Index (Force Field X 1.0.0 Test API)

A B C D E F G H I L M N O P Q R S T U V W X Z
All Classes and Interfaces|All Packages|Constant Field Values

A

after() - Method in class ffx.potential.bonded.LoopClosureTest
after() - Method in class ffx.potential.groovy.SolvatorTest
amoebaPlusChargeTransferEnergy - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
amoebaPlusIndDipoleEnergyOH - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
amoebaPlusIndDipoleEnergyOO - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
amoebaPlusMPoleEnergyOH - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
amoebaPlusMPoleEnergyOO - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
AMOEBAPlusMultipoleTensorGlobalTest - Class in ffx.numerics.multipole
AMOEBAPlusMultipoleTensorGlobalTest(String, int, Operator) - Constructor for class ffx.numerics.multipole.AMOEBAPlusMultipoleTensorGlobalTest
Angle_getCommonBond() - Method in class ffx.potential.bonded.AngleTest
Angle_getOtherBond() - Method in class ffx.potential.bonded.AngleTest
AngleTest - Class in ffx.potential.bonded: Unit tests for the Angle class.
AngleTest() - Constructor for class ffx.potential.bonded.AngleTest
Atom_addTrajectoryCoords() - Method in class ffx.potential.bonded.AtomTest
Atom_constructor() - Method in class ffx.potential.bonded.AtomTest
Atom_constructor3() - Method in class ffx.potential.bonded.AtomTest
Atom_constructor4() - Method in class ffx.potential.bonded.AtomTest
Atom_destroy() - Method in class ffx.potential.bonded.AtomTest
Atom_equals() - Method in class ffx.potential.bonded.AtomTest
Atom_getBond() - Method in class ffx.potential.bonded.AtomTest
Atom_getNumBonds() - Method in class ffx.potential.bonded.AtomTest
Atom_isBonded() - Method in class ffx.potential.bonded.AtomTest
AtomTest - Class in ffx.potential.bonded: Unit tests for the Atom class.
AtomTest() - Constructor for class ffx.potential.bonded.AtomTest

B

BARDualTopologyTest - Class in ffx.algorithms.groovy
BARDualTopologyTest() - Constructor for class ffx.algorithms.groovy.BARDualTopologyTest
BARFilesTest - Class in ffx.algorithms.groovy
BARFilesTest() - Constructor for class ffx.algorithms.groovy.BARFilesTest
BARSingleTopologyTest - Class in ffx.algorithms.groovy
BARSingleTopologyTest() - Constructor for class ffx.algorithms.groovy.BARSingleTopologyTest
before() - Method in class ffx.algorithms.groovy.DynamicsOpenMMRESPANVETest
before() - Method in class ffx.algorithms.groovy.DynamicsOpenMMStochasticTest
before() - Method in class ffx.potential.groovy.PrepareSpaceGroupsTest
BiotypeTest - Class in ffx.potential.groovy: Test the Biotype script.
BiotypeTest() - Constructor for class ffx.potential.groovy.BiotypeTest
Bond_constructor() - Method in class ffx.potential.bonded.BondTest
Bond_formsAngleWith() - Method in class ffx.potential.bonded.BondTest
Bond_getCommonAtom() - Method in class ffx.potential.bonded.BondTest
Bond_getOtherAtom() - Method in class ffx.potential.bonded.BondTest
Bond_getOtherAtom2() - Method in class ffx.potential.bonded.BondTest
Bond_update() - Method in class ffx.potential.bonded.BondTest
BondTest - Class in ffx.potential.bonded: Unit tests for the Bond class.
BondTest() - Constructor for class ffx.potential.bonded.BondTest
bornI - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
bornK - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest

