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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.jmol.modelset.AtomCollection
org.jmol.modelset.BondCollection
org.jmol.modelset.ModelCollection
public abstract class ModelCollection
Nested Class Summary | |
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static class |
ModelCollection.StateScript
|
Nested classes/interfaces inherited from class org.jmol.modelset.AtomCollection |
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AtomCollection.AtomSorter |
Field Summary | |
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private javax.vecmath.Point3f |
averageAtomPoint
|
private java.util.BitSet |
bboxAtoms
|
private java.util.BitSet |
bboxModels
|
private BoxInfo |
boxInfo
|
protected java.util.BitSet |
bsAll
|
protected java.util.BitSet |
bsSymmetry
|
protected java.util.BitSet[] |
elementsPresent
|
protected java.lang.String[] |
frameTitles
|
protected int |
groupCount
|
protected Group[] |
groups
|
protected boolean |
haveBioClasses
|
private static float |
hbondMin
|
private boolean |
isBbcageDefault
|
protected boolean |
isPDB
|
protected boolean |
isXYZ
|
protected JmolBioResolver |
jbr
|
private javax.vecmath.Matrix3f |
matInv
|
private javax.vecmath.Matrix3f |
matTemp
|
protected int |
modelCount
|
protected int[] |
modelFileNumbers
|
protected java.lang.String[] |
modelNames
|
protected int[] |
modelNumbers
|
protected java.lang.String[] |
modelNumbersForAtomLabel
|
protected Model[] |
models
|
protected java.util.Hashtable |
modelSetAuxiliaryInfo
|
protected java.lang.String |
modelSetName
|
protected java.util.Properties |
modelSetProperties
|
private static java.lang.String[] |
pdbRecords
|
(package private) boolean |
proteinStructureTainted
|
private javax.vecmath.Point3f |
ptTemp
|
private int |
selectedMoleculeCount
|
private java.util.BitSet |
selectedMolecules
|
protected ShapeManager |
shapeManager
|
private static boolean |
showRebondTimes
|
protected boolean |
someModelsHaveAromaticBonds
|
protected boolean |
someModelsHaveFractionalCoordinates
|
protected boolean |
someModelsHaveSymmetry
|
protected java.util.List |
stateScripts
|
private SymmetryInterface |
symTemp
|
private int |
thisStateModel
|
protected java.util.List |
trajectorySteps
|
(package private) SymmetryInterface[] |
unitCells
|
Fields inherited from class org.jmol.modelset.BondCollection |
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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 |
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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 Summary | |
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ModelCollection()
|
Method Summary | |
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protected Atom |
addAtom(int modelIndex,
Group group,
short atomicAndIsotopeNumber,
java.lang.String atomName,
int atomSerial,
int atomSite,
float x,
float y,
float z)
|
protected Atom |
addAtom(int modelIndex,
Group group,
short atomicAndIsotopeNumber,
java.lang.String atomName,
int atomSerial,
int atomSite,
float x,
float y,
float z,
float radius,
float vectorX,
float vectorY,
float vectorZ,
int formalCharge,
float partialCharge,
int occupancy,
float bfactor,
java.lang.Object[] ellipsoid,
boolean isHetero,
char alternateLocationID,
byte specialAtomID,
java.util.BitSet atomSymmetry)
|
protected void |
addBioPolymerToModel(Polymer polymer,
Model model)
|
private boolean |
addMolFile(java.lang.StringBuffer mol,
java.util.BitSet bsAtoms,
java.util.BitSet bsBonds,
boolean asV3000,
Quaternion q)
|
ModelCollection.StateScript |
addStateScript(java.lang.String script1,
java.util.BitSet bsBonds,
java.util.BitSet bsAtoms1,
java.util.BitSet bsAtoms2,
java.lang.String script2,
boolean addFrameNumber,
boolean postDefinitions)
|
void |
appendLoadStates(java.lang.StringBuffer commands)
|
void |
assignAtom(int atomIndex,
java.lang.String type,
boolean autoBond)
|
private int |
autoBond_Pre_11_9_24(java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsExclude,
java.util.BitSet bsBonds,
short mad)
|
int |
autoBond(java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsExclude,
java.util.BitSet bsBonds,
