#include <BasicReaction.hpp>

Inheritance diagram for CDPL::Chem::BasicReaction:

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

typedef boost::indirect_iterator< ComponentList::iterator, BasicMolecule >	ComponentIterator

typedef boost::indirect_iterator< ComponentList::const_iterator, const BasicMolecule >	ConstComponentIterator

Public Types inherited from CDPL::Chem::Reaction
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
	BasicReaction ()
	Constructs an empty `BasicReaction` instance. More...

	BasicReaction (const BasicReaction &rxn)
	Constructs a copy of the `BasicReaction` instance rxn. More...

	BasicReaction (const Reaction &rxn)
	Constructs a copy of the Chem::Reaction instance rxn. More...

	~BasicReaction ()
	Destructor. More...

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

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

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

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

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

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

ConstComponentIterator	getComponentsBegin () const

ComponentIterator	getComponentsBegin ()

ConstComponentIterator	getComponentsEnd () const

ComponentIterator	getComponentsEnd ()

ConstComponentIterator	getComponentsBegin (unsigned int role) const

ComponentIterator	getComponentsBegin (unsigned int role)

ConstComponentIterator	getComponentsEnd (unsigned int role) const

ComponentIterator	getComponentsEnd (unsigned int role)

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

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

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

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

BasicMolecule &	addComponent (unsigned int role)
	Creates a new reaction component with the specified role. More...

BasicMolecule &	addComponent (unsigned int role, const Molecule &mol)
	Creates a new reaction component with the specified role that is a copy of the molecule mol. More...

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

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

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

ComponentIterator	removeComponent (const ComponentIterator &it)

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

Reaction::SharedPointer	clone () const
	Creates a copy of the current reaction state. More...

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

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

void	copy (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...

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::Chem::Reaction
virtual	~Reaction ()
	Virtual destructor. 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...

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

Additional Inherited Members
Static Public Member Functions inherited from CDPL::Chem::Reaction
static void	registerCopyPostprocessingFunction (const CopyPostprocessingFunction &func)

Protected Member Functions inherited from CDPL::Chem::Reaction
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

BasicReaction.

Member Typedef Documentation

◆ SharedPointer

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

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

◆ ComponentIterator

typedef boost::indirect_iterator<ComponentList::iterator, BasicMolecule> CDPL::Chem::BasicReaction::ComponentIterator

◆ ConstComponentIterator

typedef boost::indirect_iterator<ComponentList::const_iterator, const BasicMolecule> CDPL::Chem::BasicReaction::ConstComponentIterator

Constructor & Destructor Documentation

◆ BasicReaction() [1/3]

CDPL::Chem::BasicReaction::BasicReaction ( )

Constructs an empty BasicReaction instance.

◆ BasicReaction() [2/3]

CDPL::Chem::BasicReaction::BasicReaction ( const BasicReaction & rxn )

Constructs a copy of the BasicReaction instance rxn.

Parameters

rxn	The other `Reaction` instance to copy.

◆ BasicReaction() [3/3]

CDPL::Chem::BasicReaction::BasicReaction ( const Reaction & rxn )

Constructs a copy of the Chem::Reaction instance rxn.

Parameters

rxn	The other Chem::Reaction instance to copy.

◆ ~BasicReaction()

CDPL::Chem::BasicReaction::~BasicReaction ( )

Destructor.

Destroys the BasicReaction instance and frees all allocated resources.

Member Function Documentation

◆ getComponentRole()

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

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).

Implements CDPL::Chem::Reaction.

◆ getComponentIndex()

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

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.

Implements CDPL::Chem::Reaction.

◆ containsComponent()

bool CDPL::Chem::BasicReaction::containsComponent ( const Molecule & mol ) const

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.

Implements CDPL::Chem::Reaction.

◆ clear()

void CDPL::Chem::BasicReaction::clear ( )

virtual

Removes all components and clears all properties of the reaction.

Implements CDPL::Chem::Reaction.

◆ getNumComponents() [1/2]

std::size_t CDPL::Chem::BasicReaction::getNumComponents ( ) const

virtual

Returns the number of reaction components.

Returns: The number of reaction components.

Implements CDPL::Chem::Reaction.

◆ getNumComponents() [2/2]

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

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.

Implements CDPL::Chem::Reaction.

