public abstract class ModelSet extends ModelCollection
ModelCollection.StateScript
AtomCollection.AtomSorter
Modifier and Type | Field and Description |
---|---|
protected Atom[] |
closest |
private boolean |
echoShapeActive |
protected java.lang.String |
modelSetTypeName |
private SymmetryInterface |
pointGroup |
private boolean |
selectionHaloEnabled |
bsAll, bsSymmetry, elementsPresent, frameTitles, groupCount, groups, haveBioClasses, isPDB, isXYZ, jbr, modelCount, modelFileNumbers, modelNames, modelNumbers, modelNumbersForAtomLabel, models, modelSetAuxiliaryInfo, modelSetName, modelSetProperties, proteinStructureTainted, shapeManager, someModelsHaveAromaticBonds, someModelsHaveFractionalCoordinates, someModelsHaveSymmetry, stateScripts, trajectorySteps, unitCells
BOND_GROWTH_INCREMENT, bondCount, bonds, bsAromatic, bsHBondsRasmol, defaultCovalentMad, freeBonds, MAX_BONDS_LENGTH_TO_CACHE, MAX_NUM_TO_CACHE, moleculeCount, molecules, numCached
atomCount, atomNames, atoms, atomSerials, atomTypes, bfactor100s, bspf, ellipsoids, g3d, haveStraightness, ionicRadii, maxBondingRadius, occupancies, partialCharges, preserveState, surfaceDistance100s, TAINT_ATOMNAME, TAINT_ATOMNO, TAINT_ATOMTYPE, TAINT_COORD, TAINT_ELEMENT, TAINT_FORMALCHARGE, TAINT_MAX, tainted, vibrationVectors, viewer
Constructor and Description |
---|
ModelSet() |
Modifier and Type | Method and Description |
---|---|
java.util.BitSet |
addHydrogens(java.util.List vConnections,
javax.vecmath.Point3f[] pts)
these are hydrogens that are being added due to a load 2D command and are
therefore not to be flagged as NEW
|
protected void |
assignAromaticBonds(boolean isUserCalculation) |
java.lang.String |
calculatePointGroup(java.util.BitSet bsAtoms) |
private java.lang.Object |
calculatePointGroupForFirstModel(java.util.BitSet bsAtoms,
boolean doAll,
boolean asDraw,
boolean asInfo,
java.lang.String type,
int index,
float scale) |
java.lang.String |
calculateStructures(java.util.BitSet bsAtoms,
boolean asDSSP,
boolean dsspIgnoreHydrogen,
boolean setStructure) |
int |
calculateStruts(java.util.BitSet bs1,
java.util.BitSet bs2)
see comments in org.jmol.modelsetbio.AlphaPolymer.java
Struts are calculated for atoms in bs1 connecting to atoms in bs2.
