public class ModelSet extends ModelCollection
ModelCollection.StateScript
AtomCollection.AtomSorter
Modifier and Type | Field and Description |
---|---|
protected Atom[] |
closest |
private boolean |
echoShapeActive |
private javax.vecmath.Matrix4f |
mat4 |
private javax.vecmath.Matrix4f |
mat4t |
private javax.vecmath.Matrix3f |
matInv |
private javax.vecmath.Matrix3f |
matTemp |
protected java.lang.String |
modelSetTypeName |
private SymmetryInterface |
pointGroup |
private boolean |
selectionHaloEnabled |
private javax.vecmath.Vector3f |
vTemp |
bsAll, bsSymmetry, elementsPresent, frameTitles, isPDB, isXYZ, modelCount, modelFileNumbers, modelNames, modelNumbers, modelNumbersForAtomLabel, models, modelSetAuxiliaryInfo, modelSetName, modelSetProperties, proteinStructureTainted, ptTemp, shapeManager, 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, atomTypes, bfactor100s, bspf, canSkipLoad, ellipsoids, g3d, haveStraightness, hydrophobicities, ionicRadii, maxBondingRadius, occupancies, partialCharges, preserveState, surfaceDistance100s, TAINT_ATOMNAME, TAINT_ATOMNO, TAINT_ATOMTYPE, TAINT_COORD, TAINT_ELEMENT, TAINT_FORMALCHARGE, TAINT_HYDROPHOBICITY, TAINT_MAX, tainted, vibrationVectors, viewer
Constructor and Description |
---|
ModelSet(Viewer viewer,
java.lang.String name) |
Modifier and Type | Method and Description |
---|---|
java.util.BitSet |
addHydrogens(java.util.List<Atom> 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 |
deleteAllBonds() |
java.util.BitSet |
deleteModels(java.util.BitSet bsAtoms) |
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 |
getDefaultStructure(java.util.BitSet bsAtoms,
java.util.BitSet bsAllAtoms) |
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.Map<java.lang.String,java.lang.Object> |
getPointGroupInfo(java.util.BitSet bsAtoms) |
boolean |
getSelectionHaloEnabled() |
java.lang.String |
getState(java.lang.StringBuffer sfunc,
boolean isAll,
boolean withProteinStructure) |
java.lang.String |
getTrajectoryInfo() |
private void |
includeAllRelatedFrames(java.util.BitSet bsModels) |
void |
invertSelected(javax.vecmath.Point3f pt,
javax.vecmath.Point4f plane,
int iAtom,
java.util.BitSet invAtoms,
java.util.BitSet bs) |
int[] |
makeConnections(float minDistance,
float maxDistance,
int order,
int connectOperation,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds,
boolean isBonds,
boolean addGroup,
float energy) |
private java.util.BitSet |
modelsOf(java.util.BitSet bsAtoms,
java.util.BitSet bsAllAtoms) |
void |
moveAtoms(javax.vecmath.Matrix3f mNew,
javax.vecmath.Matrix3f matrixRotate,
javax.vecmath.Vector3f translation,
java.util.BitSet bs,
javax.vecmath.Point3f center,
boolean isInternal) |
void |
recalculatePositionDependentQuantities(java.util.BitSet bs,
javax.vecmath.Matrix4f mat) |
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) |
private void |
setAtomPositions(int baseModelIndex,
int modelIndex,
javax.vecmath.Point3f[] trajectory,
javax.vecmath.Vector3f[] vibrations,
boolean isFractional)
A generic way to set atom positions, possibly from trajectories but also
possibly from an array.
|
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, addStateScript, adjustAtomArrays, allowSpecAtom, appendLoadStates, assignAtom, autoBond, autoHbond, calcAtomsMinMax, calcBoundBoxDimensions, calcRasmolHydrogenBonds, calcRotationRadius, calcRotationRadius, calcSelectedGroupsCount, calcSelectedMoleculesCount, calcSelectedMonomersCount, calculateMolecularDipole, calculatePolymers, calculateStraightness, calculateStructuresAllExcept, clearDataFrameReference, connect, deleteAtoms, deleteBonds, deleteModel, fillAtomData, freezeModels, getAllAtomInfo, getAllBondInfo, getAllChainInfo, getAllPolymerInfo, getAltLocCountInModel, getAltLocIndexInModel, getAltLocListInModel, getAtomBitsMaybeDeleted, getAtomCountInModel, getAtomGroupQuaternions, getAtomIdentityInfo, getAtomsConnected, getAtomSetCenter, getAtomsWithin, getAtomsWithin, getAuxiliaryInfo, getAverageAtomPoint, getBaseModelBitSet, getBboxVertices, getBioPolymerCount, getBioPolymerCountInModel, getBondCountInModel, getBoundBoxCenter, getBoundBoxCommand, getBoundBoxCornerVector, getBoundBoxInfo, getBoundBoxModels, getBoxInfo, getCellInfos, getCenterAndPoints, getChainCount, getChainCountInModel, getChimeInfo, getConformation, getDefaultVdwType, getElementsPresentBitSet, getFileHeader, getFrameDelayMs, getFrameTitle, getGroupAtom, getGroupCount, getGroupCountInModel, getGroups, getGroupsWithin, getHeteroList, getInlineData, getInsertionCodeIndexInModel, getInsertionCountInModel, getIterativeModels, getJmolDataFrameIndex, getJmolDataSourceFrame, getJmolFrameType, getLigandInfo, getMergeTrajectoryCount, getModelAtomBitSetIncludingDeleted, getModelAtomBitSetIncludingDeleted, getModelAtomProperty, getModelAuxiliaryInfo, getModelAuxiliaryInfo, getModelAuxiliaryInfoBoolean, getModelAuxiliaryInfoInt, getModelBitSet, getModelCellRange, getModelCml, getModelCount, getModelDipole, getModelExtract, getModelFileInfo, getModelFileName, getModelFileNumber, getModelFileType, getModelIndexFromId, 