#include <Reaction.hpp>

Inheritance diagram for CDPL::Chem::Reaction:

Public Types
typedef std::shared_ptr< Reaction >	SharedPointer
	A reference-counted smart pointer [SHPTR] for dynamically allocated `Reaction` instances. More...

typedef Util::IndexedElementIterator< const Molecule, ConstComponentAccessor >	ConstComponentIterator
	A constant random access iterator used to iterate over the components of the reaction. More...

typedef Util::IndexedElementIterator< Molecule, ComponentAccessor >	ComponentIterator
	A mutable random access iterator used to iterate over the components of the reaction. More...

typedef std::function< void(Reaction &, const Reaction &)>	CopyPostprocessingFunction

Public Types inherited from CDPL::Base::PropertyContainer
typedef PropertyMap::value_type	PropertyEntry
	A Base::LookupKey / Base::Any pair that stores the property value for a given property key. More...

typedef PropertyMap::const_iterator	ConstPropertyIterator
	A constant iterator used to iterate over the property entries. More...

Public Member Functions
virtual	~Reaction ()
	Virtual destructor. More...

virtual void	clear ()=0
	Removes all components and clears all properties of the reaction. More...

virtual std::size_t	getNumComponents () const =0
	Returns the number of reaction components. More...

virtual std::size_t	getNumComponents (unsigned int role) const =0
	Returns the number of reaction components with the specified role. More...

virtual unsigned int	getComponentRole (const Molecule &mol) const =0
	Returns the reaction role of the specified component. More...

virtual std::size_t	getComponentIndex (const Molecule &mol) const =0
	Returns the index of the specified reaction component. More...

virtual bool	containsComponent (const Molecule &mol) const =0
	Tells whether the specified molecule is a component of this reaction. More...

ConstComponentIterator	getComponentsBegin () const
	Returns a constant iterator pointing to the beginning of the reaction components. More...

ComponentIterator	getComponentsBegin ()
	Returns a mutable iterator pointing to the beginning of the reaction components. More...

ConstComponentIterator	getComponentsEnd () const
	Returns a constant iterator pointing to the end of the reaction components. More...

ComponentIterator	getComponentsEnd ()
	Returns a mutable iterator pointing to the end of the reaction components. More...

ConstComponentIterator	begin () const
	Returns a constant iterator pointing to the beginning of the reaction components. More...

ComponentIterator	begin ()
	Returns a mutable iterator pointing to the beginning of the reaction components. More...

ConstComponentIterator	end () const
	Returns a constant iterator pointing to the end of the reaction components. More...

ComponentIterator	end ()
	Returns a mutable iterator pointing to the end of the reaction components. More...

ConstComponentIterator	getComponentsBegin (unsigned int role) const
	Returns a constant iterator pointing to the beginning of the reaction components with the specified role. More...

ComponentIterator	getComponentsBegin (unsigned int role)
	Returns a mutable iterator pointing to the beginning of the reaction components with the specified role. More...

ConstComponentIterator	getComponentsEnd (unsigned int role) const
	Returns a constant iterator pointing to the end of the reaction components with the specified role. More...

ComponentIterator	getComponentsEnd (unsigned int role)
	Returns a mutable iterator pointing to the end of the reaction components with the specified role. More...

virtual const Molecule &	getComponent (std::size_t idx) const =0
	Returns a `const` reference to the reaction component at index idx. More...

virtual Molecule &	getComponent (std::size_t idx)=0
	Returns a non-`const` reference to the reaction component at index idx. More...

virtual const Molecule &	getComponent (std::size_t idx, unsigned int role) const =0
	Returns a `const` reference to the reaction component at index idx in the list of components with the specified role. More...

virtual Molecule &	getComponent (std::size_t idx, unsigned int role)=0
	Returns a non-`const` reference to the reaction component at index idx in the list of components with the specified role. More...

virtual Molecule &	addComponent (unsigned int role)=0
	Creates a new reaction component with the specified role. More...

virtual void	swapComponentRoles (unsigned int role1, unsigned int role2)=0
	Swaps the reaction roles of the component sets specified by role1 and role2. More...

virtual void	removeComponent (std::size_t idx)=0
	Removes the reaction component at the specified index. More...

virtual void	removeComponent (std::size_t idx, unsigned int role)=0
	Removes the reaction component at index idx in the list of components with the specified role. More...

