org.jmol.modelset
Class ModelSet
java.lang.Object
org.jmol.modelset.AtomCollection
org.jmol.modelset.BondCollection
org.jmol.modelset.ModelCollection
org.jmol.modelset.ModelSet
- Direct Known Subclasses:
- ModelLoader
public abstract class ModelSet
- extends ModelCollection
Fields inherited from class org.jmol.modelset.ModelCollection |
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 |
Fields inherited from class org.jmol.modelset.BondCollection |
BOND_GROWTH_INCREMENT, bondCount, bonds, bsAromatic, bsHBondsRasmol, defaultCovalentMad, freeBonds, MAX_BONDS_LENGTH_TO_CACHE, MAX_NUM_TO_CACHE, moleculeCount, molecules, numCached |
Fields inherited from class org.jmol.modelset.AtomCollection |
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 |
Method Summary |
BitSet |
addHydrogens(List 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 |
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 |
deleteAllBonds()
|
BitSet |
deleteModels(BitSet bsAtoms)
|
void |
fillAtomData(AtomData atomData,
int mode)
|
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 |
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)
|
Hashtable |
getPointGroupInfo(BitSet bsAtoms)
|
boolean |
getSelectionHaloEnabled()
|
private BitSet |
getSpecModel(int modelNumber)
|
String |
getState(StringBuffer sfunc,
boolean isAll,
boolean withProteinStructure)
|
String |
getTrajectoryInfo()
|
private void |
includeAllRelatedFrames(BitSet bsModels)
|
int[] |
makeConnections(float minDistance,
float maxDistance,
int order,
int connectOperation,
BitSet bsA,
BitSet bsB,
BitSet bsBonds,
boolean isBonds,
float energy)
|
private BitSet |
modelsOf(BitSet bsAtoms,
BitSet bsAllAtoms)
|
void |
recalculatePositionDependentQuantities(BitSet bs)
|
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)
|
Methods inherited from class org.jmol.modelset.ModelCollection |
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 |
Methods inherited from class org.jmol.modelset.BondCollection |
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 |
Methods inherited from class org.jmol.modelset.AtomCollection |
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 |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
selectionHaloEnabled
private boolean selectionHaloEnabled
echoShapeActive
private boolean echoShapeActive
modelSetTypeName
protected String modelSetTypeName
closest
protected final Atom[] closest
pointGroup
private SymmetryInterface pointGroup
ModelSet
public ModelSet()
releaseModelSet
protected void releaseModelSet()
- Overrides:
releaseModelSet
in class ModelCollection
setSelectionHaloEnabled
public void setSelectionHaloEnabled(boolean selectionHaloEnabled)
getSelectionHaloEnabled
public boolean getSelectionHaloEnabled()
getEchoStateActive
public boolean getEchoStateActive()
setEchoStateActive
public void setEchoStateActive(boolean TF)
getModelSetTypeName
public String getModelSetTypeName()
getModelNumberIndex
public int getModelNumberIndex(int modelNumber,
boolean useModelNumber,
boolean doSetTrajectory)
getTrajectoryInfo
public String getTrajectoryInfo()
getBitSetTrajectories
public BitSet getBitSetTrajectories()
setTrajectory
public void setTrajectory(BitSet bsModels)
setTrajectory
public void setTrajectory(int modelIndex)
getFrameOffsets
public Point3f[] getFrameOffsets(BitSet bsAtoms)
getAtomBits
public BitSet getAtomBits(int tokType,
Object specInfo)
- general lookup for integer type -- from Eval
- Overrides:
getAtomBits
in class ModelCollection
- Parameters:
tokType
- specInfo
-
- Returns:
- bitset; null only if we mess up with name
getAtomLabel
public String getAtomLabel(int i)
getSpecModel
private BitSet getSpecModel(int modelNumber)
findNearestAtomIndex
public int findNearestAtomIndex(int x,
int y,
BitSet bsNot)
fillAtomData
public void fillAtomData(AtomData atomData,
int mode)
- Overrides:
fillAtomData
in class AtomCollection
calculateStructures
public String calculateStructures(BitSet bsAtoms,
boolean asDSSP,
boolean dsspIgnoreHydrogen,
boolean setStructure)
calculatePointGroup
public String calculatePointGroup(BitSet bsAtoms)
getPointGroupInfo
public Hashtable getPointGroupInfo(BitSet bsAtoms)
getPointGroupAsString
public String getPointGroupAsString(BitSet bsAtoms,
boolean asDraw,
String type,
int index,
float scale)
calculatePointGroupForFirstModel
private Object calculatePointGroupForFirstModel(BitSet bsAtoms,
boolean doAll,
boolean asDraw,
boolean asInfo,
String type,
int index,
float scale)
modelsOf
private BitSet modelsOf(BitSet bsAtoms,
BitSet bsAllAtoms)
assignAromaticBonds
protected void assignAromaticBonds(boolean isUserCalculation)
makeConnections
public int[] makeConnections(float minDistance,
float maxDistance,
int order,
int connectOperation,
BitSet bsA,
BitSet bsB,
BitSet bsBonds,
boolean isBonds,
float energy)
- Overrides:
makeConnections
in class ModelCollection
setPdbConectBonding
public void setPdbConectBonding(int baseAtomIndex,
int baseModelIndex,
BitSet bsExclude)
deleteAllBonds
public void deleteAllBonds()
- Overrides:
deleteAllBonds
in class BondCollection
getDefinedState
public String getDefinedState(StringBuffer sfunc,
boolean isAll)
getState
public String getState(StringBuffer sfunc,
boolean isAll,
boolean withProteinStructure)
includeAllRelatedFrames
private void includeAllRelatedFrames(BitSet bsModels)
deleteModels
public BitSet deleteModels(BitSet bsAtoms)
setAtomProperty
public void setAtomProperty(BitSet bs,
int tok,
int iValue,
float fValue,
String sValue,
float[] values,
String[] list)
- Overrides:
setAtomProperty
in class ModelCollection
getFileData
public Object getFileData(int modelIndex)
calculateStruts
public 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.
The two bitsets may overlap.
- Overrides:
calculateStruts
in class ModelCollection
- Parameters:
bs1
- bs2
-
- Returns:
- number of struts found
addHydrogens
public BitSet addHydrogens(List 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
- Parameters:
vConnections
- pts
-
- Returns:
- BitSet of new atoms
setAtomCoordRelative
public void setAtomCoordRelative(Tuple3f offset,
BitSet bs)
setAtomCoord
public void setAtomCoord(BitSet bs,
int tokType,
Object xyzValues)
- Overrides:
setAtomCoord
in class AtomCollection
recalculatePositionDependentQuantities
public void recalculatePositionDependentQuantities(BitSet bs)
connect
public void connect(float[][] connections)