org.jmol.modelset
Class ModelSet
java.lang.Object
org.jmol.modelset.AtomCollection
org.jmol.modelset.BondCollection
org.jmol.modelset.ModelCollection
org.jmol.modelset.ModelSet
public class ModelSet
- extends ModelCollection
Fields inherited from class org.jmol.modelset.ModelCollection |
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 |
Fields inherited from class org.jmol.modelset.BondCollection |
BOND_GROWTH_INCREMENT, bondCount, bonds, bsAromatic, bsHBondsRasmol, defaultCovalentMad, freeBonds, haveHiddenBonds, 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, 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 |
Method Summary |
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 |
boolean |
allowSpecAtom()
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protected void |
assignAromaticBonds(boolean isUserCalculation)
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java.lang.String |
calculatePointGroup(java.util.BitSet bsAtoms)
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private java.lang.Object |
calculatePointGroupForFirstModel(java.util.BitSet bsAtoms,
boolean doAll,
boolean asDraw,
boolean asInfo,
java.lang.String type,
int index,
float scale)
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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 |
connect(float[][] connections)
|
void |
createAtomDataSet(int tokType,
java.lang.Object atomSetCollection,
java.util.BitSet bsSelected)
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void |
deleteAllBonds()
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java.util.BitSet |
deleteModels(java.util.BitSet bsAtoms)
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int |
findNearestAtomIndex(int x,
int y,
java.util.BitSet bsNot)
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java.util.BitSet |
getAtomBits(int tokType,
java.lang.Object specInfo)
general lookup for integer type -- from Eval |
java.lang.String |
getAtomLabel(int i)
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java.util.BitSet |
getBitSetTrajectories()
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java.lang.String |
getDefaultStructure(java.util.BitSet bsAtoms,
java.util.BitSet bsAllAtoms)
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java.lang.String |
getDefinedState(java.lang.StringBuffer sfunc,
boolean isAll)
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boolean |
getEchoStateActive()
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java.lang.Object |
getFileData(int modelIndex)
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javax.vecmath.Point3f[] |
getFrameOffsets(java.util.BitSet bsAtoms)
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int |
getModelNumberIndex(int modelNumber,
boolean useModelNumber,
boolean doSetTrajectory)
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java.lang.String |
getModelSetTypeName()
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java.lang.String |
getPointGroupAsString(java.util.BitSet bsAtoms,
boolean asDraw,
java.lang.String type,
int index,
float scale)
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java.util.Map<java.lang.String,java.lang.Object> |
getPointGroupInfo(java.util.BitSet bsAtoms)
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boolean |
getSelectionHaloEnabled()
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java.lang.String |
getState(java.lang.StringBuffer sfunc,
boolean isAll,
boolean withProteinStructure)
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java.lang.String |
getTrajectoryInfo()
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private void |
includeAllRelatedFrames(java.util.BitSet bsModels)
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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)
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private java.util.BitSet |
modelsOf(java.util.BitSet bsAtoms,
java.util.BitSet bsAllAtoms)
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void |
moveAtoms(javax.vecmath.Matrix3f mNew,
javax.vecmath.Matrix3f matrixRotate,
javax.vecmath.Vector3f translation,
java.util.BitSet bs,
javax.vecmath.Point3f center,
boolean isInternal)
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void |
recalculatePositionDependentQuantities(java.util.BitSet bs,
javax.vecmath.Matrix4f mat)
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protected void |
releaseModelSet()
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void |
setAtomCoord(java.util.BitSet bs,
int tokType,
java.lang.Object xyzValues)
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void |
setAtomCoordRelative(javax.vecmath.Tuple3f offset,
java.util.BitSet bs)
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void |
setAtomProperty(java.util.BitSet bs,
int tok,
int iValue,
float fValue,
java.lang.String sValue,
float[] values,
java.lang.String[] list)
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void |
setEchoStateActive(boolean TF)
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void |
setPdbConectBonding(int baseAtomIndex,
int baseModelIndex,
java.util.BitSet bsExclude)
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void |
