#include <Pathway.h>

Inheritance diagram for bio::molecular::Pathway:

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Collaboration diagram for bio::molecular::Pathway:

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Public Member Functions
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS (chemical, Pathway, filter::Chemical()) virtual ~Pathway()

virtual chemical::Products	Process (Pointer< chemical::Reactants > reactants)

virtual bool	ReactantsMeetRequirements (Pointer< const chemical::Reactants > toCheck) const

Public Member Functions inherited from bio::chemical::Class< Pathway >
virtual Pointer< ::bio::physical::Wave >	Clone () const

Pointer< ::bio::physical::Wave >	AsWave ()

Pointer< const ::bio::physical::Wave >	AsWave () const

	operator Pointer< ::bio::physical::Wave > ()

virtual Pointer< ::bio::physical::Wave >	Modulate (Pointer< ::bio::physical::Wave > signal)

virtual Pointer< ::bio::physical::Wave >	Demodulate ()

virtual Pointer< const ::bio::physical::Wave >	Demodulate () const

virtual Pointer< ::bio::physical::Wave >	Superpose (const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern)

virtual bool	Superpose (Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern)

	Class (Pointer< Pathway > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Pathway > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Pathway > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (const Class &other)

virtual	~Class ()

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

virtual Code	Attenuate (Pointer< const physical::Wave > other)

virtual Code	Disattenuate (Pointer< const physical::Wave > other)

Public Member Functions inherited from bio::physical::Class< T >
	Class (Pointer< T > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< T > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< T >	GetWaveObject ()

virtual Pointer< const T >	GetWaveObject () const

virtual	operator T& ()

virtual	operator const T & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::physical::Wave
	Wave (Pointer< Symmetry > symmetry=NULL)

	Wave (const Wave &other)

Wave &	operator= (const Wave &other)

virtual	~Wave ()

Pointer< const Symmetry >	GetSymmetry () const

virtual bool	Superpose (Pointer< const Wave > displacement, Pointer< Interference > pattern)

virtual Pointer< Wave >	Superpose (const ConstWaves &displacement, Pointer< Interference > pattern)

virtual Pointer< Wave >	Modulate (Pointer< Wave > signal)

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual void	operator\| (Pointer< Symmetry > symmetry)

virtual Pointer< Wave >	operator* (Pointer< Wave > signal)

virtual Pointer< Wave >	operator* ()

virtual Pointer< const Wave >	operator* () const

virtual void	operator+ (Pointer< const Wave > other)

virtual void	operator- (Pointer< const Wave > other)

uint16_t	GetTypeId () const

void	SetTypeId (uint16_t typeId)

Public Member Functions inherited from bio::physical::Identifiable< Id >
	Identifiable (Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Name &name, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (Identifier id, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Identifiable &other)

virtual	~Identifiable ()

virtual	operator Id () const

virtual bool	operator== (const Identifier id) const

virtual bool	operator== (const Name &name) const

virtual bool	operator== (const Identifiable< Id > &other) const

virtual Name	GetName () const

virtual Identifier	GetId () const

virtual bool	SetName (const Name &name)

virtual bool	SetId (Identifier id)

virtual bool	IsName (const Name &name) const

virtual bool	IsNameInsensitive (const Name &name) const

virtual bool	IsId (Identifier id) const

virtual void	SetPerspective (Pointer< Perspective< Id > > perspective)

Public Member Functions inherited from bio::physical::Observer< PERSPECTIVE >
	Observer (Pointer< Perspective > perspective=NULL)

	Observer (const Observer &other)

virtual	~Observer ()

virtual void	SetPerspective (Pointer< Perspective > perspective)

virtual Pointer< Perspective >	GetPerspective () const

Public Member Functions inherited from bio::log::Writer
	Writer ()

	Writer (Filter logFilter)

virtual	~Writer ()

virtual Pointer< const Writer >	AsLogWriter () const

bool	IsEnabled (LogLevel level) const

virtual void	Log (LogLevel level, const char *format, va_list args) const

Public Member Functions inherited from bio::physical::Class< Writer >
	Class (Pointer< Writer > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Writer > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Writer >	GetWaveObject ()

virtual Pointer< const Writer >	GetWaveObject () const

virtual	operator Writer & ()

virtual	operator const Writer & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::physical::Filterable
	Filterable ()

	Filterable (Filter filter)

virtual	~Filterable ()

virtual void	InitializeImplementation (ByteStreams &args)

virtual void	SetFilter (Filter filter)

