Default concrete implementation of the Chem::Reaction abstract interface. More...

#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
	A mutable random access iterator used to iterate over the stored Chem::BasicMolecule reaction components. More...

typedef boost::indirect_iterator< ComponentList::const_iterator, const BasicMolecule >	ConstComponentIterator
	A constant random access iterator used to iterate over the stored `const` Chem::BasicMolecule reaction components. More...

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
	Type of a functor invoked after a reaction copy operation to post-process 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
	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 component mol (see namespace Chem::ReactionRole). More...

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

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

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

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

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

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

ComponentIterator	getComponentsBegin ()
	Returns a mutable iterator pointing to the first component of the reaction. More...

ConstComponentIterator	getComponentsEnd () const
	Returns a constant iterator pointing one past the last component of the reaction. More...

ComponentIterator	getComponentsEnd ()
	Returns a mutable iterator pointing one past the last component of the reaction. More...

ConstComponentIterator	getComponentsBegin (unsigned int role) const
	Returns a constant iterator pointing to the first component with the given reaction role. More...

ComponentIterator	getComponentsBegin (unsigned int role)
	Returns a mutable iterator pointing to the first component with the given reaction role. More...

ConstComponentIterator	getComponentsEnd (unsigned int role) const
	Returns a constant iterator pointing one past the last component with the given reaction role. More...

ComponentIterator	getComponentsEnd (unsigned int role)
	Returns a mutable iterator pointing one past the last component with the given reaction role. More...

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

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

const BasicMolecule &	getComponent (std::size_t idx, unsigned int role) const
	Returns a `const` reference to the component at the given index within its reaction role. More...

BasicMolecule &	getComponent (std::size_t idx, unsigned int role)
	Returns a reference to the component at the given index within its reaction role. More...

BasicMolecule &	addComponent (unsigned int role)
	Adds a new empty component with the specified reaction 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 two component groups. More...

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

void	removeComponent (std::size_t idx, unsigned int role)
	Removes the component at the given index within its reaction role. More...

ComponentIterator	removeComponent (const ComponentIterator &it)
	Removes the component referenced by the given iterator. More...

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

Reaction::SharedPointer	clone () const
	Creates a deep copy of the reaction. 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)
	Registers a global post-processing function invoked after every reaction copy operation. More...

Protected Member Functions inherited from CDPL::Chem::Reaction
void	invokeCopyPostprocessingFunctions (const Reaction &src_rxn)
	Invokes all registered copy post-processing functions with `this` as the target reaction and src_rxn* as the source. 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

Default concrete implementation of the Chem::Reaction abstract interface.

BasicReaction stores reaction components as Chem::BasicMolecule instances grouped by reaction role (reactant, agent, product). Components are pooled via a Util::ObjectPool to minimize allocation overhead in batch processing scenarios.

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

A mutable random access iterator used to iterate over the stored Chem::BasicMolecule reaction components.

◆ ConstComponentIterator

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

A constant random access iterator used to iterate over the stored const Chem::BasicMolecule reaction components.

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 component mol (see namespace Chem::ReactionRole).

Parameters

mol	The molecule whose role is requested.

Returns: The reaction role of the component.

Implements CDPL::Chem::Reaction.

◆ getComponentIndex()

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

virtual

Returns the index of the component mol in the reaction.

Parameters

mol	The molecule whose index is requested.

Returns: The zero-based index of the component.

Implements CDPL::Chem::Reaction.

◆ containsComponent()

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

virtual

Tells whether mol is a component of the reaction.

Parameters

mol	The molecule to look up.

Returns: true if mol is a component of the 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 total number of components in the reaction.

Returns: The total number of components.

Implements CDPL::Chem::Reaction.

◆ getNumComponents() [2/2]

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

virtual

Returns the number of components with the given reaction role.

Parameters

role	The reaction role (see namespace Chem::ReactionRole).

Returns: The number of components with the specified role.

