#include <Pathway.h>

Inheritance diagram for bio::molecular::Pathway:

Collaboration diagram for bio::molecular::Pathway:

Public Member Functions
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, Pathway) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(chemical

&	chemical::ReactionPerspective::Instance ()

	filter::Chemical ()) virtual ~Pathway()

virtual chemical::Products	Process (chemical::Reactants *reactants)

virtual bool	ReactantsMeetRequirements (const chemical::Reactants *toCheck) const

Public Member Functions inherited from bio::chemical::Class< Pathway >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Pathway) Class(Pathway *object

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

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

T *	Convert (Wave *wave)

virtual	operator T* ()

virtual	operator Wave * ()

Public Member Functions inherited from bio::physical::Wave
	Wave (Symmetry *symmetry=NULL)

virtual	~Wave ()

virtual chemical::Atom *	AsAtom ()

virtual const chemical::Atom *	AsAtom () const

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Code	Attenuate (const Wave *other)

virtual Wave *	Clone () const

virtual Wave *	Demodulate ()

virtual const Wave *	Demodulate () const

virtual Code	Disattenuate (const Wave *other)

virtual Properties	GetProperties () const

virtual Wave *	Modulate (Wave *signal)

virtual Wave *	operator* ()

virtual const Wave *	operator* () const

virtual Wave *	operator* (Wave *signal)

virtual void	operator+ (const Wave *other)

virtual void	operator- (const Wave *other)

virtual void	operator\| (Symmetry *symmetry)

virtual Code	Reify (Symmetry *symmetry)

virtual Symmetry *	Spin () const

Public Member Functions inherited from bio::physical::Identifiable< StandardDimension >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Identifiable< StandardDimension >) explicit Identifiable(Perspective< StandardDimension > *perspective

void	CloneIntoName (Name name)

Public Member Functions inherited from bio::physical::Observer< Perspective< StandardDimension > >
	Observer (const Observer &other)

	Observer (Perspective *perspective=NULL)

virtual	~Observer ()

virtual Perspective *	GetPerspective () const

virtual void	SetPerspective (Perspective *perspective)

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

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Identifiable< StandardDimension > *	Convert (Wave *wave)

virtual	operator Identifiable< StandardDimension > * ()

virtual	operator Wave * ()

Public Member Functions inherited from bio::log::Writer
	Writer (Engine *logEngine, Filter logFilter)

virtual	~Writer ()

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Writer) Writer()

void	ExternalLog (Filter logFilter, Level level, const char *format,...) const

Engine *	GetLogEngine ()

const Engine *	GetLogEngine () const

bool	HasLogEngine () const

virtual void	SetLogEngine (Engine *logEngine)

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

virtual	~Filterable ()

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Filterable) Filterable()

Filter	GetFilter () const

virtual void	InitializeImplementation (ByteStreams args)

virtual Code	Reify (Symmetry *symmetry)

virtual void	SetFilter (Filter filter)

virtual Symmetry *	Spin () const

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

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Filterable *	Convert (Wave *wave)

virtual	operator Filterable * ()

virtual	operator Wave * ()

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

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Writer *	Convert (Wave *wave)

virtual	operator Wave * ()

virtual	operator Writer * ()

Public Member Functions inherited from bio::chemical::Atom
	Atom (const Atom &other)

virtual	~Atom ()

template<typename T >
T	As ()

template<typename T >
const T	As () const

template<typename T >
T	AsBonded ()

template<typename T >
const T	AsBonded () const

template<typename T >
T	AsBondedQuantum ()

template<typename T >
const T	AsBondedQuantum () const

virtual Code	Attenuate (const Wave *other)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Atom) explicit Atom()

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

virtual Code	Disattenuate (const Wave *other)