Filter	GetFilter () const

virtual Pointer< const Symmetry >	Spin () const

virtual Code	Reify (Pointer< const Symmetry > symmetry)

Public Member Functions inherited from bio::physical::Class< Filterable >
	Class (Pointer< Filterable > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Filterable > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Filterable >	GetWaveObject ()

virtual Pointer< const Filterable >	GetWaveObject () const

virtual	operator Filterable & ()

virtual	operator const Filterable & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::chemical::Atom
	Atom ()

	Atom (const Atom &other)

virtual	~Atom ()

void	CloneBondsFrom (const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy)

virtual Pointer< const physical::Symmetry >	Spin () const

virtual Code	Reify (Pointer< const physical::Symmetry > symmetry)

Pointer< physical::Wave >	GetBonded (Valence position)

Pointer< const physical::Wave >	GetBonded (Valence position) const

Pointer< const physical::Wave >	ResolveBondedForReadById (AtomicNumber bondId) const

Pointer< physical::Wave >	ResolveBondedForWriteById (AtomicNumber bondId)

template<typename T >
Cow< T >	AsBonded () const

template<typename T >
Pointer< T >	AsBondedQuantum () const

template<typename T >
atom_detail::AsResultType< T, type::IsWaveImplementation< typenametype::RemovePointer< T >::Type >::sValue >::Type	As () const

template<typename T >
	operator T () const

template<typename T >
Valence	FormBond (T toBond, BondType type=bond_type::Unknown())

template<typename T >
bool	BreakBond (T toDisassociate, BondType type=bond_type::Unknown())

Valence	GetBondPosition (AtomicNumber bondedId) const

Valence	GetBondPosition (const Name &typeName) const

Valence	GetBondPositionLocked (AtomicNumber bondedId) const

template<typename T >
Valence	GetBondPosition () const

BondType	GetBondType (Valence position) const

template<typename T >
BondType	GetBondType () const

Pointer< Bonds >	GetAllBonds ()

Pointer< const Bonds >	GetAllBonds () const

void	ForEachBond (BondVisitor visitor, void *context=NULL) const

void	ForEachBondMutable (BondMutator mutator, void *context=NULL)

virtual Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type)

Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

Valence	FormBondImplementationLocked (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

virtual bool	BreakBondImplementation (AtomicNumber id, BondType type)

bool	BreakBondImplementationLocked (AtomicNumber id, BondType type)

Public Member Functions inherited from bio::physical::Class< Atom >
	Class (Pointer< Atom > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Atom > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Atom >	GetWaveObject ()

virtual Pointer< const Atom >	GetWaveObject () const

virtual	operator Atom & ()

virtual	operator const Atom & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Public Member Functions inherited from bio::ThreadSafe
	ThreadSafe ()

	ThreadSafe (const ThreadSafe &toCopy)

ThreadSafe &	operator= (const ThreadSafe &toCopy)

	~ThreadSafe ()

void	LockThread () const

void	UnlockThread () const

void	LockMutexShared () const

void	UnlockMutexShared () const

Public Member Functions inherited from bio::chemical::Reaction
	BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS (chemical, Reaction, filter::Chemical(), symmetry_type::Operation()) explicit Reaction(const Name &name

virtual void	Require (Pointer< Reactant > reactant)

void	Require (const Name &typeName, Pointer< const Substance > substance)

void	Require (const Name &typeName, const UnorderedMotif< Property > &properties, const UnorderedMotif< State > &states)

template<typename T >
void	Require ()

template<typename T >
void	Require (Pointer< const T > substance)

template<typename T >
void	Require (Pointer< const typename UnorderedMotif< Property >::Contents > properties, Pointer< const typename UnorderedMotif< State >::Contents > states)

virtual Products	Process (Pointer< Reactants > reactants) const

virtual Products	operator() (Pointer< Reactants > reactants) const

Public Member Functions inherited from bio::chemical::Class< Reaction >
virtual Pointer< ::bio::physical::Wave >	Clone () const

Pointer< ::bio::physical::Wave >	AsWave ()

