#include <Reaction.h>

Inheritance diagram for bio::chemical::Reaction:

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Collaboration diagram for bio::chemical::Reaction:

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Public Member Functions
	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 bool	ReactantsMeetRequirements (Pointer< const Reactants > toCheck) 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::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::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)

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

Public Attributes
Pointer< const Reactants >	reactants

Protected Attributes
Reactants	mRequiredReactants

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

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)

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)

Detailed Description

A chemical::Reaction takes in Reactants and produces Products, performing some work in between.
For more info, see Reactants.h, Reactant.h (singular), Products.h, and Substance.h
This is basically a fancy functor that takes advantage of Atom::Bonds and Substance Properties and States to do argument validation.

Reactions, like those in real life, will often deal with the changing of chemical Bonds and Properties.
Both Excitation and Reaction are functors but the behavior and minimum requirements for using each are different.
Reactions are for turning iron into gold. All lesser magicks can be performed with Excitation!
In a more real sense, Excitations should not make or break Bonds (except in rare circumstances) whereas Reactions, when fully Processed, should change the Reactants in some significant way, hence their return as Products.
Another difference between Reactants and Excitations is that Excitations act ON a Wave (i.e. wave->someMethod()) while Reactions act WITH Substances.
Additionally, Excitations store their arguments as members, requiring each kind of Excitation function call to be a new object (e.g. to call firstObject->method(firstArg) and secondObject->method(firstArg) is 1 Excitation while firstObject->method(secondArg) would require a new Excitation).
Reactions, on the other hand, are more traditional functors and do not (by default) maintain any state between calls, meaning the same Reaction object can be used for all invokations.

A real life corollary:
Imagine a sound wave hitting a wall. This could be modeled as an Excitation: the energy from the air molecules excite those in the wall, passing energy between them. We might write this as soundEnergyTransferExcitation = EnergyTransferExcitation(sound); soundEnergyTransferExcitation(wall), which could produce code like wall->ExchangeEnergy(sound) and could be used on anything the sound wave hit (e.g. soundEnergyTransferExcitation(floor)).
A similar, but inappropriate Reaction could be EnergyTransferReaction(wall, sound) which might produce code like wall->ExchangeEnergy(sound); return {wall, sound}, saying that a sound wave hitting a wall creates a new wall and sound wave. The same Reaction would have to be called again for each object the sound wave impacted.
A more appropriate Reaction would be something like Burn(fuel, air), which might return {flame, ash, smoke, air}, where you could then check the flame->GetColor(), smoke->GetSmell(), reactantAir->GetQuantity("Oxygen") - productAir->GetQuantity("Oxygen"), and so on.
The inappropriate Excitation analog, airBurnExcitation = BurnExcitation(air); airBurnExcitation(fuel), would call fuel->burn(air), which could work but would require that anything capable of being burned implement the burn method.

While the semantic difference between the implementations of Excitation and Reaction is subtle and possibly pedantic, the use case of calling a class method vs calling a function with a class should be clear cut.
In reality, you'll probably want to use Excitations in your Reactions and vice-versa. For instance, hitting a wall with a nuclear blast would be far more complex than modeling a sound wave.
See Excitation.h for more info.

To make a Reaction, you must overload Process (virtual chemical::Products Process(chemical::Substances& reactants) = 0;)
Then, preferably in your constructor, state the Require()ments.
Each Require()d Reactant* will be checked against the reactants (Substances&) provided to *this. ORDER MATTERS! The reactants must follow the same order as the Required Reactants!

To invoke a Reaction, use the operator(), providing reactants.
For example: MyReaction r; r(MyReactants);
Doing so will do all necessary input checking and then call Process(), if all is good. Otherwise no Products are returned and you will get a code::FailedReaction().

Other ways to invoke a reaction include:
Reaction::Attempt<MyReaction>(myReactants);
myReaction = Reaction::Initiate<MyReaction>(); myReaction(myReactants);

Member Function Documentation

◆ Attempt() [1/3]

template<typename T >

static Products bio::chemical::Reaction::Attempt ( Pointer< Reactants > reactants )

inlinestatic

Invokes a reaction of the given id using the provided reactants.

Template Parameters

T	a reaction type

Parameters

reactants the reactants to provide to T.

Returns: operator() of the given reaction; else reactants.

◆ Attempt() [2/3]

template<typename T >

static Products bio::chemical::Reaction::Attempt	(	Pointer< Substance >	reactant1,
		Pointer< Substance >	reactant2 = `Pointer< Substance >()`,
		Pointer< Substance >	reactant3 = `Pointer< Substance >()`
	)

inlinestatic

Ease of use helper for invoking Reactions without creating a vector
(Mostly useful for C++98)

Template Parameters

T

Parameters

reactant1
reactant2
reactant3

Returns: Attempt<T> with the given reactants.

