Enum Class AlignmentProperties.FlexibilityMode

All Implemented Interfaces:
Serializable, Comparable<AlignmentProperties.FlexibilityMode>, java.lang.constant.Constable
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 Details


      public static final AlignmentProperties.FlexibilityMode KEEP_BOTH_RIGID
      Keep both structures conformationally rigid during the alignment.

      public static final AlignmentProperties.FlexibilityMode KEEP_BOTH_FLEXIBLE
      Keep both structures flexible during the alignment.

      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 Details