|
void |
connect(float[][] connections) |
void |
deleteAllBonds() |
java.util.BitSet |
deleteModels(java.util.BitSet bsAtoms) |
void |
fillAtomData(AtomData atomData,
int mode) |
int |
findNearestAtomIndex(int x,
int y,
java.util.BitSet bsNot) |
java.util.BitSet |
getAtomBits(int tokType,
java.lang.Object specInfo)
general lookup for integer type -- from Eval
|
java.lang.String |
getAtomLabel(int i) |
java.util.BitSet |
getBitSetTrajectories() |
java.lang.String |
getDefinedState(java.lang.StringBuffer sfunc,
boolean isAll) |
boolean |
getEchoStateActive() |
java.lang.Object |
getFileData(int modelIndex) |
javax.vecmath.Point3f[] |
getFrameOffsets(java.util.BitSet bsAtoms) |
int |
getModelNumberIndex(int modelNumber,
boolean useModelNumber,
boolean doSetTrajectory) |
java.lang.String |
getModelSetTypeName() |
java.lang.String |
getPointGroupAsString(java.util.BitSet bsAtoms,
boolean asDraw,
java.lang.String type,
int index,
float scale) |
java.util.Hashtable |
getPointGroupInfo(java.util.BitSet bsAtoms) |
boolean |
getSelectionHaloEnabled() |
private java.util.BitSet |
getSpecModel(int modelNumber) |
java.lang.String |
getState(java.lang.StringBuffer sfunc,
boolean isAll,
boolean withProteinStructure) |
java.lang.String |
getTrajectoryInfo() |
private void |
includeAllRelatedFrames(java.util.BitSet bsModels) |
int[] |
makeConnections(float minDistance,
float maxDistance,
int order,
int connectOperation,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds,
boolean isBonds,
float energy) |
private java.util.BitSet |
modelsOf(java.util.BitSet bsAtoms,
java.util.BitSet bsAllAtoms) |
void |
recalculatePositionDependentQuantities(java.util.BitSet bs) |
protected void |
releaseModelSet() |
void |
setAtomCoord(java.util.BitSet bs,
int tokType,
java.lang.Object xyzValues) |
void |
setAtomCoordRelative(javax.vecmath.Tuple3f offset,
java.util.BitSet bs) |
void |
setAtomProperty(java.util.BitSet bs,
int tok,
int iValue,
float fValue,
java.lang.String sValue,
float[] values,
java.lang.String[] list) |
void |
setEchoStateActive(boolean TF) |
void |
setPdbConectBonding(int baseAtomIndex,
int baseModelIndex,
java.util.BitSet bsExclude) |
void |
setSelectionHaloEnabled(boolean selectionHaloEnabled) |
void |
setTrajectory(java.util.BitSet bsModels) |
void |
setTrajectory(int modelIndex) |
addAtom, addAtom, addBioPolymerToModel, addStateScript, appendLoadStates, assignAtom, autoBond, autoHbond, calcAtomsMinMax, calcBoundBoxDimensions, calcRasmolHydrogenBonds, calcRotationRadius, calcRotationRadius, calcSelectedGroupsCount, calcSelectedMoleculesCount, calcSelectedMonomersCount, calculateMolecularDipole, calculatePolymers, calculateStraightness, calculateStructuresAllExcept, clearDataFrameReference, clearRasmolHydrogenBonds, deleteAtoms, deleteBonds, deleteModel, getAllAtomInfo, getAllBondInfo, getAllChainInfo, getAllPolymerInfo, getAltLocCountInModel, getAltLocIndexInModel, getAltLocListInModel, getAtomCountInModel, getAtomGroupQuaternions, getAtomIdentityInfo, getAtomsConnected, getAtomSetCenter, getAtomsWithin, getAtomsWithin, getAuxiliaryInfo, getAverageAtomPoint, getBboxVertices, getBioPolymerCount, getBioPolymerCountInModel, getBondCountInModel, getBoundBoxCenter, getBoundBoxCommand, getBoundBoxCornerVector, getBoundBoxInfo, getBoundBoxModels, getBoxInfo, getCellInfos, getCenterAndPoints, getChainCount, getChainCountInModel, getChimeInfo, getConformation, getDefaultVdwType, getElementsPresentBitSet, getFileHeader, getFrameTitle, getGroupAtom, getGroupCount, getGroupCountInModel, getGroupsWithin, getHeteroList, getInlineData, getInsertionCodeIndexInModel, getInsertionCountInModel, getIterativeModels, getJmolDataFrameIndex, getJmolDataSourceFrame, getJmolFrameType, getModelAtomBitSetIncludingDeleted, getModelAtomBitSetIncludingDeleted, getModelAuxiliaryInfo, getModelAuxiliaryInfo, getModelAuxiliaryInfoBoolean, getModelAuxiliaryInfoInt, getModelBitSet, getModelCellRange, getModelCml, getModelCount, getModelDipole, getModelExtract, getModelFileInfo, getModelFileName, getModelFileNumber, getModelFileType, getModelInfo, getModelInfoAsString, getModelKitStateBitset, getModelName, getModelNumber, getModelNumberDotted, getModelNumberForAtomLabel, getModelOrientation, getModelProperties, getModelProperty, getModels, getModelSetAuxiliaryInfo, getModelSetAuxiliaryInfo, getModelSetAuxiliaryInfoBoolean, getModelSetName, getModelSetProperties, getModelSetProperty, getModelSymmetryCount, getModelTitle, getMoInfo, getMoleculeBitSet, getMoleculeBitSet, getMoleculeCountInModel, getMoleculeIndex, getMoleculeInfo, getMolecules, getNotionalUnitcell, getPdbAtomData, getPdbData, getPDBHeader, getPlaneIntersection, getPolymerLeadMidPoints, getPolymerPointsAndVectors, getProteinStructureState, getSelectedAtomIterator, getSequenceBits, getSpaceGroupInfo, getSymmetryInfo, getSymmetryInfoAsString, getSymmetryOperation, getTrajectoryCount, getTrajectoryIndex, getUnitCell, getUnitCellInfoText, growAtomArrays, hasCalculatedHBonds, haveModelKit, initializeBspf, initializeBspt, invertSelected, isAtomAssignable, isAtomPDB, isJmolDataFrame, isTrajectory, isTrajectory, isTrajectorySubFrame, mergeModelArrays, mergeModels, modelFileNumberFromFloat, modelHasVibrationVectors, recalculateLeadMidpointsAndWingVectors, rotateAtoms, saveModelOrientation, selectDisplayedTrajectories, setAtomNamesAndNumbers, setBoundBox, setConformation, setCrystallographicDefaults, setFrameTitle, setIteratorForAtom, setIteratorForPoint, setJmolDataFrame, setModelAuxiliaryInfo, setProteinType, setRotationRadius, setStructureIds
addHBond, assignAromaticBonds, assignAromaticBonds, bondAtoms, bondMutually, checkValencesAndBond, deleteConnections, getBondAt, getBondAtom1, getBondAtom2, getBondColix1, getBondColix2, getBondCount, getBondIterator, getBondIterator, getBondModelIndex, getBondOrder, getBondOrder, getBondRadius, getBonds, getBondsForSelectedAtoms, getDefaultMadFromOrder, getRasmolHydrogenBonds, removeUnnecessaryBonds, resetAromatic, setBond, setBondOrder
calculateHydrogens, calculateSurface, calculateVolume, clearBfactorRange, deleteModelAtoms, findAtomsInRectangle, findMaxRadii, findNearestAtomIndex, getAtomChain, getAtomColix, getAtomCount, getAtomicCharges, getAtomicPropertyState, getAtomicPropertyState, getAtomIndexFromAtomNumber, getAtomIndices, getAtomInfo, getAtomInfoXYZ, getAtomModelIndex, getAtomName, getAtomNumber, getAtomPoint3f, getAtomPointVector, getAtomRadius, getAtomSequenceCode, getAtomsWithin, getAtomTypes, getAtomVdwRadius, getBfactor100Hi, getBfactor100Lo, getBFactors, getChainBits, getClickableSet, getElementName, getElementNumber, getElementSymbol, getEllipsoid, getHaveStraightness, getHelixData, getHybridizationAndAxes, getIonicRadii, getMaxVanderwaalsRadius, getPartialCharges, getQuaternion, getRadiusVdwJmol, getSeqcodeBits, getSurfaceDistance100, getSurfaceDistanceMax, getTaintedAtoms, getUserSettableType, getVibrationCoord, getVibrationVector, getVisibleSet, isAtomHidden, isCursorOnTopOf, mergeAtomArrays, modelSetHasVibrationVectors, setAtomCoord, setAtomCoordRelative, setAtomCoordRelative, setAtomData, setAtomName, setAtomNumber, setAtomType, setBFactor, setBsHidden, setElement, setEllipsoid, setFormalCharges, setHaveStraightness, setIonicRadius, setOccupancy, setPartialCharge, setPreserveState, setTaintedAtoms, setVibrationVector, taint, taint, unTaintAtoms
