Class Atom

Method Details

• setAtom

  public Atom setAtom(int modelIndex, int atomIndex, P3 xyz, float radius, BS atomSymmetry, int atomSite, short atomicAndIsotopeNumber, int formalCharge, boolean isHetero, boolean isNegDisorder)

  Parameters:

  modelIndex -

  atomIndex -

  xyz -

  radius -

  atomSymmetry -

  atomSite -

  atomicAndIsotopeNumber -

  formalCharge -

  isHetero -

  isNegDisorder - TODO -- never implemented as such

  Returns:

  this

• setShapeVisibility

  public final void setShapeVisibility(int flag, boolean isVisible)

• isCovalentlyBonded

  public boolean isCovalentlyBonded(Atom atomOther)

• isBonded

  public boolean isBonded(Atom atomOther)

• getBond

  public Bond getBond(Atom atomOther)

• getBondedAtomIndex

  public int getBondedAtomIndex(int bondIndex)

  Specified by:

  getBondedAtomIndex in interface Node

• setMadAtom

  public void setMadAtom(Viewer vwr, RadiusData rd)

• calculateMad

  public short calculateMad(Viewer vwr, RadiusData rd)

• getADPMinMax

  public float getADPMinMax(boolean isMax)

• getTensors

  public Object[] getTensors()

• getRasMolRadius

  public int getRasMolRadius()

• getEdges

  public Edge[] getEdges()

  Description copied from interface: SimpleNode

  Get the bond array, including hydrogen bonds.

  Specified by:

  getEdges in interface Node

  Specified by:

  getEdges in interface SimpleNode

  Returns:

  number of bonds

• getBondCount

  public int getBondCount()

  Description copied from interface: SimpleNode

  Get the total number of bonds, including hydrogen bonds.

  Specified by:

  getBondCount in interface SimpleNode

  Returns:

  number of bonds

• setTranslucent

  public void setTranslucent(boolean isTranslucent, float translucentLevel)

• getElementNumber

  public int getElementNumber()

  Specified by:

  getElementNumber in interface Node

  Specified by:

  getElementNumber in interface SimpleNode

  Returns:

  the atomic number for this atom

• getIsotopeNumber

  public int getIsotopeNumber()

  Specified by:

  getIsotopeNumber in interface Node

  Specified by:

  getIsotopeNumber in interface SimpleNode

• getAtomicAndIsotopeNumber

  public int getAtomicAndIsotopeNumber()

  Specified by:

  getAtomicAndIsotopeNumber in interface Node

• setAtomicAndIsotopeNumber

  public void setAtomicAndIsotopeNumber(int n)

• getElementSymbolIso

  public String getElementSymbolIso(boolean withIsotope)

• getElementSymbol

  public String getElementSymbol()

• isHetero

  public boolean isHetero()

• hasVibration

  public boolean hasVibration()

• setFormalCharge

  public void setFormalCharge(int charge)

  Parameters:

  charge - from -3 to 7

• getFormalCharge

  public int getFormalCharge()

  Specified by:

  getFormalCharge in interface Node

  Specified by:

  getFormalCharge in interface SimpleNode

  Returns:

  the formal charge for this atom

• getOccupancy100

  public int getOccupancy100()

• isOccupied

  public boolean isOccupied()

• getBfactor100

  public int getBfactor100()

• getHydrophobicity

  public float getHydrophobicity()

• setRadius

  public boolean setRadius(float radius)

• delete

  public void delete(BS bsBonds)

• isDeleted

  public boolean isDeleted()

  Specified by:

  isDeleted in interface Node

• setValence

  public void setValence(int nBonds)

• getValence

  public int getValence()

  return the total bond order for this atom

  Specified by:

  getValence in interface Node

  Specified by:

  getValence in interface SimpleNode

  Returns:

  the sum of the bond orders for this atom

• getCovalentBondCount

  public int getCovalentBondCount()

  Description copied from interface: SimpleNode

  Get the total number of covalent bonds, thus not including hydrogen bonds.

  Specified by:

  getCovalentBondCount in interface Node

  Specified by:

  getCovalentBondCount in interface SimpleNode

  Returns:

  number of bonds

• getCovalentOrPartialBondCount

  public int getCovalentOrPartialBondCount()

• getCovalentHydrogenCount

  public int getCovalentHydrogenCount()

  Specified by:

  getCovalentHydrogenCount in interface Node

• getImplicitHydrogenCount

  public int getImplicitHydrogenCount()

  Description copied from interface: Node

  can be > 0 for PDB model with no H atoms or for SMILES string CCC

  Specified by:

  getImplicitHydrogenCount in interface Node

  Returns:

  number of missing H atoms

• getTotalHydrogenCount

  public int getTotalHydrogenCount()

  Specified by:

  getTotalHydrogenCount in interface Node

• getTotalValence

  public int getTotalValence()

