Enum AlignmentProperties.FlexibilityMode

  • All Implemented Interfaces:
    Serializable, Comparable<AlignmentProperties.FlexibilityMode>
    Enclosing class:

    public static enum AlignmentProperties.FlexibilityMode
    extends Enum<AlignmentProperties.FlexibilityMode>
    Conformational flexibility treatment during the alignment for a pair of a molecule. If the reference molecule is set as rigid its coordinates remains intact, while if it is set for the second molecule, that will translate and rotate as a rigid body. If any molecule is set flexible it will translate and rotate and also, and if it has rotatable bonds, the dihedral angles around these bonds are tweaked in a continuous manner enabling the conformation to change to maximize the overlay.
    • Enum Constant Detail


        public static final AlignmentProperties.FlexibilityMode KEEP_FIRST_RIGID_SECOND_FLEXIBLE
        Keep the first reference structure rigid, and the second as flexible during the alignment.

        public static final AlignmentProperties.FlexibilityMode KEEP_FIRST_RIGID_SECOND_FLEXIBLE_EXTRA
        As of KEEP_FIRST_RIGID_SECOND_FLEXIBLE with an extension of some otherwise rigid bond is kept flexible.(e.g.: double or amide bonds). So the cis amide in second molecule can be tweaked to trans if it is favored by the alignment.
    • Method Detail

      • values

        public static AlignmentProperties.FlexibilityMode[] values()
        Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:
        for (AlignmentProperties.FlexibilityMode c : AlignmentProperties.FlexibilityMode.values())
        an array containing the constants of this enum type, in the order they are declared
      • valueOf

        public static AlignmentProperties.FlexibilityMode valueOf​(String name)
        Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (Extraneous whitespace characters are not permitted.)
        name - the name of the enum constant to be returned.
        the enum constant with the specified name
        IllegalArgumentException - if this enum type has no constant with the specified name
        NullPointerException - if the argument is null