public final class ModelLoader extends ModelSet
ModelCollection.StateScript
AtomCollection.AtomSorter
Modifier and Type | Field and Description |
---|---|
private int |
adapterModelCount |
private int |
adapterTrajectoryCount |
private boolean |
appendNew |
private int |
baseAtomIndex |
private int |
baseGroupIndex |
private int |
baseModelCount |
private int |
baseModelIndex |
private int |
baseTrajectoryCount |
private Chain[] |
chainOf |
private Chain |
currentChain |
private char |
currentChainID |
private java.lang.String |
currentGroup3 |
private char |
currentGroupInsertionCode |
private int |
currentGroupSequenceNumber |
private Model |
currentModel |
private int |
currentModelIndex |
private static int |
defaultGroupCount |
private boolean |
doMinimize |
private java.lang.String |
fileHeader |
private int[] |
firstAtomIndexes |
private int[][] |
group3Counts |
private java.lang.String[] |
group3Lists |
private java.lang.String[] |
group3Of |
private java.util.Map |
htAtomMap |
private boolean |
is2D |
private boolean |
isTrajectory |
private java.lang.String |
jmolData |
private ModelLoader |
mergeModelSet |
private boolean |
merging |
private boolean |
noAutoBond |
private Group |
nullGroup |
private int[] |
seqcodes |
private boolean |
someModelsHaveUnitcells |
private int[] |
specialAtomIndexes |
private java.util.BitSet |
structuresDefinedInFile |
private java.util.List |
vStereo |
closest, modelSetTypeName
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
BOND_GROWTH_INCREMENT, bondCount, bonds, bsAromatic, bsHBondsRasmol, defaultCovalentMad, freeBonds, MAX_BONDS_LENGTH_TO_CACHE, MAX_NUM_TO_CACHE, moleculeCount, molecules, numCached
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
Constructor and Description |
---|
ModelLoader(Viewer viewer,
java.lang.String name) |
ModelLoader(Viewer viewer,
java.lang.StringBuffer loadScript,
java.lang.Object atomSetCollection,
ModelLoader mergeModelSet,
java.lang.String modelSetName,
java.util.BitSet bsNew) |
Modifier and Type | Method and Description |
---|---|
private void |
addAtom(boolean isPDB,
java.util.BitSet atomSymmetry,
int atomSite,
java.lang.Object atomUid,
short atomicAndIsotopeNumber,
java.lang.String atomName,
int formalCharge,
float partialCharge,
java.lang.Object[] ellipsoid,
int occupancy,
float bfactor,
float x,
float y,
float z,
boolean isHetero,
int atomSerial,
char chainID,
java.lang.String group3,
int groupSequenceNumber,
char groupInsertionCode,
float vectorX,
float vectorY,
float vectorZ,
char alternateLocationID,
float radius) |
private void |
addGroup(Chain chain,
Group group) |
private void |
applyStereochemistry() |
private void |
bondAtoms(java.lang.Object atomUid1,
java.lang.Object atomUid2,
short order) |
private void |
checkNewGroup(char chainID,
java.lang.String group3,
int groupSequenceNumber,
char groupInsertionCode) |
private void |
countGroup(int modelIndex,
java.lang.String code,
java.lang.String group3) |
void |
createAtomDataSet(int tokType,
java.lang.Object atomSetCollection,
java.util.BitSet bsSelected) |
private void |
createModelSet(JmolAdapter adapter,
java.lang.Object atomSetCollection,
java.util.BitSet bsNew) |
private void |
defineStructure(int modelIndex,
int subType,
java.lang.String structureID,
int serialID,
int strandCount,
char startChainID,
int startSequenceNumber,
char startInsertionCode,
char endChainID,
int endSequenceNumber,
char endInsertionCode) |
private void |
distinguishAndPropagateGroup(int groupIndex,
Chain chain,
java.lang.String group3,
int seqcode,
int firstAtomIndex,
int maxAtomIndex) |
private void |
finalizeGroupBuild() |
private void |
finalizeModels(int baseModelCount)
Model numbers are considerably more complicated in Jmol 11.
