Class GeometryCalculator


  • public class GeometryCalculator
    extends java.lang.Object
    Utility class to perform 3D geometry calculations on molecules
    • Constructor Detail

      • GeometryCalculator

        public GeometryCalculator()
    • Method Detail

      • getAngle

        public static final double getAngle​(StereoMolecule mol,
                                            int a1,
                                            int a2,
                                            int a3)
        Gets the Angle between 3 atoms
        Parameters:
        mol -
        a1 -
        a2 -
        a3 -
        Returns:
        the angle
      • getDihedral

        public static final double getDihedral​(StereoMolecule mol,
                                               int a1,
                                               int a2,
                                               int a3,
                                               int a4)
        Gets the Dihedral Angle between 4 atoms
        Parameters:
        mol -
        a1 -
        a2 -
        a3 -
        a4 -
        Returns:
        the angle
      • getCenterGravity

        public static final Coordinates getCenterGravity​(StereoMolecule mol)
        Gets the center of Gravity of a molecule
        Parameters:
        mol -
        Returns:
      • getBounds

        public static final Coordinates[] getBounds​(StereoMolecule molecule)
        Gets the Bounds of a molecule
        Parameters:
        molecule -
        Returns:
        an Array of Coordinares [lowerBounds, upperbounds]
      • translate

        public static final void translate​(StereoMolecule molecule,
                                           Coordinates c)
        Translate a Molecule
        Parameters:
        molecule -
        c -