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

Bonds *	GetAllBonds ()

const Bonds *	GetAllBonds () const

Wave *	GetBonded (Valence position)

const Wave *	GetBonded (Valence position) const

template<typename T >
Valence	GetBondPosition () const

Valence	GetBondPosition (AtomicNumber bondedId) const

Valence	GetBondPosition (Name typeName) const

template<typename T >
BondType	GetBondType () const

BondType	GetBondType (Valence position) const

template<typename T >
	operator T ()

virtual Code	Reify (physical::Symmetry *symmetry)

virtual physical::Symmetry *	Spin () const

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

virtual	~Class ()

virtual Wave *	AsWave ()

virtual const Wave *	AsWave () const

virtual Wave *	Clone () const

Atom *	Convert (Wave *wave)

virtual	operator Atom * ()

virtual	operator Wave * ()

Public Member Functions inherited from bio::chemical::Reaction
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, Reaction) BIO_DEFAULT_IDENTIFIABLE_CONSTRUCTORS(chemical

	filter::Chemical ()

virtual Products	operator() (Reactants *reactants) const

virtual Products	Process (Reactants *reactants) const

virtual bool	ReactantsMeetRequirements (const Reactants *toCheck) const

&	ReactionPerspective::Instance ()

template<typename T >
void	Require ()

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

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

void	Require (Name typeName, const Substance *substance)

void	Require (Name typeName, const typename UnorderedMotif< Property >::Contents properties, const typename UnorderedMotif< State >::Contents states)

virtual void	Require (Reactant *reactant)

	symmetry_type::Operation ()) explicit Reaction(Name name

Public Member Functions inherited from bio::chemical::Class< Reaction >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, Reaction) Class(Reaction *object

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 >
void	Clear ()

template<typename T >
Container *	GetAll ()

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

template<typename T >
std::vector< T >	GetAllAsVector ()

template<typename T >
const std::vector< T >	GetAllAsVector () const

template<typename T >
unsigned long	GetCount () const

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

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

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

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

template<typename T >
void	Import (const std::vector< T > &other)

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

Code	ImportAll (const physical::Wave *other)

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

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

	ThreadSafe (const ThreadSafe &toCopy)

virtual	~ThreadSafe ()

void	LockThread () const

void	UnlockThread () const

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

virtual	~LinearStructureInterface ()

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

template<typename T >
T	GetById (StandardDimension id)

template<typename T >
const T	GetById (StandardDimension id) const

template<typename T >
T	GetByName (Name name)

template<typename T >
const T	GetByName (Name name) const

template<typename T >
T	GetOrCreateById (StandardDimension id)

template<typename T >
T	GetOrCreateByName (Name name)

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

Public Member Functions inherited from bio::chemical::LinearMotif< chemical::Reaction * >
	LinearMotif (const Contents contents, physical::Perspective< StandardDimension > perspective=NULL)

	LinearMotif (const LinearMotif< chemical::Reaction * > &toCopy)

	LinearMotif (physical::Perspective< StandardDimension > *perspective=NULL)

virtual	~LinearMotif ()

virtual chemical::Reaction *	AddImplementation (chemical::Reaction * content)

virtual Code	Attenuate (const physical::Wave *other)

	BIO_DISAMBIGUATE_REQUIRED_CLASS_METHODS (chemical, LinearMotif< chemical::Reaction * >) BIO_DISAMBIGUATE_OPTIONAL_CLASS_METHODS(physical

virtual void	ClearImplementation ()

virtual chemical::Reaction *	CreateImplementation (StandardDimension id)

virtual Code	Disattenuate (const physical::Wave *other)

virtual Emission	ForEachImplementation (ExcitationBase *excitation)

virtual chemical::Reaction *	GetByIdImplementation (StandardDimension id)

virtual const chemical::Reaction *	GetByIdImplementation (StandardDimension id) const

virtual chemical::Reaction *	GetByNameImplementation (Name name)

virtual const chemical::Reaction *	GetByNameImplementation (Name name) const

virtual chemical::Reaction *	GetOrCreateByIdImplementation (StandardDimension id)

virtual chemical::Reaction *	GetOrCreateByNameImplementation (Name name)

virtual std::string	GetStringFromImplementation (std::string separator=", ")

physical::Perspective< StandardDimension > *	GetStructuralPerspective ()

const physical::Perspective< StandardDimension > *	GetStructuralPerspective () const

virtual bool	HasImplementation (const chemical::Reaction * &content) const

virtual void	ImportImplementation (const LinearMotif< chemical::Reaction * > *other)

virtual Code	InsertImplementation (chemical::Reaction * toAdd, const Position position=BOTTOM, const StandardDimension optionalPositionArg=0, const bool transferSubContents=false)

