public class ModelSet extends ModelCollection
ModelCollection.StateScript
AtomCollection.AtomSorter
Modifier and Type | Field and Description |
---|---|
protected Atom[] |
closest |
private boolean |
echoShapeActive |
private Matrix4f |
mat4 |
private Matrix4f |
mat4t |
private Matrix3f |
matInv |
private Matrix3f |
matTemp |
protected java.lang.String |
modelSetTypeName |
private SymmetryInterface |
pointGroup |
private boolean |
selectionHaloEnabled |
private V3 |
vTemp |
bsAll, bsSymmetry, elementsPresent, frameTitles, haveUnitCells, htPeaks, isPDB, isXYZ, modelCount, modelFileNumbers, modelNames, modelNumbers, modelNumbersForAtomLabel, models, modelSetAuxiliaryInfo, modelSetName, modelSetProperties, proteinStructureTainted, ptTemp, shapeManager, showRebondTimes, someModelsHaveAromaticBonds, someModelsHaveFractionalCoordinates, someModelsHaveSymmetry, stateScripts, trajectorySteps, unitCells, vibrationSteps
BOND_GROWTH_INCREMENT, bondCount, bonds, bsAromatic, defaultCovalentMad, freeBonds, haveHiddenBonds, MAX_BONDS_LENGTH_TO_CACHE, MAX_NUM_TO_CACHE, moleculeCount, molecules, numCached
atomCount, atomNames, atoms, atomSerials, atomTensorList, atomTensors, atomTypes, bfactor100s, bspf, canSkipLoad, g3d, haveStraightness, hydrophobicities, ionicRadii, maxBondingRadius, occupancies, partialCharges, preserveState, surfaceDistance100s, TAINT_ATOMNAME, TAINT_ATOMNO, TAINT_ATOMTYPE, TAINT_COORD, TAINT_ELEMENT, TAINT_FORMALCHARGE, TAINT_HYDROPHOBICITY, TAINT_IONICRADIUS, TAINT_MAX, TAINT_OCCUPANCY, TAINT_PARTIALCHARGE, TAINT_TEMPERATURE, TAINT_VALENCE, TAINT_VANDERWAALS, TAINT_VIBRATION, tainted, userSettableValues, vibrations, viewer
Constructor and Description |
---|
ModelSet(Viewer viewer,
java.lang.String name) |
Modifier and Type | Method and Description |
---|---|
BS |
addHydrogens(JmolList<Atom> vConnections,
P3[] pts)
these are hydrogens that are being added due to a load 2D command and are
therefore not to be flagged as NEW
|
java.lang.String |
calculatePointGroup(BS bsAtoms) |
private java.lang.Object |
calculatePointGroupForFirstModel(BS bsAtoms,
boolean doAll,
boolean asDraw,
boolean asInfo,
java.lang.String type,
int index,
float scale) |
java.lang.String |
calculateStructures(BS bsAtoms,
boolean asDSSP,
boolean dsspIgnoreHydrogen,
boolean setStructure) |
int |
calculateStruts(BS bs1,
BS bs2)
see comments in org.jmol.modelsetbio.AlphaPolymer.java
Struts are calculated for atoms in bs1 connecting to atoms in bs2.
