public class DebugReaction extends Reaction implements IReaction
IReaction.Direction
agents, growArraySize, map, mappingCount, products, reactants
Constructor and Description |
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DebugReaction() |
Modifier and Type | Method and Description |
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void |
addAgent(IAtomContainer agent)
Adds an agent to this reaction.
|
void |
addListener(IChemObjectListener col)
Use this to add yourself to this IChemObject as a listener.
|
void |
addProduct(IAtomContainer product)
Adds a product to this reaction.
|
void |
addProduct(IAtomContainer product,
Double coefficient)
Adds a product to this reaction.
|
void |
addProperties(Map<Object,Object> properties)
Sets the properties of this object.
|
void |
addReactant(IAtomContainer reactant)
Adds a reactant to this reaction.
|
void |
addReactant(IAtomContainer reactant,
Double coefficient)
Adds a reactant to this reaction with a stoichiometry coefficient.
|
Object |
clone()
Clones this
Reaction and its content. |
IAtomContainerSet |
getAgents()
Returns a MoleculeSet containing the agents in this reaction.
|
IChemObjectBuilder |
getBuilder()
Returns a
IChemObjectBuilder for the data classes that extend
this class. |
IReaction.Direction |
getDirection()
Returns the direction of the reaction.
|
boolean |
getFlag(int flagType)
Returns the value of a given flag.
|
boolean[] |
getFlags()
Returns the whole set of flags.
|
String |
getID()
Returns the identifier (ID) of this object.
|
int |
getListenerCount()
Returns the number of ChemObjectListeners registered with this object.
|
Double |
getProductCoefficient(IAtomContainer product)
Returns the stoichiometry coefficient of the given product.
|
Double[] |
getProductCoefficients()
Returns an array of double with the stoichiometric coefficients
of the products.
|
int |
getProductCount()
Returns the number of products in this reaction.
|
IAtomContainerSet |
getProducts()
Returns a MoleculeSet containing the products of this reaction.
|
Map<Object,Object> |
getProperties()
Returns a Map with the IChemObject's properties.
|
<T> T |
getProperty(Object description)
Returns a property for the IChemObject.
|
Double |
getReactantCoefficient(IAtomContainer reactant)
Returns the stoichiometry coefficient of the given reactant.
|
Double[] |
getReactantCoefficients()
Returns an array of double with the stoichiometric coefficients
of the reactants.
|
int |
getReactantCount()
Returns the number of reactants in this reaction.
|
IAtomContainerSet |
getReactants()
Returns a MoleculeSet containing the reactants in this reaction.
|
void |
notifyChanged()
This should be triggered by an method that changes the content of an object
to that the registered listeners can react to it.
|
void |
notifyChanged(IChemObjectChangeEvent evt)
This should be triggered by an method that changes the content of an object
to that the registered listeners can react to it.
|
void |
removeListener(IChemObjectListener col)
Use this to remove a ChemObjectListener from the ListenerList of this
IChemObject.
|
void |
removeProperty(Object description)
Removes a property for a IChemObject.
|
void |
setDirection(IReaction.Direction direction)
Sets the direction of the reaction.
|
void |
setFlag(int flagType,
boolean flagValue)
Sets the value of some flag.
|
void |
setFlags(boolean[] flagsNew)
Sets the whole set of flags.
|
void |
setID(String identifier)
Sets the identifier (ID) of this object.
|
boolean |
setProductCoefficient(IAtomContainer product,
Double coefficient)
Sets the coefficient of a a product to a given value.
|
boolean |
setProductCoefficients(Double[] coefficients)
Sets the coefficient of the products.
|
void |
setProducts(IAtomContainerSet products)
Assigns a MoleculeSet to the products of this reaction.
|
void |
setProperty(Object description,
Object property)
Sets a property for a IChemObject.
|
boolean |
setReactantCoefficient(IAtomContainer reactant,
Double coefficient)
Sets the coefficient of a a reactant to a given value.
|
boolean |
setReactantCoefficients(Double[] coefficients)
Sets the coefficients of the reactants.
|
void |
setReactants(IAtomContainerSet reactants)
Assigns a MoleculeSet to the reactants in this reaction.
