Package org.biojava.nbio.protmod

Class ModificationLinkage

  • public class ModificationLinkage
extends java.lang.Object

    • Constructor Detail

      • ModificationLinkage

        public ModificationLinkage​(java.util.List<Component> components,
                           int indexOfComponent1,
                           int indexOfComponent2)
        Parameters:
        components - Components involved in a modification.
        indexOfComponent1 - index of the first component.
        indexOfComponent2 - index of the second component.

      • ModificationLinkage

        public ModificationLinkage​(java.util.List<Component> components,
                           int indexOfComponent1,
                           java.lang.String pdbNameOfAtomsOnComponent1,
                           int indexOfComponent2,
                           java.lang.String pdbNameOfAtomsOnComponent2)
        Parameters:
        components - Components involved in a modification.
        indexOfComponent1 - index of the first component.
        labelOfAtomOnComponent1 - label of the atom on the first component.
        indexOfComponent2 - index of the second component.
        labelOfAtomOnComponent2 - label of the atom on the second component.

      • ModificationLinkage

        public ModificationLinkage​(java.util.List<Component> components,
                           int indexOfComponent1,
                           java.util.List<java.lang.String> pdbNameOfPotentialAtomsOnComponent1,
                           int indexOfComponent2,
                           java.util.List<java.lang.String> pdbNameOfPotentialAtomsOnComponent2)
        Parameters:
        components - Components involved in a modification.
        indexOfComponent1 - index of the first component.
        labelOfAtomOnComponent1 - label of the atom on the first component.
        indexOfComponent2 - index of the second component.
        labelOfAtomOnComponent2 - label of the atom on the second component.

      • ModificationLinkage

        public ModificationLinkage​(java.util.List<Component> components,
                           int indexOfComponent1,
                           java.util.List<java.lang.String> pdbNameOfPotentialAtomsOnComponent1,
                           java.lang.String labelOfAtomOnComponent1,
                           int indexOfComponent2,
                           java.util.List<java.lang.String> pdbNameOfPotentialAtomsOnComponent2,
                           java.lang.String labelOfAtomOnComponent2)
        Parameters:
        components - Components involved in a modification.
        indexOfComponent1 - index of the first component.
        pdbNameOfPotentialAtomsOnComponent1 - a list of PDB names of potential atoms on the first component.
        labelOfAtomOnComponent1 - label of the atom on the first component.
        indexOfComponent2 - index of the second component.
        pdbNameOfPotentialAtomsOnComponent2 - a list of PDB names of potential atoms on the second component.
        labelOfAtomOnComponent2 - label of the atom on the second component.

    • Method Detail

      • getIndexOfComponent1

        public int getIndexOfComponent1()
        Returns:
        index of the first component.

      • getIndexOfComponent2

        public int getIndexOfComponent2()
        Returns:
        index of the second component.

      • getComponent1

        public Component getComponent1()
        Returns:
        the first component.

      • getComponent2

        public Component getComponent2()
        Returns:
        the second component.

      • getPDBNameOfPotentialAtomsOnComponent1

        public java.util.List<java.lang.String> getPDBNameOfPotentialAtomsOnComponent1()
        Returns:
        a list of PDB names of potential atoms on the first component.

      • getPDBNameOfPotentialAtomsOnComponent2

        public java.util.List<java.lang.String> getPDBNameOfPotentialAtomsOnComponent2()
        Returns:
        a list of PDB names of potential atoms on the second component.

      • getLabelOfAtomOnComponent1

        public java.lang.String getLabelOfAtomOnComponent1()
        Returns:
        label of the atom on the first component.

      • getLabelOfAtomOnComponent2

        public java.lang.String getLabelOfAtomOnComponent2()
        Returns:
        label of the atom on the second component.

      • toString

        public java.lang.String toString()
        Overrides:
        toString in class java.lang.Object