short mad,
boolean preJmol11_9_24)
|
private int[] |
autoBond(int order,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds,
boolean isBonds,
boolean matchHbond)
|
int |
autoHbond(java.util.BitSet bsA,
java.util.BitSet bsB)
a generalized formation of HBONDS, carried out in relation to calculate HBONDS {atomsFrom} {atomsTo}. |
int |
calcAtomsMinMax(java.util.BitSet bs,
BoxInfo boxInfo)
|
void |
calcBoundBoxDimensions(java.util.BitSet bs,
float scale)
|
void |
calcRasmolHydrogenBonds(java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.List vHBonds,
boolean nucleicOnly,
int nMax,
boolean dsspIgnoreHydrogens)
These are not actual hydrogen bonds. |
float |
calcRotationRadius(java.util.BitSet bs)
|
float |
calcRotationRadius(int modelIndex,
javax.vecmath.Point3f center)
|
void |
calcSelectedGroupsCount(java.util.BitSet bsSelected)
|
void |
calcSelectedMoleculesCount(java.util.BitSet bsSelected)
|
void |
calcSelectedMonomersCount(java.util.BitSet bsSelected)
|
javax.vecmath.Vector3f |
calculateMolecularDipole(int modelIndex)
|
protected void |
calculatePolymers(int baseGroupIndex,
java.util.BitSet alreadyDefined)
|
void |
calculateStraightness()
|
protected java.lang.String |
calculateStructuresAllExcept(java.util.BitSet alreadyDefined,
boolean asDSSP,
boolean doReport,
boolean dsspIgnoreHydrogen,
boolean setStructure,
boolean includeAlpha)
allows rebuilding of PDB structures; also accessed by ModelManager from Eval |
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. |
private void |
calcUnitCellMinMax()
|
private static javax.vecmath.Point3f |
checkMinAttachedAngle(Atom atom1,
float minAngle,
javax.vecmath.Vector3f v1,
javax.vecmath.Vector3f v2,
boolean haveHAtoms)
|
protected void |
clearDataFrameReference(int modelIndex)
|
void |
clearRasmolHydrogenBonds(int baseIndex,
java.util.BitSet bsAtoms)
|
void |
deleteAtoms(java.util.BitSet bs)
|
void |
deleteBonds(java.util.BitSet bsBonds,
boolean isFullModel)
|
protected void |
deleteModel(int modelIndex,
int firstAtomIndex,
int nAtoms,
java.util.BitSet bsAtoms,
java.util.BitSet bsBonds)
|
private void |
freezeModels()
|
java.util.List |
getAllAtomInfo(java.util.BitSet bs)
|
java.util.List |
getAllBondInfo(java.util.BitSet bs)
|
java.util.Hashtable |
getAllChainInfo(java.util.BitSet bs)
|
java.util.Hashtable |
getAllPolymerInfo(java.util.BitSet bs)
|
int |
getAltLocCountInModel(int modelIndex)
|
int |
getAltLocIndexInModel(int modelIndex,
char alternateLocationID)
|
java.lang.String |
getAltLocListInModel(int modelIndex)
|
java.util.BitSet |
getAtomBits(int tokType,
java.lang.Object specInfo)
general unqualified lookup of atom set type |
int |
getAtomCountInModel(int modelIndex)
|
Quaternion[] |
getAtomGroupQuaternions(java.util.BitSet bsAtoms,
int nMax,
char qtype)
|
void |
getAtomIdentityInfo(int i,
java.util.Hashtable info)
|
private java.util.Hashtable |
getAtomInfoLong(int i)
|
private void |
getAtomRecordMOL(java.lang.StringBuffer sb,
int i,
Atom a,
Quaternion q,
javax.vecmath.Point3f pTemp,
boolean asV3000)
|
private static void |
getAtomResidueInfo(java.lang.StringBuffer info,
Atom atom)
|
java.util.BitSet |
getAtomsConnected(float min,
float max,
int intType,
java.util.BitSet bs)
|
javax.vecmath.Point3f |
getAtomSetCenter(java.util.BitSet bs)
|
java.util.BitSet |
getAtomsWithin(float distance,
java.util.BitSet bs,
boolean withinAllModels)
Get atoms within a specific distance of any atom in a specific set of atoms either within all models or within just the model(s) of those atoms |
java.util.BitSet |
getAtomsWithin(float distance,
javax.vecmath.Point3f coord,
java.util.BitSet bsResult,
int modelIndex)
|
java.util.Hashtable |
getAuxiliaryInfo(java.util.BitSet bsModels)
|
javax.vecmath.Point3f |
getAverageAtomPoint()
|
private java.util.BitSet |
getBasePairBits(java.lang.String specInfo)
|
private java.lang.String |
getBasePairInfo(java.util.BitSet bs)
|
Point3fi[] |
getBboxVertices()
|
int |
getBioPolymerCount()
|
int |
getBioPolymerCountInModel(int modelIndex)
|
int |
getBondCountInModel(int modelIndex)
for general use |
private java.util.Hashtable |
getBondInfo(int i)
|
private void |
getBondRecordMOL(int n,
