Package org.jmol.util

Interface Node

    • Method Detail

      • getAtomicAndIsotopeNumber

        int getAtomicAndIsotopeNumber()
      • 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
      • 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

        javajs.util.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
      • getCovalentBondCountPlusMissingH

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

        int getTotalHydrogenCount()
      • getTotalValence

        int getTotalValence()
      • getCIPChirality

        String getCIPChirality​(boolean doCalculate)
      • getCIPChiralityCode

        int getCIPChiralityCode()
      • getXYZ

        javajs.util.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​(javajs.util.Lst<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()