Package ffx.potential.utils


@ParametersAreNonnullByDefault package ffx.potential.utils
The Utils package implements core functionality needed for using the Potential package, such as opening and closing structure files, basic force field energy evaluations, etc.
Since:
1.0
Author:
Michael J. Schnieders
  • Class
    Description
    Cluster contains methods utilized in the Cluster.groovy file.
    Class for cluster objects.
    This ConvexHullOps class uses the QuickHull3D package by John E.
    This Exception class indicates an error in calculating energy or gradients.
     
    GradientUtils is a utility class for testing the gradient of a potential.
    Loop class.
    LoopClosure class.
    The PotentialsFileOpener class specifies a Runnable object which is constructed with a File and, when run, allows returning any opened MolecularAssembly objects and their associated properties.
    PotentialsFunctions describes core functionality for many Force Field X algorithms and scripts, such as opening and closing structure files, basic force field energy evaluations, etc.
    PotentialsUtils implements core functionality for many Force Field X algorithms and scripts, such as opening and closing structure files, basic force field evaluations, etc.
    PotentialTest extends BaseFFXTest to include support for:
    1) Creating a Groovy Binding before each test.
    Class ProgressiveAlignmentOfCrystals holds the majority of the functionality necessary to quantify crystal similarity following the PAC method.
    Structure Metrics contains functionality to calculate characteristics of coordinate systems.