Modifier and Type | Class and Description |
---|---|
class |
AtomContainerSet
A set of AtomContainers.
|
class |
RingSet
Maintains a set of Ring objects.
|
class |
Substance
An implementation of the
ISubstance interface. |
Modifier and Type | Field and Description |
---|---|
protected IAtomContainerSet |
Reaction.agents
These are the used solvent, catalysts etc that normally appear above
the reaction arrow
|
protected IAtomContainerSet |
Reaction.products |
protected IAtomContainerSet |
Reaction.reactants |
protected IAtomContainerSet |
ChemModel.setOfMolecules
A MoleculeSet.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainerSet |
Reaction.getAgents()
Returns a MoleculeSet containing the agents in this reaction.
|
IAtomContainerSet |
ChemModel.getMoleculeSet()
Returns the MoleculeSet of this ChemModel.
|
IAtomContainerSet |
Reaction.getProducts()
Returns a MoleculeSet containing the products of this reaction.
|
IAtomContainerSet |
Reaction.getReactants()
Returns a MoleculeSet containing the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainerSet.add(IAtomContainerSet atomContainerSet)
Adds all atomContainers in the AtomContainerSet to this container.
|
void |
ChemModel.setMoleculeSet(IAtomContainerSet setOfMolecules)
Sets the MoleculeSet of this ChemModel.
|
void |
Reaction.setProducts(IAtomContainerSet setOfMolecules)
Assigns a MoleculeSet to the products of this reaction.
|
void |
Reaction.setReactants(IAtomContainerSet setOfMolecules)
Assigns a MoleculeSet to the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
double[][] |
GasteigerPEPEPartialCharges.assignrPiMarsilliFactors(IAtomContainerSet setAc)
Method which stores and assigns the factors a,b,c and CHI+.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugAtomContainerSet
Debugging data class.
|
class |
DebugRingSet
Debugging data class.
|
class |
DebugSubstance
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainerSet |
DebugReaction.getAgents()
Returns a MoleculeSet containing the agents in this reaction.
|
IAtomContainerSet |
DebugChemModel.getMoleculeSet()
Returns the MoleculeSet of this ChemModel.
|
IAtomContainerSet |
DebugReaction.getProducts()
Returns a MoleculeSet containing the products of this reaction.
|
IAtomContainerSet |
DebugReaction.getReactants()
Returns a MoleculeSet containing the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugAtomContainerSet.add(IAtomContainerSet atomContainerSet)
Adds all atomContainers in the AtomContainerSet to this container.
|
void |
DebugSubstance.add(IAtomContainerSet atomContainerSet)
Adds all atomContainers in the AtomContainerSet to this container.
|
void |
DebugChemModel.setMoleculeSet(IAtomContainerSet setOfMolecules)
Sets the MoleculeSet of this ChemModel.
|
void |
DebugReaction.setProducts(IAtomContainerSet products)
Assigns a MoleculeSet to the products of this reaction.
|
void |
DebugReaction.setReactants(IAtomContainerSet reactants)
Assigns a MoleculeSet to the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
static IAtomContainerSet |
ConnectivityChecker.partitionIntoMolecules(IAtomContainer container)
Partitions the atoms in an AtomContainer into covalently connected components.
|
static IAtomContainerSet |
ConnectivityChecker.partitionIntoMolecules(IAtomContainer container,
int[] components) |
Modifier and Type | Method and Description |
---|---|
static IAtomContainerSet |
ConjugatedPiSystemsDetector.detect(IAtomContainer ac)
Detect all conjugated pi systems in an AtomContainer.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IRingSet
Maintains a set of Ring objects.
|
interface |
ISubstance
A chemical substance that consists of one or more chemical structures.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainerSet |
IReaction.getAgents()
Returns a IAtomContaineSet containing the agents in this reaction.
|
IAtomContainerSet |
IChemModel.getMoleculeSet()
Returns the IAtomContainerSet of this ChemModel.
|
IAtomContainerSet |
IReaction.getProducts()
Returns a IAtomContaineSet containing the products of this reaction.
|
IAtomContainerSet |
IReaction.getReactants()
Returns a IAtomContaineSet containing the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
void |
IAtomContainerSet.add(IAtomContainerSet atomContainerSet)
Adds all atomContainers in the AtomContainerSet to this container.