ComponentIterator	removeComponent (const ComponentIterator &it)
	Removes the reaction component specified by the iterator it. More...

virtual void	removeComponents (unsigned int role)=0
	Removes all components with the specified role. More...

virtual SharedPointer	clone () const =0
	Creates a copy of the current reaction state. More...

virtual void	copy (const Reaction &rxn)=0
	Replaces the current set of reaction components and properties by a copy of the components and properties of the reaction rxn. More...

Reaction &	operator= (const Reaction &rxn)
	Replaces the current set of reaction components and properties by a copy of the components and properties of the reaction rxn. More...

Public Member Functions inherited from CDPL::Base::PropertyContainer
std::size_t	getNumProperties () const
	Returns the number of property entries. More...

template<typename T >
void	setProperty (const LookupKey &key, T &&val)
	Sets the value of the property specified by key to val. More...

template<typename T >
const T &	getProperty (const LookupKey &key) const
	Returns the value of the property specified by key as a `const` reference to an object of type T. More...

template<typename T >
const T &	getPropertyOrDefault (const LookupKey &key, const T &def_val) const
	Returns the value of the property specified by key as a `const` reference to an object of type T, or the default value def_val if a stored value does not exist. More...

const Any &	getProperty (const LookupKey &key, bool throw_=false) const
	Returns the value of the property specified by key. More...

bool	isPropertySet (const LookupKey &key) const
	Tells whether or not a value has been assigned to the property specified by key. More...

ConstPropertyIterator	getPropertiesBegin () const
	Returns a constant iterator pointing to the beginning of the property entries. More...

ConstPropertyIterator	getPropertiesEnd () const
	Returns a constant iterator pointing to the end of the property entries. More...

ConstPropertyIterator	begin () const
	Returns a constant iterator pointing to the beginning of the property entries. More...

ConstPropertyIterator	end () const
	Returns a constant iterator pointing to the end of the property entries. More...

bool	removeProperty (const LookupKey &key)
	Clears the value of the property specified by key. More...

void	clearProperties ()
	Clears all property values. More...

void	addProperties (const PropertyContainer &cntnr)
	Adds the property value entries in the `PropertyContainer` instance cntnr. More...

void	copyProperties (const PropertyContainer &cntnr)
	Replaces the current set of properties by a copy of the entries in cntnr. More...

void	swap (PropertyContainer &cntnr)
	Exchanges the properties of this container with the properties of the container cntnr. More...

const PropertyContainer &	getProperties () const
	Returns a `const` reference to itself. More...

Static Public Member Functions
static void	registerCopyPostprocessingFunction (const CopyPostprocessingFunction &func)

Protected Member Functions
void	invokeCopyPostprocessingFunctions (const Reaction &src_rxn)

Protected Member Functions inherited from CDPL::Base::PropertyContainer
	PropertyContainer ()
	Constructs an empty `PropertyContainer` instance. More...

	PropertyContainer (const PropertyContainer &cntnr)
	Constructs a copy of the `PropertyContainer` instance cntnr. More...

virtual	~PropertyContainer ()
	Virtual destructor. More...

PropertyContainer &	operator= (const PropertyContainer &cntnr)
	Assignment operator. More...

Detailed Description

Reaction.

Member Typedef Documentation

◆ SharedPointer

typedef std::shared_ptr<Reaction> CDPL::Chem::Reaction::SharedPointer

A reference-counted smart pointer [SHPTR] for dynamically allocated Reaction instances.