◆ Attempt() [3/3]

template<typename T >

static Products bio::chemical::Reaction::Attempt ( Substances & substances )

inlinestatic

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS()

bio::chemical::Reaction::BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS	(	chemical	,
		Reaction	,
		filter::Chemical()	,
		symmetry_type::Operation()
	)		const &

Ensure virtual methods point to Class implementations.
Standard constructors.

Parameters

name
reactants

◆ Initiate() [1/2]

template<typename T >

static Pointer< const T > bio::chemical::Reaction::Initiate ( )

inlinestatic

Get a Reaction!
This should be used to avoid unnecessary new and deletes.
This only works for Reactions that have a name matching their type (i.e. were constructed with name=SafelyAccess<PeriodicTable>()->GetNameFromType(*this)), which is true for all Reactions in the core Biology framework.

Template Parameters

T

Returns: a Reaction* of the given type or NULL, if no Reaction exists matching the TypeName of the given T.

◆ Initiate() [2/2]

Pointer< const Reaction > bio::chemical::Reaction::Initiate ( const AtomicNumber & id )

static

Get a Reaction!
This should be used to avoid unnecessary new and deletes.
Use when the TypeName does not match the Name or when you have the id of the Reaction you want.

Parameters

id

Returns: a Reaction* with the given id or NULL.

◆ operator()()

Products bio::chemical::Reaction::operator() ( Pointer< Reactants > reactants ) const

virtual

A Reaction takes in some Reactants and checks if they match the Reactants for *this.
If the inputs check out, the Reaction occurs and the products are returned.

Parameters

reactants

Returns: Products of this->Process(...) or empty Products with a code::FailedReaction() Code.

◆ Process()

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

inlinevirtual

User defined reaction process.
The actual work of *this.

Parameters

reactants

Returns: Products containing a Code and some set of new Substances or just the reactants. Up to you!

Reimplemented in bio::chemical::Mix.

◆ ReactantsMeetRequirements()

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

virtual

Checks if the given Substances match the Reactants in *this.
ORDER MATTERS!
NOTE: toCheck may have MORE substances than just the reactants needed for this->Process but must have AT LEAST the required Reactants.

Parameters

toCheck

Returns: true if all Substances match; false otherwise.

Reimplemented in bio::molecular::Pathway, and bio::chemical::Mix.

◆ Require() [1/6]

template<typename T >

void bio::chemical::Reaction::Require ( )

inline

Wrapper around Require(Reactant*).
Constructs Reactant from args, adding the Enabled() State as a requirement.
NOTE: T should not have pointer type (unless you're using **).

Template Parameters

T	the T* which will be used in the Reaction (without the *)

◆ Require() [2/6]

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

Wrapper around Require(Reactant*).
Constructs Reactant from args

Parameters

typeName
properties
states

◆ Require() [3/6]

void bio::chemical::Reaction::Require	(	const Name &	typeName,
		Pointer< const Substance >	substance
	)

Wrapper around Require(Reactant*).
Constructs Reactant from args

Parameters

typeName
substance

◆ Require() [4/6]

template<typename T >

void bio::chemical::Reaction::Require ( Pointer< const T > substance )

inline

Wrapper around Require(Reactant*).
Constructs Reactant from args

Template Parameters

T	of the T* which will be used in the Reaction (without the *)

Parameters

substance the T* to use (with the *).

◆ Require() [5/6]

template<typename T >

void bio::chemical::Reaction::Require	(	Pointer< const typename UnorderedMotif< Property >::Contents >	properties,
		Pointer< const typename UnorderedMotif< State >::Contents >	states
	)

inline

Wrapper around Require(Reactant*).
Constructs Reactant from args

Template Parameters

T	the T* which will be used in the Reaction (without the *)

◆ Require() [6/6]

void bio::chemical::Reaction::Require ( Pointer< Reactant > reactant )

virtual

Add a required Reactant to *this.
NOTE: ORDER MATTERS!
The order of requirements MUST be the order of arguments provided to operator().

Parameters

reactant

Member Data Documentation

◆ mRequiredReactants

Reactants bio::chemical::Reaction::mRequiredReactants

protected

◆ reactants

Pointer< const Reactants > bio::chemical::Reaction::reactants

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

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ Attempt() [1/3]

◆ Attempt() [2/3]

◆ Attempt() [3/3]

◆ BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS()

◆ Initiate() [1/2]

◆ Initiate() [2/2]

◆ operator()()

◆ Process()

◆ ReactantsMeetRequirements()

◆ Require() [1/6]

◆ Require() [2/6]

◆ Require() [3/6]

◆ Require() [4/6]

◆ Require() [5/6]

◆ Require() [6/6]

Member Data Documentation

◆ mRequiredReactants

◆ reactants