|
addMapping, getMapping, getMappingCount, mappings, removeMapping, toString
compare, getFlagValue, getNotification, getProperty, setNotification, setProperties, shallowCopy
equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
addMapping, getMapping, getMappingCount, mappings, removeMapping
getFlagValue, getNotification, getProperty, setNotification, setProperties, toString
public void addListener(IChemObjectListener col)
addListener
in interface IChemObject
addListener
in class ChemObject
col
- the ChemObjectListenerChemObject.removeListener(org.openscience.cdk.interfaces.IChemObjectListener)
public int getListenerCount()
getListenerCount
in interface IChemObject
getListenerCount
in class ChemObject
public void removeListener(IChemObjectListener col)
removeListener
in interface IChemObject
removeListener
in class ChemObject
col
- The ChemObjectListener to be removedChemObject.addListener(org.openscience.cdk.interfaces.IChemObjectListener)
public void notifyChanged()
notifyChanged
in interface IChemObject
notifyChanged
in class ChemObject
public void notifyChanged(IChemObjectChangeEvent evt)
notifyChanged
in interface IChemObject
notifyChanged
in class ChemObject
evt
- A ChemObjectChangeEvent pointing to the source of where
the change happenedpublic void setProperty(Object description, Object property)
setProperty
in interface IChemObject
setProperty
in class ChemObject
description
- An object description of the property (most likely a
unique string)property
- An object with the property itselfChemObject.getProperty(java.lang.Object)
,
ChemObject.removeProperty(java.lang.Object)
public void removeProperty(Object description)
removeProperty
in interface IChemObject
removeProperty
in class ChemObject
description
- The object description of the property (most likely a
unique string)ChemObject.setProperty(java.lang.Object, java.lang.Object)
,
ChemObject.getProperty(java.lang.Object)
public <T> T getProperty(Object description)
getProperty
in interface IChemObject
getProperty
in class ChemObject
T
- generic return typedescription
- An object description of the property (most likely a
unique string)ChemObject.setProperty(java.lang.Object, java.lang.Object)
,
ChemObject.removeProperty(java.lang.Object)
public Map<Object,Object> getProperties()
getProperties
in interface IChemObject
getProperties
in class ChemObject
ChemObject.addProperties(java.util.Map<java.lang.Object, java.lang.Object>)
public String getID()
getID
in interface IChemObject
getID
in class ChemObject
ChemObject.setID(java.lang.String)
public void setID(String identifier)
setID
in interface IChemObject
setID
in class ChemObject
identifier
- a String representing the ID valueChemObject.getID()
public void setFlag(int flagType, boolean flagValue)
CDKConstants.ISAROMATIC
or CDKConstants.VISITED
). The flags are
intrinsic internal properties and should not be used to store custom
values, please use IChemObject.setProperty(Object, Object)
.
// set this chem object to be aromatic
chemObject.setFlag(CDKConstants.ISAROMATIC, Boolean.TRUE);
// ...
// indicate we have visited this chem object
chemObject.setFlag(CDKConstants.VISITED, Boolean.TRUE);
setFlag
in interface IChemObject
setFlag
in class ChemObject
flagType
- flag to set the value forflagValue
- value to assign to flagIChemObject.getFlag(int)
,
CDKConstants
public boolean getFlag(int flagType)
CDKConstants.ISAROMATIC
).
if(chemObject.getFlag(CDKConstants.ISAROMATIC)){
// handle aromatic flag on this chem object
}
getFlag
in interface IChemObject
getFlag
in class ChemObject
flagType
- flag to retrieve the value offlag_type
is setIChemObject.setFlag(int, boolean)
,
CDKConstants
public void addProperties(Map<Object,Object> properties)
addProperties
in interface IChemObject
addProperties
in class ChemObject
properties
- a Hashtable specifying the property valuesChemObject.getProperties()
public void setFlags(boolean[] flagsNew)
setFlags
in interface IChemObject
setFlags
in class ChemObject
flagsNew
- the new flags.ChemObject.getFlags()
public boolean[] getFlags()
getFlags
in interface IChemObject
getFlags
in class ChemObject
ChemObject.setFlags(boolean[])
public Object clone() throws CloneNotSupportedException
Reaction
and its content.clone
in interface IChemObject
clone
in class Reaction
CloneNotSupportedException
- if the IChemObject cannot be clonedpublic IChemObjectBuilder getBuilder()
IChemObjectBuilder
for the data classes that extend
this class.getBuilder
in interface ICDKObject
getBuilder
in class ChemObject
IChemObjectBuilder
matching this ICDKObject
public int getReactantCount()
getReactantCount
in interface IReaction
getReactantCount
in class Reaction
public int getProductCount()
