public class ModelSet extends ModelCollection
AtomCollection.AtomSorter
Modifier and Type | Field and Description |
---|---|
protected Atom[] |
closest |
private boolean |
echoShapeActive |
private javajs.util.M4 |
mat4 |
private javajs.util.M4 |
mat4t |
private javajs.util.M3 |
matInv |
private javajs.util.M3 |
matTemp |
protected String |
modelSetTypeName |
private SymmetryInterface |
pointGroup |
private boolean |
selectionHaloEnabled |
private javajs.util.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, bsModulated, bspf, canSkipLoad, g3d, haveStraightness, hydrophobicities, ionicRadii, labeler, 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
Modifier and Type | Method and Description |
---|---|
BS |
addHydrogens(javajs.util.List<Atom> vConnections,
javajs.util.P3[] pts)
these are hydrogens that are being added due to a load 2D command and are
therefore not to be flagged as NEW
|
String |
calculatePointGroup(BS bsAtoms) |
private Object |
calculatePointGroupForFirstModel(BS bsAtoms,
boolean doAll,
boolean asDraw,
boolean asInfo,
String type,
int index,
float scale) |
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,
Object specInfo)
general lookup for integer type -- from Eval
|
String |
getAtomLabel(int i) |
BS |
getBitSetTrajectories() |
BS[] |
getBsBranches(float[] dihedralList) |
String |
getDefaultStructure(BS bsAtoms,
BS bsAllAtoms) |
boolean |
getEchoStateActive() |
Object |
getFileData(int modelIndex) |
javajs.util.P3[] |
getFrameOffsets(BS bsAtoms) |
int |
getModelNumberIndex(int modelNumber,
boolean useModelNumber,
boolean doSetTrajectory) |
String |
getModelSetTypeName() |
String |
getPointGroupAsString(BS bsAtoms,
boolean asDraw,
String type,
int index,
float scale) |
Map<String,Object> |
getPointGroupInfo(BS bsAtoms) |
boolean |
getSelectionHaloEnabled() |
javajs.util.M4[] |
getSymMatrices(int modelIndex) |
private void |
includeAllRelatedFrames(BS bsModels) |
void |
invertSelected(javajs.util.P3 pt,
javajs.util.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(javajs.util.M3 mNew,
javajs.util.M3 matrixRotate,
javajs.util.V3 translation,
BS bs,
javajs.util.P3 center,
boolean isInternal,
boolean translationOnly) |
void |
recalculatePositionDependentQuantities(BS bs,
javajs.util.M4 mat) |
protected void |
releaseModelSet() |
void |
setAtomCoords(BS bs,
int tokType,
Object xyzValues) |
void |
setAtomCoordsRelative(javajs.util.T3 offset,
BS bs) |
private void |
setAtomPositions(int baseModelIndex,
int modelIndex,
javajs.util.P3[] t1,
javajs.util.P3[] t2,
float f,
javajs.util.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,
String sValue,
float[] values,
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, getBoundBoxOrientation, getBoxInfo, getCenterAndPoints, getChainCount, getChainCountInModel, getConformation, getDefaultVdwType, getDihedralMap, getDynamicAtom, getElementsPresentBitSet, getFileHeader, getFrameDelayMs, getFrameTitle, getGroupAtom, getGroupCount, getGroupCountInModel, getGroups, getGroupsWithin, getHeteroList, getInlineData, getInsertionCodeIndexInModel, getInsertionCountInModel, getIterativeModels, getJmolDataFrameIndex, getJmolDataSourceFrame, getJmolFrameType, getLastVibrationVector, 