Pointer< const ::bio::physical::Wave >	AsWave () const

	operator Pointer< ::bio::physical::Wave > ()

virtual Pointer< ::bio::physical::Wave >	Modulate (Pointer< ::bio::physical::Wave > signal)

virtual Pointer< ::bio::physical::Wave >	Demodulate ()

virtual Pointer< const ::bio::physical::Wave >	Demodulate () const

virtual Pointer< ::bio::physical::Wave >	Superpose (const ::bio::physical::ConstWaves &displacement, Pointer< ::bio::physical::Interference > pattern)

virtual bool	Superpose (Pointer< const ::bio::physical::Wave > displacement, Pointer< ::bio::physical::Interference > pattern)

	Class (Pointer< Reaction > object, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Reaction > object, const Name &name, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (Pointer< Reaction > object, const Id &id, Filter filter=filter::Default(), SymmetryType symmetryType=symmetry_type::Object())

	Class (const Class &other)

virtual	~Class ()

virtual bool	RegisterProperties (const Properties &properties)

virtual Properties	GetProperties () const

virtual Pointer< Atom >	AsAtom ()

virtual Pointer< const Atom >	AsAtom () const

virtual Code	Attenuate (Pointer< const physical::Wave > other)

virtual Code	Disattenuate (Pointer< const physical::Wave > other)

Public Member Functions inherited from bio::chemical::Structure
	Structure ()

virtual	~Structure ()

Public Member Functions inherited from bio::chemical::UnorderedStructureInterface
	UnorderedStructureInterface ()

virtual	~UnorderedStructureInterface ()

template<typename T >
T	Add (const T t)

template<typename T >
Pointer< T >	Add (Pointer< T > t)

template<typename T >
Code	Remove (const T t)

template<typename T >
Code	Remove (Pointer< T > t)

template<typename T >
void	Import (Pointer< const UnorderedMotif< T > > other)

template<typename T >
void	Import (Pointer< const LinearMotif< T > > other)

template<typename T >
void	Import (const ::bio::Arrangement< T > &other)

Code	ImportAll (Pointer< const physical::Wave > other)

template<typename T >
Index	GetCount () const

template<typename T >
Pointer< Container >	GetAll ()

template<typename T >
Pointer< const Container >	GetAll () const

template<typename T >
bool	Has (T content) const

template<typename T >
bool	Has (Pointer< T > content) const

template<typename T >
unsigned int	GetNumMatching (Pointer< const Container > other) const

template<typename T >
bool	HasAll (Pointer< const Container > contents) const

template<typename T >
void	Clear ()

template<typename T >
std::string	GetStringFrom (std::string separator=", ")

template<typename T >
void	Log (const LogLevel &level=log_level::Info(), const Filter &filter=FilterPerspective::InvalidId())

Public Member Functions inherited from bio::chemical::LinearStructureInterface
	LinearStructureInterface ()

virtual	~LinearStructureInterface ()

template<typename T >
Code	Insert (typename LinearStructureRequest< T >::PointerType toAdd, const Position position=BOTTOM, const Id optionalPositionArg=0, const bool transferSubContents=false)

template<typename T >
LinearStructureRequest< T >::PointerType	GetById (const Id &id)

template<typename T >
const LinearStructureRequest< T >::PointerType	GetById (const Id &id) const

template<typename T >
LinearStructureRequest< T >::PointerType	GetByName (const Name &name)

template<typename T >
const LinearStructureRequest< T >::PointerType	GetByName (const Name &name) const

template<typename T >
LinearStructureRequest< T >::PointerType	GetOrCreateById (Id id)

template<typename T >
LinearStructureRequest< T >::PointerType	GetOrCreateByName (const Name &name)

template<typename T >
Code	RemoveById (const Id &id)

template<typename T >
Code	RemoveByName (const Name &name)

template<typename T >
LinearMotif< typenameLinearStructureRequest< T >::Pointee >::Contents	GetAllLike (Pointer< const Affinity > affinity) const

template<typename T >
Emission	ForEach (Pointer< ExcitationBase > excitation)

Public Member Functions inherited from bio::Covalent< chemical::LinearMotif< chemical::Reaction > >
	Covalent ()

	Covalent (const Covalent &other)

virtual	~Covalent ()

Covalent &	operator= (const Covalent &other)

Pointer< chemical::LinearMotif< chemical::Reaction > >	Object ()

Pointer< const chemical::LinearMotif< chemical::Reaction > >	Object () const

Additional Inherited Members
Public Types inherited from bio::physical::Identifiable< Id >
typedef Id	Identifier

typedef Arrangement< Identifier >	Ids

Public Types inherited from bio::physical::Observer< PERSPECTIVE >
typedef PERSPECTIVE	Perspective