◆ ConstComponentIterator

typedef Util::IndexedElementIterator<const Molecule, ConstComponentAccessor> CDPL::Chem::Reaction::ConstComponentIterator

A constant random access iterator used to iterate over the components of the reaction.

◆ ComponentIterator

typedef Util::IndexedElementIterator<Molecule, ComponentAccessor> CDPL::Chem::Reaction::ComponentIterator

A mutable random access iterator used to iterate over the components of the reaction.

◆ CopyPostprocessingFunction

typedef std::function<void(Reaction&, const Reaction&)> CDPL::Chem::Reaction::CopyPostprocessingFunction

Constructor & Destructor Documentation

◆ ~Reaction()

virtual CDPL::Chem::Reaction::~Reaction ( )

inlinevirtual

Virtual destructor.

Member Function Documentation

◆ clear()

virtual void CDPL::Chem::Reaction::clear ( )

pure virtual

Removes all components and clears all properties of the reaction.

Implemented in CDPL::Chem::BasicReaction.

◆ getNumComponents() [1/2]

virtual std::size_t CDPL::Chem::Reaction::getNumComponents ( ) const

pure virtual

Returns the number of reaction components.

Returns: The number of reaction components.

Implemented in CDPL::Chem::BasicReaction.

◆ getNumComponents() [2/2]

virtual std::size_t CDPL::Chem::Reaction::getNumComponents ( unsigned int role ) const

pure virtual

Returns the number of reaction components with the specified role.

Parameters

role	A flag that specifies the reaction role (see namespace Chem::ReactionRole).

Returns: The number of reaction components with the specified role.

Exceptions

Base::ValueError if the value of role is not equal to Chem::ReactionRole::REACTANT, Chem::ReactionRole::AGENT or Chem::ReactionRole::PRODUCT.

Implemented in CDPL::Chem::BasicReaction.

◆ getComponentRole()

virtual unsigned int CDPL::Chem::Reaction::getComponentRole ( const Molecule & mol ) const

pure virtual

Returns the reaction role of the specified component.

If the specified molecule is not a component of this reaction, Chem::ReactionRole::NONE will be returned.

Parameters

mol	The component for which to return the reaction role.

Returns: A flag that specifies the reaction role of the component (see namespace Chem::ReactionRole).

Implemented in CDPL::Chem::BasicReaction.

◆ getComponentIndex()

virtual std::size_t CDPL::Chem::Reaction::getComponentIndex ( const Molecule & mol ) const

pure virtual

Returns the index of the specified reaction component.

Parameters

mol	The component for which to return the index.

Returns: The zero-based index of the specified reaction component.

Exceptions

Base::ItemNotFound if the specified molecule is not a component of this reaction.

Implemented in CDPL::Chem::BasicReaction.

◆ containsComponent()

virtual bool CDPL::Chem::Reaction::containsComponent ( const Molecule & mol ) const

pure virtual

Tells whether the specified molecule is a component of this reaction.

Parameters

mol	The molecule to look for.

Returns: true if the specified molecule is a component of this reaction, and false otherwise.

Implemented in CDPL::Chem::BasicReaction.

◆ getComponentsBegin() [1/4]

ConstComponentIterator CDPL::Chem::Reaction::getComponentsBegin ( ) const

Returns a constant iterator pointing to the beginning of the reaction components.

Returns: A constant iterator pointing to the beginning of the reaction components.

◆ getComponentsBegin() [2/4]

ComponentIterator CDPL::Chem::Reaction::getComponentsBegin ( )

Returns a mutable iterator pointing to the beginning of the reaction components.

Returns: A mutable iterator pointing to the beginning of the reaction components.

◆ getComponentsEnd() [1/4]

ConstComponentIterator CDPL::Chem::Reaction::getComponentsEnd ( ) const

Returns a constant iterator pointing to the end of the reaction components.

Returns: A constant iterator pointing to the end of the reaction components.

◆ getComponentsEnd() [2/4]

ComponentIterator CDPL::Chem::Reaction::getComponentsEnd ( )

Returns a mutable iterator pointing to the end of the reaction components.

