Modifier and Type | Class and Description |
---|---|
class |
ChemModel
An object containing multiple MoleculeSet and
the other lower level concepts like rings, sequences,
fragments, etc.
|
Modifier and Type | Field and Description |
---|---|
protected IChemModel[] |
ChemSequence.chemModels
Array of ChemModels.
|
Modifier and Type | Method and Description |
---|---|
IChemModel |
ChemSequence.getChemModel(int number)
Returns the ChemModel at position
number in the
container. |
Modifier and Type | Method and Description |
---|---|
Iterable<IChemModel> |
ChemSequence.chemModels()
Returns an Iterable to ChemModels in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
ChemSequence.addChemModel(IChemModel chemModel)
Adds an chemModel to this container.
|
Modifier and Type | Class and Description |
---|---|
class |
DebugChemModel
Debugging data class.
|
Modifier and Type | Method and Description |
---|---|
IChemModel |
DebugChemSequence.getChemModel(int number)
Returns the ChemModel at position
number in the
container. |
Modifier and Type | Method and Description |
---|---|
Iterable<IChemModel> |
DebugChemSequence.chemModels()
Returns an Iterable to ChemModels in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
DebugChemSequence.addChemModel(IChemModel chemModel)
Adds an chemModel to this container.
|
Modifier and Type | Method and Description |
---|---|
static boolean |
GeometryTools.has3DCoordinates(IChemModel chemModel)
Deprecated.
Determines if this model contains 3D coordinates for all atoms.
|
static boolean |
GeometryUtil.has3DCoordinates(IChemModel chemModel)
Determines if this model contains 3D coordinates for all atoms.
|
Modifier and Type | Method and Description |
---|---|
IChemModel |
IChemSequence.getChemModel(int number)
Returns the ChemModel at position
number in the
container. |
Modifier and Type | Method and Description |
---|---|
Iterable<IChemModel> |
IChemSequence.chemModels()
Returns an Iterable to ChemModels in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
IChemSequence.addChemModel(IChemModel chemModel)
Adds an chemModel to this container.
|
Modifier and Type | Field and Description |
---|---|
protected IChemModel |
CMLCoreModule.currentChemModel |
Modifier and Type | Method and Description |
---|---|
IChemModel |
IteratingPCSubstancesXMLReader.next() |
Modifier and Type | Method and Description |
---|---|
IChemModel |
PubChemXMLHelper.parseSubstance(XMLStreamReader parser) |
Modifier and Type | Method and Description |
---|---|
org.xmlcml.cml.element.CMLList |
Convertor.cdkChemModelToCMLList(IChemModel model) |
Modifier and Type | Method and Description |
---|---|
List<IGenerator<IChemModel>> |
ChemModelRenderer.getGenerators()
Returns a
List of IGenerator s for this renderer. |
Modifier and Type | Method and Description |
---|---|
static double |
AverageBondLengthCalculator.calculateAverageBondLength(IChemModel model)
Calculate the average bond length for the bonds in a chem model.
|
static Rectangle2D |
BoundsCalculator.calculateBounds(IChemModel chemModel)
Calculate the bounding rectangle for a chem model.
|
Rectangle |
ChemModelRenderer.calculateDiagramBounds(IChemModel model)
Given a chem model, calculates the bounding rectangle in screen space.
|
Rectangle |
ChemModelRenderer.paint(IChemModel chemModel,
IDrawVisitor drawVisitor)
Paint an IChemModel using the IDrawVisitor at a scale determined by the
bond length in RendererModel.
|
void |
ChemModelRenderer.paint(IChemModel chemModel,
IDrawVisitor drawVisitor,
Rectangle2D bounds,
boolean resetCenter)
Paint a ChemModel.
|
void |
ChemModelRenderer.setScale(IChemModel chemModel)
Set the scale for an IChemModel.