java.lang.StringBuffer sb,
int i,
int[] atomMap,
boolean asV3000)
|
javax.vecmath.Point3f |
getBoundBoxCenter(int modelIndex)
|
java.lang.String |
getBoundBoxCommand(boolean withOptions)
|
javax.vecmath.Vector3f |
getBoundBoxCornerVector()
|
java.util.Hashtable |
getBoundBoxInfo()
|
java.util.BitSet |
getBoundBoxModels()
|
BoxInfo |
getBoxInfo(java.util.BitSet bs,
float scale)
|
SymmetryInterface[] |
getCellInfos()
|
javax.vecmath.Point3f[][] |
getCenterAndPoints(java.util.List vAtomSets,
boolean addCenters)
|
int |
getChainCount(boolean addWater)
|
int |
getChainCountInModel(int modelIndex,
boolean countWater)
|
private java.util.List |
getChainInfo(int modelIndex,
java.util.BitSet bs)
|
java.lang.String |
getChimeInfo(int tok,
java.util.BitSet bs)
|
java.util.BitSet |
getConformation(int modelIndex,
int conformationIndex,
boolean doSet)
|
private java.util.BitSet |
getCovalentBondsForAtoms(java.util.BitSet bsAtoms)
|
int |
getDefaultVdwType(int modelIndex)
|
java.util.BitSet |
getElementsPresentBitSet(int modelIndex)
|
java.lang.String |
getFileHeader(int modelIndex)
|
java.lang.String |
getFrameTitle(int modelIndex)
|
private java.lang.String |
getFullPDBHeader(int modelIndex)
|
int |
getGroupAtom(Atom atom,
int offset,
java.lang.String name)
|
int |
getGroupCount()
|
int |
getGroupCountInModel(int modelIndex)
|
java.util.BitSet |
getGroupsWithin(int nResidues,
java.util.BitSet bs)
|
java.util.Hashtable |
getHeteroList(int modelIndex)
|
java.lang.String |
getInlineData(int modelIndex)
|
int |
getInsertionCodeIndexInModel(int modelIndex,
char insertionCode)
|
int |
getInsertionCountInModel(int modelIndex)
|
private java.lang.String |
getInsertionListInModel(int modelIndex)
|
java.util.BitSet |
getIterativeModels(boolean allowJmolData)
only some models can be iterated through. |
int |
getJmolDataFrameIndex(int modelIndex,
java.lang.String type)
|
int |
getJmolDataSourceFrame(int modelIndex)
|
java.lang.String |
getJmolFrameType(int modelIndex)
|
java.util.BitSet |
getModelAtomBitSetIncludingDeleted(java.util.BitSet bsModels)
note -- this method returns ALL atoms, including deleted. |
java.util.BitSet |
getModelAtomBitSetIncludingDeleted(int modelIndex,
boolean asCopy)
Note that this method returns all atoms, included deleted ones. |
java.util.Hashtable |
getModelAuxiliaryInfo(int modelIndex)
|
java.lang.Object |
getModelAuxiliaryInfo(int modelIndex,
java.lang.String key)
|
protected boolean |
getModelAuxiliaryInfoBoolean(int modelIndex,
java.lang.String keyName)
|
protected int |
getModelAuxiliaryInfoInt(int modelIndex,
java.lang.String keyName)
|
java.util.BitSet |
getModelBitSet(java.util.BitSet atomList,
boolean allTrajectories)
|
int[] |
getModelCellRange(int modelIndex)
|
java.lang.String |
getModelCml(java.util.BitSet bs,
int atomsMax,
boolean addBonds)
|
int |
getModelCount()
|
javax.vecmath.Vector3f |
getModelDipole(int modelIndex)
|
java.lang.String |
getModelExtract(java.util.BitSet bs,
boolean doTransform,
boolean isModelKit,
boolean asSDF,
boolean asV3000)
|
java.lang.String |
getModelFileInfo(java.util.BitSet frames)
|
java.lang.String |
getModelFileName(int modelIndex)
|
int |
getModelFileNumber(int modelIndex)
|
java.lang.String |
getModelFileType(int modelIndex)
|
java.util.Hashtable |
getModelInfo(java.util.BitSet bsModels)
|
java.lang.String |
getModelInfoAsString()
|
java.util.BitSet |
getModelKitStateBitset(java.util.BitSet bs,
java.util.BitSet bsDeleted)
|
java.lang.String |
getModelName(int modelIndex)
|
int |
getModelNumber(int modelIndex)
|
java.lang.String |
getModelNumberDotted(int modelIndex)
|
java.lang.String |
getModelNumberForAtomLabel(int modelIndex)
|
StateManager.Orientation |
getModelOrientation(int modelIndex)
|
java.util.Properties |
getModelProperties(int modelIndex)
|
java.lang.String |
getModelProperty(int modelIndex,
java.lang.String property)
|
Model[] |
getModels()
|
java.util.Hashtable |
getModelSetAuxiliaryInfo()
|
java.lang.Object |
getModelSetAuxiliaryInfo(java.lang.String keyName)
|
protected boolean |
getModelSetAuxiliaryInfoBoolean(java.lang.String keyName)
|
java.lang.String |
getModelSetName()
|
java.util.Properties |
getModelSetProperties()