|
void |
IChemModel.setMoleculeSet(IAtomContainerSet setOfMolecules)
Sets the IAtomContainerSet of this ChemModel.
|
void |
IReaction.setProducts(IAtomContainerSet products)
Assigns a IAtomContaineSet to the products of this reaction.
|
void |
IReaction.setReactants(IAtomContainerSet reactants)
Assigns a IAtomContaineSet to the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
void |
SMILESWriter.writeAtomContainerSet(IAtomContainerSet som)
Writes a list of molecules to an OutputStream.
|
Modifier and Type | Field and Description |
---|---|
protected IAtomContainerSet |
CMLCoreModule.currentMoleculeSet |
Modifier and Type | Method and Description |
---|---|
IAtomContainerSet |
PubChemXMLHelper.parseCompoundsBlock(XMLStreamReader parser) |
Modifier and Type | Method and Description |
---|---|
IAtomContainerSet |
TemplateHandler.getMappedSubstructures(IAtomContainer molecule)
Checks if one of the loaded templates is a substructure in the given
Molecule and returns all matched substructures in a IAtomContainerSet.
|
Modifier and Type | Method and Description |
---|---|
org.xmlcml.cml.element.CMLMoleculeList |
Convertor.cdkAtomContainerSetToCMLList(IAtomContainerSet moleculeSet) |
Modifier and Type | Method and Description |
---|---|
void |
TemplateExtractor.writeChemModel(IAtomContainerSet som,
String file,
String endFix) |
Modifier and Type | Method and Description |
---|---|
IReaction |
IReactionMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReactionSet |
IReactionProcess.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiates the process for the given Reaction.
|
Modifier and Type | Method and Description |
---|---|
IReaction |
SharingElectronMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
TautomerizationMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RemovingSEofNBMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RemovingSEofBMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RadicalSiteIonizationMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
HeterolyticCleavageMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
HomolyticCleavageMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
AdductionPBMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RearrangementChargeMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
AdductionLPMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
IReaction |
RadicalSiteRearrangementMechanism.initiate(IAtomContainerSet atomContainerSet,
ArrayList<IAtom> atomList,
ArrayList<IBond> bondList)
Initiates the process for the given mechanism.
|
Modifier and Type | Method and Description |
---|---|
IReactionSet |
RadicalSiteRrAlphaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RearrangementRadicalReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteInitiationReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
PiBondingMovementReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
HyperconjugationReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RearrangementCationReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrDeltaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RearrangementLonePairReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
AdductionProtonPBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrAlphaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactNBEReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalChargeSiteInitiationReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
SharingChargeDBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
SharingAnionReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrDeltaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactSDBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrBetaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrBetaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RearrangementAnionReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
HeterolyticCleavagePBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteRrGammaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
SharingLonePairReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalChargeSiteInitiationHReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
AdductionSodiumLPReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
TautomerizationReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
HeterolyticCleavageSBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
HomolyticCleavageReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteHrGammaReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
CarbonylEliminationReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
ElectronImpactPDBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
SharingChargeSBReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
AdductionProtonLPReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
IReactionSet |
RadicalSiteInitiationHReaction.initiate(IAtomContainerSet reactants,
IAtomContainerSet agents)
Initiate process.
|
Modifier and Type | Method and Description |
---|---|
List<IGenerator<IAtomContainerSet>> |
MoleculeSetRenderer.getGenerators()
Returns a
List of IGenerator s for this renderer. |
Modifier and Type | Method and Description |
---|---|
static double |
AverageBondLengthCalculator.calculateAverageBondLength(IAtomContainerSet moleculeSet)
Calculate the average bond length for the bonds in a molecule set.
|
static Rectangle2D |
BoundsCalculator.calculateBounds(IAtomContainerSet moleculeSet)
Calculate the bounding rectangle for a molecule set.
|
Rectangle |
MoleculeSetRenderer.calculateDiagramBounds(IAtomContainerSet moleculeSet)
Given a
IChemObject , calculates the bounding rectangle in screen
space. |
IRenderingElement |
MoleculeSetRenderer.generateDiagram(IAtomContainerSet 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(IAtomContainerSet moleculeSet,
IDrawVisitor drawVisitor)
Paint an IChemObject.