◆ getComponentsBegin() [1/4]

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

◆ getComponentsBegin() [2/4]

ComponentIterator CDPL::Chem::BasicReaction::getComponentsBegin ( )

◆ getComponentsEnd() [1/4]

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

◆ getComponentsEnd() [2/4]

ComponentIterator CDPL::Chem::BasicReaction::getComponentsEnd ( )

◆ getComponentsBegin() [3/4]

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

◆ getComponentsBegin() [4/4]

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

◆ getComponentsEnd() [3/4]

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

◆ getComponentsEnd() [4/4]

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

◆ getComponent() [1/4]

const BasicMolecule& CDPL::Chem::BasicReaction::getComponent ( std::size_t idx ) const

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].

Implements CDPL::Chem::Reaction.

◆ getComponent() [2/4]

BasicMolecule& CDPL::Chem::BasicReaction::getComponent ( std::size_t idx )

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].

Implements CDPL::Chem::Reaction.

◆ getComponent() [3/4]

const BasicMolecule& CDPL::Chem::BasicReaction::getComponent	(	std::size_t	idx,
		unsigned int	role
	)		const

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.

Implements CDPL::Chem::Reaction.

◆ getComponent() [4/4]

BasicMolecule& CDPL::Chem::BasicReaction::getComponent	(	std::size_t	idx,
		unsigned int	role
	)

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.

Implements CDPL::Chem::Reaction.

◆ addComponent() [1/2]

BasicMolecule& CDPL::Chem::BasicReaction::addComponent ( unsigned int role )

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.

Implements CDPL::Chem::Reaction.

◆ addComponent() [2/2]

BasicMolecule& CDPL::Chem::BasicReaction::addComponent	(	unsigned int	role,
		const Molecule &	mol
	)

Creates a new reaction component with the specified role that is a copy of the molecule mol.

Parameters

role	A flag specifying the reaction role of the new component (see namespace Chem::ReactionRole).
mol	Specifies a molecule that provides the data for the new reaction component (note that only explicitly assigned molecule, atom and bond properties will be copied).

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.

◆ swapComponentRoles()

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

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.

Implements CDPL::Chem::Reaction.

◆ removeComponent() [1/3]

void CDPL::Chem::BasicReaction::removeComponent ( std::size_t idx )

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].

Implements CDPL::Chem::Reaction.

◆ removeComponent() [2/3]

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

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.

Implements CDPL::Chem::Reaction.

◆ removeComponent() [3/3]

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

◆ removeComponents()

void CDPL::Chem::BasicReaction::removeComponents ( unsigned int role )

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.

Implements CDPL::Chem::Reaction.

◆ clone()

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

virtual

Creates a copy of the current reaction state.

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

Implements CDPL::Chem::Reaction.

◆ operator=() [1/2]

BasicReaction& CDPL::Chem::BasicReaction::operator= ( const BasicReaction & 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.

◆ copy() [1/2]

void CDPL::Chem::BasicReaction::copy ( const BasicReaction & rxn )

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.

◆ copy() [2/2]

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

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.

Implements CDPL::Chem::Reaction.

◆ operator=() [2/2]

Reaction& CDPL::Chem::Reaction::operator=

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.

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

BasicReaction.hpp

Public Types

Public Member Functions

Additional Inherited Members

Detailed Description

Member Typedef Documentation

◆ SharedPointer

◆ ComponentIterator

◆ ConstComponentIterator

Constructor & Destructor Documentation

◆ BasicReaction() [1/3]

◆ BasicReaction() [2/3]

◆ BasicReaction() [3/3]

◆ ~BasicReaction()

Member Function Documentation

◆ getComponentRole()

◆ getComponentIndex()

◆ containsComponent()

◆ clear()

◆ getNumComponents() [1/2]

◆ getNumComponents() [2/2]

◆ getComponentsBegin() [1/4]

◆ getComponentsBegin() [2/4]

◆ getComponentsEnd() [1/4]

◆ getComponentsEnd() [2/4]

◆ 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() [1/2]

◆ addComponent() [2/2]

◆ swapComponentRoles()

◆ removeComponent() [1/3]

◆ removeComponent() [2/3]

◆ removeComponent() [3/3]

◆ removeComponents()

◆ clone()

◆ operator=() [1/2]

◆ copy() [1/2]

◆ copy() [2/2]

◆ operator=() [2/2]