Returns: A mutable iterator pointing to the end of the reaction components.

◆ begin() [1/2]

ConstComponentIterator CDPL::Chem::Reaction::begin ( ) const

Returns a constant iterator pointing to the beginning of the reaction components.

Returns: A constant iterator pointing to the beginning of the reaction components.

◆ begin() [2/2]

ComponentIterator CDPL::Chem::Reaction::begin ( )

Returns a mutable iterator pointing to the beginning of the reaction components.

Returns: A mutable iterator pointing to the beginning of the reaction components.

◆ end() [1/2]

ConstComponentIterator CDPL::Chem::Reaction::end ( ) const

Returns a constant iterator pointing to the end of the reaction components.

Returns: A constant iterator pointing to the end of the reaction components.

◆ end() [2/2]

ComponentIterator CDPL::Chem::Reaction::end ( )

Returns a mutable iterator pointing to the end of the reaction components.

Returns: A mutable iterator pointing to the end of the reaction components.

◆ getComponentsBegin() [3/4]

ConstComponentIterator CDPL::Chem::Reaction::getComponentsBegin ( unsigned int role ) const

Returns a constant iterator pointing to the beginning of the reaction components with the specified role.

Parameters

role	A flag that specifies the reaction role (see namespace Chem::ReactionRole).

Returns: A constant iterator pointing to the beginning of the reaction components with the specified role.

Exceptions

Base::ValueError if the value of role is not equal to Chem::ReactionRole::REACTANT, Chem::ReactionRole::AGENT or Chem::ReactionRole::PRODUCT.

◆ getComponentsBegin() [4/4]

ComponentIterator CDPL::Chem::Reaction::getComponentsBegin ( unsigned int role )

Returns a mutable iterator pointing to the beginning of the reaction components with the specified role.

Parameters

role	A flag that specifies the reaction role (see namespace Chem::ReactionRole).

Returns: A mutable iterator pointing to the beginning of the reaction components with the specified role.

Exceptions

Base::ValueError if the value of role is not equal to Chem::ReactionRole::REACTANT, Chem::ReactionRole::AGENT or Chem::ReactionRole::PRODUCT.

◆ getComponentsEnd() [3/4]

ConstComponentIterator CDPL::Chem::Reaction::getComponentsEnd ( unsigned int role ) const

Returns a constant iterator pointing to the end of the reaction components with the specified role.

Parameters

role	A flag that specifies the reaction role (see namespace Chem::ReactionRole).

Returns: A constant iterator pointing to the end of the reaction components with the specified role.

Exceptions

Base::ValueError if the value of role is not equal to Chem::ReactionRole::REACTANT, Chem::ReactionRole::AGENT or Chem::ReactionRole::PRODUCT.

◆ getComponentsEnd() [4/4]

ComponentIterator CDPL::Chem::Reaction::getComponentsEnd ( unsigned int role )

Returns a mutable iterator pointing to the end of the reaction components with the specified role.

Parameters

role	A flag that specifies the reaction role (see namespace Chem::ReactionRole).

Returns: A mutable iterator pointing to the end of the reaction components with the specified role.

Exceptions

Base::ValueError if the value of role is not equal to Chem::ReactionRole::REACTANT, Chem::ReactionRole::AGENT or Chem::ReactionRole::PRODUCT.

◆ getComponent() [1/4]

virtual const Molecule& CDPL::Chem::Reaction::getComponent ( std::size_t idx ) const

pure virtual

Returns a const reference to the reaction component at index idx.

Parameters

idx	The zero-based index of the reaction component to return.

Returns: A const reference to the reaction component at the specified index.

Exceptions

Base::IndexError if the number of components is zero or idx is not in the range [0, getNumComponents() - 1].

Implemented in CDPL::Chem::BasicReaction.

◆ getComponent() [2/4]

virtual Molecule& CDPL::Chem::Reaction::getComponent ( std::size_t idx )

pure virtual

Returns a non-const reference to the reaction component at index idx.