|
java.lang.String |
getModelSetProperty(java.lang.String propertyName)
|
int |
getModelSymmetryCount(int modelIndex)
|
java.lang.String |
getModelTitle(int modelIndex)
|
java.lang.String |
getMoInfo(int modelIndex)
|
java.util.BitSet |
getMoleculeBitSet(java.util.BitSet bs)
|
java.util.BitSet |
getMoleculeBitSet(int atomIndex)
|
int |
getMoleculeCountInModel(int modelIndex)
|
int |
getMoleculeIndex(int atomIndex)
|
java.util.List |
getMoleculeInfo(java.util.BitSet bsAtoms)
|
JmolMolecule[] |
getMolecules()
|
float[] |
getNotionalUnitcell()
deprecated due to multimodel issues, but required by an interface -- do NOT remove. |
java.lang.String |
getPdbAtomData(java.util.BitSet bs,
OutputStringBuffer sb)
|
java.lang.String |
getPdbData(int modelIndex,
java.lang.String type,
java.util.BitSet bsSelected,
java.lang.Object[] parameters,
OutputStringBuffer sb)
|
java.lang.String |
getPDBHeader(int modelIndex)
|
java.util.List |
getPlaneIntersection(int type,
javax.vecmath.Point4f plane,
float scale,
int flags,
int modelIndex)
|
javax.vecmath.Point3f[] |
getPolymerLeadMidPoints(int iModel,
int iPolymer)
|
void |
getPolymerPointsAndVectors(java.util.BitSet bs,
java.util.List vList)
|
java.lang.String |
getProteinStructureState(java.util.BitSet bsAtoms,
boolean taintedOnly,
boolean needPhiPsi,
boolean pdbFormat)
|
AtomIndexIterator |
getSelectedAtomIterator(java.util.BitSet bsSelected,
boolean isGreaterOnly,
boolean modelZeroBased,
boolean hemisphereOnly)
|
java.util.BitSet |
getSequenceBits(java.lang.String specInfo,
java.util.BitSet bs)
|
java.util.Hashtable |
getSpaceGroupInfo(int modelIndex,
java.lang.String spaceGroup,
int symOp,
javax.vecmath.Point3f pt1,
javax.vecmath.Point3f pt2,
java.lang.String drawID)
|
java.lang.Object |
getSymmetryInfo(java.util.BitSet bsAtoms,
java.lang.String xyz,
int op,
javax.vecmath.Point3f pt,
javax.vecmath.Point3f pt2,
java.lang.String id,
int type)
|
java.lang.String |
getSymmetryInfoAsString()
|
private java.lang.String |
getSymmetryInfoAsString(int modelIndex)
|
java.lang.String |
getSymmetryOperation(int modelIndex,
java.lang.String spaceGroup,
int symOp,
javax.vecmath.Point3f pt1,
javax.vecmath.Point3f pt2,
java.lang.String drawID,
boolean labelOnly)
|
private void |
getSymTemp(boolean forceNew)
|
protected int |
getTrajectoryCount()
|
int |
getTrajectoryIndex(int modelIndex)
|
SymmetryInterface |
getUnitCell(int modelIndex)
|
java.lang.String |
getUnitCellInfoText()
|
protected void |
growAtomArrays(int newLength)
|
boolean |
hasCalculatedHBonds(java.util.BitSet bs)
|
boolean |
haveModelKit()
|
protected void |
initializeBspf()
|
protected void |
initializeBspt(int modelIndex)
|
void |
invertSelected(javax.vecmath.Point3f pt,
javax.vecmath.Point4f plane,
int iAtom,
java.util.BitSet invAtoms,
java.util.BitSet bs)
|
boolean |
isAtomAssignable(int i)
|
boolean |
isAtomPDB(int i)
|
private boolean |
isInLatticeCell(int i,
javax.vecmath.Point3f cell,
javax.vecmath.Point3f pt,
boolean isAbsolute)
|
private boolean |
isJmolDataFrame(Atom atom)
|
boolean |
isJmolDataFrame(int modelIndex)
|
boolean |
isTrajectory(int modelIndex)
|
boolean |
isTrajectory(int[] countPlusIndices)
|
protected boolean |
isTrajectorySubFrame(int i)
|
protected int[] |
makeConnections(float minDistance,
float maxDistance,
int order,
int connectOperation,
java.util.BitSet bsA,
java.util.BitSet bsB,
java.util.BitSet bsBonds,
boolean isBonds,
float energy)
|
protected void |
mergeModelArrays(ModelSet mergeModelSet)
initial transfer of model data from old to new model set. |
protected void |
mergeModels(ModelSet mergeModelSet)
|
static int |
modelFileNumberFromFloat(float fDotM)
|
boolean |
modelHasVibrationVectors(int modelIndex)
|
void |
recalculateLeadMidpointsAndWingVectors(int modelIndex)
|
protected void |
releaseModelSet()
|
void |
rotateAtoms(javax.vecmath.Matrix3f mNew,
javax.vecmath.Matrix3f matrixRotate,
java.util.BitSet bsAtoms,
boolean fullMolecule,
javax.vecmath.Point3f center,
boolean isInternal)
|
void |
saveModelOrientation(int modelIndex,
StateManager.Orientation orientation)
|
void |
selectDisplayedTrajectories(java.util.BitSet bs)
|
void |
setAtomNamesAndNumbers(int iFirst,