|
private void |
finalizeShapes() |
private void |
findElementsPresent() |
private void |
freeze() |
private java.util.BitSet |
getBranch2dZ(int atomIndex,
int atomIndexNot,
java.util.BitSet bs0,
java.util.BitSet bsBranch,
javax.vecmath.Vector3f v,
javax.vecmath.Vector3f v0,
javax.vecmath.Vector3f v1) |
private Chain |
getOrAllocateChain(Model model,
char chainID) |
private void |
initializeAtomBondModelCounts(int nAtoms) |
private void |
initializeBonding() |
private void |
initializeInfo(java.lang.String name,
java.util.Map info) |
private void |
initializeUnitCellAndSymmetry() |
private void |
iterateOverAllNewAtoms(JmolAdapter adapter,
java.lang.Object atomSetCollection) |
private void |
iterateOverAllNewBonds(JmolAdapter adapter,
java.lang.Object atomSetCollection) |
private void |
iterateOverAllNewModels(JmolAdapter adapter,
java.lang.Object atomSetCollection) |
private void |
iterateOverAllNewStructures(JmolAdapter adapter,
java.lang.Object atomSetCollection)
Pull in all spans of helix, etc.
|
private void |
mergeGroups() |
protected void |
releaseModelSet() |
private void |
set2dZ(int iatom1,
int iatom2) |
private static void |
setAtom2dZ(Atom atomRef,
Atom atom2,
javax.vecmath.Vector3f v,
javax.vecmath.Vector3f v0,
javax.vecmath.Vector3f v1) |
private void |
setAtomProperties() |
private static void |
setBranch2dZ(Atom atom,
java.util.BitSet bs,
java.util.BitSet bsToTest,
javax.vecmath.Vector3f v,
javax.vecmath.Vector3f v0,
javax.vecmath.Vector3f v1) |
private void |
setDefaultRendering(int maxAtoms) |
private boolean |
setModelNameNumberProperties(int modelIndex,
int trajectoryBaseIndex,
java.lang.String modelName,
int modelNumber,
java.util.Properties modelProperties,
java.util.Hashtable modelAuxiliaryInfo,
java.lang.String jmolData) |
addHydrogens, assignAromaticBonds, calculatePointGroup, calculateStructures, calculateStruts, connect, deleteAllBonds, deleteModels, fillAtomData, findNearestAtomIndex, getAtomBits, getAtomLabel, getBitSetTrajectories, getDefinedState, getEchoStateActive, getFileData, getFrameOffsets, getModelNumberIndex, getModelSetTypeName, getPointGroupAsString, getPointGroupInfo, getSelectionHaloEnabled, getState, getTrajectoryInfo, makeConnections, recalculatePositionDependentQuantities, setAtomCoord, setAtomCoordRelative, setAtomProperty, setEchoStateActive, setPdbConectBonding, setSelectionHaloEnabled, setTrajectory, setTrajectory
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
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
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
private ModelLoader mergeModelSet
private boolean merging
private java.lang.String jmolData
private final int[] specialAtomIndexes
private java.lang.String[] group3Lists
private int[][] group3Counts
private boolean someModelsHaveUnitcells
private boolean isTrajectory
private boolean doMinimize
private java.lang.String fileHeader
private final java.util.Map htAtomMap
private static final int defaultGroupCount
private Chain[] chainOf
private java.lang.String[] group3Of
private int[] seqcodes
private int[] firstAtomIndexes
private int currentModelIndex
private Model currentModel
private char currentChainID
private Chain currentChain
private int currentGroupSequenceNumber
private char currentGroupInsertionCode
private java.lang.String currentGroup3
private Group nullGroup
private int baseModelIndex
private int baseModelCount
private int baseAtomIndex
private int baseGroupIndex
private int baseTrajectoryCount
private boolean appendNew
private int adapterModelCount
private int adapterTrajectoryCount
private boolean noAutoBond