getProductCount
in interface IReaction
getProductCount
in class Reaction
public IAtomContainerSet getReactants()
getReactants
in interface IReaction
getReactants
in class Reaction
IReaction.setReactants(org.openscience.cdk.interfaces.IAtomContainerSet)
public void setReactants(IAtomContainerSet reactants)
setReactants
in interface IReaction
setReactants
in class Reaction
reactants
- The new set of reactantsReaction.getReactants()
public IAtomContainerSet getProducts()
getProducts
in interface IReaction
getProducts
in class Reaction
IReaction.setProducts(org.openscience.cdk.interfaces.IAtomContainerSet)
public void setProducts(IAtomContainerSet products)
setProducts
in interface IReaction
setProducts
in class Reaction
products
- The new set of productsReaction.getProducts()
public IAtomContainerSet getAgents()
getAgents
in interface IReaction
getAgents
in class Reaction
Reaction.addAgent(org.openscience.cdk.interfaces.IAtomContainer)
public void addReactant(IAtomContainer reactant)
addReactant
in interface IReaction
addReactant
in class Reaction
reactant
- Molecule added as reactant to this reactionReaction.getReactants()
public void addAgent(IAtomContainer agent)
addAgent
in interface IReaction
addAgent
in class Reaction
agent
- Molecule added as agent to this reactionReaction.getAgents()
public void addReactant(IAtomContainer reactant, Double coefficient)
addReactant
in interface IReaction
addReactant
in class Reaction
reactant
- Molecule added as reactant to this reactioncoefficient
- Stoichiometry coefficient for this moleculeReaction.getReactants()
public void addProduct(IAtomContainer product)
addProduct
in interface IReaction
addProduct
in class Reaction
product
- Molecule added as product to this reactionReaction.getProducts()
public void addProduct(IAtomContainer product, Double coefficient)
addProduct
in interface IReaction
addProduct
in class Reaction
product
- Molecule added as product to this reactioncoefficient
- Stoichiometry coefficient for this moleculeReaction.getProducts()
public Double getReactantCoefficient(IAtomContainer reactant)
getReactantCoefficient
in interface IReaction
getReactantCoefficient
in class Reaction
reactant
- Reactant for which the coefficient is returned.Reaction.setReactantCoefficient(org.openscience.cdk.interfaces.IAtomContainer, java.lang.Double)
public Double getProductCoefficient(IAtomContainer product)
getProductCoefficient
in interface IReaction
getProductCoefficient
in class Reaction
product
- Product for which the coefficient is returned.Reaction.setProductCoefficient(org.openscience.cdk.interfaces.IAtomContainer, java.lang.Double)
public boolean setReactantCoefficient(IAtomContainer reactant, Double coefficient)
setReactantCoefficient
in interface IReaction
setReactantCoefficient
in class Reaction
reactant
- Reactant for which the coefficient is setcoefficient
- The new coefficient for the given reactantReaction.getReactantCoefficient(org.openscience.cdk.interfaces.IAtomContainer)
public boolean setProductCoefficient(IAtomContainer product, Double coefficient)
setProductCoefficient
in interface IReaction
setProductCoefficient
in class Reaction
product
- Product for which the coefficient is setcoefficient
- The new coefficient for the given productReaction.getProductCoefficient(org.openscience.cdk.interfaces.IAtomContainer)
public Double[] getReactantCoefficients()
getReactantCoefficients
in interface IReaction
getReactantCoefficients
in class Reaction
Reaction.setReactantCoefficients(java.lang.Double[])
public Double[] getProductCoefficients()
getProductCoefficients
in interface IReaction
getProductCoefficients
in class Reaction
Reaction.setProductCoefficients(java.lang.Double[])
public boolean setReactantCoefficients(Double[] coefficients)
setReactantCoefficients
in interface IReaction
setReactantCoefficients
in class Reaction
coefficients
- An array of double's containing the coefficients of the reactantsReaction.getReactantCoefficients()
public boolean setProductCoefficients(Double[] coefficients)
setProductCoefficients
in interface IReaction
setProductCoefficients
in class Reaction
coefficients
- An array of double's containing the coefficients of the productsReaction.getProductCoefficients()
public void setDirection(IReaction.Direction direction)
setDirection
in interface IReaction
setDirection
in class Reaction
direction
- The new reaction directionReaction.getDirection()
public IReaction.Direction getDirection()
getDirection
in interface IReaction
getDirection
in class Reaction
IReaction.Direction
,
Reaction.setDirection(org.openscience.cdk.interfaces.IReaction.Direction)
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