Uses of Class org.jmol.modelset.ModelSet (Jmol 16.3.55 API)

Packages that use ModelSet

Package

Description

org.jmol.adapter.readers.pdb

Uses of ModelSet in org.jmol.adapter.readers.pdb

Methods in org.jmol.adapter.readers.pdb with parameters of type ModelSet

Modifier and Type

Method

Description

void

JmolDataReader.setJmolDataFrame(ModelSet ms, String type, int modelIndex, int modelDataIndex)

Set up the JmolDataFrame initially
Uses of ModelSet in org.jmol.api

Methods in org.jmol.api with parameters of type ModelSet

Modifier and Type

Method

Description

void

JmolAnnotationParser.getAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData, String dataType)

String

JmolAnnotationParser.getHBonds(ModelSet ms, int modelIndex, Lst<Bond> vHBonds, boolean doReport)

Map<String,Object>

SymmetryInterface.getSpaceGroupInfo(ModelSet modelSet, String spaceGroup, int modelIndex, boolean isFull, float[] cellParams)

boolean

SymmetryInterface.getState(ModelSet ms, int modelIndex, SB commands)

Object

SymmetryInterface.getSymmetryInfoAtom(ModelSet ms, int iatom, String xyz, int op, P3 translation, P3 pt, P3 pt2, String id, int type, float scaleFactor, int nth, int options, int[] oplist)

BS

SymmetryInterface.notInCentroid(ModelSet modelSet, BS bsAtoms, int[] minmax)

BS

SymmetryInterface.removeDuplicates(ModelSet ms, BS bs, boolean highPrec)

void

JmolRepaintManager.render(GData gdata, ModelSet modelSet, boolean isFirstPass, int[] navMinMax)

String

JmolRepaintManager.renderExport(GData gdata, ModelSet modelSet, Map<String,Object> params)

void

JmolAnnotationParser.setGroup1(ModelSet ms, int modelIndex)

void

AtomIndexIterator.setModel(ModelSet modelSet, int modelIndex, int zeroBase, int atomIndex, T3 center, float distance, RadiusData rd)
Uses of ModelSet in org.jmol.dssx

Methods in org.jmol.dssx with parameters of type ModelSet

Modifier and Type

Method

Description

void

AnnotationParser.getAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData, String dataType)

void

DSSR1.getAtomicDSSRData(ModelSet ms, int modelIndex, float[] dssrData, String dataType)

String

AnnotationParser.getHBonds(ModelSet ms, int modelIndex, Lst<Bond> vHBonds, boolean doReport)

String

DSSR1.getHBonds(ModelSet ms, int modelIndex, Lst<Bond> vHBonds, boolean doReport)

void

AnnotationParser.setGroup1(ModelSet ms, int modelIndex)

void

DSSR1.setGroup1(ModelSet ms, int modelIndex)
Uses of ModelSet in org.jmol.minimize

Methods in org.jmol.minimize with parameters of type ModelSet

Modifier and Type

Method

Description

void

Minimizer.calculatePartialCharges(ModelSet ms, BS bsAtoms, BS bsReport)
Uses of ModelSet in org.jmol.modelkit

Fields in org.jmol.modelkit declared as ModelSet

Modifier and Type

Field

Description

protected ModelSet

ModelKit.lastModelSet
Uses of ModelSet in org.jmol.modelset

Fields in org.jmol.modelset declared as ModelSet

Modifier and Type

Field

Description

ModelSet

Measurement.ms

ModelSet

Model.ms

BE CAREFUL: FAILURE TO NULL REFERENCES TO modelSet WILL PREVENT FINALIZATION AND CREATE A MEMORY LEAK.

ModelSet

ModelLoader.ms

Methods in org.jmol.modelset with parameters of type ModelSet

Modifier and Type

Method

Description

static String

ModelLoader.createAtomDataSet(Viewer vwr, ModelSet modelSet, int tokType, Object asc, BS bsSelected)

void

MeasurementData.define(JmolMeasurementClient client, ModelSet modelSet)

called by the client to generate a set of measurements

int[]

BondSet.getAssociatedAtoms(ModelSet ms)

protected void

ModelSet.mergeModelArrays(ModelSet mergeModelSet)

initial transfer of model data from old to new model set.