|
void |
MoleculeSetRenderer.paint(IAtomContainerSet molecules,
IDrawVisitor drawVisitor,
Rectangle2D bounds,
boolean resetCenter)
Paint a set of molecules.
|
void |
MoleculeSetRenderer.setScale(IAtomContainerSet moleculeSet)
Set the scale for an
IAtomContainerSet . |
void |
MoleculeSetRenderer.setup(IAtomContainerSet moleculeSet,
Rectangle screen)
Setup the transformations necessary to draw this
IAtomContainerSet . |
Modifier and Type | Field and Description |
---|---|
protected IAtomContainerSet |
Reaction.agents
These are the used solvent, catalysts etc that normally appear above
the reaction arrow
|
protected IAtomContainerSet |
Reaction.products |
protected IAtomContainerSet |
Reaction.reactants |
protected IAtomContainerSet |
ChemModel.setOfMolecules
A MoleculeSet.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainerSet |
Reaction.getAgents()
Returns a MoleculeSet containing the agents in this reaction.
|
IAtomContainerSet |
ChemModel.getMoleculeSet()
Returns the MoleculeSet of this ChemModel.
|
IAtomContainerSet |
Reaction.getProducts()
Returns a MoleculeSet containing the products of this reaction.
|
IAtomContainerSet |
Reaction.getReactants()
Returns a MoleculeSet containing the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
void |
AtomContainerSet.add(IAtomContainerSet atomContainerSet)
Adds all atomContainers in the AtomContainerSet to this container.
|
void |
ChemModel.setMoleculeSet(IAtomContainerSet setOfMolecules)
Sets the MoleculeSet of this ChemModel.
|
void |
Reaction.setProducts(IAtomContainerSet setOfMolecules)
Assigns a MoleculeSet to the products of this reaction.
|
void |
Reaction.setReactants(IAtomContainerSet setOfMolecules)
Assigns a MoleculeSet to the reactants in this reaction.
|
Modifier and Type | Method and Description |
---|---|
protected IAtomContainerSet |
CDKSubGraphHandler.getUncommon(IAtomContainer mol,
IAtomContainer mcss,
boolean shouldMatchBonds)
Deprecated.
|
protected IAtomContainerSet |
CDKMCSHandler.getUncommon(IAtomContainer mol,
IAtomContainer mcss,
boolean shouldMatchBonds)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainer |
PartialFilledStructureMerger.generate(IAtomContainerSet atomContainers)
Randomly generates a single, connected, correctly bonded structure from
a number of fragments.
|
Modifier and Type | Method and Description |
---|---|
IAtomContainerSet |
StructureResonanceGenerator.getContainers(IAtomContainer molecule)
Get the container which is found resonance from a
IAtomContainer . |
IAtomContainerSet |
StructureResonanceGenerator.getStructures(IAtomContainer molecule)
Get the resonance structures from an
IAtomContainer . |
Modifier and Type | Method and Description |
---|---|
static IAtomContainerSet |
ReactionManipulator.getAllAgents(IReaction reaction) |
static IAtomContainerSet |
ReactionSchemeManipulator.getAllAtomContainers(IReactionScheme scheme)
get all AtomContainers object from a set of Reactions.
|
static IAtomContainerSet |
ReactionSchemeManipulator.getAllAtomContainers(IReactionScheme scheme,
IAtomContainerSet molSet)
Get all molecule objects from a set of Reactions given a
IAtomContainerSet to add. |
static IAtomContainerSet |
ReactionManipulator.getAllMolecules(IReaction reaction)
Get all molecule of a
IReaction : reactants + products. |
static IAtomContainerSet |
ReactionSetManipulator.getAllMolecules(IReactionSet set)
get all Molecules object from a set of Reactions.
|
static IAtomContainerSet |
ReactionManipulator.getAllProducts(IReaction reaction)
get all products of a IReaction
|
static IAtomContainerSet |
ReactionManipulator.getAllReactants(IReaction reaction)
get all reactants of a IReaction
|
Modifier and Type | Method and Description |
---|---|
static ArrayList<IAtomContainerSet> |
ReactionSchemeManipulator.getAtomContainerSet(IAtomContainer origenMol,
IAtomContainer finalMol,
IReactionScheme reactionScheme)
Extract the list of AtomContainers taking part in the IReactionScheme to originate a
product given a reactant.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
AtomContainerSetManipulator.containsByID(IAtomContainerSet atomContainerSet,
String id)
Tells if an AtomContainerSet contains at least one AtomContainer with the
same ID as atomContainer.