private boolean selectionHaloEnabled
private boolean echoShapeActive
protected java.lang.String modelSetTypeName
protected final Atom[] closest
private SymmetryInterface pointGroup
protected void releaseModelSet()
releaseModelSet
in class ModelCollection
public void setSelectionHaloEnabled(boolean selectionHaloEnabled)
public boolean getSelectionHaloEnabled()
public boolean getEchoStateActive()
public void setEchoStateActive(boolean TF)
public java.lang.String getModelSetTypeName()
public int getModelNumberIndex(int modelNumber, boolean useModelNumber, boolean doSetTrajectory)
public java.lang.String getTrajectoryInfo()
public java.util.BitSet getBitSetTrajectories()
public void setTrajectory(java.util.BitSet bsModels)
public void setTrajectory(int modelIndex)
public javax.vecmath.Point3f[] getFrameOffsets(java.util.BitSet bsAtoms)
public java.util.BitSet getAtomBits(int tokType, java.lang.Object specInfo)
getAtomBits
in class ModelCollection
tokType
- specInfo
- public java.lang.String getAtomLabel(int i)
private java.util.BitSet getSpecModel(int modelNumber)
public int findNearestAtomIndex(int x, int y, java.util.BitSet bsNot)
public void fillAtomData(AtomData atomData, int mode)
fillAtomData
in class AtomCollection
public java.lang.String calculateStructures(java.util.BitSet bsAtoms, boolean asDSSP, boolean dsspIgnoreHydrogen, boolean setStructure)
public java.lang.String calculatePointGroup(java.util.BitSet bsAtoms)
public java.util.Hashtable getPointGroupInfo(java.util.BitSet bsAtoms)
public java.lang.String getPointGroupAsString(java.util.BitSet bsAtoms, boolean asDraw, java.lang.String type, int index, float scale)
private java.lang.Object calculatePointGroupForFirstModel(java.util.BitSet bsAtoms, boolean doAll, boolean asDraw, boolean asInfo, java.lang.String type, int index, float scale)
private java.util.BitSet modelsOf(java.util.BitSet bsAtoms, java.util.BitSet bsAllAtoms)
protected void assignAromaticBonds(boolean isUserCalculation)
public int[] makeConnections(float minDistance, float maxDistance, int order, int connectOperation, java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsBonds, boolean isBonds, float energy)
makeConnections
in class ModelCollection
public void setPdbConectBonding(int baseAtomIndex, int baseModelIndex, java.util.BitSet bsExclude)
public void deleteAllBonds()
deleteAllBonds
in class BondCollection
public java.lang.String getDefinedState(java.lang.StringBuffer sfunc, boolean isAll)
public java.lang.String getState(java.lang.StringBuffer sfunc, boolean isAll, boolean withProteinStructure)
private void includeAllRelatedFrames(java.util.BitSet bsModels)
public java.util.BitSet deleteModels(java.util.BitSet bsAtoms)
public void setAtomProperty(java.util.BitSet bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.String[] list)
setAtomProperty
in class ModelCollection
public java.lang.Object getFileData(int modelIndex)
public int calculateStruts(java.util.BitSet bs1, java.util.BitSet bs2)
calculateStruts
in class ModelCollection
bs1
- bs2
- public java.util.BitSet addHydrogens(java.util.List vConnections, javax.vecmath.Point3f[] pts)
vConnections
- pts
- public void setAtomCoordRelative(javax.vecmath.Tuple3f offset, java.util.BitSet bs)
public void setAtomCoord(java.util.BitSet bs, int tokType, java.lang.Object xyzValues)
setAtomCoord
in class AtomCollection
public void recalculatePositionDependentQuantities(java.util.BitSet bs)
public void connect(float[][] connections)