Parameters

idx	The zero-based index of the reaction component to return.

Returns: A non-const reference to the reaction component at the specified index.

Exceptions

Base::IndexError if the number of components is zero or idx is not in the range [0, getNumComponents() - 1].

Implemented in CDPL::Chem::BasicReaction.

◆ getComponent() [3/4]

virtual const Molecule& CDPL::Chem::Reaction::getComponent	(	std::size_t	idx,
		unsigned int	role
	)		const

pure virtual

Returns a const reference to the reaction component at index idx in the list of components with the specified role.

Parameters

idx	The zero-based index of the reaction component to return.
role	A flag indicating the reaction role of the component (see namespace Chem::ReactionRole).

Returns: A const reference to the reaction component with the specified role and index.

Exceptions

Base::IndexError if the number of components with the specified role is zero or idx is not in the range [0, getNumComponents(role) - 1]. Base::ValueError if the value of role is not equal to Chem::ReactionRole::REACTANT, Chem::ReactionRole::AGENT or Chem::ReactionRole::PRODUCT.

Implemented in CDPL::Chem::BasicReaction.

◆ getComponent() [4/4]

virtual Molecule& CDPL::Chem::Reaction::getComponent	(	std::size_t	idx,
		unsigned int	role
	)

pure virtual

Returns a non-const reference to the reaction component at index idx in the list of components with the specified role.

Parameters

idx	The zero-based index of the reaction component to return.
role	A flag indicating the reaction role of the component (see namespace Chem::ReactionRole).

Returns: A non-const reference to the reaction component with the specified role and index.

Exceptions

Base::IndexError if the number of components with the specified role is zero or idx is not in the range [0, getNumComponents(role) - 1]. Base::ValueError if the value of role is not equal to Chem::ReactionRole::REACTANT, Chem::ReactionRole::AGENT or Chem::ReactionRole::PRODUCT.

Implemented in CDPL::Chem::BasicReaction.

◆ addComponent()

virtual Molecule& CDPL::Chem::Reaction::addComponent ( unsigned int role )

pure virtual

Creates a new reaction component with the specified role.

Parameters

role	A flag specifying the reaction role of the new component (see namespace Chem::ReactionRole).

Returns: A reference to the newly created component molecule.

Exceptions

Base::ValueError if the value of role is not Chem::ReactionRole::REACTANT, Chem::ReactionRole::AGENT or Chem::ReactionRole::PRODUCT.

Implemented in CDPL::Chem::BasicReaction.

◆ swapComponentRoles()

virtual void CDPL::Chem::Reaction::swapComponentRoles	(	unsigned int	role1,
		unsigned int	role2
	)

pure virtual

Swaps the reaction roles of the component sets specified by role1 and role2.

If role1 is equal to role2, the method has no effect.

Parameters

role1	A flag specifying the reaction role of the first component set (see namespace Chem::ReactionRole).
role2	A flag specifying the reaction role of the second component set (see namespace Chem::ReactionRole).

Exceptions

Base::ValueError if the value of role1 and/or role2 is not equal to Chem::ReactionRole::REACTANT, Chem::ReactionRole::AGENT or Chem::ReactionRole::PRODUCT.

Implemented in CDPL::Chem::BasicReaction.

◆ removeComponent() [1/3]

virtual void CDPL::Chem::Reaction::removeComponent ( std::size_t idx )

pure virtual

Removes the reaction component at the specified index.

Parameters

idx	The zero-based index of the component to remove.

Exceptions

Base::IndexError if the number of components is zero or idx is not in the range [0, getNumComponents() - 1].

Implemented in CDPL::Chem::BasicReaction.

◆ removeComponent() [2/3]

virtual void CDPL::Chem::Reaction::removeComponent	(	std::size_t	idx,
		unsigned int	role
	)

pure virtual

Removes the reaction component at index idx in the list of components with the specified role.