  Specified by:

  getTotalValence in interface Node

• getCovalentBondCountPlusMissingH

  public int getCovalentBondCountPlusMissingH()

  Description copied from interface: Node

  includes actual + missing

  Specified by:

  getCovalentBondCountPlusMissingH in interface Node

  Returns:

  actual + missing

• getDimensionValue

  public float getDimensionValue(int dimension)

• getVanderwaalsRadiusFloat

  public float getVanderwaalsRadiusFloat(Viewer vwr, VDW type)

• getBondingRadius

  public float getBondingRadius()

• getRadius

  public float getRadius()

• getIndex

  public int getIndex()

  Specified by:

  getIndex in interface Node

  Specified by:

  getIndex in interface SimpleNode

  Returns:

  the unique ID number associated with this atom (which in Jmol is its position in the atoms[] array

• getAtomSite

  public int getAtomSite()

  Specified by:

  getAtomSite in interface Node

• getGroupBits

  public void getGroupBits(BS bs)

  Specified by:

  getGroupBits in interface Node

• getAtomName

  public String getAtomName()

  Specified by:

  getAtomName in interface Node

  Specified by:

  getAtomName in interface SimpleNode

• getAtomType

  public String getAtomType()

  Specified by:

  getAtomType in interface Node

• getAtomNumber

  public int getAtomNumber()

  Specified by:

  getAtomNumber in interface Node

• getSeqID

  public int getSeqID()

• isVisible

  public boolean isVisible(int flags)

• getPartialCharge

  public float getPartialCharge()

• getSymmetryTranslation

  public int getSymmetryTranslation(int symop, int[] cellRange, int nOps)

  Given a symmetry operation number, the set of cells in the model, and the number of operations, this method returns either 0 or the cell number (555, 666) of the translated symmetry operation corresponding to this atom. atomSymmetry is a bitset that is created in adapter.smarter.AtomSetCollection It is arranged as follows: |--overall--|---cell1---|---cell2---|---cell3---|... |012..nOps-1|012..nOps-1|012..nOp-1s|012..nOps-1|... If a bit is set, it means that the atom was created using that operator operating on the base file set and translated for that cell. If any bit is set in any of the cell blocks, then the same bit will also be set in the overall block. This allows for rapid determination of special positions and also of atom membership in any operation set. Note that it is not necessarily true that an atom is IN the designated cell, because one can load {nnn mmm 0}, and then, for example, the {-x,-y,-z} operator sends atoms from 555 to 444. Still, those atoms would be marked as cell 555 here, because no translation was carried out. That is, the numbers 444 in symop=3444 do not refer to a cell, per se. What they refer to is the file-designated operator plus a translation of {-1 -1 -1/1}.

  Parameters:

  symop - = 0, 1, 2, 3, ....

  cellRange - = {444, 445, 446, 454, 455, 456, .... }

  nOps - = 2 for x,y,z;-x,-y,-z, for example

  Returns:

  cell number such as 565

• getCellTranslation

  public int getCellTranslation(int cellNNN, int[] cellRange, int nOps)

  Looks for a match in the cellRange list for this atom within the specified translation set select symop=0NNN for this

  Parameters:

  cellNNN -

  cellRange -

  nOps -

  Returns:

  matching cell number, if applicable

• getModelIndex

  public int getModelIndex()

  Specified by:

  getModelIndex in interface Node

• getMoleculeNumber

  public int getMoleculeNumber(boolean inModel)

  Specified by:

  getMoleculeNumber in interface Node

• getXYZ

  public P3 getXYZ()

  Specified by:

  getXYZ in interface Node

  Specified by:

  getXYZ in interface SimpleNode

  Returns:

  the position of this atom

• getFractionalCoordPt

  public P3 getFractionalCoordPt(boolean fixJavaFloat, boolean ignoreOffset, P3 pt)

• setFractionalCoordPt

  public void setFractionalCoordPt(P3 pt, P3 ptNew, boolean asAbsolute)

• getInfo

  public String getInfo()

• getIdentityXYZ

  public String getIdentityXYZ(P3 pt, int mode)

• getGroup3

  public String getGroup3(boolean allowNull)

  Specified by:

  getGroup3 in interface Node

• getGroup1

  public String getGroup1(char c0)

  Specified by:

  getGroup1 in interface Node

• getBioSmilesType

  public char getBioSmilesType()

  Specified by:

  getBioSmilesType in interface Node

• isPurine

  public boolean isPurine()

  Specified by:

  isPurine in interface Node

• isPyrimidine

  public boolean isPyrimidine()

  Specified by:

  isPyrimidine in interface Node

• getResno

  public int getResno()

  Specified by:

  getResno in interface Node

• isClickable

  public boolean isClickable()

• setClickable

  public void setClickable(int flag)

• checkVisible

  public boolean checkVisible()

• isLeadAtom

  public boolean isLeadAtom()

  Specified by:

  isLeadAtom in interface Node

• getChainID

  public int getChainID()

