Field Detail

• almost180

  private static final float almost180

  See Also:

  Constant Field Values

• sqrt3_2

  private static final float sqrt3_2

• vRef

  private static final javajs.util.V3 vRef

• vwr

  public Viewer vwr

• g3d

  protected GData g3d

• bioModelset

  public BioModelSet bioModelset

  If any model in the collection is a BioModel, then it is also indicated here as a "bioModelset", meaning

• at

  public Atom[] at

• ac

  public int ac

• trajectory

  public Trajectory trajectory

• labeler

  private LabelToken labeler

• maxBondingRadius

  protected float maxBondingRadius

• maxVanderwaalsRadius

  private float maxVanderwaalsRadius

• hasBfactorRange

  private boolean hasBfactorRange

• bfactor100Lo

  private int bfactor100Lo

• bfactor100Hi

  private int bfactor100Hi

• haveBSVisible

  private boolean haveBSVisible

• haveBSClickable

  private boolean haveBSClickable

• bsSurface

  private BS bsSurface

• nSurfaceAtoms

  private int nSurfaceAtoms

• surfaceDistanceMax

  private int surfaceDistanceMax

• averageAtomPoint

  protected javajs.util.P3 averageAtomPoint

• bspf

  protected Bspf bspf

  Binary Space Partitioning Forest

• preserveState

  protected boolean preserveState

• canSkipLoad

  public boolean canSkipLoad

• haveStraightness

  public boolean haveStraightness

• bsHidden

  private BS bsHidden

• bsVisible

  public BS bsVisible

• bsClickable

  public BS bsClickable

• bsModulated

  public BS bsModulated

• atomTensorList

  public java.lang.Object[][] atomTensorList

• atomTensors

  public java.util.Map<java.lang.String,​javajs.util.Lst<java.lang.Object>> atomTensors

• surfaceDistance100s

  protected int[] surfaceDistance100s

• tainted

  public BS[] tainted

• userSettableValues

  public static java.lang.String[] userSettableValues

• TAINT_ATOMNAME

  public static final int TAINT_ATOMNAME

  See Also:

  Constant Field Values

• TAINT_ATOMTYPE

  public static final int TAINT_ATOMTYPE

  See Also:

  Constant Field Values

• TAINT_COORD

  public static final int TAINT_COORD

  See Also:

  Constant Field Values

• TAINT_ELEMENT

  public static final int TAINT_ELEMENT

  See Also:

  Constant Field Values

• TAINT_FORMALCHARGE

  public static final int TAINT_FORMALCHARGE

  See Also:

  Constant Field Values

• TAINT_HYDROPHOBICITY

  public static final int TAINT_HYDROPHOBICITY

  See Also:

  Constant Field Values

• TAINT_BONDINGRADIUS

  public static final int TAINT_BONDINGRADIUS

  See Also:

  Constant Field Values

• TAINT_OCCUPANCY

  public static final int TAINT_OCCUPANCY

  See Also:

  Constant Field Values

• TAINT_PARTIALCHARGE

  public static final int TAINT_PARTIALCHARGE

  See Also:

  Constant Field Values

• TAINT_TEMPERATURE

  public static final int TAINT_TEMPERATURE

  See Also:

  Constant Field Values

• TAINT_VALENCE

  public static final int TAINT_VALENCE

  See Also:

  Constant Field Values

• TAINT_VANDERWAALS

  public static final int TAINT_VANDERWAALS

  See Also:

  Constant Field Values

• TAINT_VIBRATION

  public static final int TAINT_VIBRATION

  See Also:

  Constant Field Values

• TAINT_ATOMNO

  public static final int TAINT_ATOMNO

  See Also:

  Constant Field Values

• TAINT_SEQID

  public static final int TAINT_SEQID

  See Also:

  Constant Field Values

• TAINT_RESNO

  public static final int TAINT_RESNO

  See Also:

  Constant Field Values

• TAINT_CHAIN

  public static final int TAINT_CHAIN

  See Also:

  Constant Field Values

• TAINT_MAX

  public static final int TAINT_MAX

  See Also:

  Constant Field Values

• atomNames

  java.lang.String[] atomNames

• atomTypes

  java.lang.String[] atomTypes

• atomSerials

  int[] atomSerials

• atomResnos

  int[] atomResnos

• atomSeqIDs

  int[] atomSeqIDs

• vibrations

  public Vibration[] vibrations

• occupancies

  public float[] occupancies

• bfactor100s

  short[] bfactor100s

• partialCharges

  float[] partialCharges

• bondingRadii

  float[] bondingRadii

• hydrophobicities

  float[] hydrophobicities

• bsPartialCharges

  public BS bsPartialCharges

• aaRet

  int[] aaRet

• atomCapacity

  private int atomCapacity

Constructor Detail

• AtomCollection

  public AtomCollection()

Method Detail

• setupAC

  protected void setupAC()

• releaseModelSetAC

  protected void releaseModelSetAC()

• mergeAtomArrays

  protected void mergeAtomArrays​(AtomCollection mergeModelSet)

• getAtomPointVector

  public javajs.util.Lst<javajs.util.P3> getAtomPointVector​(BS bs)

• modelSetHasVibrationVectors

  public boolean modelSetHasVibrationVectors()

• getAtomTypes

  public java.lang.String[] getAtomTypes()

• getPartialCharges

  public float[] getPartialCharges()

• getBondingRadii

  public float[] getBondingRadii()

• getBFactors

  public short[] getBFactors()

• getHydrophobicity

  public float[] getHydrophobicity()

• setBsHidden

  public void setBsHidden​(BS bs)

• isAtomHidden

  public boolean isAtomHidden​(int iAtom)

• getLabeler

  public LabelToken getLabeler()

• getAtomInfo

  public java.lang.String getAtomInfo​(int i,
                                      java.lang.String format,
                                      javajs.util.P3 ptTemp)

• getElementName

  public java.lang.String getElementName​(int i)

• getQuaternion

  public javajs.util.Quat getQuaternion​(int i,
                                        char qtype)

• getFirstAtomIndexFromAtomNumber

  public int getFirstAtomIndexFromAtomNumber​(int atomNumber,
                                             BS bsVisibleFrames)

• setFormalCharges

  public void setFormalCharges​(BS bs,
                               int formalCharge)

• getAtomicCharges

  public float[] getAtomicCharges()

• getRadiusVdwJmol

  protected float getRadiusVdwJmol​(Atom atom)

• getMaxVanderwaalsRadius

  public float getMaxVanderwaalsRadius()

• findMaxRadii

  protected void findMaxRadii()

• clearBfactorRange

  public void clearBfactorRange()

• calcBfactorRange

  private void calcBfactorRange​(BS bs)

• setBf

  private void setBf​(int i)

• getBfactor100Lo

  public int getBfactor100Lo()

• getBfactor100Hi

  public int getBfactor100Hi()

• getSurfaceDistanceMax

  public int getSurfaceDistanceMax()

• calculateVolume

  public float calculateVolume​(BS bs,
                               VDW vType)

• getSurfaceDistance100

  int getSurfaceDistance100​(int atomIndex)

• calcSurfaceDistances

  private void calcSurfaceDistances()

• calculateSurface

  public javajs.util.P3[] calculateSurface​(BS bsSelected,
                                           float envelopeRadius)

• setAtomCoord2

  protected void setAtomCoord2​(BS bs,
                               int tokType,
                               java.lang.Object xyzValues)

• setAtomVibrationVector

  private void setAtomVibrationVector​(int atomIndex,
                                      javajs.util.T3 vib)

• setAtomCoord

  public void setAtomCoord​(int atomIndex,
                           float x,
                           float y,
                           float z)

• fixTrajectory

  private void fixTrajectory​(Atom a)

• setAtomCoordRelative

  public void setAtomCoordRelative​(int atomIndex,
                                   float x,
                                   float y,
                                   float z)

• setAtomsCoordRelative

  protected void setAtomsCoordRelative​(BS bs,
                                       float x,
                                       float y,
                                       float z)

• setAPa

  protected void setAPa​(BS bs,
                        int tok,
                        int iValue,
                        float fValue,
                        java.lang.String sValue,
                        float[] values,
                        java.lang.String[] list)

• getVibCoord

  public float getVibCoord​(int atomIndex,
                           char c)

  also handles modulation info

  Parameters:

  atomIndex -

  c -

  Returns:

  value or NaN

• getVibration

  public Vibration getVibration​(int atomIndex,
                                boolean forceNew)