Public Types inherited from bio::chemical::Atom
typedef BondCloneAction(*	BondClonePolicy) (const Bond &bond)

typedef void(*	BondVisitor) (const Bond &bond, void *context)

typedef BondCloneAction(*	BondMutator) (Bond &bond, void *context)

Static Public Member Functions inherited from bio::physical::Class< T >
static Pointer< T >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::physical::Wave
static Properties	GetResonanceBetween (ConstWaves waves)

static Properties	GetResonanceBetween (Pointer< const Wave > wave1, Pointer< const Wave > wave2)

static Properties	GetResonanceBetween (Pointer< const Wave > wave, const Properties &properties)

Static Public Member Functions inherited from bio::log::Writer
static void	Log (Pointer< const Writer > writer, LogLevel level, const char *format,...)

static bool	ShouldLog (Pointer< const Writer > writer, LogLevel level)

Static Public Member Functions inherited from bio::physical::Class< Writer >
static Pointer< Writer >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::physical::Class< Filterable >
static Pointer< Filterable >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::chemical::Atom
static BondCloneAction	DefaultBondClonePolicy (const Bond &bond)

template<typename T >
static AtomicNumber	GetBondId ()

Static Public Member Functions inherited from bio::physical::Class< Atom >
static Pointer< Atom >	Convert (Pointer< Wave > wave)

Static Public Member Functions inherited from bio::chemical::Reaction
static Pointer< const Reaction >	Initiate (const AtomicNumber &id)

template<typename T >
static Pointer< const T >	Initiate ()

template<typename T >
static Products	Attempt (Pointer< Reactants > reactants)

template<typename T >
static Products	Attempt (Substances &substances)

template<typename T >
static Products	Attempt (Pointer< Substance > reactant1, Pointer< Substance > reactant2=Pointer< Substance >(), Pointer< Substance > reactant3=Pointer< Substance >())

Static Public Member Functions inherited from bio::chemical::UnorderedStructureInterface
static void	ImportAllCollectVisitor (const chemical::Bond &bond, void *ctx)

Public Attributes inherited from bio::chemical::Reaction
Pointer< const Reactants >	reactants

Protected Types inherited from bio::physical::Identifiable< Id >
typedef Id	Identifier

typedef Arrangement< Identifier >	Ids

Protected Types inherited from bio::physical::Observer< PERSPECTIVE >
typedef PERSPECTIVE	Perspective

Protected Types inherited from bio::chemical::Atom
typedef BondCloneAction(*	BondClonePolicy) (const Bond &bond)

typedef void(*	BondVisitor) (const Bond &bond, void *context)

typedef BondCloneAction(*	BondMutator) (Bond &bond, void *context)

Protected Member Functions inherited from bio::chemical::Elementary< T >
void	RegisterType ()

	Elementary (const Properties properties)

	Elementary ()

virtual	~Elementary ()

Protected Member Functions inherited from bio::physical::Identifiable< Id >
virtual void	InitializeImplementation (ByteStreams &args)

friend::std::ostream &	operator<< (std::ostream &out, const Identifiable< Id > &t)

	Identifiable (Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Name &name, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (Identifier id, Pointer< Perspective< Id > > perspective=NULL)

	Identifiable (const Identifiable &other)

virtual	~Identifiable ()

virtual	operator Id () const

virtual bool	operator== (const Identifier id) const

virtual bool	operator== (const Name &name) const

virtual bool	operator== (const Identifiable< Id > &other) const

virtual Name	GetName () const

virtual Identifier	GetId () const

virtual bool	SetName (const Name &name)

virtual bool	SetId (Identifier id)

virtual bool	IsName (const Name &name) const

virtual bool	IsNameInsensitive (const Name &name) const

virtual bool	IsId (Identifier id) const

virtual void	SetPerspective (Pointer< Perspective< Id > > perspective)

Protected Member Functions inherited from bio::physical::Observer< PERSPECTIVE >
	Observer (Pointer< Perspective > perspective=NULL)

	Observer (const Observer &other)

virtual	~Observer ()

virtual void	SetPerspective (Pointer< Perspective > perspective)

virtual Pointer< Perspective >	GetPerspective () const

Protected Member Functions inherited from bio::VirtualBase
	VirtualBase ()

virtual	~VirtualBase ()

void	Initialize (ByteStreams &args)

void	Initialize (ByteStream arg1)

void	Initialize (ByteStream arg1, ByteStream arg2)

void	Initialize (ByteStream arg1, ByteStream arg2, ByteStream arg3)

