Package org.jmol.util

Interface Node

All Superinterfaces:
SimpleNode
All Known Implementing Classes:
Atom, SmilesAtom
public interface Node extends SimpleNode

  • Method Details

    • getAtomicAndIsotopeNumber

      int getAtomicAndIsotopeNumber()

    • getAtomName

      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 atom

    • 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(String property)
      Parameters:
      property - "property_xxxx"
      Returns:
      value or Float.NaN

    • findAtomsLike

      BS findAtomsLike(String substring)

    • getAtomType

      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

    • getExplicitHydrogenCount

      int getExplicitHydrogenCount()
      [CH2] for example
      Returns:
      number of H atoms in brackets

    • getCovalentBondCountPlusMissingH

      int getCovalentBondCountPlusMissingH()
      includes actual + missing
      Returns:
      actual + missing

    • getTotalHydrogenCount

      int getTotalHydrogenCount()

    • getTotalValence

      int getTotalValence()

    • getCIPChirality

      String getCIPChirality(boolean doCalculate)

    • getCIPChiralityCode

      int getCIPChiralityCode()

    • setCIPChirality

      void setCIPChirality(int c)
      Specified by:
      setCIPChirality in interface SimpleNode

    • getXYZ

      P3 getXYZ()
      Specified by:
      getXYZ in interface SimpleNode
      Returns:
      the position of this atom

    • modelIsRawPDB

      boolean modelIsRawPDB()

    • getBioStructureTypeName

      String getBioStructureTypeName()

    • getGroup1

      String getGroup1(char c0)

    • getGroup3

      String getGroup3(boolean allowNull)

    • getResno

      int getResno()

    • getInsertionCode

      char getInsertionCode()

    • getChainID

      int getChainID()

    • getChainIDStr

      String getChainIDStr()

    • getOffsetResidueAtom

      int getOffsetResidueAtom(String name, int offset)

    • getCrossLinkVector

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

    • getGroupBits

      void getGroupBits(BS bs)

    • isLeadAtom

      boolean isLeadAtom()

    • isCrossLinked

      boolean isCrossLinked(Node node)

    • isPurine

      boolean isPurine()

    • isPyrimidine

      boolean isPyrimidine()

    • isDeleted

      boolean isDeleted()

    • getBioSmilesType

      char getBioSmilesType()