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, getModulationList, getMoInfo, getMoleculeBitSet, getMoleculeBitSetForAtom, getMoleculeCountInModel, getMoleculeIndex, getMolecules, getNotionalUnitcell, getPdbAtomData, getPdbData, getPDBHeader, getPlaneIntersection, getPolymerLeadMidPoints, getPolymerPointsAndVectors, getProteinStructureState, getSelectedAtomIterator, getSequenceBits, getStructureList, getSymmetryInfoAsString, getSymmetryInfoString, getSymTemp, getTrajectoryIndex, getUnitCell, getUnitCellForAtom, getUnitCellInfoText, growAtomArrays, haveModelKit, initializeBspf, initializeBspt, intersectPlane, isAtomAssignable, isAtomPDB, isJmolDataFrameForModel, isTrajectory, isTrajectoryMeasurement, isTrajectorySubFrame, makeConnections2, mergeModelArrays, mergeTrajectories, modelFileNumberFromFloat, recalculateLeadMidpointsAndWingVectors, saveModelOrientation, selectDisplayedTrajectories, setAPm, setAtomNamesAndNumbers, setBoundBox, setCentroid, setConformation, setCrystallographicDefaults, setDefaultStructure, setFrameDelayMs, setFrameTitle, setIteratorForAtom, setIteratorForPoint, setJmolDataFrame, setModelAuxiliaryInfo, setModelCage, setModulation, 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, chainToUpper, 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, getLabeler, getMaxVanderwaalsRadius, getPartialCharges, getQuaternion, getRadiusVdwJmol, getSeqcodeBits, getSurfaceDistance100, getSurfaceDistanceMax, getTaintedAtoms, getUserSettableType, getVibration, getVibrationCoord, getVisibleSet, isAtomHidden, isCursorOnTopOf, isModulated, 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 String modelSetTypeName
protected final Atom[] closest
private SymmetryInterface pointGroup
private final javajs.util.M3 matTemp
private final javajs.util.M3 matInv
private final javajs.util.M4 mat4
private final javajs.util.M4 mat4t
private final javajs.util.V3 vTemp
protected void releaseModelSet()
releaseModelSet
in class ModelCollection
public void setSelectionHaloEnabled(boolean selectionHaloEnabled)
public boolean getSelectionHaloEnabled()
public boolean getEchoStateActive()
public void setEchoStateActive(boolean TF)
public 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, javajs.util.P3[] t1, javajs.util.P3[] t2, float f, javajs.util.V3[] vibs, boolean isFractional)
baseModelIndex
- modelIndex
- t1
- t2
- f
- vibs
- isFractional
- public javajs.util.P3[] getFrameOffsets(BS bsAtoms)
public BS getAtomBits(int tokType, Object specInfo)
tokType
- specInfo
- public String getAtomLabel(int i)
public int findNearestAtomIndex(int x, int y, BS bsNot, int min)
public String calculateStructures(BS bsAtoms, boolean asDSSP, boolean dsspIgnoreHydrogen, boolean setStructure)
public String getPointGroupAsString(BS bsAtoms, boolean asDraw, String type, int index, float scale)
private Object calculatePointGroupForFirstModel(BS bsAtoms, boolean doAll, boolean asDraw, boolean asInfo, 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, String sValue, float[] values, String[] list)
public Object getFileData(int modelIndex)
public int calculateStruts(BS bs1, BS bs2)
calculateStruts
in class ModelCollection
bs1
- bs2
- public BS addHydrogens(javajs.util.List<Atom> vConnections, javajs.util.P3[] pts)
vConnections
- pts
- public void setAtomCoordsRelative(javajs.util.T3 offset, BS bs)
public void invertSelected(javajs.util.P3 pt, javajs.util.P4 plane, int iAtom, BS invAtoms, BS bs)
public void setDihedrals(float[] dihedralList, BS[] bsBranches, float f)
public void moveAtoms(javajs.util.M3 mNew, javajs.util.M3 matrixRotate, javajs.util.V3 translation, BS bs, javajs.util.P3 center, boolean isInternal, boolean translationOnly)
public void recalculatePositionDependentQuantities(BS bs, javajs.util.M4 mat)
public BS[] getBsBranches(float[] dihedralList)
public javajs.util.M4[] getSymMatrices(int modelIndex)