|
void |
deleteAllBonds() |
BS |
deleteModels(BS bsAtoms) |
int |
findNearestAtomIndex(int x,
int y,
BS bsNot,
int min) |
BS |
getAtomBits(int tokType,
java.lang.Object specInfo)
general lookup for integer type -- from Eval
|
java.lang.String |
getAtomLabel(int i) |
BS |
getBitSetTrajectories() |
BS[] |
getBsBranches(float[] dihedralList) |
java.lang.String |
getDefaultStructure(BS bsAtoms,
BS bsAllAtoms) |
boolean |
getEchoStateActive() |
java.lang.Object |
getFileData(int modelIndex) |
P3[] |
getFrameOffsets(BS bsAtoms) |
int |
getModelNumberIndex(int modelNumber,
boolean useModelNumber,
boolean doSetTrajectory) |
java.lang.String |
getModelSetTypeName() |
java.lang.String |
getPointGroupAsString(BS bsAtoms,
boolean asDraw,
java.lang.String type,
int index,
float scale) |
java.util.Map<java.lang.String,java.lang.Object> |
getPointGroupInfo(BS bsAtoms) |
boolean |
getSelectionHaloEnabled() |
private void |
includeAllRelatedFrames(BS bsModels) |
void |
invertSelected(P3 pt,
P4 plane,
int iAtom,
BS invAtoms,
BS bs) |
int[] |
makeConnections(float minDistance,
float maxDistance,
int order,
int connectOperation,
BS bsA,
BS bsB,
BS bsBonds,
boolean isBonds,
boolean addGroup,
float energy) |
private BS |
modelsOf(BS bsAtoms,
BS bsAllAtoms) |
void |
morphTrajectories(int m1,
int m2,
float f) |
void |
moveAtoms(Matrix3f mNew,
Matrix3f matrixRotate,
V3 translation,
BS bs,
P3 center,
boolean isInternal) |
void |
recalculatePositionDependentQuantities(BS bs,
Matrix4f mat) |
protected void |
releaseModelSet() |
void |
setAtomCoords(BS bs,
int tokType,
java.lang.Object xyzValues) |
void |
setAtomCoordsRelative(Tuple3f offset,
BS bs) |
private void |
setAtomPositions(int baseModelIndex,
int modelIndex,
P3[] t1,
P3[] t2,
float f,
V3[] vibs,
boolean isFractional)
A generic way to set atom positions, possibly from trajectories but also
possibly from an array.
|
void |
setAtomProperty(BS bs,
int tok,
int iValue,
float fValue,
java.lang.String sValue,
float[] values,
java.lang.String[] list) |
void |
setDihedrals(float[] dihedralList,
BS[] bsBranches,
float f) |
void |
setEchoStateActive(boolean TF) |
void |
setPdbConectBonding(int baseAtomIndex,
int baseModelIndex,
BS bsExclude) |
void |
setSelectionHaloEnabled(boolean selectionHaloEnabled) |
void |
setTrajectory(int modelIndex) |
void |
setTrajectoryBs(BS bsModels) |
addAtom, addStateScript, adjustAtomArrays, allowSpecAtom, assignAtom, autoBondBs4, autoHbond, calcAtomsMinMax, calcBoundBoxDimensions, calcRasmolHydrogenBonds, calcRotationRadius, calcRotationRadiusBs, calcSelectedGroupsCount, calcSelectedMoleculesCount, calcSelectedMonomersCount, calculateMolecularDipole, calculatePolymers, calculateStraightness, calculateStructuresAllExcept, calculateStrutsMC, clearDataFrameReference, connect, createModels, deleteAtoms, deleteBonds, deleteModel, fillAtomData, freezeModels, getAltLocCountInModel, getAltLocIndexInModel, getAltLocListInModel, getAtomBitsMaybeDeleted, getAtomCountInModel, getAtomGroupQuaternions, getAtomsConnected, getAtomSetCenter, getAtomsWithin, getAtomsWithinRD, getAuxiliaryInfo, getAverageAtomPoint, getBboxVertices, getBioPolymerCount, getBioPolymerCountInModel, getBondCountInModel, getBoundBoxCenter, getBoundBoxCommand, getBoundBoxCornerVector, getBoundBoxInfo, getBoundBoxModels, getBoxInfo, getCenterAndPoints, getChainCount, getChainCountInModel, getConformation, getDefaultVdwType, getDihedralMap, getElementsPresentBitSet, getFileHeader, getFrameDelayMs, getFrameTitle, getGroupAtom, getGroupCount, getGroupCountInModel, getGroups, getGroupsWithin, getHeteroList, getInlineData, getInsertionCodeIndexInModel, getInsertionCountInModel, getIterativeModels, getJmolDataFrameIndex, getJmolDataSourceFrame, getJmolFrameType, getModelAtomBitSetIncludingDeleted, getModelAtomBitSetIncludingDeletedBs, getModelAtomProperty, getModelAuxiliaryInfo, getModelAuxiliaryInfoBoolean, getModelAuxiliaryInfoInt, getModelAuxiliaryInfoValue, getModelBitSet, getModelCellRange, getModelCml, getModelDipole, getModelFileName, getModelFileNumber, getModelFileType, getModelIndexFromId, getModelInfoAsString, getModelKitStateBitset, getModelName, getModelNumber, getModelNumberDotted, getModelNumberForAtomLabel, getModelOrientation, getModelProperties, getModelProperty, getModelSetAuxiliaryInfo, getModelSetAuxiliaryInfoBoolean, getModelSetAuxiliaryInfoValue, getModelSetProperties, getModelSetProperty, getModelSymmetryCount, getModelTitle, getMoInfo, getMoleculeBitSet, getMoleculeBitSetForAtom, getMoleculeCountInModel, getMoleculeIndex, getMolecules, getNotionalUnitcell, getPdbAtomData, getPdbData, getPDBHeader, getPlaneIntersection, getPolymerLeadMidPoints, getPolymerPointsAndVectors, getProteinStructureState, getSelectedAtomIterator, getSequenceBits, getStructureList, getSymmetryInfoAsString, getSymmetryOperation, getSymTemp, getTrajectoryIndex, getUnitCell, getUnitCellInfoText, growAtomArrays, haveModelKit, initializeBspf, initializeBspt, isAtomAssignable, isAtomPDB, isJmolDataFrameForModel, isTrajectory, isTrajectoryMeasurement, isTrajectorySubFrame, makeConnections2, mergeModelArrays, mergeTrajectories, modelFileNumberFromFloat, modelHasVibrationVectors, recalculateLeadMidpointsAndWingVectors, saveModelOrientation, selectDisplayedTrajectories, setAPm, setAtomNamesAndNumbers, setBoundBox, setCentroid, setConformation, setCrystallographicDefaults, setDefaultStructure, setFrameDelayMs, setFrameTitle, setIteratorForAtom, setIteratorForPoint, setJmolDataFrame, setModelAuxiliaryInfo, setModelCage, setProteinType, setRotationRadius, setStructureIndexes, setStructureList, setUnitCellOffset
addHBond, assignAromaticBonds, assignAromaticBondsBs, bondAtoms, bondMutually, checkValencesAndBond, dBb, dBm, deleteAllBonds2, deleteConnections, displayBonds, getAtomBitsMDb, getBondAt, getBondAtom1, getBondAtom2, getBondColix1, getBondColix2, getBondIterator, getBondIteratorForType, getBondModelIndex, getBondOrder, getBondOrderFull, getBondRadius, getBondsForSelectedAtoms, getDefaultMadFromOrder, releaseModelSetBC, removeUnnecessaryBonds, resetAromatic, resetMolecules, setBond, setBondOrder, setBondParameters, setBondParametersBS
addTensor, calculateHydrogens, calculateSurface, calculateVolume, clearBfactorRange, deleteModelAtoms, fillADa, findAtomsInRectangle, findMaxRadii, findNearest2, fixFormalCharges, getAllAtomTensors, getAtomBitsMDa, getAtomChain, getAtomColix, getAtomCount, getAtomicCharges, getAtomIdentityInfo, getAtomIndexFromAtomNumber, getAtomIndices, getAtomInfo, getAtomInfoXYZ, getAtomName, getAtomNumber, getAtomPoint3f, getAtomPointVector, getAtomRadius, getAtomsWithin, getAtomsWithinBs, getAtomTensor, getAtomTensorList, getAtomTypes, getAtomVdwRadius, getBfactor100Hi, getBfactor100Lo, getBFactors, getChainBits, getClickableSet, getElementName, getElementNumber, getElementSymbol, getHaveStraightness, getHelixData, getHybridizationAndAxes, getHydrophobicity, getImplicitHydrogenCount, getIonicRadii, getMaxVanderwaalsRadius, getPartialCharges, getQuaternion, getRadiusVdwJmol, getSeqcodeBits, getSurfaceDistance100, getSurfaceDistanceMax, getTaintedAtoms, getUserSettableType, getVibration, getVibrationCoord, getVisibleSet, isAtomHidden, isCursorOnTopOf, mergeAtomArrays, modelSetHasVibrationVectors, releaseModelSetAC, setAPa, setAtomCoord, setAtomCoord2, setAtomCoordRelative, setAtomData, setAtomName, setAtomNumber, setAtomsCoordRelative, setAtomTensors, setAtomType, setBFactor, setBsHidden, setElement, setFormalCharges, setHaveStraightness, setHydrophobicity, setIonicRadius, setOccupancy, setPartialCharge, setPreserveState, setTaintedAtoms, setVibrationVector, taintAtom, taintAtoms, unTaintAtoms, validateBspf, validateBspfForModel
private boolean selectionHaloEnabled
private boolean echoShapeActive
protected java.lang.String modelSetTypeName
protected final Atom[] closest
private SymmetryInterface pointGroup
private final Matrix3f matTemp
private final Matrix3f matInv
private final Matrix4f mat4
private final Matrix4f mat4t
private final V3 vTemp
public ModelSet(Viewer viewer, java.lang.String name)
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 BS getBitSetTrajectories()
public void setTrajectoryBs(BS bsModels)
public void setTrajectory(int modelIndex)
public void morphTrajectories(int m1, int m2, float f)
private void setAtomPositions(int baseModelIndex, int modelIndex, P3[] t1, P3[] t2, float f, V3[] vibs, boolean isFractional)
baseModelIndex
- modelIndex
- t1
- t2
- f
- vibs
- isFractional
- public BS getAtomBits(int tokType, java.lang.Object specInfo)
tokType
- specInfo
- public java.lang.String getAtomLabel(int i)
public int findNearestAtomIndex(int x, int y, BS bsNot, int min)
public java.lang.String calculateStructures(BS bsAtoms, boolean asDSSP, boolean dsspIgnoreHydrogen, boolean setStructure)
public java.lang.String calculatePointGroup(BS bsAtoms)
public java.util.Map<java.lang.String,java.lang.Object> getPointGroupInfo(BS bsAtoms)
public java.lang.String getPointGroupAsString(BS bsAtoms, boolean asDraw, java.lang.String type, int index, float scale)
private java.lang.Object calculatePointGroupForFirstModel(BS bsAtoms, boolean doAll, boolean asDraw, boolean asInfo, java.lang.String type, int index, float scale)
public int[] makeConnections(float minDistance, float maxDistance, int order, int connectOperation, BS bsA, BS bsB, BS bsBonds, boolean isBonds, boolean addGroup, float energy)
public void setPdbConectBonding(int baseAtomIndex, int baseModelIndex, BS bsExclude)
public void deleteAllBonds()
private void includeAllRelatedFrames(BS bsModels)
public void setAtomProperty(BS bs, int tok, int iValue, float fValue, java.lang.String sValue, float[] values, java.lang.String[] list)
public java.lang.Object getFileData(int modelIndex)
public int calculateStruts(BS bs1, BS bs2)
calculateStruts
in class ModelCollection
bs1
- bs2
- public BS addHydrogens(JmolList<Atom> vConnections, P3[] pts)
vConnections
- pts
- public void setAtomCoords(BS bs, int tokType, java.lang.Object xyzValues)
public void setDihedrals(float[] dihedralList, BS[] bsBranches, float f)
public void moveAtoms(Matrix3f mNew, Matrix3f matrixRotate, V3 translation, BS bs, P3 center, boolean isInternal)
public void recalculatePositionDependentQuantities(BS bs, Matrix4f mat)
public BS[] getBsBranches(float[] dihedralList)