MeasurementPending

MeasurementPending.set(ModelSet modelSet)

Model

Model.set(ModelSet modelSet, int modelIndex, int trajectoryBaseIndex, Map<String,Object> jmolData, Properties properties, Map<String,Object> auxiliaryInfo)

Measurement

Measurement.setM(ModelSet modelSet, Measurement m, float value, short colix, String strFormat, int index)

void

AtomIteratorWithinModel.setModel(ModelSet modelSet, int modelIndex, int firstModelAtom, int atomIndex, T3 center, float distance, RadiusData rd)

MeasurementData

MeasurementData.setModelSet(ModelSet m)

Measurement

Measurement.setPoints(ModelSet modelSet, int[] indices, Point3fi[] points, TickInfo tickInfo)

Constructors in org.jmol.modelset with parameters of type ModelSet

Modifier

Constructor

Description

ModelLoader(Viewer vwr, String modelSetName, SB loadScript, Object asc, ModelSet modelSet0, BS bsNew)
Uses of ModelSet in org.jmol.modelsetbio

Methods in org.jmol.modelsetbio with parameters of type ModelSet

Modifier and Type

Method

Description

BioModelSet

BioResolver.getBioModelSet(ModelSet modelSet)

BioModelSet

BioModelSet.set(Viewer vwr, ModelSet ms)
Uses of ModelSet in org.jmol.render

Fields in org.jmol.render declared as ModelSet

Modifier and Type

Field

Description

protected ModelSet

ShapeRenderer.ms

Methods in org.jmol.render with parameters of type ModelSet

Modifier and Type

Method

Description

void

RepaintManager.render(GData gdata, ModelSet modelSet, boolean isFirstPass, int[] navMinMax)

//////// actual rendering ///////////

String

RepaintManager.renderExport(GData gdata, ModelSet modelSet, Map<String,Object> params)

boolean

ShapeRenderer.renderShape(JmolRendererInterface g3d, ModelSet modelSet, Shape shape, int flags)

void

ShapeRenderer.setup(JmolRendererInterface g3d, ModelSet modelSet, Shape shape)
Uses of ModelSet in org.jmol.shape

Fields in org.jmol.shape declared as ModelSet

Modifier and Type

Field

Description

ModelSet

Shape.ms

Methods in org.jmol.shape with parameters of type ModelSet

Modifier and Type

Method

Description

final void

Shape.initializeShape(Viewer vwr, ModelSet modelSet, int shapeID)

void

Shape.setModelSet(ModelSet modelSet)
Uses of ModelSet in org.jmol.symmetry

Methods in org.jmol.symmetry with parameters of type ModelSet

Modifier and Type

Method

Description

Map<String,Object>

Symmetry.getSpaceGroupInfo(ModelSet modelSet, String sgName, int modelIndex, boolean isFull, float[] cellParams)

boolean

Symmetry.getState(ModelSet ms, int modelIndex, SB commands)

Object

Symmetry.getSymmetryInfoAtom(ModelSet modelSet, int iatom, String xyz, int op, P3 translation, P3 pt, P3 pt2, String id, int type, float scaleFactor, int nth, int options, int[] opList)

BS

Symmetry.notInCentroid(ModelSet modelSet, BS bsAtoms, int[] minmax)

BS

Symmetry.removeDuplicates(ModelSet ms, BS bs, boolean highPrec)

SymmetryDesc

SymmetryDesc.set(ModelSet modelSet)

void

UnitCellIterator.setModel(ModelSet modelSet, int modelIndex, int zeroBase, int atomIndex, T3 center, float distance, RadiusData rd)

void

Symmetry.setSymmetryInfoFromFile(ModelSet ms, int modelIndex, float[] unitCellParams)

Set space group and unit cell from the auxiliary info generated by XtalSymmetry specific to a given model.
Uses of ModelSet in org.jmol.util

Methods in org.jmol.util with parameters of type ModelSet

Modifier and Type

Method

Description

static Atom

Vibration.find(ModelSet modelSet, BS bs, Vibration v0)

int

Vibration.rotateModelSpinVectors(ModelSet ms, int modelIndex, M3 rot, boolean isdx)
Uses of ModelSet in org.jmol.viewer

Fields in org.jmol.viewer declared as ModelSet

Modifier and Type

Field

Description

ModelSet

Viewer.ms

Methods in org.jmol.viewer with parameters of type ModelSet

Modifier and Type

Method

Description

void

ShapeManager.loadDefaultShapes(ModelSet newModelSet)

void

ShapeManager.setModelSet(ModelSet modelSet)

void

Viewer.setModelSet(ModelSet modelSet)

Uses of Classorg.jmol.modelset.ModelSet

Uses of ModelSet in org.jmol.adapter.readers.pdb

Uses of ModelSet in org.jmol.api

Uses of ModelSet in org.jmol.dssx

Uses of ModelSet in org.jmol.minimize

Uses of ModelSet in org.jmol.modelkit

Uses of ModelSet in org.jmol.modelset

Uses of ModelSet in org.jmol.modelsetbio

Uses of ModelSet in org.jmol.render

Uses of ModelSet in org.jmol.shape

Uses of ModelSet in org.jmol.symmetry

Uses of ModelSet in org.jmol.util

Uses of ModelSet in org.jmol.viewer

Uses of Class
org.jmol.modelset.ModelSet