int baseAtomIndex,
AtomCollection mergeSet)
|
void |
setAtomProperty(java.util.BitSet bs,
int tok,
int iValue,
float fValue,
java.lang.String sValue,
float[] values,
java.lang.String[] list)
|
void |
setBoundBox(javax.vecmath.Point3f pt1,
javax.vecmath.Point3f pt2,
boolean byCorner,
float scale)
|
java.util.BitSet |
setConformation(java.util.BitSet bsAtoms)
|
boolean |
setCrystallographicDefaults()
|
void |
setFrameTitle(java.util.BitSet bsFrames,
java.lang.String title)
|
void |
setIteratorForAtom(AtomIndexIterator iterator,
int modelIndex,
int atomIndex,
float distance)
|
void |
setIteratorForPoint(AtomIndexIterator iterator,
int modelIndex,
javax.vecmath.Point3f pt,
float distance)
|
void |
setJmolDataFrame(java.lang.String type,
int modelIndex,
int modelDataIndex)
|
void |
setModelAuxiliaryInfo(int modelIndex,
java.lang.Object key,
java.lang.Object value)
|
void |
setProteinType(java.util.BitSet bs,
byte iType)
|
boolean |
setRotationRadius(int modelIndex,
float angstroms)
|
(package private) void |
setStructureIds()
|
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
---|
protected java.util.BitSet bsSymmetry
protected java.lang.String modelSetName
protected Model[] models
protected int modelCount
SymmetryInterface[] unitCells
protected int[] modelNumbers
protected int[] modelFileNumbers
protected java.lang.String[] modelNumbersForAtomLabel
protected java.lang.String[] modelNames
protected java.lang.String[] frameTitles
protected java.util.BitSet[] elementsPresent
protected boolean isXYZ
protected boolean isPDB
protected java.util.Properties modelSetProperties
protected java.util.Hashtable modelSetAuxiliaryInfo
protected Group[] groups
protected int groupCount
protected boolean haveBioClasses
protected JmolBioResolver jbr
protected boolean someModelsHaveSymmetry
protected boolean someModelsHaveAromaticBonds
protected boolean someModelsHaveFractionalCoordinates
private final javax.vecmath.Matrix3f matTemp
private final javax.vecmath.Matrix3f matInv
private final javax.vecmath.Point3f ptTemp
private final javax.vecmath.Point3f averageAtomPoint
private boolean isBbcageDefault
private java.util.BitSet bboxModels
private java.util.BitSet bboxAtoms
private final BoxInfo boxInfo
protected java.util.List stateScripts
private int thisStateModel
protected java.util.List trajectorySteps
private static final java.lang.String[] pdbRecords
private java.util.BitSet selectedMolecules
private int selectedMoleculeCount
private static final boolean showRebondTimes
protected java.util.BitSet bsAll
protected ShapeManager shapeManager
private static float hbondMin
boolean proteinStructureTainted
private SymmetryInterface symTemp
Constructor Detail |
---|
public ModelCollection()
Method Detail |
---|
protected void mergeModelArrays(ModelSet mergeModelSet)
mergeModelSet
- protected void mergeModels(ModelSet mergeModelSet)
protected void releaseModelSet()
releaseModelSet
in class BondCollection
public java.lang.String getModelSetName()
public Model[] getModels()
public int getModelCount()
public SymmetryInterface[] getCellInfos()
public SymmetryInterface getUnitCell(int modelIndex)
public java.util.List getPlaneIntersection(int type, javax.vecmath.Point4f plane, float scale, int flags, int modelIndex)
type
- plane
- scale
- modelIndex
- flags
- 1 -- edges only 2 -- triangles only 3 -- both
public java.lang.String getModelName(int modelIndex)
public java.lang.String getModelTitle(int modelIndex)
public java.lang.String getModelFileName(int modelIndex)
public void setFrameTitle(java.util.BitSet bsFrames, java.lang.String title)
public java.lang.String getFrameTitle(int modelIndex)
public java.lang.String getModelNumberForAtomLabel(int modelIndex)
protected void calculatePolymers(int baseGroupIndex, java.util.BitSet alreadyDefined)
protected void addBioPolymerToModel(Polymer polymer, Model model)
public float[] getNotionalUnitcell()
public boolean setCrystallographicDefaults()
public javax.vecmath.Point3f getAverageAtomPoint()
public javax.vecmath.Point3f getBoundBoxCenter(int modelIndex)
public javax.vecmath.Vector3f getBoundBoxCornerVector()
public Point3fi[] getBboxVertices()
public java.util.Hashtable getBoundBoxInfo()
public java.util.BitSet getBoundBoxModels()
public void setBoundBox(javax.vecmath.Point3f pt1, javax.vecmath.Point3f pt2, boolean byCorner, float scale)
public java.lang.String getBoundBoxCommand(boolean withOptions)
public int getDefaultVdwType(int modelIndex)
public boolean setRotationRadius(int modelIndex, float angstroms)
public float calcRotationRadius(int modelIndex, javax.vecmath.Point3f center)
public void calcBoundBoxDimensions(java.util.BitSet bs, float scale)
public BoxInfo getBoxInfo(java.util.BitSet bs, float scale)
public int calcAtomsMinMax(java.util.BitSet bs, BoxInfo boxInfo)
private void calcUnitCellMinMax()
public float calcRotationRadius(java.util.BitSet bs)
public javax.vecmath.Point3f[][] getCenterAndPoints(java.util.List vAtomSets, boolean addCenters)
vAtomSets
- addCenters
-
public javax.vecmath.Point3f getAtomSetCenter(java.util.BitSet bs)
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 AtomCollection
public ModelCollection.StateScript addStateScript(java.lang.String script1, java.util.BitSet bsBonds, java.util.BitSet bsAtoms1, java.util.BitSet bsAtoms2, java.lang.String script2, boolean addFrameNumber, boolean postDefinitions)
protected java.lang.String calculateStructuresAllExcept(java.util.BitSet alreadyDefined, boolean asDSSP, boolean doReport, boolean dsspIgnoreHydrogen, boolean setStructure, boolean includeAlpha)
alreadyDefined
- set to skip calculationasDSSP
- doReport
- dsspIgnoreHydrogen
- setStructure
- includeAlpha
-
public void setProteinType(java.util.BitSet bs, byte iType)
private void freezeModels()
public java.util.BitSet setConformation(java.util.BitSet bsAtoms)
public java.util.BitSet getConformation(int modelIndex, int conformationIndex, boolean doSet)
public java.util.Hashtable getHeteroList(int modelIndex)
public java.util.Properties getModelSetProperties()
public java.util.Hashtable getModelSetAuxiliaryInfo()
public java.lang.String getModelSetProperty(java.lang.String propertyName)
public java.lang.Object getModelSetAuxiliaryInfo(java.lang.String keyName)
protected boolean getModelSetAuxiliaryInfoBoolean(java.lang.String keyName)
protected int getTrajectoryCount()
public int getTrajectoryIndex(int modelIndex)
public boolean isTrajectory(int modelIndex)
public boolean isTrajectory(int[] countPlusIndices)
protected boolean isTrajectorySubFrame(int i)
public java.util.BitSet getModelBitSet(java.util.BitSet atomList, boolean allTrajectories)
public java.util.BitSet getIterativeModels(boolean allowJmolData)
allowJmolData
-
public void selectDisplayedTrajectories(java.util.BitSet bs)
public java.lang.String getModelNumberDotted(int modelIndex)
public int getModelNumber(int modelIndex)
public int getModelFileNumber(int modelIndex)
public java.util.Properties getModelProperties(int modelIndex)
public java.lang.String getModelProperty(int modelIndex, java.lang.String property)
public java.util.Hashtable getModelAuxiliaryInfo(int modelIndex)
public void setModelAuxiliaryInfo(int modelIndex, java.lang.Object key, java.lang.Object value)
public java.lang.Object getModelAuxiliaryInfo(int modelIndex, java.lang.String key)
protected boolean getModelAuxiliaryInfoBoolean(int modelIndex, java.lang.String keyName)
protected int getModelAuxiliaryInfoInt(int modelIndex, java.lang.String keyName)
public int getInsertionCountInModel(int modelIndex)
public java.lang.String getModelFileType(int modelIndex)
public static int modelFileNumberFromFloat(float fDotM)
public int getAltLocCountInModel(int modelIndex)
public int getChainCount(boolean addWater)
public int getBioPolymerCount()
public int getBioPolymerCountInModel(int modelIndex)
public void getPolymerPointsAndVectors(java.util.BitSet bs, java.util.List vList)
public void recalculateLeadMidpointsAndWingVectors(int modelIndex)
public javax.vecmath.Point3f[] getPolymerLeadMidPoints(int iModel, int iPolymer)
public int getChainCountInModel(int modelIndex, boolean countWater)
public int getGroupCount()
public int getGroupCountInModel(int modelIndex)
public void calcSelectedGroupsCount(java.util.BitSet bsSelected)
public void calcSelectedMonomersCount(java.util.BitSet bsSelected)
