org.jmol.modelset
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 String |
modelSetTypeName |
private SymmetryInterface |
pointGroup |
private boolean |
selectionHaloEnabled |
private 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, bsHBondsRasmol, defaultCovalentMad, freeBonds, haveHiddenBonds, MAX_BONDS_LENGTH_TO_CACHE, MAX_NUM_TO_CACHE, moleculeCount, molecules, numCached
atomCount, atomNames, atoms, atomSerials, atomTypes, bfactor100s, bspf, 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
Modifier and Type | Method and Description |
---|---|
BitSet |
addHydrogens(List<Atom> vConnections,
Point3f[] pts)
these are hydrogens that are being added due to a load 2D command and are
therefore not to be flagged as NEW
|
boolean |
allowSpecAtom() |
protected void |
assignAromaticBonds(boolean isUserCalculation) |
String |
calculatePointGroup(BitSet bsAtoms) |
private Object |
calculatePointGroupForFirstModel(BitSet bsAtoms,
boolean doAll,
boolean asDraw,
boolean asInfo,
String type,
int index,
float scale) |
String |
calculateStructures(BitSet bsAtoms,
boolean asDSSP,
boolean dsspIgnoreHydrogen,
boolean setStructure) |
int |
calculateStruts(BitSet bs1,
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 |
createAtomDataSet(int tokType,
Object atomSetCollection,
BitSet bsSelected) |
void |
deleteAllBonds() |
BitSet |
deleteModels(BitSet bsAtoms) |
int |
findNearestAtomIndex(int x,
int y,
BitSet bsNot) |
BitSet |
getAtomBits(int tokType,
Object specInfo)
general lookup for integer type -- from Eval
|
String |
getAtomLabel(int i) |
BitSet |
getBitSetTrajectories() |
String |
getDefaultStructure(BitSet bsAtoms,
BitSet bsAllAtoms) |
String |
getDefinedState(StringBuffer sfunc,
boolean isAll) |
boolean |
getEchoStateActive() |
Object |
getFileData(int modelIndex) |
Point3f[] |
getFrameOffsets(BitSet bsAtoms) |
int |
getModelNumberIndex(int modelNumber,
boolean useModelNumber,
boolean doSetTrajectory) |
String |
getModelSetTypeName() |
String |
getPointGroupAsString(BitSet bsAtoms,
boolean asDraw,
String type,
int index,
float scale) |
Map<String,Object> |
getPointGroupInfo(BitSet bsAtoms) |
boolean |
getSelectionHaloEnabled() |
String |
getState(StringBuffer sfunc,
boolean isAll,
boolean withProteinStructure) |
String |
getTrajectoryInfo() |
private void |
includeAllRelatedFrames(BitSet bsModels) |
void |
invertSelected(Point3f pt,
Point4f plane,
int iAtom,
BitSet invAtoms,
BitSet bs) |
int[] |
makeConnections(float minDistance,
float maxDistance,
int order,
int connectOperation,
BitSet bsA,
BitSet bsB,
BitSet bsBonds,
boolean isBonds,
boolean addGroup,
float energy) |
private BitSet |
modelsOf(BitSet bsAtoms,
BitSet bsAllAtoms) |
void |
moveAtoms(Matrix3f mNew,
Matrix3f matrixRotate,
Vector3f translation,
BitSet bs,
Point3f center,
boolean isInternal) |
void |
recalculatePositionDependentQuantities(BitSet bs,
Matrix4f mat) |
protected void |
releaseModelSet() |
void |
setAtomCoord(BitSet bs,
int tokType,
Object xyzValues) |
void |
setAtomCoordRelative(Tuple3f offset,
BitSet bs) |
void |
setAtomProperty(BitSet bs,
int tok,
int iValue,
float fValue,
String sValue,
float[] values,
String[] list) |
void |
setEchoStateActive(boolean TF) |
void |
setPdbConectBonding(int baseAtomIndex,
int baseModelIndex,
BitSet bsExclude) |
void |
setSelectionHaloEnabled(boolean selectionHaloEnabled) |
void |
setTrajectory(BitSet bsModels) |
void |
setTrajectory(int modelIndex) |
addAtom, addAtom, addBioPolymerToModel, addStateScript, adjustAtomArrays, appendLoadStates, assignAtom, autoBond, autoHbond, calcAtomsMinMax, calcBoundBoxDimensions, calcRasmolHydrogenBonds, calcRotationRadius, calcRotationRadius, calcSelectedGroupsCount, calcSelectedMoleculesCount, calcSelectedMonomersCount, calculateMolecularDipole, calculatePolymers, calculateStraightness, calculateStructuresAllExcept, clearDataFrameReference, clearRasmolHydrogenBonds, deleteAtoms, deleteBonds, deleteModel, fillAtomData, freezeModels, getAllAtomInfo, getAllBondInfo, getAllChainInfo, getAllPolymerInfo, getAltLocCountInModel, getAltLocIndexInModel, getAltLocListInModel, getAtomBitsMaybeDeleted, 