Protected Member Functions inherited from bio::log::Writer
	Writer ()

	Writer (Filter logFilter)

virtual	~Writer ()

virtual Pointer< const Writer >	AsLogWriter () const

bool	IsEnabled (LogLevel level) const

virtual void	Log (LogLevel level, const char *format, va_list args) const

Protected Member Functions inherited from bio::physical::Class< Writer >
	Class (Pointer< Writer > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Writer > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Writer >	GetWaveObject ()

virtual Pointer< const Writer >	GetWaveObject () const

virtual	operator Writer & ()

virtual	operator const Writer & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::physical::Filterable
	Filterable ()

	Filterable (Filter filter)

virtual	~Filterable ()

virtual void	InitializeImplementation (ByteStreams &args)

virtual void	SetFilter (Filter filter)

Filter	GetFilter () const

virtual Pointer< const Symmetry >	Spin () const

virtual Code	Reify (Pointer< const Symmetry > symmetry)

Protected Member Functions inherited from bio::physical::Class< Filterable >
	Class (Pointer< Filterable > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Filterable > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Filterable >	GetWaveObject ()

virtual Pointer< const Filterable >	GetWaveObject () const

virtual	operator Filterable & ()

virtual	operator const Filterable & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::chemical::Atom
void	IndexBond (AtomicNumber bondedId, Valence position)

void	UnindexBond (AtomicNumber bondedId)

	Atom ()

	Atom (const Atom &other)

virtual	~Atom ()

void	CloneBondsFrom (const Atom &other, BondClonePolicy policy=&Atom::DefaultBondClonePolicy)

virtual Pointer< const physical::Symmetry >	Spin () const

virtual Code	Reify (Pointer< const physical::Symmetry > symmetry)

Pointer< physical::Wave >	GetBonded (Valence position)

Pointer< const physical::Wave >	GetBonded (Valence position) const

Pointer< const physical::Wave >	ResolveBondedForReadById (AtomicNumber bondId) const

Pointer< physical::Wave >	ResolveBondedForWriteById (AtomicNumber bondId)

template<typename T >
Cow< T >	AsBonded () const

template<typename T >
Pointer< T >	AsBondedQuantum () const

template<typename T >
atom_detail::AsResultType< T, type::IsWaveImplementation< typenametype::RemovePointer< T >::Type >::sValue >::Type	As () const

template<typename T >
	operator T () const

template<typename T >
Valence	FormBond (T toBond, BondType type=bond_type::Unknown())

template<typename T >
bool	BreakBond (T toDisassociate, BondType type=bond_type::Unknown())

Valence	GetBondPosition (AtomicNumber bondedId) const

Valence	GetBondPosition (const Name &typeName) const

Valence	GetBondPositionLocked (AtomicNumber bondedId) const

template<typename T >
Valence	GetBondPosition () const

BondType	GetBondType (Valence position) const

template<typename T >
BondType	GetBondType () const

Pointer< Bonds >	GetAllBonds ()

Pointer< const Bonds >	GetAllBonds () const

void	ForEachBond (BondVisitor visitor, void *context=NULL) const

void	ForEachBondMutable (BondMutator mutator, void *context=NULL)

virtual Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type)

Valence	FormBondImplementation (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

Valence	FormBondImplementationLocked (Pointer< physical::Wave > toBond, AtomicNumber id, BondType type, bool ownsBonded)

virtual bool	BreakBondImplementation (AtomicNumber id, BondType type)

bool	BreakBondImplementationLocked (AtomicNumber id, BondType type)

Protected Member Functions inherited from bio::physical::Class< Atom >
	Class (Pointer< Atom > object, Pointer< Symmetry > symmetry=NULL)

	Class (Pointer< Atom > object, SymmetryFactory symmetryFactory)

	Class (const Class &other)

virtual Pointer< Atom >	GetWaveObject ()

virtual Pointer< const Atom >	GetWaveObject () const

virtual	operator Atom & ()

virtual	operator const Atom & () const

Pointer< Wave >	AsWave ()

Pointer< const Wave >	AsWave () const

virtual	operator Pointer< Wave > ()

Protected Member Functions inherited from bio::ThreadSafe
	ThreadSafe ()

	ThreadSafe (const ThreadSafe &toCopy)

ThreadSafe &	operator= (const ThreadSafe &toCopy)