private boolean is2D
private java.util.List vStereo
private java.util.BitSet structuresDefinedInFile
public ModelLoader(Viewer viewer, java.lang.String name)
public ModelLoader(Viewer viewer, java.lang.StringBuffer loadScript, java.lang.Object atomSetCollection, ModelLoader mergeModelSet, java.lang.String modelSetName, java.util.BitSet bsNew)
private void initializeInfo(java.lang.String name, java.util.Map info)
private void createModelSet(JmolAdapter adapter, java.lang.Object atomSetCollection, java.util.BitSet bsNew)
private void setDefaultRendering(int maxAtoms)
private void setAtomProperties()
protected void releaseModelSet()
releaseModelSet
in class ModelSet
private void initializeAtomBondModelCounts(int nAtoms)
private void mergeGroups()
private void iterateOverAllNewModels(JmolAdapter adapter, java.lang.Object atomSetCollection)
private boolean setModelNameNumberProperties(int modelIndex, int trajectoryBaseIndex, java.lang.String modelName, int modelNumber, java.util.Properties modelProperties, java.util.Hashtable modelAuxiliaryInfo, java.lang.String jmolData)
private void finalizeModels(int baseModelCount)
baseModelCount
- private void iterateOverAllNewAtoms(JmolAdapter adapter, java.lang.Object atomSetCollection)
private void addAtom(boolean isPDB, java.util.BitSet atomSymmetry, int atomSite, java.lang.Object atomUid, short atomicAndIsotopeNumber, java.lang.String atomName, int formalCharge, float partialCharge, java.lang.Object[] ellipsoid, int occupancy, float bfactor, float x, float y, float z, boolean isHetero, int atomSerial, char chainID, java.lang.String group3, int groupSequenceNumber, char groupInsertionCode, float vectorX, float vectorY, float vectorZ, char alternateLocationID, float radius)
private void checkNewGroup(char chainID, java.lang.String group3, int groupSequenceNumber, char groupInsertionCode)
private void iterateOverAllNewBonds(JmolAdapter adapter, java.lang.Object atomSetCollection)
private void bondAtoms(java.lang.Object atomUid1, java.lang.Object atomUid2, short order)
private void iterateOverAllNewStructures(JmolAdapter adapter, java.lang.Object atomSetCollection)
adapter
- atomSetCollection
- private void defineStructure(int modelIndex, int subType, java.lang.String structureID, int serialID, int strandCount, char startChainID, int startSequenceNumber, char startInsertionCode, char endChainID, int endSequenceNumber, char endInsertionCode)
private void initializeUnitCellAndSymmetry()
private void initializeBonding()
private void finalizeGroupBuild()
private void distinguishAndPropagateGroup(int groupIndex, Chain chain, java.lang.String group3, int seqcode, int firstAtomIndex, int maxAtomIndex)
private void countGroup(int modelIndex, java.lang.String code, java.lang.String group3)
private void freeze()
private void findElementsPresent()
private void applyStereochemistry()
private void set2dZ(int iatom1, int iatom2)
private java.util.BitSet getBranch2dZ(int atomIndex, int atomIndexNot, java.util.BitSet bs0, java.util.BitSet bsBranch, javax.vecmath.Vector3f v, javax.vecmath.Vector3f v0, javax.vecmath.Vector3f v1)
atomIndex
- atomIndexNot
- bs0
- bsBranch
- v
- v0
- v1
- private static void setBranch2dZ(Atom atom, java.util.BitSet bs, java.util.BitSet bsToTest, javax.vecmath.Vector3f v, javax.vecmath.Vector3f v0, javax.vecmath.Vector3f v1)
private static void setAtom2dZ(Atom atomRef, Atom atom2, javax.vecmath.Vector3f v, javax.vecmath.Vector3f v0, javax.vecmath.Vector3f v1)
private void finalizeShapes()
public void createAtomDataSet(int tokType, java.lang.Object atomSetCollection, java.util.BitSet bsSelected)