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, getPeakAtomRecord, getPlaneIntersection, getPolymerLeadMidPoints, getPolymerPointsAndVectors, getProteinStructureState, getSelectedAtomIterator, getSequenceBits, getSpaceGroupInfo, getStructureList, getSymmetryInfo, getSymmetryInfoAsString, getSymmetryOperation, getTrajectoryIndex, getUnitCell, getUnitCellInfoText, growAtomArrays, haveModelKit, haveUnitCells, initializeBspf, initializeBspt, isAtomAssignable, isAtomPDB, isJmolDataFrame, isTrajectory, isTrajectory, isTrajectorySubFrame, mergeModelArrays, modelFileNumberFromFloat, modelHasVibrationVectors, recalculateLeadMidpointsAndWingVectors, saveModelOrientation, selectDisplayedTrajectories, setAtomNamesAndNumbers, setBoundBox, setCentroid, setConformation, setCrystallographicDefaults, setDefaultStructure, setFrameDelayMs, setFrameTitle, setIteratorForAtom, setIteratorForPoint, setJmolDataFrame, setModelAuxiliaryInfo, setProteinType, setRotationRadius, setStructureIds, setStructureList, setUnitCell, setUnitCellOffset
addHBond, assignAromaticBonds, assignAromaticBonds, bondAtoms, bondMutually, checkValencesAndBond, deleteConnections, displayBonds, getBondAt, getBondAtom1, getBondAtom2, getBondColix1, getBondColix2, getBondCount, getBondIterator, getBondIterator, getBondModelIndex, getBondOrder, getBondOrder, getBondRadius, getBonds, getBondsForSelectedAtoms, getDefaultMadFromOrder, removeUnnecessaryBonds, resetAromatic, resetMolecules, setBond, setBondOrder
calculateHydrogens, calculateSurface, calculateVolume, clearBfactorRange, deleteModelAtoms, findAtomsInRectangle, findMaxRadii, findNearestAtomIndex, getAtomChain, getAtomColix, getAtomCount, getAtomicCharges, getAtomicPropertyState, getAtomicPropertyState, getAtomIndexFromAtomNumber, getAtomIndices, getAtomInfo, getAtomInfoXYZ, getAtomName, getAtomNumber, getAtomPoint3f, getAtomPointVector, getAtomRadius, getAtomsWithin, getAtomsWithin, getAtomTypes, getAtomVdwRadius, getBfactor100Hi, getBfactor100Lo, getBFactors, getChainBits, getClickableSet, getElementName, getElementNumber, getElementSymbol, getEllipsoid, getHaveStraightness, getHelixData, getHybridizationAndAxes, getHydrophobicity, getImplicitHydrogenCount, 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, setHydrophobicity, setIonicRadius, setOccupancy, setPartialCharge, setPreserveState, setTaintedAtoms, setVibrationVector, taint, taint, unTaintAtoms, validateBspf, validateBspf
private boolean selectionHaloEnabled
private boolean echoShapeActive
protected java.lang.String modelSetTypeName
protected final Atom[] closest
private SymmetryInterface pointGroup
private final javax.vecmath.Matrix3f matTemp
private final javax.vecmath.Matrix3f matInv
private final javax.vecmath.Matrix4f mat4
private final javax.vecmath.Matrix4f mat4t
private final javax.vecmath.Vector3f 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 java.lang.String getTrajectoryInfo()
public java.util.BitSet getBitSetTrajectories()
public void setTrajectory(java.util.BitSet bsModels)
public void setTrajectory(int modelIndex)
private void setAtomPositions(int baseModelIndex, int modelIndex, javax.vecmath.Point3f[] trajectory, javax.vecmath.Vector3f[] vibrations, boolean isFractional)
baseModelIndex
- modelIndex
- trajectory
- vibrations
- isFractional
- 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)
public int findNearestAtomIndex(int x, int y, java.util.BitSet bsNot)
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.Map<java.lang.String,java.lang.Object> 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)
public java.lang.String getDefaultStructure(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, boolean addGroup, 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<Atom> 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 invertSelected(javax.vecmath.Point3f pt, javax.vecmath.Point4f plane, int iAtom, java.util.BitSet invAtoms, java.util.BitSet bs)
public void moveAtoms(javax.vecmath.Matrix3f mNew, javax.vecmath.Matrix3f matrixRotate, javax.vecmath.Vector3f translation, java.util.BitSet bs, javax.vecmath.Point3f center, boolean isInternal)
public void recalculatePositionDependentQuantities(java.util.BitSet bs, javax.vecmath.Matrix4f mat)