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

	Elementary (const Properties properties)

virtual	~Elementary ()

void	RegisterProperties (const Properties properties)

Public Member Functions inherited from bio::chemical::Class< LinearMotif< chemical::Reaction * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, LinearMotif< chemical::Reaction * >) Class(LinearMotif< chemical::Reaction * > *object

Public Member Functions inherited from bio::chemical::UnorderedMotif< chemical::Reaction * >
	UnorderedMotif (const Contents *contents)

	UnorderedMotif (const UnorderedMotif< chemical::Reaction * > *toCopy)

virtual	~UnorderedMotif ()

virtual chemical::Reaction *	AddImplementation (const chemical::Reaction * content)

	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (chemical, UnorderedMotif< chemical::Reaction * >) UnorderedMotif()

virtual void	ClearImplementation ()

virtual unsigned long	GetCountImplementation () const

virtual unsigned int	GetNumMatchingImplementation (const Container *other) const

virtual std::string	GetStringFromImplementation (std::string separator=", ")

virtual bool	HasAllImplementation (const Container *contents) const

virtual bool	HasImplementation (const chemical::Reaction * content) const

virtual void	ImportImplementation (const UnorderedMotif< chemical::Reaction * > *other)

virtual chemical::Reaction *	RemoveImplementation (const chemical::Reaction * content)

Public Member Functions inherited from bio::chemical::Class< UnorderedMotif< chemical::Reaction * > >
	BIO_DISAMBIGUATE_ALL_CLASS_METHODS (physical, UnorderedMotif< chemical::Reaction * >) Class(UnorderedMotif< chemical::Reaction * > *object

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

virtual	~AbstractMotif ()

virtual void	ClearImplementation ()

virtual Container *	GetAllImplementation ()

virtual const Container *	GetAllImplementation () const

virtual unsigned long	GetCountImplementation () const

virtual std::string	GetStringFromImplementation (std::string separator=", ")

virtual void	ImportImplementation (const void *other)

Public Attributes
	Pathway

Public Attributes inherited from bio::chemical::Class< Pathway >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::physical::Identifiable< StandardDimension >
Id	m_id

Public Attributes inherited from bio::chemical::Reaction
	Reaction

const Reactants *	reactants

Public Attributes inherited from bio::chemical::Class< Reaction >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::LinearMotif< chemical::Reaction * >
physical::Perspective< StandardDimension > *	m_perspective

Public Attributes inherited from bio::chemical::Class< LinearMotif< chemical::Reaction * > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

Public Attributes inherited from bio::chemical::Class< UnorderedMotif< chemical::Reaction * > >
physical::Perspective< StandardDimension > Filter	filter

physical::Perspective< StandardDimension > *	perspective

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

typedef std::vector< Id >	Ids

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

Public Types inherited from bio::chemical::LinearMotif< chemical::Reaction * >
typedef physical::Line	Contents

Public Types inherited from bio::chemical::UnorderedMotif< chemical::Reaction * >
typedef physical::Arrangement< chemical::Reaction * >	Contents

Static Public Member Functions inherited from bio::physical::Wave
static Properties	GetResonanceBetween (const Wave *wave, const Properties &properties)

static Properties	GetResonanceBetween (const Wave wave1, const Wave wave2)

static Properties	GetResonanceBetween (ConstWaves waves)

Static Public Member Functions inherited from bio::chemical::Reaction
template<typename T >
static Products	Attempt (Reactants *reactants)

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

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

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

static const Reaction *	Initiate (StandardDimension id)

Static Public Member Functions inherited from bio::chemical::LinearMotif< chemical::Reaction * >
static LinearMotif< chemical::Reaction * > Properties	GetClassProperties ()

Static Public Member Functions inherited from bio::chemical::AbstractMotif
static Properties	GetClassProperties ()

Static Public Attributes inherited from bio::chemical::Elementary< LinearMotif< chemical::Reaction * > >
static bool	hasRegistered

