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
-
ClassDescriptionCluster contains methods utilized in the
Cluster.groovyfile.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.