setSelectionHaloEnabled(boolean selectionHaloEnabled)
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void |
setTrajectory(java.util.BitSet bsModels)
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void |
setTrajectory(int modelIndex)
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Methods inherited from class org.jmol.modelset.ModelCollection |
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 |
Methods inherited from class org.jmol.modelset.BondCollection |
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 |
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, 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 |
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 java.lang.String modelSetTypeName
closest
protected final Atom[] closest
pointGroup
private SymmetryInterface pointGroup
matTemp
private final javax.vecmath.Matrix3f matTemp
matInv
private final javax.vecmath.Matrix3f matInv
mat4
private final javax.vecmath.Matrix4f mat4
mat4t
private final javax.vecmath.Matrix4f mat4t
vTemp
private final javax.vecmath.Vector3f vTemp
ModelSet
public ModelSet(Viewer viewer,
java.lang.String name)
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 java.lang.String getModelSetTypeName()
getModelNumberIndex
public int getModelNumberIndex(int modelNumber,
boolean useModelNumber,
boolean doSetTrajectory)
getTrajectoryInfo
public java.lang.String getTrajectoryInfo()
getBitSetTrajectories
public java.util.BitSet getBitSetTrajectories()
setTrajectory
public void setTrajectory(java.util.BitSet bsModels)
setTrajectory
public void setTrajectory(int modelIndex)
getFrameOffsets
public javax.vecmath.Point3f[] getFrameOffsets(java.util.BitSet bsAtoms)
getAtomBits
public java.util.BitSet getAtomBits(int tokType,
java.lang.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 java.lang.String getAtomLabel(int i)
findNearestAtomIndex
public int findNearestAtomIndex(int x,
int y,
java.util.BitSet bsNot)
calculateStructures
public java.lang.String calculateStructures(java.util.BitSet bsAtoms,
boolean asDSSP,
boolean dsspIgnoreHydrogen,
boolean setStructure)
calculatePointGroup
public java.lang.String calculatePointGroup(java.util.BitSet bsAtoms)
getPointGroupInfo
public java.util.Map<java.lang.String,java.lang.Object> getPointGroupInfo(java.util.BitSet bsAtoms)
getPointGroupAsString
public java.lang.String getPointGroupAsString(java.util.BitSet bsAtoms,
boolean asDraw,
java.lang.String type,
int index,
float scale)
calculatePointGroupForFirstModel
private java.lang.Object calculatePointGroupForFirstModel(java.util.BitSet bsAtoms,
boolean doAll,
boolean asDraw,
boolean asInfo,
java.lang.String type,
int index,
float scale)
modelsOf
private java.util.BitSet modelsOf(java.util.BitSet bsAtoms,
java.util.BitSet bsAllAtoms)
getDefaultStructure
public java.lang.String getDefaultStructure(java.util.BitSet bsAtoms,
java.util.BitSet bsAllAtoms)
assignAromaticBonds
protected void assignAromaticBonds(boolean isUserCalculation)
makeConnections
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)
- Overrides:
makeConnections
in class ModelCollection
setPdbConectBonding
public void setPdbConectBonding(int baseAtomIndex,
int baseModelIndex,
java.util.BitSet bsExclude)
deleteAllBonds
public void deleteAllBonds()
- Overrides:
deleteAllBonds
in class BondCollection
getDefinedState
public java.lang.String getDefinedState(java.lang.StringBuffer sfunc,
boolean isAll)
getState
public java.lang.String getState(java.lang.StringBuffer sfunc,
boolean isAll,
boolean withProteinStructure)
includeAllRelatedFrames
private void includeAllRelatedFrames(java.util.BitSet bsModels)
deleteModels
public java.util.BitSet deleteModels(java.util.BitSet bsAtoms)
setAtomProperty
public void setAtomProperty(java.util.BitSet bs,
int tok,
int iValue,
float fValue,
java.lang.String sValue,
float[] values,
java.lang.String[] list)
- Overrides:
setAtomProperty
in class ModelCollection
getFileData
public java.lang.Object getFileData(int modelIndex)
calculateStruts
public 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.
The two bitsets may overlap.
- Overrides:
calculateStruts
in class ModelCollection
- Parameters:
bs1
- bs2
-
- Returns:
- number of struts found
addHydrogens
public 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
- Parameters:
vConnections
- pts
-
- Returns:
- BitSet of new atoms
setAtomCoordRelative
public void setAtomCoordRelative(javax.vecmath.Tuple3f offset,
java.util.BitSet bs)
setAtomCoord
public void setAtomCoord(java.util.BitSet bs,
int tokType,
java.lang.Object xyzValues)
- Overrides:
setAtomCoord
in class AtomCollection
invertSelected
public void invertSelected(javax.vecmath.Point3f pt,
javax.vecmath.Point4f plane,
int iAtom,
java.util.BitSet invAtoms,
java.util.BitSet bs)
moveAtoms
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)
recalculatePositionDependentQuantities
public void recalculatePositionDependentQuantities(java.util.BitSet bs,
javax.vecmath.Matrix4f mat)
connect
public void connect(float[][] connections)
createAtomDataSet
public void createAtomDataSet(int tokType,
java.lang.Object atomSetCollection,
java.util.BitSet bsSelected)
allowSpecAtom
public boolean allowSpecAtom()