Class Angle


  • public final class Angle
    extends java.lang.Object
    The angle type class provides static functions for getting angle and stretch bend MMFF type.
    • Constructor Summary

      Constructors 
      Constructor Description
      Angle()  
    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static int getStbnType​(Tables table, MMFFMolecule mol, int a1, int a2, int a3)
      Given three atoms which form an angle, returns the MMFF stretch-bend type of the angle.
      static int getType​(Tables table, MMFFMolecule mol, int a1, int a2, int a3)
      Gets the angle type of an angle bend.
      static boolean inRingOfSize​(MMFFMolecule mol, int a1, int a2, int a3, int size)
      Checks if an angle is in a ring of given size.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • Angle

        public Angle()
    • Method Detail

      • inRingOfSize

        public static boolean inRingOfSize​(MMFFMolecule mol,
                                           int a1,
                                           int a2,
                                           int a3,
                                           int size)
        Checks if an angle is in a ring of given size. Will also check that the atoms form an angle.
        Parameters:
        mol - The molecule that the angle is in.
        a1 - Atom 1 of the angle.
        a2 - Atom 2 of the angle.
        a3 - Atom 3 of the angle.
        size - The size of ring to check for.
        Returns:
        True if the angle is in the given size, false otherwise.
      • getType

        public static int getType​(Tables table,
                                  MMFFMolecule mol,
                                  int a1,
                                  int a2,
                                  int a3)
        Gets the angle type of an angle bend. The possible return types are as follows: 0: The angle i-j-k is a "normal" bond angle. 1: Either bond i-j or bond j-k has a bond type of 1. 2: Bonds i-j and j-k each have bond types of 1; The sum is 2. 3: The angle occurs in a three member ring. 4: The angle occurs in a four member ring. 5: The angle is in a three member ring and the sum of the bond types is 1. 6: The angle is in a three member ring and the sum of the bond types is 2. 7: The angle is in a four member ring and the sum of the bond types is 1. 8: The angle is in a four member ring and the sum of the bond types is 2.
      • getStbnType

        public static int getStbnType​(Tables table,
                                      MMFFMolecule mol,
                                      int a1,
                                      int a2,
                                      int a3)
        Given three atoms which form an angle, returns the MMFF stretch-bend type of the angle.
        Parameters:
        mol - The molecule containing the atoms.
        a1 - Atom 1 (atom i).
        a2 - Atom 2, the central atom (atom j).
        a3 - Atom 3 (atom k).
        Returns:
        The stretch-bend type.