Package io.github.WeronikaJargielo.protein_interaction_finder

Class AromaticRing

  • public final class AromaticRing
extends java.lang.Object
    Class representing single aromatic ring in protein. Considered aromatic rings are phenyl ring in Phe, Tyr and Trp and pyrrole ring in Trp.

    • Constructor Summary

      Constructors 
      Constructor Description
      AromaticRing​(java.util.List<org.biojava.nbio.structure.Atom> atoms)
      Instantiates new Aromatic ring.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      javax.vecmath.Point3d calculateAtomProjectionOnRing​(org.biojava.nbio.structure.Atom atom)
      Calculate projection of given atom on aromatic ring plane.
      double calculateAzimuthalAngleOfAtom​(org.biojava.nbio.structure.Atom atom)
      Calculate azimuthal angle for given atom.
      double calculateElevationAngleOfAtom​(org.biojava.nbio.structure.Atom atom)
      Calculate elevation angle for given atom.
      double calculateEquatorialAngleOfAtom​(org.biojava.nbio.structure.Atom atom)
      Calculate equatorial angle for given atom.
      double calculatePolarAngleOfAtom​(org.biojava.nbio.structure.Atom atom)
      Calculate polar angle for given atom.
      AminoAcid getAminoAcid()
      Returns amino acid of the aromatic ring.
      org.biojava.nbio.structure.Atom[] getAtoms()
      Returns atoms forming the aromatic ring.
      org.biojava.nbio.structure.Group getGroup()
      Returns group representing aromatic ring's amino acid.
      javax.vecmath.Vector3d getNormalVector()
      Returns normal vector to aromatic ring plane.
      org.biojava.nbio.structure.Atom getRingCentroid()
      Returns ring centroid.

      • Methods inherited from class java.lang.Object

        equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • AromaticRing

        public AromaticRing​(java.util.List<org.biojava.nbio.structure.Atom> atoms)
        Instantiates new Aromatic ring.
        Parameters:
        atoms - Atoms forming the aromatic ring.

    • Method Detail

      • getAtoms

        public org.biojava.nbio.structure.Atom[] getAtoms()
        Returns atoms forming the aromatic ring.
        Returns:
        Atoms forming the aromatic ring.

      • getGroup

        public org.biojava.nbio.structure.Group getGroup()
        Returns group representing aromatic ring's amino acid.
        Returns:
        BioJava Group representing aromatic ring's amino acid.

      • getAminoAcid

        public AminoAcid getAminoAcid()
        Returns amino acid of the aromatic ring.
        Returns:
        Amino acid of the aromatic ring.

      • getRingCentroid

        public org.biojava.nbio.structure.Atom getRingCentroid()
        Returns ring centroid.
        Returns:
        Atom representing geometrical centre of aromatic ring.

      • getNormalVector

        public javax.vecmath.Vector3d getNormalVector()
        Returns normal vector to aromatic ring plane.
        Returns:
        Normal vector to aromatic ring plane.

      • calculatePolarAngleOfAtom

        public double calculatePolarAngleOfAtom​(org.biojava.nbio.structure.Atom atom)
        Calculate polar angle for given atom. See angle β here.
        Parameters:
        atom - Atom to calculate the polar angle for.
        Returns:
        Polar angle for given atom.

      • calculateAzimuthalAngleOfAtom

        public double calculateAzimuthalAngleOfAtom​(org.biojava.nbio.structure.Atom atom)
        Calculate azimuthal angle for given atom. See angle α here.
        Parameters:
        atom - Atom to calculate the azimuthal angle for.
        Returns:
        Azimuthal angle for given atom.

      • calculateElevationAngleOfAtom

        public double calculateElevationAngleOfAtom​(org.biojava.nbio.structure.Atom atom)
        Calculate elevation angle for given atom. See angle β here.
        Parameters:
        atom - Atom to calculate the elevation angle for.
        Returns:
        Elevation angle for given atom.

      • calculateEquatorialAngleOfAtom

        public double calculateEquatorialAngleOfAtom​(org.biojava.nbio.structure.Atom atom)
        Calculate equatorial angle for given atom. See angle α here.
        Parameters:
        atom - Atom to calculate the equatorial angle for.
        Returns:
        Equatorial angle for given atom.

      • calculateAtomProjectionOnRing

        public javax.vecmath.Point3d calculateAtomProjectionOnRing​(org.biojava.nbio.structure.Atom atom)
        Calculate projection of given atom on aromatic ring plane.
        Parameters:
        atom - Atom to calculate the projection of.
        Returns:
        Point representing projection of atom on aromatic ring plane.