|
static List<IAtomContainer> |
MoleculeSetManipulator.getAllAtomContainers(IAtomContainerSet set)
Returns all the AtomContainer's of a MoleculeSet.
|
static List<IAtomContainer> |
AtomContainerSetManipulator.getAllAtomContainers(IAtomContainerSet set)
Returns all the AtomContainer's of a MoleculeSet.
|
static IAtomContainerSet |
ReactionSchemeManipulator.getAllAtomContainers(IReactionScheme scheme,
IAtomContainerSet molSet)
Get all molecule objects from a set of Reactions given a
IAtomContainerSet to add. |
static List<IChemObject> |
MoleculeSetManipulator.getAllChemObjects(IAtomContainerSet set) |
static List<IChemObject> |
AtomContainerSetManipulator.getAllChemObjects(IAtomContainerSet set)
Does not recursively return the contents of the AtomContainer.
|
static List<String> |
MoleculeSetManipulator.getAllIDs(IAtomContainerSet set) |
static List<String> |
AtomContainerSetManipulator.getAllIDs(IAtomContainerSet set) |
static int |
MoleculeSetManipulator.getAtomCount(IAtomContainerSet set) |
static int |
AtomContainerSetManipulator.getAtomCount(IAtomContainerSet set) |
static int |
MoleculeSetManipulator.getBondCount(IAtomContainerSet set) |
static int |
AtomContainerSetManipulator.getBondCount(IAtomContainerSet set) |
static IAtomContainer |
MoleculeSetManipulator.getRelevantAtomContainer(IAtomContainerSet moleculeSet,
IAtom atom) |
static IAtomContainer |
AtomContainerSetManipulator.getRelevantAtomContainer(IAtomContainerSet containerSet,
IAtom atom) |
static IAtomContainer |
MoleculeSetManipulator.getRelevantAtomContainer(IAtomContainerSet moleculeSet,
IBond bond) |
static IAtomContainer |
AtomContainerSetManipulator.getRelevantAtomContainer(IAtomContainerSet containerSet,
IBond bond) |
static double |
MoleculeSetManipulator.getTotalCharge(IAtomContainerSet set) |
static double |
AtomContainerSetManipulator.getTotalCharge(IAtomContainerSet set) |
static double |
MoleculeSetManipulator.getTotalFormalCharge(IAtomContainerSet set) |
static double |
AtomContainerSetManipulator.getTotalFormalCharge(IAtomContainerSet set) |
static int |
MoleculeSetManipulator.getTotalHydrogenCount(IAtomContainerSet set) |
static int |
AtomContainerSetManipulator.getTotalHydrogenCount(IAtomContainerSet set) |
static void |
MoleculeSetManipulator.removeAtomAndConnectedElectronContainers(IAtomContainerSet set,
IAtom atom) |
static void |
AtomContainerSetManipulator.removeAtomAndConnectedElectronContainers(IAtomContainerSet set,
IAtom atom) |
static void |
MoleculeSetManipulator.removeElectronContainer(IAtomContainerSet set,
IElectronContainer electrons) |
static void |
AtomContainerSetManipulator.removeElectronContainer(IAtomContainerSet set,
IElectronContainer electrons) |
static void |
MoleculeSetManipulator.setAtomProperties(IAtomContainerSet set,
Object propKey,
Object propVal) |
static void |
AtomContainerSetManipulator.setAtomProperties(IAtomContainerSet set,
Object propKey,
Object propVal) |
static void |
AtomContainerSetManipulator.sort(IAtomContainerSet atomContainerSet)
Sorts the IAtomContainers in the given IAtomContainerSet by the following
criteria with decreasing priority:
|
Modifier and Type | Method and Description |
---|---|
ValidationReport |
AbstractValidator.validateMoleculeSet(IAtomContainerSet subject) |
ValidationReport |
IValidator.validateMoleculeSet(IAtomContainerSet subject) |
ValidationReport |
ValidatorEngine.validateMoleculeSet(IAtomContainerSet subject) |
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