Implements CDPL::Chem::Reaction.

◆ getComponentsBegin() [1/4]

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

Returns a constant iterator pointing to the first component of the reaction.

Returns: A constant iterator pointing to the first component.

◆ getComponentsBegin() [2/4]

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

Returns a mutable iterator pointing to the first component of the reaction.

Returns: A mutable iterator pointing to the first component.

◆ getComponentsEnd() [1/4]

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

Returns a constant iterator pointing one past the last component of the reaction.

Returns: A constant iterator pointing one past the last component.

◆ getComponentsEnd() [2/4]

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

Returns a mutable iterator pointing one past the last component of the reaction.

Returns: A mutable iterator pointing one past the last component.

◆ getComponentsBegin() [3/4]

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

Returns a constant iterator pointing to the first component with the given reaction role.

Parameters

role	The reaction role (see namespace Chem::ReactionRole).

Returns: A constant iterator pointing to the first component with the specified role.

◆ getComponentsBegin() [4/4]

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

Returns a mutable iterator pointing to the first component with the given reaction role.

Parameters

role	The reaction role (see namespace Chem::ReactionRole).

Returns: A mutable iterator pointing to the first component with the specified role.

◆ getComponentsEnd() [3/4]

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

Returns a constant iterator pointing one past the last component with the given reaction role.

Parameters

role	The reaction role (see namespace Chem::ReactionRole).

Returns: A constant iterator pointing one past the last component with the specified role.

◆ getComponentsEnd() [4/4]

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

Returns a mutable iterator pointing one past the last component with the given reaction role.

Parameters

role	The reaction role (see namespace Chem::ReactionRole).

Returns: A mutable iterator pointing one past the last component with the specified role.

◆ getComponent() [1/4]

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

virtual

Returns a const reference to the component at the specified index.

Parameters

idx	The zero-based component index.

Returns: A const reference to the component.

Implements CDPL::Chem::Reaction.

◆ getComponent() [2/4]

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

virtual

Returns a reference to the component at the specified index.

Parameters

idx	The zero-based component index.

Returns: A reference to the component.

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 component at the given index within its reaction role.

Parameters

idx	The zero-based component index within the role.
role	The reaction role (see namespace Chem::ReactionRole).

Returns: A const reference to the component.

Implements CDPL::Chem::Reaction.

◆ getComponent() [4/4]

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

virtual

Returns a reference to the component at the given index within its reaction role.

Parameters

idx	The zero-based component index within the role.
role	The reaction role (see namespace Chem::ReactionRole).

Returns: A reference to the component.

Implements CDPL::Chem::Reaction.

◆ addComponent() [1/2]

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

virtual

Adds a new empty component with the specified reaction role.

Parameters

role	The reaction role of the new component (see namespace Chem::ReactionRole).

Returns: A reference to the newly created component molecule.

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 two component groups.

Parameters

role1	The first reaction role.
role2	The second reaction role.

Implements CDPL::Chem::Reaction.

◆ removeComponent() [1/3]

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

virtual

Removes the component at the specified index.

Parameters

idx	The zero-based component index.

Implements CDPL::Chem::Reaction.

◆ removeComponent() [2/3]

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

virtual

Removes the component at the given index within its reaction role.

Parameters

idx	The zero-based component index within the role.
role	The reaction role (see namespace Chem::ReactionRole).

Implements CDPL::Chem::Reaction.

◆ removeComponent() [3/3]

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

Removes the component referenced by the given iterator.

Parameters

it	Iterator referencing the component to remove.

Returns: A mutable iterator pointing to the component following the removed one.

◆ removeComponents()

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

virtual

Removes all components with the specified reaction role.

Parameters

role	The reaction role of the components to remove (see namespace Chem::ReactionRole).

Implements CDPL::Chem::Reaction.

◆ clone()

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

virtual

Creates a deep copy of the reaction.

Returns: A smart pointer to the cloned 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]