public void calcRasmolHydrogenBonds(java.util.BitSet bsA, java.util.BitSet bsB, java.util.List vHBonds, boolean nucleicOnly, int nMax, boolean dsspIgnoreHydrogens)
bsA
- bsB
- vHBonds
- vector of bonds to fill; if null, creates the HBondsnucleicOnly
- nMax
- dsspIgnoreHydrogens
- public void calculateStraightness()
public Quaternion[] getAtomGroupQuaternions(java.util.BitSet bsAtoms, int nMax, char qtype)
public java.lang.String getPdbAtomData(java.util.BitSet bs, OutputStringBuffer sb)
public java.lang.String getPdbData(int modelIndex, java.lang.String type, java.util.BitSet bsSelected, java.lang.Object[] parameters, OutputStringBuffer sb)
public boolean isJmolDataFrame(int modelIndex)
private boolean isJmolDataFrame(Atom atom)
public void setJmolDataFrame(java.lang.String type, int modelIndex, int modelDataIndex)
public int getJmolDataFrameIndex(int modelIndex, java.lang.String type)
protected void clearDataFrameReference(int modelIndex)
public java.lang.String getJmolFrameType(int modelIndex)
public int getJmolDataSourceFrame(int modelIndex)
public void saveModelOrientation(int modelIndex, StateManager.Orientation orientation)
public StateManager.Orientation getModelOrientation(int modelIndex)
private java.lang.String getFullPDBHeader(int modelIndex)
public java.lang.String getPDBHeader(int modelIndex)
public java.lang.String getFileHeader(int modelIndex)
public java.util.Hashtable getModelInfo(java.util.BitSet bsModels)
public int getAltLocIndexInModel(int modelIndex, char alternateLocationID)
public int getInsertionCodeIndexInModel(int modelIndex, char insertionCode)
public java.lang.String getAltLocListInModel(int modelIndex)
private java.lang.String getInsertionListInModel(int modelIndex)
public int getModelSymmetryCount(int modelIndex)
public java.lang.String getSymmetryOperation(int modelIndex, java.lang.String spaceGroup, int symOp, javax.vecmath.Point3f pt1, javax.vecmath.Point3f pt2, java.lang.String drawID, boolean labelOnly)
public int[] getModelCellRange(int modelIndex)
public boolean modelHasVibrationVectors(int modelIndex)
public java.util.BitSet getElementsPresentBitSet(int modelIndex)
private java.lang.String getSymmetryInfoAsString(int modelIndex)
public java.util.List getMoleculeInfo(java.util.BitSet bsAtoms)
public int getMoleculeIndex(int atomIndex)
public java.util.BitSet getMoleculeBitSet(java.util.BitSet bs)
public java.util.BitSet getMoleculeBitSet(int atomIndex)
public void rotateAtoms(javax.vecmath.Matrix3f mNew, javax.vecmath.Matrix3f matrixRotate, java.util.BitSet bsAtoms, boolean fullMolecule, javax.vecmath.Point3f center, boolean isInternal)
public void invertSelected(javax.vecmath.Point3f pt, javax.vecmath.Point4f plane, int iAtom, java.util.BitSet invAtoms, java.util.BitSet bs)
public javax.vecmath.Vector3f getModelDipole(int modelIndex)
public javax.vecmath.Vector3f calculateMolecularDipole(int modelIndex)
public int getMoleculeCountInModel(int modelIndex)
public void calcSelectedMoleculesCount(java.util.BitSet bsSelected)
public JmolMolecule[] getMolecules()
public boolean hasCalculatedHBonds(java.util.BitSet bs)
public void clearRasmolHydrogenBonds(int baseIndex, java.util.BitSet bsAtoms)
protected void initializeBspf()
protected void initializeBspt(int modelIndex)
public void setIteratorForPoint(AtomIndexIterator iterator, int modelIndex, javax.vecmath.Point3f pt, float distance)
public void setIteratorForAtom(AtomIndexIterator iterator, int modelIndex, int atomIndex, float distance)
public AtomIndexIterator getSelectedAtomIterator(java.util.BitSet bsSelected, boolean isGreaterOnly, boolean modelZeroBased, boolean hemisphereOnly)
public int getBondCountInModel(int modelIndex)
BondCollection
getBondCountInModel
in class BondCollection
modelIndex
- the model of interest or -1 for all
public int calculateStruts(java.util.BitSet bs1, java.util.BitSet bs2)
bs1
- bs2
-
public int getAtomCountInModel(int modelIndex)
public java.util.BitSet getModelAtomBitSetIncludingDeleted(java.util.BitSet bsModels)
bsModels
-
public java.util.BitSet getModelAtomBitSetIncludingDeleted(int modelIndex, boolean asCopy)
modelIndex
- asCopy
- MUST BE TRUE IF THE BITSET IS GOING TO BE MODIFIED!
