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RDKit
Open-source cheminformatics and machine learning.
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Base class for enumerating chemical reactions from collections of. More...
#include <EnumerateBase.h>
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 ChemicalReaction & | getReaction () const |
returns the underlying chemical reaction More... | |
const EnumerationStrategyBase & | getEnumerator () |
return the current enumeration strategy More... | |
virtual std::vector< MOL_SPTR_VECT > | next ()=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::RGROUPS & | getPosition () 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< EnumerationStrategyBase > | m_enumerator |
boost::shared_ptr< EnumerationStrategyBase > | m_initialEnumerator |
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 62 of file EnumerateBase.h.
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inline |
default constructor
Definition at line 70 of file EnumerateBase.h.
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inline |
construct with a chemical reaction and an enumeration strategy
Definition at line 73 of file EnumerateBase.h.
References RDKit::ChemicalReaction::initReactantMatchers().
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inline |
Copy constructor.
Definition at line 82 of file EnumerateBase.h.
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inlinevirtual |
Definition at line 87 of file EnumerateBase.h.
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inline |
return the current enumeration strategy
Definition at line 106 of file EnumerateBase.h.
References getPosition(), getState(), m_enumerator, next(), nextSmiles(), PRECONDITION, resetState(), setState(), and toStream().
const EnumerationTypes::RGROUPS& RDKit::EnumerateLibraryBase::getPosition | ( | ) | const |
Get the current position into the reagent vectors.
Referenced by getEnumerator().
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inline |
returns the underlying chemical reaction
Definition at line 103 of file EnumerateBase.h.
References m_rxn.
std::string RDKit::EnumerateLibraryBase::getState | ( | ) | const |
Get the current state of the enumerator.
Referenced by getEnumerator().
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pure virtual |
initializes from a stream pickle
Implemented in RDKit::EnumerateLibrary.
Referenced by initFromString(), and Serialize().
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inlinevirtual |
initializes from a string pickle
Definition at line 156 of file EnumerateBase.h.
References RDKit::EnumerationStrategyPickler::fromPickle(), RDKit::ChemicalReaction::getNumAgentTemplates(), RDKit::ChemicalReaction::getNumProductTemplates(), RDKit::ChemicalReaction::getNumReactantTemplates(), initFromStream(), m_enumerator, RDKit::EnumerationStrategyPickler::pickle(), RDKit::ReactionPickler::pickleReaction(), and RDKit::ReactionPickler::reactionFromPickle().
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pure virtual |
get the next set of products (See run_Reactants) for details
Implemented in RDKit::EnumerateLibrary.
Referenced by getEnumerator().
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virtual |
get the next set of products as smiles
Referenced by getEnumerator().
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inlinevirtual |
Are there any enumerations left?
Definition at line 90 of file EnumerateBase.h.
References PRECONDITION.
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inline |
reset the enumeration to the beginning.
Definition at line 96 of file EnumerateBase.h.
void RDKit::EnumerateLibraryBase::resetState | ( | ) |
Reset the enumerator to the beginning.
Referenced by getEnumerator().
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inlinevirtual |
returns a string with a serialized (pickled) representation
Definition at line 146 of file EnumerateBase.h.
References initFromStream(), and toStream().
void RDKit::EnumerateLibraryBase::setState | ( | const std::string & | ) |
Set the current state of the enumerator.
Referenced by getEnumerator().
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pure virtual |
serializes (pickles) to a stream
Implemented in RDKit::EnumerateLibrary.
Referenced by getEnumerator(), and Serialize().
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protected |
Definition at line 65 of file EnumerateBase.h.
Referenced by getEnumerator(), and initFromString().
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protected |
Definition at line 66 of file EnumerateBase.h.
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protected |
Definition at line 64 of file EnumerateBase.h.
Referenced by getReaction().