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, getGroups, getGroupsWithin, getHeteroList, getInlineData, getInsertionCodeIndexInModel, getInsertionCountInModel, getIterativeModels, getJbr, getJmolDataFrameIndex, getJmolDataSourceFrame, getJmolFrameType, getLigandInfo, getModelAtomBitSetIncludingDeleted, getModelAtomBitSetIncludingDeleted, getModelAtomProperty, 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, getStructureList, getSymmetryInfo, getSymmetryInfoAsString, getSymmetryOperation, getTrajectoryCount, getTrajectoryIndex, getUnitCell, getUnitCellInfoText, growAtomArrays, hasCalculatedHBonds, haveModelKit, initializeBspf, initializeBspt, isAtomAssignable, isAtomPDB, isJmolDataFrame, isTrajectory, isTrajectory, isTrajectorySubFrame, mergeModelArrays, mergeModels, modelFileNumberFromFloat, modelHasVibrationVectors, recalculateLeadMidpointsAndWingVectors, saveModelOrientation, selectDisplayedTrajectories, setAtomNamesAndNumbers, setBoundBox, setConformation, setCrystallographicDefaults, setDefaultStructure, setFrameTitle, setIteratorForAtom, setIteratorForPoint, setJmolDataFrame, setModelAuxiliaryInfo, setProteinType, setRotationRadius, setStructureIds, setStructureList, setUnitCellOffset
addHBond, assignAromaticBonds, assignAromaticBonds, bondAtoms, bondMutually, checkValencesAndBond, deleteConnections, displayBonds, getBondAt, getBondAtom1, getBondAtom2, getBondColix1, getBondColix2, getBondCount, getBondIterator, getBondIterator, getBondModelIndex, getBondOrder, getBondOrder, getBondRadius, getBonds, getBondsForSelectedAtoms, getDefaultMadFromOrder, getRasmolHydrogenBonds, removeUnnecessaryBonds, resetAromatic, resetMolecules, 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, 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 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 Vector3f 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 String getTrajectoryInfo()
public BitSet getBitSetTrajectories()
public void setTrajectory(BitSet bsModels)
public void setTrajectory(int modelIndex)
public BitSet getAtomBits(int tokType, Object specInfo)
getAtomBits
in class ModelCollection
tokType
- specInfo
- public String getAtomLabel(int i)
public int findNearestAtomIndex(int x, int y, BitSet bsNot)
public String calculateStructures(BitSet bsAtoms, boolean asDSSP, boolean dsspIgnoreHydrogen, boolean setStructure)
public String getPointGroupAsString(BitSet bsAtoms, boolean asDraw, String type, int index, float scale)
private Object calculatePointGroupForFirstModel(BitSet bsAtoms, boolean doAll, boolean asDraw, boolean asInfo, String type, int index, float scale)
protected void assignAromaticBonds(boolean isUserCalculation)
public int[] makeConnections(float minDistance, float maxDistance, int order, int connectOperation, BitSet bsA, BitSet bsB, BitSet bsBonds, boolean isBonds, boolean addGroup, float energy)
makeConnections
in class ModelCollection
public void setPdbConectBonding(int baseAtomIndex, int baseModelIndex, BitSet bsExclude)
public void deleteAllBonds()
deleteAllBonds
in class BondCollection
public String getDefinedState(StringBuffer sfunc, boolean isAll)
public String getState(StringBuffer sfunc, boolean isAll, boolean withProteinStructure)
private void includeAllRelatedFrames(BitSet bsModels)
public void setAtomProperty(BitSet bs, int tok, int iValue, float fValue, String sValue, float[] values, String[] list)
setAtomProperty
in class ModelCollection
public Object getFileData(int modelIndex)
public int calculateStruts(BitSet bs1, BitSet bs2)
calculateStruts
in class ModelCollection
bs1
- bs2
- public BitSet addHydrogens(List<Atom> vConnections, Point3f[] pts)
vConnections
- pts
- public void setAtomCoord(BitSet bs, int tokType, Object xyzValues)
setAtomCoord
in class AtomCollection
public void invertSelected(Point3f pt, Point4f plane, int iAtom, BitSet invAtoms, BitSet bs)
public void moveAtoms(Matrix3f mNew, Matrix3f matrixRotate, Vector3f translation, BitSet bs, Point3f center, boolean isInternal)
public void recalculatePositionDependentQuantities(BitSet bs, Matrix4f mat)
public void connect(float[][] connections)
public void createAtomDataSet(int tokType, Object atomSetCollection, BitSet bsSelected)
public boolean allowSpecAtom()