  Specified by:

  getChainID in interface Node

• getChainIDStr

  public String getChainIDStr()

  Specified by:

  getChainIDStr in interface Node

• getSurfaceDistance100

  public int getSurfaceDistance100()

• getVibrationVector

  public Vibration getVibrationVector()

• getModulation

  public JmolModulationSet getModulation()

• getModelNumberForLabel

  public String getModelNumberForLabel()

• getModelNumber

  public int getModelNumber()

• getBioStructureTypeName

  public String getBioStructureTypeName()

  Specified by:

  getBioStructureTypeName in interface Node

• equals

  public boolean equals(Object obj)

  Description copied from class: T3

  Returns true if all of the data members of Tuple3f t1 are equal to the corresponding data members in this

  Overrides:

  equals in class T3

  Parameters:

  obj - the vector with which the comparison is made.

• hashCode

  public int hashCode()

  Description copied from class: T3

  Returns a hash number based on the data values in this object. Two different Tuple3f objects with identical data values (ie, returns true for equals(Tuple3f) ) will return the same hash number. Two vectors with different data members may return the same hash value, although this is not likely.

  Overrides:

  hashCode in class T3

• findAromaticNeighbor

  public Atom findAromaticNeighbor(int notAtomIndex)

• atomPropertyInt

  public int atomPropertyInt(Viewer vwr, int tokWhat)

  called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()

  Parameters:

  vwr -

  tokWhat -

  Returns:

  int value or Integer.MIN_VALUE

• atomPropertyFloat

  public float atomPropertyFloat(Viewer vwr, int tokWhat, P3 ptTemp)

  called by isosurface and int comparator via atomProperty() and also by getBitsetProperty()

  Parameters:

  vwr -

  tokWhat -

  ptTemp -

  Returns:

  float value or value*100 (asInt=true) or throw an error if not found

• getVib

  public float getVib(char ch)

• getNominalMass

  public int getNominalMass()

• getMass

  public float getMass()

  Specified by:

  getMass in interface Node

  Specified by:

  getMass in interface SimpleNode

  Returns:

  the mass or, if specified, the mass number

• atomPropertyString

  public String atomPropertyString(Viewer vwr, int tokWhat)

• getWyckoffPosition

  public String getWyckoffPosition(boolean withMultiplicity)

• getCIPChirality

  public String getCIPChirality(boolean doCalculate)

  Determine R/S chirality at this position; non-H atoms only; cached in formalChargeAndFlags

  Specified by:

  getCIPChirality in interface Node

  Parameters:

  doCalculate -

  Returns:

  one of "", "R", "S", "E", "Z", "r", "s", "?"

• getCIPChiralityRule

  public String getCIPChiralityRule()

• setCIPChirality

  public void setCIPChirality(int c)

  Specified by:

  setCIPChirality in interface Node

  Specified by:

  setCIPChirality in interface SimpleNode

  Parameters:

  c - [0:unknown; 3:none; 1: R; 2: S; 5: Z; 6: E; 9: M, 10: P, +r,s

• getCIPChiralityCode

  public int getCIPChiralityCode()

  Specified by:

  getCIPChiralityCode in interface Node

• getInsertionCode

  public char getInsertionCode()

  Specified by:

  getInsertionCode in interface Node

• atomPropertyTuple

  public T3 atomPropertyTuple(Viewer vwr, int tok, P3 ptTemp)

• getOffsetResidueAtom

  public int getOffsetResidueAtom(String name, int offset)

  Specified by:

  getOffsetResidueAtom in interface Node

• isCrossLinked

  public boolean isCrossLinked(Node node)

  Specified by:

  isCrossLinked in interface Node

• getCrossLinkVector

  public boolean getCrossLinkVector(Lst<Integer> vReturn, boolean crosslinkCovalent, boolean crosslinkHBond)

  Used by SMILES to get vector of cross-links

  Specified by:

  getCrossLinkVector in interface Node

• toString

  public String toString()

  Description copied from class: T3

  Returns a string that contains the values of this Tuple3f. The form is (x,y,z).

  Overrides:

  toString in class T3

  Returns:

  the String representation

• findAtomsLike

  public BS findAtomsLike(String atomExpression)

  Specified by:

  findAtomsLike in interface Node

• getUnitID

  public String getUnitID(int flags)

• getFloatProperty

  public float getFloatProperty(String property)

  Specified by:

  getFloatProperty in interface Node

  Parameters:

  property - "property_xxxx"

  Returns:

  value or Float.NaN

• modelIsRawPDB

  public boolean modelIsRawPDB()

  Specified by:

  modelIsRawPDB in interface Node

• setSymop

  public void setSymop(int isym, boolean andClear)

• getExplicitHydrogenCount

  public int getExplicitHydrogenCount()

  Description copied from interface: Node

  [CH2] for example

  Specified by:

  getExplicitHydrogenCount in interface Node

  Returns:

  number of H atoms in brackets