• getModulation

  public JmolModulationSet getModulation​(int iAtom)

• setVibrationVector

  protected void setVibrationVector​(int atomIndex,
                                    javajs.util.T3 vib)

• setVibrationVector2

  private void setVibrationVector2​(int atomIndex,
                                   int tok,
                                   float fValue)

• setAtomName

  public void setAtomName​(int atomIndex,
                          java.lang.String name,
                          boolean doTaint)

• setAtomType

  private void setAtomType​(int atomIndex,
                           java.lang.String type)

• setChainID

  private void setChainID​(int atomIndex,
                          java.lang.String id)

• setAtomNumber

  public void setAtomNumber​(int atomIndex,
                            int atomno,
                            boolean doTaint)

• setElement

  protected void setElement​(Atom atom,
                            int atomicNumber,
                            boolean doTaint)

• setAtomResno

  private void setAtomResno​(int atomIndex,
                            int resno)

• setAtomSeqID

  private void setAtomSeqID​(int atomIndex,
                            int seqID)

• setOccupancy

  protected void setOccupancy​(int atomIndex,
                              float occupancy,
                              boolean doTaint)

• setPartialCharge

  protected void setPartialCharge​(int atomIndex,
                                  float partialCharge,
                                  boolean doTaint)

• setBondingRadius

  private void setBondingRadius​(int atomIndex,
                                float radius)

• setBFactor

  protected void setBFactor​(int atomIndex,
                            float bfactor,
                            boolean doTaint)

• setHydrophobicity

  private void setHydrophobicity​(int atomIndex,
                                 float value)

• setAtomData

  public void setAtomData​(int type,
                          java.lang.String name,
                          java.lang.String dataString,
                          boolean isDefault)

• loadCoordinates

  private void loadCoordinates​(java.lang.String data,
                               boolean isVibrationVectors,
                               boolean doTaint)

• validateBspf

  public void validateBspf​(boolean isValid)

• validateBspfForModel

  void validateBspfForModel​(int modelIndex,
                            boolean isValid)

• setPreserveState

  public void setPreserveState​(boolean TF)

• getUserSettableType

  public static int getUserSettableType​(java.lang.String dataType)

• getTaintedAtoms

  public BS getTaintedAtoms​(int type)

• taintAtoms

  public void taintAtoms​(BS bsAtoms,
                         int type)

• taintAtom

  protected void taintAtom​(int atomIndex,
                           int type)

• untaint

  private void untaint​(int atomIndex,
                       int type)

• setTaintedAtoms

  public void setTaintedAtoms​(BS bs,
                              int type)

• unTaintAtoms

  public void unTaintAtoms​(BS bs,
                           int type)

• findNearest2

  protected void findNearest2​(int x,
                              int y,
                              Atom[] closest,
                              BS bsNot,
                              int min)

• isCursorOnTopOf

  boolean isCursorOnTopOf​(Atom contender,
                          int x,
                          int y,
                          int radius,
                          Atom champion)

  used by Frame and AminoMonomer and NucleicMonomer -- does NOT check for clickability

  Parameters:

  contender -

  x -

  y -

  radius -

  champion -

  Returns:

  true if user is pointing to this atom

• fillADa

  protected void fillADa​(AtomData atomData,
                         int mode)

• getWorkingRadius

  private float getWorkingRadius​(Atom atom,
                                 AtomData atomData)

• calculateHydrogens

  public javajs.util.P3[][] calculateHydrogens​(BS bs,
                                               int[] nTotal,
                                               boolean doAll,
                                               boolean justCarbon,
                                               javajs.util.Lst<Atom> vConnect)

  get a list of potential H atom positions based on elemental valence and formal charge

  Parameters:

  bs -

  nTotal -

  doAll - -- whether we add to C that already have H or not.

  justCarbon -

  vConnect -

  Returns:

  array of arrays of points added to specific atoms

• isAdjacentSp2

  private boolean isAdjacentSp2​(Atom atom)

• getMissingHydrogenCount

  int getMissingHydrogenCount​(Atom atom,
                              boolean allowNegative)

• fixFormalCharges

  public int fixFormalCharges​(BS bs)

• getHybridizationAndAxes

  public java.lang.String getHybridizationAndAxes​(int atomIndex,
                                                  int atomicNumber,
                                                  javajs.util.V3 z,
                                                  javajs.util.V3 x,
                                                  java.lang.String lcaoTypeRaw,
                                                  boolean hybridizationCompatible,
                                                  boolean doAlignZ)

