::EnumerateLibraryBase::reset ( )

inline

reset the enumeration to the beginning.

Definition at line 97 of file EnumerateBase.h.

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.

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.

Member Data Documentation

m_enumerator

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

protected

Definition at line 66 of file EnumerateBase.h.

m_initialEnumerator

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

protected

Definition at line 67 of file EnumerateBase.h.

m_rxn

ChemicalReaction RDKit::EnumerateLibraryBase::m_rxn

protected

Definition at line 65 of file EnumerateBase.h.

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

• EnumerateBase.h