Protected Member Functions inherited from bio::physical::Observer< Perspective< StandardDimension > >
virtual void	InitializeImplementation (ByteStreams args)

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

virtual	~VirtualBase ()

void	Initialize (ByteStream arg1)

void	Initialize (ByteStream arg1, ByteStream arg2)

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

void	Initialize (ByteStreams args)

virtual void	InitializeImplementation (ByteStreams args)=0

Protected Member Functions inherited from bio::log::Writer
virtual void	InitializeImplementation (ByteStreams args)

void	Log (Level level, const char *format,...) const

Protected Member Functions inherited from bio::chemical::Atom
virtual bool	BreakBondImplementation (Wave *toDisassociate, AtomicNumber id, BondType type)

virtual bool	FormBondImplementation (Wave *toBond, AtomicNumber id, BondType type)

Protected Attributes inherited from bio::physical::Class< T >
T *	m_object

Protected Attributes inherited from bio::physical::Wave
Wave *	m_signal

Symmetry *	m_symmetry

Protected Attributes inherited from bio::VirtualBase
bool	m_hasBeenInitialized

Protected Attributes inherited from bio::physical::Class< Identifiable< StandardDimension > >
Identifiable< StandardDimension > *	m_object

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

Protected Attributes inherited from bio::physical::Class< Filterable >
Filterable *	m_object

Protected Attributes inherited from bio::physical::Class< Writer >
Writer *	m_object

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

Protected Attributes inherited from bio::physical::Class< Atom >
Atom *	m_object

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

Protected Attributes inherited from bio::chemical::AbstractMotif
Container *	m_contents

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.

Definition at line 46 of file Pathway.h.

Member Function Documentation

◆ BIO_DISAMBIGUATE_ALL_CLASS_METHODS()

bio::molecular::Pathway::BIO_DISAMBIGUATE_ALL_CLASS_METHODS	(	chemical	,
		Pathway
	)

Ensure virtual methods point to Class implementations. Standard ctors.

◆ chemical::ReactionPerspective::Instance()

& bio::molecular::Pathway::chemical::ReactionPerspective::Instance ( )

◆ filter::Chemical()

bio::molecular::Pathway::filter::Chemical ( )

◆ Process()

chemical::Products bio::molecular::Pathway::Process ( 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.

Definition at line 36 of file Pathway.cpp.

{
    BIO_SANITIZE(reactants,,return code::BadArgument1())
 
    chemical::Products products(reactants);
    Reaction* reactionBuffer;
    for (
        SmartIterator rct = GetAll< Reaction* >()->Begin();
        !rct.IsAtEnd();
        ++rct
        )
    {
        if (products == code::Success() && products != code::NoErrorNoSuccess())
        {
            chemical::Reactants nextReactants(products);
            reactionBuffer = rct;
            products = (*reactionBuffer)(&nextReactants);
        }
        else
        {
            break;
        }
    }
    return products;
}

References bio::chemical::Reaction::Reaction, bio::code::BadArgument1(), BIO_SANITIZE, bio::SmartIterator::IsAtEnd(), bio::code::NoErrorNoSuccess(), bio::chemical::Reaction::reactants, and bio::code::Success().

◆ ReactantsMeetRequirements()

bool bio::molecular::Pathway::ReactantsMeetRequirements ( 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.

Definition at line 62 of file Pathway.cpp.

{
    BIO_SANITIZE(GetCount< chemical::Reaction* >(),,return false)
    return GetAll< chemical::Reaction* >()->Begin().As< chemical::Reaction* >()->ReactantsMeetRequirements(toCheck);
}

References BIO_SANITIZE, and ReactantsMeetRequirements().

Referenced by ReactantsMeetRequirements().

Member Data Documentation

◆ Pathway

bio::molecular::Pathway::Pathway

Definition at line 61 of file Pathway.h.

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

/home/eons/git/biology/lib_bio/inc/bio/molecular/Pathway.h
/home/eons/git/biology/lib_bio/src/molecular/Pathway.cpp

Public Member Functions

Public Attributes

Additional Inherited Members