Package ffx.algorithms.groovy

Class ManyBodyTest

java.lang.Object
ffx.utilities.FFXTest
ffx.algorithms.misc.AlgorithmsTest
ffx.algorithms.groovy.ManyBodyTest
public class ManyBodyTest extends ffx.algorithms.misc.AlgorithmsTest
Tests many body optimization and the many body groovy script under global, box and monte carlo parameter conditions.
Author:
Mallory R. Tollefson

  • Field Summary

    Fields inherited from class ffx.algorithms.misc.AlgorithmsTest

    algorithmsScript, binding

    Fields inherited from class ffx.utilities.FFXTest

    ffxCI, ffxOpenMM, logger

  • Constructor Summary

    Constructors
    Constructor
    Description
    ManyBodyTest()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    testManyBodyBoxOptimization()
    Tests ManyBody.groovy and RotamerOptimization.java by running a box optimization simulation on a small pdb file.
    void
    testManyBodyBoxRestart()
    Tests the restart file functionality for box optimization.
    void
    testManyBodyGlobal()
     
    void
    testManyBodyHelp()
     
    void
    testManyBodyMonteCarlo()
    Tests ManyBody.groovy and RotamerOptimization.java by running a monte carlo optimization simulation on a small pdb file.
    void
    testManyBodyRestart()
    Tests the restart file functionality.
    void
    testManyBodyTitration()
     

    Methods inherited from class ffx.algorithms.misc.AlgorithmsTest

    afterTest, beforeClass, beforeTest, getResourceFile, getResourcePath

    Methods inherited from class ffx.utilities.FFXTest

    afterClass, registerTemporaryDirectory

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • ManyBodyTest

      public ManyBodyTest()

  • Method Details

    • testManyBodyBoxOptimization

      public void testManyBodyBoxOptimization()
      Tests ManyBody.groovy and RotamerOptimization.java by running a box optimization simulation on a small pdb file.

    • testManyBodyBoxRestart

      public void testManyBodyBoxRestart()
      Tests the restart file functionality for box optimization. The test applies a 1.5 angstrom 2-body and 3-body cutoff but the restart file was generated using 2-body and 3-body cutoffs of 2 angstroms.

    • testManyBodyGlobal

      public void testManyBodyGlobal()

    • testManyBodyHelp

      public void testManyBodyHelp()

    • testManyBodyMonteCarlo

      public void testManyBodyMonteCarlo()
      Tests ManyBody.groovy and RotamerOptimization.java by running a monte carlo optimization simulation on a small pdb file. Elimination criteria are not used during this test. A Monte Carlo search is done on the permutations.

    • testManyBodyRestart

      public void testManyBodyRestart()
      Tests the restart file functionality. The test applies a 1.5 angstrom 2-body and 3-body cutoff but the restart file was generated using 2-body and 3-body cutoffs of 2 angstroms.

    • testManyBodyTitration

      public void testManyBodyTitration()