Modifier and Type | Class and Description |
---|---|
class |
MoleculeSet
A set of molecules, for example those taking part in a reaction.
|
Modifier and Type | Method and Description |
---|---|
IMoleculeSet |
Reaction.getAgents()
Returns a MoleculeSet containing the agents in this reaction.
|
IMoleculeSet |
ChemModel.getMoleculeSet()
Returns the MoleculeSet of this ChemModel.
|
IMoleculeSet |
Reaction.getProducts()
Returns a MoleculeSet containing the products of this reaction.
|
IMoleculeSet |
Reaction.getReactants()
Returns a MoleculeSet containing the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
void |
MoleculeSet.add(IMoleculeSet moleculeSet)
Adds all molecules in the MoleculeSet to this container.
|
void |
ChemModel.setMoleculeSet(IMoleculeSet setOfMolecules)
Sets the MoleculeSet of this ChemModel.
|
void |
Reaction.setProducts(IMoleculeSet setOfMolecules)
Assigns a MoleculeSet to the products of this reaction.
|
void |
Reaction.setReactants(IMoleculeSet setOfMolecules)
Assigns a MoleculeSet to the reactants in this reaction.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugMoleculeSet
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
IMoleculeSet |
DebugReaction.getAgents() |
IMoleculeSet |
DebugChemModel.getMoleculeSet() |
IMoleculeSet |
DebugReaction.getProducts() |
IMoleculeSet |
DebugReaction.getReactants() |
Modifier and Type | Method and Description |
---|---|
void |
DebugMoleculeSet.add(IMoleculeSet moleculeSet) |
void |
DebugChemModel.setMoleculeSet(IMoleculeSet setOfMolecules) |
void |
DebugReaction.setProducts(IMoleculeSet products) |
void |
DebugReaction.setReactants(IMoleculeSet reactants) |
Modifier and Type | Method and Description |
---|---|
static IMoleculeSet |
ConnectivityChecker.partitionIntoMolecules(IAtomContainer atomContainer)
Partitions the atoms in an AtomContainer into covalently connected components.
|
Modifier and Type | Method and Description |
---|---|
IMoleculeSet |
IReaction.getAgents()
Returns a IMoleculeSet containing the agents in this reaction.
|
IMoleculeSet |
IChemModel.getMoleculeSet()
Returns the MoleculeSet of this ChemModel.
|
IMoleculeSet |
IReaction.getProducts()
Returns a IMoleculeSet containing the products of this reaction.
|
IMoleculeSet |
IReaction.getReactants()
Returns a IMoleculeSet containing the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
void |
IMoleculeSet.add(IMoleculeSet moleculeSet)
Adds all molecules in the MoleculeSet to this container.
|
void |
IChemModel.setMoleculeSet(IMoleculeSet setOfMolecules)
Sets the MoleculeSet of this ChemModel.
|
void |
IReaction.setProducts(IMoleculeSet products)
Assigns a IMoleculeSet to the products of this reaction.
|
void |
IReaction.setReactants(IMoleculeSet reactants)
Assigns a IMoleculeSet to the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
void |
SMILESWriter.writeMoleculeSet(IMoleculeSet som)
Writes a list of molecules to an OutputStream
|
Modifier and Type | Method and Description |
---|---|
IMoleculeSet |
PubChemXMLHelper.parseCompoundsBlock(org.xmlpull.v1.XmlPullParser parser) |
Modifier and Type | Method and Description |
---|---|
org.xmlcml.cml.element.CMLMoleculeList |
Convertor.cdkMoleculeSetToCMLList(IMoleculeSet moleculeSet) |
Modifier and Type | Method and Description |
---|---|
void |
TemplateExtractor.writeChemModel(IMoleculeSet som,
String file,
String endFix) |
Modifier and Type | Class and Description |
---|---|
class |
NNMoleculeSet
Deprecated.
Use the
MoleculeSet instead. |
Modifier and Type | Method and Description |
---|---|
IReaction |
IReactionMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReactionSet |
IReactionProcess.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiates the process for the given Reaction.
|
Modifier and Type | Method and Description |
---|---|
IReaction |
TautomerizationMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
SharingElectronMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RemovingSEofNBMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RemovingSEofBMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RearrangementChargeMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RadicalSiteRearrangementMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RadicalSiteIonizationMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
HomolyticCleavageMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
HeterolyticCleavageMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
AdductionPBMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
AdductionLPMechanism.initiate(IMoleculeSet moleculeSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
Modifier and Type | Method and Description |
---|---|
IReactionSet |
TautomerizationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
SharingLonePairReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
SharingChargeSBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
SharingChargeDBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
SharingAnionReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RearrangementRadicalReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RearrangementLonePairReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RearrangementCationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RearrangementAnionReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrGammaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrDeltaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrBetaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrAlphaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteInitiationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteInitiationHReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrGammaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrDeltaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrBetaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrAlphaReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalChargeSiteInitiationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
RadicalChargeSiteInitiationHReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
PiBondingMovementReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
HyperconjugationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
HomolyticCleavageReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
HeterolyticCleavageSBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
HeterolyticCleavagePBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactSDBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactPDBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactNBEReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
CarbonylEliminationReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
AdductionSodiumLPReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
AdductionProtonPBReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
IReactionSet |
AdductionProtonLPReaction.initiate(IMoleculeSet reactants,
IMoleculeSet agents)
Initiate process.
|
Modifier and Type | Method and Description |
---|---|
List<IGenerator<IMoleculeSet>> |
MoleculeSetRenderer.getGenerators()
Returns a
List of IGenerator s for this renderer. |
Modifier and Type | Method and Description |
---|---|
static double |
AverageBondLengthCalculator.calculateAverageBondLength(IMoleculeSet moleculeSet)
Calculate the average bond length for the bonds in a molecule set.
