Abstract base class for chemical reactions composed of role-tagged reaction components of type Chem::Molecule. More...

#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 stored `const` Chem::Molecule objects. More...

typedef Util::IndexedElementIterator< Molecule, ComponentAccessor >	ComponentIterator
	A mutable random access iterator used to iterate over the stored Chem::Molecule objects. More...

typedef std::function< void(Reaction &, const Reaction &)>	CopyPostprocessingFunction
	Type of a functor invoked after a reaction copy operation to postprocess the target reaction (first argument) using information from the source reaction (second argument). More...

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 total 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 deep 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)
	Registers a global postprocessing function invoked after every reaction copy operation. More...

Protected Member Functions
void	invokeCopyPostprocessingFunctions (const Reaction &src_rxn)
	Invokes all registered copy postprocessing functions with `this` as the target and src_rxn* as the source reaction. More...

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

Abstract base class for chemical reactions composed of role-tagged reaction components of type Chem::Molecule.

Each component carries a reaction role that is specified by one of the constants declared in namespace Chem::ReactionRole. Reaction roles divide the components into three different subsets: reactants, agents/catalysts and products. For component management/access the methods getComponentRole(), getNumComponents(), getComponent(), getComponentsBegin() and getComponentsEnd() are available. For reaction editing the methods addComponent(), removeComponent(), swapComponentRoles() and clear(). The method clone() allows the creation of polymorphic deep copies and reaction properties can be stored/retrieved via the methods of the Base::PropertyContainer base class.

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 stored const Chem::Molecule objects.

◆ ComponentIterator

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

A mutable random access iterator used to iterate over the stored Chem::Molecule objects.

◆ CopyPostprocessingFunction

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

Type of a functor invoked after a reaction copy operation to postprocess the target reaction (first argument) using information from the source reaction (second argument).

Functions registered with registerCopyPostprocessingFunction() are run by invokeCopyPostprocessingFunctions() inside subclasses' copy() implementations.

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 total number of reaction components.

Returns: The total 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	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: 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	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	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	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	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 idx is not in the range [0, getNumComponents()).

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 idx is not in the range [0, getNumComponents()).

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 idx is not in the range [0, getNumComponents(role)). 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 idx is not in the range [0, getNumComponents(role)). 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	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	The reaction role of the first component set (see namespace Chem::ReactionRole).
role2	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 idx is not in the range [0, getNumComponents()).

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 component (see namespace Chem::ReactionRole).

Exceptions

Base::IndexError if idx is not in the range [0, getNumComponents(role)). 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 it is not in the range [getComponentsBegin(), getComponentsEnd()).

◆ removeComponents()

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

pure virtual

Removes all components with the specified role.

Parameters

role	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 deep 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

Registers a global postprocessing function invoked after every reaction copy operation.

Parameters

func	The function to register.

◆ invokeCopyPostprocessingFunctions()

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

protected

Invokes all registered copy postprocessing functions with *this as the target and src_rxn as the source reaction.

Parameters

src_rxn The source reaction the copy was made from.

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()