	~ThreadSafe ()

void	LockThread () const

void	UnlockThread () const

void	LockMutexShared () const

void	UnlockMutexShared () const

Protected Member Functions inherited from bio::chemical::LinearStructureInterface
template<typename T >
Pointer< LinearMotif< T > >	ResolveLinearMotif ()

template<typename T >
Pointer< const LinearMotif< T > >	ResolveLinearMotif () const

Static Protected Member Functions inherited from bio::log::Writer
static void	Log (Pointer< const Writer > writer, LogLevel level, const char *format,...)

static bool	ShouldLog (Pointer< const Writer > writer, LogLevel level)

Static Protected Member Functions inherited from bio::physical::Class< Writer >
static Pointer< Writer >	Convert (Pointer< Wave > wave)

Static Protected Member Functions inherited from bio::physical::Class< Filterable >
static Pointer< Filterable >	Convert (Pointer< Wave > wave)

Static Protected Member Functions inherited from bio::chemical::Atom
static BondCloneAction	DefaultBondClonePolicy (const Bond &bond)

template<typename T >
static AtomicNumber	GetBondId ()

Static Protected Member Functions inherited from bio::physical::Class< Atom >
static Pointer< Atom >	Convert (Pointer< Wave > wave)

Protected Attributes inherited from bio::physical::Class< T >
Pointer< T >	mObject

Protected Attributes inherited from bio::physical::Wave
LazyPointer< Symmetry >	mSymmetry

bool	mHasSignal

uint16_t	mTypeId

Protected Attributes inherited from bio::VirtualBase
bool	mHasBeenInitialized

Protected Attributes inherited from bio::physical::Class< Writer >
Pointer< Writer >	mObject

Protected Attributes inherited from bio::physical::Filterable
Filter	mFilter

Protected Attributes inherited from bio::physical::Class< Filterable >
Pointer< Filterable >	mObject

Protected Attributes inherited from bio::chemical::Atom
Bonds	mBonds

::std::map< AtomicNumber, Valence >	mBondIndex

Arrangement< Pointer< const physical::Wave > >	mBackflowPreventer

Protected Attributes inherited from bio::physical::Class< Atom >
Pointer< Atom >	mObject

Protected Attributes inherited from bio::chemical::Reaction
Reactants	mRequiredReactants

Protected Attributes inherited from bio::Covalent< chemical::LinearMotif< chemical::Reaction > >
Pointer< chemical::LinearMotif< chemical::Reaction > >	mT

Detailed Description

A Pathway is a series chemical::Reactions that accomplishes some larger goal.
Pathways, are themselves Reactions and can be invoked using the same calls (e.g. chemical::Reaction::Initiate<MyPathway>.
NOTE: in real life, pathways often include protein-catalyzed reactions. You can do that here too!

NOTE: while Pathways are Reactions, they should not have any Requirements / Reactants nor should they perform any Process of their own. Instead, they should rely entirely on the Reactions added to them.
With the above stated, Pathways can be treated like Reactions for the purpose of being added to other Pathways ;)

Pathways are First-In-First-Out (FIFO) ordered.
The first call to Add<Reaction*>() will be the first Reaction run by this and the Reaction that determines the required Reactants to even begin *this Process.
The last call to Add<Reaction>() will be the last Reaction called and will determine the ultimate Products returned by *this Process, should it successfully run to completion.
i.e. return last(middle(first(reactants)));

TODO: Add switching logic for Products Code.

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS()

bio::molecular::Pathway::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS	(	chemical	,
		Pathway	,
		filter::Chemical()
	)

Ensure virtual methods point to Class implementations.
Standard constructors.

◆ Process()

chemical::Products bio::molecular::Pathway::Process ( Pointer< chemical::Reactants > reactants )

virtual

The Process of a Pathway is the series of Reactions it includes.
This is FIFO ordering (see class description for details).

Parameters

reactants

Returns: the Products from the last Reaction or a code::FailedReaction(), if any step did not succeed.

◆ ReactantsMeetRequirements()

bool bio::molecular::Pathway::ReactantsMeetRequirements ( Pointer< const chemical::Reactants > toCheck ) const

virtual

*this shouldn't have an Requirements / Reactants, so instead we check the first Reaction in *this.

Parameters

toCheck

Returns: whether or not the first Reaction in *this can use the given Substances.

Reimplemented from bio::chemical::Reaction.

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

Public Member Functions

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS()

◆ Process()

◆ ReactantsMeetRequirements()