Method Detail

• getAtomicAndIsotopeNumber

  int getAtomicAndIsotopeNumber()

• getAtomName

  java.lang.String getAtomName()

  Specified by:

  getAtomName in interface SimpleNode

• getAtomSite

  int getAtomSite()

• getBondedAtomIndex

  int getBondedAtomIndex​(int j)

• getCovalentBondCount

  int getCovalentBondCount()

  Description copied from interface: SimpleNode
  Get the total number of covalent bonds, thus not including hydrogen bonds.

  Specified by:

  getCovalentBondCount in interface SimpleNode

  Returns:

  number of bonds

• getCovalentHydrogenCount

  int getCovalentHydrogenCount()

• getEdges

  Edge[] getEdges()

  Description copied from interface: SimpleNode
  Get the bond array, including hydrogen bonds.

  Specified by:

  getEdges in interface SimpleNode

  Returns:

  number of bonds

• getElementNumber

  int getElementNumber()

  Specified by:

  getElementNumber in interface SimpleNode

  Returns:

  the atomic number for this aotm

• getFormalCharge

  int getFormalCharge()

  Specified by:

  getFormalCharge in interface SimpleNode

  Returns:

  the formal charge for this atom

• getIndex

  int getIndex()

  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

• getIsotopeNumber

  int getIsotopeNumber()

  Specified by:

  getIsotopeNumber in interface SimpleNode

• getValence

  int getValence()

  Specified by:

  getValence in interface SimpleNode

  Returns:

  the sum of the bond orders for this atom

• set

  void set​(float x,
           float y,
           float z)

• getMoleculeNumber

  int getMoleculeNumber​(boolean inModel)

• getMass

  float getMass()

  Specified by:

  getMass in interface SimpleNode

  Returns:

  the mass or, if specified, the mass number

• getFloatProperty

  float getFloatProperty​(java.lang.String property)

  Parameters:

  property - "property_xxxx"

  Returns:

  value or Float.NaN

• findAtomsLike

  javajs.util.BS findAtomsLike​(java.lang.String substring)

• getAtomType

  java.lang.String getAtomType()

• getModelIndex

  int getModelIndex()

• getAtomNumber

  int getAtomNumber()

• getImplicitHydrogenCount

  int getImplicitHydrogenCount()

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

  Returns:

  number of missing H atoms

• getCovalentBondCountPlusMissingH

  int getCovalentBondCountPlusMissingH()

  includes actual + missing

  Returns:

  actual + missing

• getTotalHydrogenCount

  int getTotalHydrogenCount()

• getTotalValence

  int getTotalValence()

• getCIPChirality

  java.lang.String getCIPChirality​(boolean doCalculate)

• getCIPChiralityCode

  int getCIPChiralityCode()

• setCIPChirality

  void setCIPChirality​(int c)

  Specified by:

  setCIPChirality in interface SimpleNode

• getXYZ

  javajs.util.P3 getXYZ()

  Specified by:

  getXYZ in interface SimpleNode

  Returns:

  the position of this atom

• modelIsRawPDB

  boolean modelIsRawPDB()

• getBioStructureTypeName

  java.lang.String getBioStructureTypeName()

• getGroup1

  java.lang.String getGroup1​(char c0)

• getGroup3

  java.lang.String getGroup3​(boolean allowNull)

• getResno

  int getResno()

• getInsertionCode

  char getInsertionCode()

• getChainID

  int getChainID()

• getChainIDStr

  java.lang.String getChainIDStr()

• getOffsetResidueAtom

  int getOffsetResidueAtom​(java.lang.String name,
                           int offset)

• getCrossLinkVector

  boolean getCrossLinkVector​(javajs.util.Lst<java.lang.Integer> vReturn,
                             boolean crosslinkCovalent,
                             boolean crosslinkHBond)

• getGroupBits

  void getGroupBits​(javajs.util.BS bs)

• isLeadAtom

  boolean isLeadAtom()

• isCrossLinked

  boolean isCrossLinked​(Node node)

• isPurine

  boolean isPurine()

• isPyrimidine

  boolean isPyrimidine()

• isDeleted

  boolean isDeleted()

• getBioSmilesType

  char getBioSmilesType()