|
static Rectangle2D |
BoundsCalculator.calculateBounds(IMoleculeSet moleculeSet)
Calculate the bounding rectangle for a molecule set.
|
Rectangle |
MoleculeSetRenderer.calculateDiagramBounds(IMoleculeSet moleculeSet)
Given a
IChemObject , calculates the bounding rectangle in screen
space. |
IRenderingElement |
MoleculeSetRenderer.generateDiagram(IMoleculeSet molecules)
The main method of the renderer, that uses each of the generators
to create a different set of
IRenderingElement s grouped
together into a tree. |
Rectangle |
MoleculeSetRenderer.paint(IMoleculeSet moleculeSet,
IDrawVisitor drawVisitor)
Paint an IChemObject.
|
void |
MoleculeSetRenderer.paint(IMoleculeSet molecules,
IDrawVisitor drawVisitor,
Rectangle2D bounds,
boolean resetCenter)
Paint a set of molecules.
|
void |
MoleculeSetRenderer.setScale(IMoleculeSet moleculeSet)
Set the scale for an IMoleculeSet.
|
void |
MoleculeSetRenderer.setup(IMoleculeSet moleculeSet,
Rectangle screen)
Setup the transformations necessary to draw this
IMoleculeSet . |
Modifier and Type | Method and Description |
---|---|
IMoleculeSet |
Reaction.getAgents()
Returns a MoleculeSet containing the agents in this reaction.
|
IMoleculeSet |
ChemModel.getMoleculeSet()
Returns the MoleculeSet of this ChemModel.
|
IMoleculeSet |
Reaction.getProducts()
Returns a MoleculeSet containing the products of this reaction.
|
IMoleculeSet |
Reaction.getReactants()
Returns a MoleculeSet containing the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
void |
MoleculeSet.add(IMoleculeSet moleculeSet)
Adds all molecules in the MoleculeSet to this container.
|
void |
ChemModel.setMoleculeSet(IMoleculeSet setOfMolecules)
Sets the MoleculeSet of this ChemModel.
|
void |
Reaction.setProducts(IMoleculeSet setOfMolecules)
Assigns a MoleculeSet to the products of this reaction.
|
void |
Reaction.setReactants(IMoleculeSet setOfMolecules)
Assigns a MoleculeSet to the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
IMoleculeSet |
StructureResonanceGenerator.getStructures(IMolecule molecule)
Get the resonance structures from an IMolecule.
|
Modifier and Type | Method and Description |
---|---|
static IMoleculeSet |
ReactionManipulator.getAllMolecules(IReaction reaction)
get all molecule of a IReaction.
|
static IMoleculeSet |
ReactionSchemeManipulator.getAllMolecules(IReactionScheme scheme)
get all Molecules object from a set of Reactions.
|
static IMoleculeSet |
ReactionSchemeManipulator.getAllMolecules(IReactionScheme scheme,
IMoleculeSet molSet)
Get all Molecules object from a set of Reactions given a IMoleculeSet to add.
|
static IMoleculeSet |
ReactionSetManipulator.getAllMolecules(IReactionSet set)
get all Molecules object from a set of Reactions.
|
static IMoleculeSet |
ReactionManipulator.getAllProducts(IReaction reaction)
get all products of a IReaction
|
static IMoleculeSet |
ReactionManipulator.getAllReactants(IReaction reaction)
get all reactants of a IReaction
|
Modifier and Type | Method and Description |
---|---|
static ArrayList<IMoleculeSet> |
ReactionSchemeManipulator.getMoleculeSet(IMolecule origenMol,
IMolecule finalMol,
IReactionScheme reactionScheme)
Extract the list of molecules taking part in the IReactionScheme to originate a
product given a reactant.
|
Modifier and Type | Method and Description |
---|---|
static List<IAtomContainer> |
MoleculeSetManipulator.getAllAtomContainers(IMoleculeSet set)
Returns all the AtomContainer's of a MoleculeSet.
|
static List<IChemObject> |
MoleculeSetManipulator.getAllChemObjects(IMoleculeSet set) |
static List<String> |
MoleculeSetManipulator.getAllIDs(IMoleculeSet set) |
static IMoleculeSet |
ReactionSchemeManipulator.getAllMolecules(IReactionScheme scheme,
IMoleculeSet molSet)
Get all Molecules object from a set of Reactions given a IMoleculeSet to add.
|
static IAtomContainer |
MoleculeSetManipulator.getRelevantAtomContainer(IMoleculeSet moleculeSet,
IAtom atom) |
static IAtomContainer |
MoleculeSetManipulator.getRelevantAtomContainer(IMoleculeSet moleculeSet,
IBond bond) |
static double |
MoleculeSetManipulator.getTotalCharge(IMoleculeSet set) |
static double |
MoleculeSetManipulator.getTotalFormalCharge(IMoleculeSet set) |
static int |
MoleculeSetManipulator.getTotalHydrogenCount(IMoleculeSet set) |
static void |
MoleculeSetManipulator.removeAtomAndConnectedElectronContainers(IMoleculeSet set,
IAtom atom) |
static void |
MoleculeSetManipulator.removeElectronContainer(IMoleculeSet set,
IElectronContainer electrons) |
static void |
MoleculeSetManipulator.setAtomProperties(IMoleculeSet set,
Object propKey,
Object propVal) |
Modifier and Type | Method and Description |
---|---|
ValidationReport |
ValidatorEngine.validateMoleculeSet(IMoleculeSet subject) |
ValidationReport |
IValidator.validateMoleculeSet(IMoleculeSet subject) |
ValidationReport |
AbstractValidator.validateMoleculeSet(IMoleculeSet subject) |