|
void |
ChemModelRenderer.setup(IChemModel chemModel,
Rectangle screen)
Setup the transformations necessary to draw this Chem Model.
|
Modifier and Type | Method and Description |
---|---|
void |
AbstractSelection.select(IChemModel chemModel)
Perform a selection by some method.
|
void |
IChemObjectSelection.select(IChemModel chemModel)
Perform a selection by some method.
|
Modifier and Type | Field and Description |
---|---|
protected IChemModel[] |
ChemSequence.chemModels
Array of ChemModels.
|
Modifier and Type | Method and Description |
---|---|
IChemModel |
ChemSequence.getChemModel(int number)
Returns the ChemModel at position
number in the
container. |
Modifier and Type | Method and Description |
---|---|
Iterable<IChemModel> |
ChemSequence.chemModels()
Returns an Iterable to ChemModels in this container.
|
Modifier and Type | Method and Description |
---|---|
void |
ChemSequence.addChemModel(IChemModel chemModel)
Adds an chemModel to this container.
|
Modifier and Type | Method and Description |
---|---|
static IChemModel |
ChemModelManipulator.newChemModel(IAtomContainer atomContainer)
Create a new ChemModel containing an IAtomContainer.
|
Modifier and Type | Method and Description |
---|---|
static List<IChemModel> |
ChemFileManipulator.getAllChemModels(IChemFile file)
Get a list of all ChemModels inside an IChemFile.
|
Modifier and Type | Method and Description |
---|---|
static IAtomContainer |
ChemModelManipulator.createNewMolecule(IChemModel chemModel)
Adds a new Molecule to the MoleculeSet inside a given ChemModel.
|
static List<IAtomContainer> |
ChemModelManipulator.getAllAtomContainers(IChemModel chemModel)
Returns all the AtomContainer's of a ChemModel.
|
static List<IChemObject> |
ChemModelManipulator.getAllChemObjects(IChemModel chemModel)
Retrieve a List of all ChemObject objects within an IChemModel.
|
static List<String> |
ChemModelManipulator.getAllIDs(IChemModel chemModel) |
static int |
ChemModelManipulator.getAtomCount(IChemModel chemModel)
Get the total number of atoms inside an IChemModel.
|
static int |
ChemModelManipulator.getBondCount(IChemModel chemModel)
Get the total number of bonds inside an IChemModel.
|
static IAtomContainer |
ChemModelManipulator.getRelevantAtomContainer(IChemModel chemModel,
IAtom atom)
This badly named methods tries to determine which AtomContainer in the
ChemModel is best suited to contain added Atom's and Bond's.
|
static IAtomContainer |
ChemModelManipulator.getRelevantAtomContainer(IChemModel chemModel,
IBond bond)
Retrieves the first IAtomContainer containing a given IBond from an
IChemModel.
|
static IReaction |
ChemModelManipulator.getRelevantReaction(IChemModel chemModel,
IAtom atom)
Retrieves the first IReaction containing a given IAtom from an
IChemModel.
|
static void |
ChemModelManipulator.removeAtomAndConnectedElectronContainers(IChemModel chemModel,
IAtom atom)
Remove an Atom and the connected ElectronContainers from all AtomContainers
inside an IChemModel.
|
static void |
ChemModelManipulator.removeElectronContainer(IChemModel chemModel,
IElectronContainer electrons)
Remove an ElectronContainer from all AtomContainers
inside an IChemModel.
|
static void |
ChemModelManipulator.setAtomProperties(IChemModel chemModel,
Object propKey,
Object propVal)
Sets the AtomProperties of all Atoms inside an IChemModel.
|
Modifier and Type | Method and Description |
---|---|
ValidationReport |
AbstractValidator.validateChemModel(IChemModel subject) |
ValidationReport |
IValidator.validateChemModel(IChemModel subject) |
ValidationReport |
ValidatorEngine.validateChemModel(IChemModel subject) |
Copyright © 2021. All rights reserved.