RDKit
Open-source cheminformatics and machine learning.
RDKit::EnumerateLibraryBase Class Referenceabstract

Base class for enumerating chemical reactions from collections of. More...

#include <EnumerateBase.h>

Inheritance diagram for RDKit::EnumerateLibraryBase:
RDKit::EnumerateLibrary

Public Member Functions

 EnumerateLibraryBase ()
 default constructor More...
 
 EnumerateLibraryBase (const ChemicalReaction &rxn, EnumerationStrategyBase *enumerator=0)
 construct with a chemical reaction and an enumeration strategy More...
 
 EnumerateLibraryBase (const EnumerateLibraryBase &rhs)
 Copy constructor. More...
 
virtual ~EnumerateLibraryBase ()
 
virtual operator bool () const
 Are there any enumerations left? More...
 
void reset ()
 reset the enumeration to the beginning. More...
 
const ChemicalReactiongetReaction () const
 returns the underlying chemical reaction More...
 
const EnumerationStrategyBasegetEnumerator ()
 return the current enumeration strategy More...
 
virtual std::vector< MOL_SPTR_VECTnext ()=0
 get the next set of products (See run_Reactants) for details More...
 
virtual std::vector< std::vector< std::string > > nextSmiles ()
 get the next set of products as smiles More...
 
const EnumerationTypes::RGROUPSgetPosition () const
 Get the current position into the reagent vectors. More...
 
std::string getState () const
 Get the current state of the enumerator. More...
 
void setState (const std::string &)
 Set the current state of the enumerator. More...
 
void resetState ()
 Reset the enumerator to the beginning. More...
 
virtual void toStream (std::ostream &ss) const =0
 serializes (pickles) to a stream More...
 
virtual std::string Serialize () const
 returns a string with a serialized (pickled) representation More...
 
virtual void initFromStream (std::istream &ss)=0
 initializes from a stream pickle More...
 
virtual void initFromString (const std::string &text)
 initializes from a string pickle More...
 

Protected Attributes

ChemicalReaction m_rxn
 
boost::shared_ptr< EnumerationStrategyBasem_enumerator
 
boost::shared_ptr< EnumerationStrategyBasem_initialEnumerator
 

Detailed Description

Base class for enumerating chemical reactions from collections of.

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 = 0 
)
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.

◆ 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.

◆ 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

Implemented in RDKit::EnumerateLibrary.

◆ nextSmiles()

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

get the next set of products as smiles

◆ 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.

References RDLog::toStream().

◆ setState()

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

Set the current state of the enumerator.

◆ 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.


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