CDPL.Chem.Reaction Class Reference

Reaction. More...

Inheritance diagram for CDPL.Chem.Reaction:

Classes
class	ComponentSequence

Public Member Functions
None	__init__ ()
	Initializes the Reaction instance.
None	clear ()
	Removes all components and clears all properties of the reaction.
Molecule	addComponent (int role)
	Creates a new reaction component with the specified role. More...
bool	containsComponent (Molecule mol)
	Tells whether the specified molecule is a component of this reaction. More...
int	getComponentRole (Molecule mol)
	Returns the reaction role of the specified component. More...
int	getComponentIndex (Molecule mol)
	Returns the index of the specified reaction component. More...
int	getNumComponents (int role)
	Returns the number of reaction components with the specified role. More...
int	getNumComponents ()
	Returns the number of reaction components. More...
Molecule	getComponent (int idx, int role)
	Returns a reference to the reaction component at index idx in the list of components with the specified role. More...
Molecule	getComponent (int idx)
	Returns a reference to the reaction component at index idx. More...
None	removeComponents (int role)
	Removes all components with the specified role. More...
None	removeComponent (int idx, int role)
	Removes the reaction component at index idx in the list of components with the specified role. More...
None	removeComponent (int idx)
	Removes the reaction component at the specified index. More...
None	swapComponentRoles (int role1, int role2)
	Swaps the reaction roles of the component sets specified by role1 and role2. More...
Reaction	clone ()
	Creates a copy of the current reaction state. More...
None	copy (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	assign (Reaction rxn)
	Replaces the current set of reaction components and properties by a copy of the components and properties of the reaction rxn. More...
ComponentSequence	getReactants ()
ComponentSequence	getAgents ()
ComponentSequence	getProducts ()
None	invokeCopyPostprocessingFunctions (Reaction src_rxn)
tuple	__getstate__ ()
Molecule	__getitem__ (int idx)
Base.Any	__getitem__ (Base.LookupKey key)
None	__delitem__ (int idx)
bool	__delitem__ (Base.LookupKey key)
bool	__contains__ (Molecule mol)
	Returns the result of the membership test operation mol in self. More...
bool	__contains__ (Base.LookupKey key)
	Returns the result of the membership test operation key in self. More...
None	__setitem__ (Base.LookupKey key, Base.Any value)
int	__len__ ()
Public Member Functions inherited from CDPL.Base.PropertyContainer
int	getObjectID ()
	Returns the numeric identifier (ID) of the wrapped C++ class instance. More...
int	getNumProperties ()
	Returns the number of property entries. More...
Any	getPropertyOrDefault (LookupKey key, Any def_value)
list	getPropertyKeys ()
list	getPropertyValues ()
list	getProperties ()
	Returns a reference to itself. More...
None	setProperty (LookupKey key, Any value)
bool	removeProperty (LookupKey key)
	Clears the value of the property specified by key. More...
Any	getProperty (LookupKey key, bool throw_=False)
	Returns the value of the property specified by key. More...
bool	isPropertySet (LookupKey key)
	Tells whether or not a value has been assigned to the property specified by key. More...
None	clearProperties ()
	Clears all property values.
None	addProperties (PropertyContainer cntnr)
	Adds the property value entries in the PropertyContainer instance cntnr. More...
None	copyProperties (PropertyContainer cntnr)
	Replaces the current set of properties by a copy of the entries in cntnr. More...
None	swap (PropertyContainer cntnr)
	Exchanges the properties of this container with the properties of the container cntnr. More...
Any	__getitem__ (LookupKey key)
bool	__contains__ (LookupKey key)
	Returns the result of the membership test operation key in self. More...
None	__setitem__ (LookupKey key, Any value)
bool	__delitem__ (LookupKey key)

Static Public Member Functions
None	registerCopyPostprocessingFunction (VoidMoleculeMolecularGraphFunctor func)

Properties
	reactants = property(getReactants)
	agents = property(getAgents)
	products = property(getProducts)
	numComponents = property(getNumComponents)
Properties inherited from CDPL.Base.PropertyContainer
	objectID = property(getObjectID)
	propertyKeys = property(getPropertyKeys)
	propertyValues = property(getPropertyValues)
	properties = property(getProperties)
	numProperties = property(getNumProperties)

Detailed Description

Reaction.