• getHybridizationAndAxesD

  private java.lang.String getHybridizationAndAxesD​(int atomIndex,
                                                    javajs.util.V3 z,
                                                    javajs.util.V3 x,
                                                    java.lang.String lcaoType)

  dsp3 (trigonal bipyramidal, see-saw, T-shaped) or d2sp3 (square planar, square pyramidal, octahedral)

  Parameters:

  atomIndex -

  z -

  x -

  lcaoType -

  Returns:

  valid hybridization or null

• getAttached

  private Atom[] getAttached​(Atom atom,
                             int nMax,
                             boolean doSort)

• findNotAttached

  private BS findNotAttached​(int nAttached,
                             int[][] angles,
                             int[] ptrs,
                             int nPtrs)

• getAtomBitsMDa

  public BS getAtomBitsMDa​(int tokType,
                           java.lang.Object specInfo,
                           BS bs)

  general unqualified lookup of atom set type

  Parameters:

  tokType -

  specInfo -

  bs - - to be filled

  Returns:

  BitSet; or null if we mess up the type

• getChainBits

  public BS getChainBits​(int chainID)

• chainToUpper

  public int chainToUpper​(int chainID)

• isAltLoc

  private boolean isAltLoc​(char altloc,
                           java.lang.String strPattern)

• getSeqcodeBits

  public BS getSeqcodeBits​(int seqcode,
                           boolean returnEmpty)

• getIdentifierOrNull

  private BS getIdentifierOrNull​(java.lang.String identifier)

  overhauled by RMH Nov 1, 2006.

  Parameters:

  identifier -

  Returns:

  null or bs

• getSpecName

  private BS getSpecName​(java.lang.String name)

• getSpecNameOrNull

  public BS getSpecNameOrNull​(java.lang.String name,
                              boolean checkStar)

• isAtomNameMatch

  private boolean isAtomNameMatch​(Atom atom,
                                  java.lang.String strPattern,
                                  boolean checkStar,
                                  boolean allowInitialStar)

• getAtomIndices

  public int[] getAtomIndices​(BS bs)

• getAtomsNearPlane

  public BS getAtomsNearPlane​(float distance,
                              javajs.util.P4 plane)

• clearVisibleSets

  public void clearVisibleSets()

• getAtomsInFrame

  public void getAtomsInFrame​(BS bsAtoms)

• getVisibleSet

  public BS getVisibleSet​(boolean forceNew)

• getClickableSet

  public BS getClickableSet​(boolean forceNew)

• isModulated

  public boolean isModulated​(int i)

• deleteModelAtoms

  protected void deleteModelAtoms​(int firstAtomIndex,
                                  int nAtoms,
                                  BS bsAtoms)

• getAtomIdentityInfo

  public void getAtomIdentityInfo​(int i,
                                  java.util.Map<java.lang.String,​java.lang.Object> info,
                                  javajs.util.P3 ptTemp)

• getAtomTensorList

  public java.lang.Object[] getAtomTensorList​(int i)

• deleteAtomTensors

  private void deleteAtomTensors​(BS bsAtoms)

• setCapacity

  void setCapacity​(int nAtoms)

• setAtomTensors

  public void setAtomTensors​(int atomIndex,
                             javajs.util.Lst<java.lang.Object> list)

• addTensor

  public void addTensor​(Tensor t,
                        java.lang.String type)

• getTensorList

  private static java.lang.Object[] getTensorList​(javajs.util.Lst<java.lang.Object> list)

• getAtomTensor

  public Tensor getAtomTensor​(int i,
                              java.lang.String type)

• getAllAtomTensors

  public javajs.util.Lst<java.lang.Object> getAllAtomTensors​(java.lang.String type)

• scaleVectorsToMax

  public void scaleVectorsToMax​(float max)

  Scales vibrations and associated vectors such that the maximum length is the given value

  Parameters:

  max -

• getAtomsFromAtomNumberInFrame

  public BS getAtomsFromAtomNumberInFrame​(int atomNumber)

• generateCrystalClass

  public javajs.util.Lst<javajs.util.P3> generateCrystalClass​(int atomIndex,
                                                              javajs.util.P3 pt)