Class AtomCollection

Method Details

• getAtom

  public Atom getAtom(int iatom)

• setupAC

  protected void setupAC()

• releaseModelSetAC

  protected void releaseModelSetAC()

• mergeAtomArrays

  protected void mergeAtomArrays(AtomCollection mergeModelSet)

• getAtomPointVector

  public Lst<P3> getAtomPointVector(BS bs)

• modelSetHasVibrationVectors

  public boolean modelSetHasVibrationVectors()

• getAtomTypes

  public 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()

  ///////// atoms //////////////

• getAtomInfo

  public String getAtomInfo(int i, String format, P3 ptTemp)

• getElementName

  public String getElementName(int i)

• getQuaternion

  public 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()

• getBfactor100Lo

  public int getBfactor100Lo()

• getBfactor100Hi

  public int getBfactor100Hi()

• getSurfaceDistanceMax

  public int getSurfaceDistanceMax()

• calculateVolume

  public float calculateVolume(BS bs, VDW vType)

• calculateSurface

  public P3[] calculateSurface(BS bsSelected, float envelopeRadius)

• setAtomCoord2

  protected void setAtomCoord2(BS bs, int tokType, Object xyzValues)

• setAtomVibrationVector

  public Vibration setAtomVibrationVector(int atomIndex, T3 vib)

• setAtomCoord

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

• 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, String sValue, float[] values, String[] list)

• getVibCoord

  public float getVibCoord(int atomIndex, char c)

  also handles modulation info

  Parameters:

  atomIndex -

  c - generally x, y, z, but for modulation could be 1, 2, 3, or O (oh, not zero)

  Returns:

  value or NaN

• getVibration

  public Vibration getVibration(int atomIndex, boolean forceNew)

• getModulation

  public JmolModulationSet getModulation(int iAtom)

• setAtomName

  public void setAtomName(int atomIndex, String name, boolean doTaint)

• setAtomNumber

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

• setElement

  public void setElement(Atom atom, int atomicNumber, boolean doTaint)

• setSite

  public void setSite(Atom atom, int site, boolean doTaint)

• setOccupancy

  public void setOccupancy(int atomIndex, float occupancy, boolean doTaint)

• getOccupancyFloat

  public float getOccupancyFloat(int i)

• setPartialCharge

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

• setBondingRadius

  protected void setBondingRadius(int atomIndex, float radius)

• setBFactor

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

• setAtomData

  public void setAtomData(int type, String name, String dataString, boolean isDefault)

• validateBspf

  public void validateBspf(boolean isValid)

• setPreserveState

  public void setPreserveState(boolean TF)

• getUserSettableType

  public static int getUserSettableType(String dataType)

  / atom coordinate and property changing //////////

• getTaintedAtoms

  public BS getTaintedAtoms(int type)

• taintAtoms

  public void taintAtoms(BS bsAtoms, int type)

• taintAtom

  public void taintAtom(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)

  ////////////////////////////////////////

• fillADa

  protected void fillADa(AtomData atomData, int mode)

• calculateHydrogens

  public P3[][] calculateHydrogens(BS bs, int[] nTotal, Lst<Atom> vConnect, int flags)

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

  Parameters:

  bs -

  nTotal -

  vConnect -

  flags - [CALC_H_DOALL | CALC_H_JUSTC | CALC_H_HAVEH | CALC_H_QUICK

  Returns:

  array of arrays of points added to specific atoms

• getMissingHydrogenCount

  public int getMissingHydrogenCount(Atom atom, boolean allowNegative)

• fixFormalCharges

  public int fixFormalCharges(BS bs)

• getHybridizationAndAxes

  public String getHybridizationAndAxes(int atomIndex, int atomicNumber, V3 z, V3 x, String lcaoTypeRaw, boolean hybridizationCompatible, boolean doAlignZ, boolean isQuick, T3 ref)

• getAtomBitsMDa

  public BS getAtomBitsMDa(int tokType, 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)

• getSeqcodeBits

  public BS getSeqcodeBits(int seqcode, boolean returnEmpty)

• getSpecNameOrNull

  public BS getSpecNameOrNull(String name, boolean checkStar)

• getAtomIndices

  public int[] getAtomIndices(BS bs)

• getAtomsNearPlane

  public BS getAtomsNearPlane(float distance, 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, Map<String,Object> info, P3 ptTemp)

• getAtomTensorList

  public Object[] getAtomTensorList(int i)

• setAtomTensors

  public void setAtomTensors(int atomIndex, Lst<Object> list)

• addTensor

  public void addTensor(Tensor t, String type)

• getAtomTensor

  public Tensor getAtomTensor(int i, String type)

• getAllAtomTensors

  public Lst<Object> getAllAtomTensors(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 Lst<P3> generateCrystalClass(int atomIndex, P3 pt)

• isDeleted

  public static boolean isDeleted(Atom atom)