Member Function Documentation

addComponent()

Molecule CDPL.Chem.Reaction.addComponent

(

int

role

)

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.

Reimplemented in CDPL.Chem.BasicReaction.

containsComponent()

bool CDPL.Chem.Reaction.containsComponent

(

Molecule

mol

)

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.

getComponentRole()

int CDPL.Chem.Reaction.getComponentRole

(

Molecule

mol

)

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).

getComponentIndex()

int CDPL.Chem.Reaction.getComponentIndex

(

Molecule

mol

)

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.

getNumComponents() [1/2]

int CDPL.Chem.Reaction.getNumComponents

(

int

role

)

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.

getNumComponents() [2/2]

int CDPL.Chem.Reaction.getNumComponents

(

)

Returns the number of reaction components.

Returns

The number of reaction components.

getComponent() [1/2]

Molecule CDPL.Chem.Reaction.getComponent	(	int	idx,
		int	role
	)

Returns a 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 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.

getComponent() [2/2]

Molecule CDPL.Chem.Reaction.getComponent

(

int

idx

)

Returns a reference to the reaction component at index idx.

Parameters

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

Returns

A 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].

removeComponents()

None CDPL.Chem.Reaction.removeComponents

(

int

role

)

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.

removeComponent() [1/2]

None CDPL.Chem.Reaction.removeComponent	(	int	idx,
		int	role
	)

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.

removeComponent() [2/2]

None CDPL.Chem.Reaction.removeComponent

(

int

idx

)

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].

swapComponentRoles()

None CDPL.Chem.Reaction.swapComponentRoles	(	int	role1,
		int	role2
	)

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.

clone()

Reaction CDPL.Chem.Reaction.clone

(

)

Creates a copy of the current reaction state.

Returns

A smart reference to the copy of the reaction.

copy()

None CDPL.Chem.Reaction.copy

(

Reaction

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.

Reimplemented in CDPL.Chem.BasicReaction.

assign()

Reaction CDPL.Chem.Reaction.assign

(

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

self

Reimplemented in CDPL.Chem.BasicReaction.

getReactants()

ComponentSequence CDPL.Chem.Reaction.getReactants

(

)

Returns

getAgents()

ComponentSequence CDPL.Chem.Reaction.getAgents

(

)

Returns

getProducts()

ComponentSequence CDPL.Chem.Reaction.getProducts

(

)

Returns

registerCopyPostprocessingFunction()

None CDPL.Chem.Reaction.registerCopyPostprocessingFunction ( VoidMoleculeMolecularGraphFunctor  func )

static

Parameters

func

invokeCopyPostprocessingFunctions()

None CDPL.Chem.Reaction.invokeCopyPostprocessingFunctions

(

Reaction

src_rxn

)

Parameters

src_rxn

__getstate__()

tuple CDPL.Chem.Reaction.__getstate__

(

)

Parameters

arg1

Returns

__getitem__() [1/2]

Molecule CDPL.Chem.Reaction.__getitem__

(

int

idx

)

Parameters

idx

Returns

__getitem__() [2/2]

Base.Any CDPL.Chem.Reaction.__getitem__

(

Base.LookupKey

key

)

Parameters

key

Returns

__delitem__() [1/2]

None CDPL.Chem.Reaction.__delitem__

(

int

idx

)

Parameters

idx

__delitem__() [2/2]

bool CDPL.Chem.Reaction.__delitem__

(

Base.LookupKey

key

)

Parameters

key

Returns

__contains__() [1/2]

bool CDPL.Chem.Reaction.__contains__

(

Molecule

mol

)

Returns the result of the membership test operation mol in self.

Parameters

mol	The value to test for membership.

Returns

The result of the membership test operation.

__contains__() [2/2]

bool CDPL.Chem.Reaction.__contains__

(

Base.LookupKey

key

)

Returns the result of the membership test operation key in self.

Parameters

key	The value to test for membership.

Returns

The result of the membership test operation.

__setitem__()

None CDPL.Chem.Reaction.__setitem__	(	Base.LookupKey	key,
		Base.Any	value
	)

Parameters

key
value

__len__()

int CDPL.Chem.Reaction.__len__

(

)

Returns

Reimplemented from CDPL.Base.PropertyContainer.