public java.util.BitSet getAtomBits(int tokType, java.lang.Object specInfo)
getAtomBits
in class BondCollection
tokType
- specInfo
-
private boolean isInLatticeCell(int i, javax.vecmath.Point3f cell, javax.vecmath.Point3f pt, boolean isAbsolute)
public java.util.BitSet getAtomsWithin(float distance, java.util.BitSet bs, boolean withinAllModels)
distance
- bs
- withinAllModels
-
public java.util.BitSet getGroupsWithin(int nResidues, java.util.BitSet bs)
public java.util.BitSet getAtomsWithin(float distance, javax.vecmath.Point3f coord, java.util.BitSet bsResult, int modelIndex)
private java.lang.String getBasePairInfo(java.util.BitSet bs)
private static void getAtomResidueInfo(java.lang.StringBuffer info, Atom atom)
private java.util.BitSet getBasePairBits(java.lang.String specInfo)
public java.util.BitSet getSequenceBits(java.lang.String specInfo, java.util.BitSet bs)
public void deleteBonds(java.util.BitSet bsBonds, boolean isFullModel)
deleteBonds
in class BondCollection
protected int[] makeConnections(float minDistance, float maxDistance, int order, int connectOperation, java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsBonds, boolean isBonds, float energy)
public int autoBond(java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsExclude, java.util.BitSet bsBonds, short mad, boolean preJmol11_9_24)
private int autoBond_Pre_11_9_24(java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsExclude, java.util.BitSet bsBonds, short mad)
private int[] autoBond(int order, java.util.BitSet bsA, java.util.BitSet bsB, java.util.BitSet bsBonds, boolean isBonds, boolean matchHbond)
public int autoHbond(java.util.BitSet bsA, java.util.BitSet bsB)
bsA
- "from" set (must contain H if that is desired)bsB
- "to" set
private static javax.vecmath.Point3f checkMinAttachedAngle(Atom atom1, float minAngle, javax.vecmath.Vector3f v1, javax.vecmath.Vector3f v2, boolean haveHAtoms)
void setStructureIds()
public java.lang.String getProteinStructureState(java.util.BitSet bsAtoms, boolean taintedOnly, boolean needPhiPsi, boolean pdbFormat)
public java.lang.String getModelInfoAsString()
public java.lang.String getSymmetryInfoAsString()
public java.util.BitSet getAtomsConnected(float min, float max, int intType, java.util.BitSet bs)
public java.lang.String getModelExtract(java.util.BitSet bs, boolean doTransform, boolean isModelKit, boolean asSDF, boolean asV3000)
private boolean addMolFile(java.lang.StringBuffer mol, java.util.BitSet bsAtoms, java.util.BitSet bsBonds, boolean asV3000, Quaternion q)
private java.util.BitSet getCovalentBondsForAtoms(java.util.BitSet bsAtoms)
private void getAtomRecordMOL(java.lang.StringBuffer sb, int i, Atom a, Quaternion q, javax.vecmath.Point3f pTemp, boolean asV3000)
private void getBondRecordMOL(int n, java.lang.StringBuffer sb, int i, int[] atomMap, boolean asV3000)
public java.lang.String getChimeInfo(int tok, java.util.BitSet bs)
getChimeInfo
in class AtomCollection
public java.lang.String getModelFileInfo(java.util.BitSet frames)
public java.util.Hashtable getAuxiliaryInfo(java.util.BitSet bsModels)
public java.util.List getAllAtomInfo(java.util.BitSet bs)
public void getAtomIdentityInfo(int i, java.util.Hashtable info)
private java.util.Hashtable getAtomInfoLong(int i)
public java.util.List getAllBondInfo(java.util.BitSet bs)
private java.util.Hashtable getBondInfo(int i)
public java.util.Hashtable getAllChainInfo(java.util.BitSet bs)
private java.util.List getChainInfo(int modelIndex, java.util.BitSet bs)
public java.util.Hashtable getAllPolymerInfo(java.util.BitSet bs)
public java.lang.String getUnitCellInfoText()
public java.util.Hashtable getSpaceGroupInfo(int modelIndex, java.lang.String spaceGroup, int symOp, javax.vecmath.Point3f pt1, javax.vecmath.Point3f pt2, java.lang.String drawID)
public java.lang.Object getSymmetryInfo(java.util.BitSet bsAtoms, java.lang.String xyz, int op, javax.vecmath.Point3f pt, javax.vecmath.Point3f pt2, java.lang.String id, int type)
private void getSymTemp(boolean forceNew)
protected void deleteModel(int modelIndex, int firstAtomIndex, int nAtoms, java.util.BitSet bsAtoms, java.util.BitSet bsBonds)
public java.lang.String getMoInfo(int modelIndex)
public void assignAtom(int atomIndex, java.lang.String type, boolean autoBond)
public void deleteAtoms(java.util.BitSet bs)
public void appendLoadStates(java.lang.StringBuffer commands)
public java.lang.String getModelCml(java.util.BitSet bs, int atomsMax, boolean addBonds)
protected void growAtomArrays(int newLength)
protected Atom addAtom(int modelIndex, Group group, short atomicAndIsotopeNumber, java.lang.String atomName, int atomSerial, int atomSite, float x, float y, float z)
protected Atom addAtom(int modelIndex, Group group, short atomicAndIsotopeNumber, java.lang.String atomName, int atomSerial, int atomSite, float x, float y, float z, float radius, float vectorX, float vectorY, float vectorZ, int formalCharge, float partialCharge, int occupancy, float bfactor, java.lang.Object[] ellipsoid, boolean isHetero, char alternateLocationID, byte specialAtomID, java.util.BitSet atomSymmetry)
public java.lang.String getInlineData(int modelIndex)
public boolean isAtomPDB(int i)
public boolean isAtomAssignable(int i)
public int getGroupAtom(Atom atom, int offset, java.lang.String name)
public boolean haveModelKit()
public java.util.BitSet getModelKitStateBitset(java.util.BitSet bs, java.util.BitSet bsDeleted)
public void setAtomNamesAndNumbers(int iFirst, int baseAtomIndex, AtomCollection mergeSet)
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