Parameters

idx	The zero-based index of the component to remove.
role	The reaction role of the components

Exceptions

Base::IndexError if the number of components with the specified role is zero or idx is not in the range [0, getNumComponents(role) - 1]. Base::ValueError if the value of role is not Chem::ReactionRole::REACTANT, Chem::ReactionRole::AGENT or Chem::ReactionRole::PRODUCT.

Implemented in CDPL::Chem::BasicReaction.

◆ removeComponent() [3/3]

ComponentIterator CDPL::Chem::Reaction::removeComponent ( const ComponentIterator & it )

Removes the reaction component specified by the iterator it.

Parameters

it	A mutable iterator that specifies the component to remove.

Returns: A mutable iterator pointing to the next reaction component in the list.

Exceptions

Base::RangeError if the number of reaction components is zero or it is not in the range [getComponentsBegin(), getComponentsEnd() - 1].

◆ removeComponents()

virtual void CDPL::Chem::Reaction::removeComponents ( unsigned int role )

pure virtual

Removes all components with the specified role.

Parameters

role	A flag specifying the reaction role of the components to remove (see namespace Chem::ReactionRole).

Exceptions

Base::ValueError if the value of role is not Chem::ReactionRole::REACTANT, Chem::ReactionRole::AGENT or Chem::ReactionRole::PRODUCT.

Implemented in CDPL::Chem::BasicReaction.

◆ clone()

virtual SharedPointer CDPL::Chem::Reaction::clone ( ) const

pure virtual

Creates a copy of the current reaction state.

Returns: A smart pointer to the copy of the reaction.

Implemented in CDPL::Chem::BasicReaction.

◆ copy()

virtual void CDPL::Chem::Reaction::copy ( const Reaction & rxn )

pure virtual

Replaces the current set of reaction components and properties by a copy of the components and properties of the reaction rxn.

Parameters

rxn	The reaction to copy.

Implemented in CDPL::Chem::BasicReaction.

◆ operator=()

Reaction& CDPL::Chem::Reaction::operator= ( const Reaction & rxn )

Replaces the current set of reaction components and properties by a copy of the components and properties of the reaction rxn.

Internally calls copy() to perform the actual work.

Parameters

rxn	The reaction to copy.

Returns: A reference to itself.

◆ registerCopyPostprocessingFunction()

static void CDPL::Chem::Reaction::registerCopyPostprocessingFunction ( const CopyPostprocessingFunction & func )

static

◆ invokeCopyPostprocessingFunctions()

void CDPL::Chem::Reaction::invokeCopyPostprocessingFunctions ( const Reaction & src_rxn )

protected

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

Reaction.hpp

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ConstComponentIterator

◆ ComponentIterator

◆ CopyPostprocessingFunction

Constructor & Destructor Documentation

◆ ~Reaction()

Member Function Documentation

◆ clear()

◆ getNumComponents() [1/2]

◆ getNumComponents() [2/2]

◆ getComponentRole()

◆ getComponentIndex()

◆ containsComponent()

◆ getComponentsBegin() [1/4]

◆ getComponentsBegin() [2/4]

◆ getComponentsEnd() [1/4]

◆ getComponentsEnd() [2/4]

◆ begin() [1/2]

◆ begin() [2/2]

◆ end() [1/2]

◆ end() [2/2]

◆ getComponentsBegin() [3/4]

◆ getComponentsBegin() [4/4]

◆ getComponentsEnd() [3/4]

◆ getComponentsEnd() [4/4]

◆ getComponent() [1/4]

◆ getComponent() [2/4]

◆ getComponent() [3/4]

◆ getComponent() [4/4]

◆ addComponent()

◆ swapComponentRoles()

◆ removeComponent() [1/3]

◆ removeComponent() [2/3]

◆ removeComponent() [3/3]

◆ removeComponents()

◆ clone()

◆ copy()

◆ operator=()

◆ registerCopyPostprocessingFunction()

◆ invokeCopyPostprocessingFunctions()