Package org.biojava.nbio.structure.chem

Class ChemCompBond

  • All Implemented Interfaces:
    java.io.Serializable, CifBean
    public class ChemCompBond
extends java.lang.Object
implements CifBean
    Properties of a bond in a chemical component.
    Since:
    6.0.0
    Author:
    Sebastian Bittrich
    See Also:
    Serialized Form

    • Constructor Detail

      • ChemCompBond

        public ChemCompBond()

    • Method Detail

      • getLogger

        public static org.slf4j.Logger getLogger()

      • getCompId

        public java.lang.String getCompId()

      • setCompId

        public void setCompId​(java.lang.String compId)

      • getAtomId1

        public java.lang.String getAtomId1()

      • setAtomId1

        public void setAtomId1​(java.lang.String atomId1)

      • getAtomId2

        public java.lang.String getAtomId2()

      • setAtomId2

        public void setAtomId2​(java.lang.String atomId2)

      • getValueOrder

        public java.lang.String getValueOrder()

      • setValueOrder

        public void setValueOrder​(java.lang.String valueOrder)

      • getPdbxAromaticFlag

        public java.lang.String getPdbxAromaticFlag()

      • setPdbxAromaticFlag

        public void setPdbxAromaticFlag​(java.lang.String pdbxAromaticFlag)

      • getPdbxStereoConfig

        public java.lang.String getPdbxStereoConfig()

      • setPdbxStereoConfig

        public void setPdbxStereoConfig​(java.lang.String pdbxStereoConfig)

      • getPdbxOrdinal

        public int getPdbxOrdinal()

      • setPdbxOrdinal

        public void setPdbxOrdinal​(int pdbxOrdinal)

      • getNumericalBondOrder

        public int getNumericalBondOrder()
        Converts this ChemCompBond's value_order attribute into an int using the conversion: 
                SING -> 1
        DOUB -> 2
        TRIP -> 3
        QUAD -> 4
        Any other values will return -1.

        (Source: http://mmcif.rcsb.org/dictionaries/mmcif_mdb.dic/Items/_chem_comp_bond. value_order.html)

        Returns:
        the numerical value of this ChemCompBond's bond order, or -1 if the value is non-numeric or unknown.