Package io.github.WeronikaJargielo.protein_interaction_finder

Class HydrogenBond

  • public final class HydrogenBond
extends java.lang.Object
    Class representing hydrogen bond.

    • Constructor Summary

      Constructors 
      Constructor Description
      HydrogenBond​(AminoAcid donor, AminoAcid acceptor, org.biojava.nbio.structure.Atom donorAtom, org.biojava.nbio.structure.Atom hydrogenAtom, org.biojava.nbio.structure.Atom acceptorAtom, org.biojava.nbio.structure.Atom acceptorAntecedentAtom, double distanceHA, double distanceDA, double angleDHA, double angleHAAa, double angleDAAa)
      Instantiates new hydrogen bond.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      boolean equals​(java.lang.Object o)  
      AminoAcid getAcceptor()
      Returns amino acid of participant with acceptor atom.
      org.biojava.nbio.structure.Atom getAcceptorAntecedentAtom()
      Returns atom preceding hydrogen bond acceptor.
      org.biojava.nbio.structure.Atom getAcceptorAtom()
      Returns hydrogen bond acceptor.
      double getAngleDAAa()
      Returns angle between donor, acceptor and acceptor antecedent.
      double getAngleDHA()
      Returns angle between donor, hydrogen and acceptor.
      double getAngleHAAa()
      Returns angle between hydrogen, acceptor and acceptor antecedent.
      double getDistanceDA()
      Returns distance between donor and acceptor.
      double getDistanceHA()
      Returns distance between hydrogen and acceptor.
      AminoAcid getDonor()
      Returns amino acid of participant with donor atom.
      org.biojava.nbio.structure.Atom getDonorAtom()
      Returns hydrogen bond donor.
      org.biojava.nbio.structure.Atom getHydrogenAtom()
      Returns hydrogen atom bound to donor.
      int hashCode()  
      java.lang.String toString()  

      • Methods inherited from class java.lang.Object

        getClass, notify, notifyAll, wait, wait, wait

    • Constructor Detail

      • HydrogenBond

        public HydrogenBond​(AminoAcid donor,
                    AminoAcid acceptor,
                    org.biojava.nbio.structure.Atom donorAtom,
                    org.biojava.nbio.structure.Atom hydrogenAtom,
                    org.biojava.nbio.structure.Atom acceptorAtom,
                    org.biojava.nbio.structure.Atom acceptorAntecedentAtom,
                    double distanceHA,
                    double distanceDA,
                    double angleDHA,
                    double angleHAAa,
                    double angleDAAa)
        Instantiates new hydrogen bond. For parameters' full description see here.
        Parameters:
        donor - Amino acid of participant with donor atom.
        acceptor - Amino acid of participant with acceptor atom.
        donorAtom - Hydrogen bond donor.
        hydrogenAtom - Hydrogen atom covalently bound to donor atom.
        acceptorAtom - Hydrogen bond acceptor.
        acceptorAntecedentAtom - Atom preceding hydrogen bond acceptor.
        distanceHA - Distance between hydrogen and acceptor.
        distanceDA - Distance between donor and acceptor.
        angleDHA - Angle between donor, hydrogen and acceptor.
        angleHAAa - Angle between hydrogen, acceptor and acceptor antecedent.
        angleDAAa - Angle between donor, acceptor and acceptor antecedent.

    • Method Detail

      • getDonor

        public AminoAcid getDonor()
        Returns amino acid of participant with donor atom.
        Returns:
        Amino acid of participant with donor atom.

      • getAcceptor

        public AminoAcid getAcceptor()
        Returns amino acid of participant with acceptor atom.
        Returns:
        Amino acid of participant with acceptor atom.

      • getDonorAtom

        public org.biojava.nbio.structure.Atom getDonorAtom()
        Returns hydrogen bond donor.
        Returns:
        Hydrogen bond donor.

      • getHydrogenAtom

        public org.biojava.nbio.structure.Atom getHydrogenAtom()
        Returns hydrogen atom bound to donor.
        Returns:
        Hydrogen atom bound to donor.

      • getAcceptorAtom

        public org.biojava.nbio.structure.Atom getAcceptorAtom()
        Returns hydrogen bond acceptor.
        Returns:
        Hydrogen bond acceptor.

      • getAcceptorAntecedentAtom

        public org.biojava.nbio.structure.Atom getAcceptorAntecedentAtom()
        Returns atom preceding hydrogen bond acceptor.
        Returns:
        Atom preceding hydrogen bond acceptor.

      • getDistanceHA

        public double getDistanceHA()
        Returns distance between hydrogen and acceptor.
        Returns:
        Distance between hydrogen and acceptor.

      • getDistanceDA

        public double getDistanceDA()
        Returns distance between donor and acceptor.
        Returns:
        Distance between donor and acceptor.

      • getAngleDHA

        public double getAngleDHA()
        Returns angle between donor, hydrogen and acceptor.
        Returns:
        Angle between donor, hydrogen and acceptor.

      • getAngleHAAa

        public double getAngleHAAa()
        Returns angle between hydrogen, acceptor and acceptor antecedent.
        Returns:
        Angle between hydrogen, acceptor and acceptor antecedent.

      • getAngleDAAa

        public double getAngleDAAa()
        Returns angle between donor, acceptor and acceptor antecedent.
        Returns:
        Angle between donor, acceptor and acceptor antecedent.

      • equals

        public boolean equals​(java.lang.Object o)
        Overrides:
        equals in class java.lang.Object

      • hashCode

        public int hashCode()
        Overrides:
        hashCode in class java.lang.Object

      • toString

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