C

Cart2FracTest - Class in ffx.potential.groovy: Test the Cart2Frac script.
Cart2FracTest() - Constructor for class ffx.potential.groovy.Cart2FracTest
castToDoubleSetTest() - Method in class ffx.numerics.integrate.Integrate1DTest: Ensures that integration performs the same on a DoublesDataSet constructed from a function as directly from the function; uses both DoublesDataSet constructors.
chargeFiniteDifferenceTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
chargeFiniteDifferenceTest() - Method in class ffx.numerics.multipole.GKTensorQITest
chargePenAlphaHyd - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
chargePenAlphaOx - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
chargeTensorTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
chargeTensorTest() - Method in class ffx.numerics.multipole.GKTensorQITest
chrgTranParamsOx - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
CIFFilterTest - Class in ffx.xray.parsers: Test the CIF Filter.
CIFFilterTest() - Constructor for class ffx.xray.parsers.CIFFilterTest
ClusteringTest - Class in ffx.algorithms.groovy: Tests the Cluster command to assess clustering based on distances.
ClusteringTest() - Constructor for class ffx.algorithms.groovy.ClusteringTest
codeGenerationTest() - Method in class ffx.numerics.multipole.MultipoleTensorQITest
codingGenerationTest() - Method in class ffx.numerics.multipole.MultipoleTensorGlobalTest
CombinedTensorTest - Class in ffx.numerics.multipole
CombinedTensorTest(String, int, Operator) - Constructor for class ffx.numerics.multipole.CombinedTensorTest
Complex2DTest - Class in ffx.numerics.fft
Complex2DTest(String, int, int) - Constructor for class ffx.numerics.fft.Complex2DTest
Complex3DParallelTest - Class in ffx.numerics.fft
Complex3DParallelTest(String, int, int, int, int) - Constructor for class ffx.numerics.fft.Complex3DParallelTest
Complex3DTest - Class in ffx.numerics.fft
Complex3DTest(String, int, int, int) - Constructor for class ffx.numerics.fft.Complex3DTest
ComplexTest - Class in ffx.numerics.fft
ComplexTest(String, int, boolean) - Constructor for class ffx.numerics.fft.ComplexTest
CrystalReciprocalSpaceTest - Class in ffx.xray
CrystalReciprocalSpaceTest() - Constructor for class ffx.xray.CrystalReciprocalSpaceTest
CrystalVolumeDerivativeTest - Class in ffx.crystal: Test the Crystal class.
CrystalVolumeDerivativeTest(String, double, double, double, double, double, double, String) - Constructor for class ffx.crystal.CrystalVolumeDerivativeTest

D

data() - Static method in class ffx.algorithms.groovy.DynamicsBeemanBerendsenTest
data() - Static method in class ffx.algorithms.groovy.DynamicsInitVelocitiesTest
data() - Static method in class ffx.algorithms.groovy.DynamicsNVETest
data() - Static method in class ffx.algorithms.groovy.DynamicsNVTTest
data() - Static method in class ffx.algorithms.groovy.DynamicsOpenMMRESPANVETest
data() - Static method in class ffx.algorithms.groovy.DynamicsOpenMMStochasticTest
data() - Static method in class ffx.algorithms.groovy.DynamicsRESPANVETest
data() - Static method in class ffx.algorithms.groovy.DynamicsStochasticTest
data() - Static method in class ffx.algorithms.groovy.OSTGradientTest
data() - Static method in class ffx.algorithms.groovy.SimulatedAnnealingTest
data() - Static method in class ffx.algorithms.groovy.ThermodynamicsTest
data() - Static method in class ffx.algorithms.optimize.RotamerOptimizationTest
data() - Static method in class ffx.crystal.CrystalVolumeDerivativeTest
data() - Static method in class ffx.crystal.ReflectionListTest
data() - Static method in class ffx.numerics.fft.Complex2DTest
data() - Static method in class ffx.numerics.fft.Complex3DParallelTest
data() - Static method in class ffx.numerics.fft.Complex3DTest
data() - Static method in class ffx.numerics.fft.ComplexTest
data() - Static method in class ffx.numerics.fft.Real3DParallelTest
data() - Static method in class ffx.numerics.fft.Real3DTest
data() - Static method in class ffx.numerics.fft.RealTest
data() - Static method in class ffx.numerics.func1d.QuasiLinearSwitchTest
data() - Static method in class ffx.numerics.math.SquareRootTest: The expected values are found using java.lang.Math.sqrt.
data() - Static method in class ffx.numerics.multipole.AMOEBAPlusMultipoleTensorGlobalTest
data() - Static method in class ffx.numerics.multipole.CombinedTensorTest
data() - Static method in class ffx.numerics.multipole.MultipoleTensorGlobalSIMDTest
data() - Static method in class ffx.numerics.multipole.MultipoleTensorGlobalTest
data() - Static method in class ffx.numerics.multipole.MultipoleTensorQISIMDTest
data() - Static method in class ffx.numerics.multipole.MultipoleTensorQITest
data() - Static method in class ffx.numerics.multipole.MultipoleTensorTest
data() - Static method in class ffx.numerics.special.ErfTest: The expected values were found to 20 decimal points of precision using Mathematica: Erf[SetPrecision[x, 20]] Erfc[SetPrecision[x, 20]]
data() - Static method in class ffx.numerics.special.ModifiedBesselTest: The expected values were found to 20 decimal points of precision using Mathematica: SetPrecision[BesselI[0, x], 20]] SetPrecision[BesselI[1, x], 20]]
data() - Static method in class ffx.numerics.spline.UniformBSplineTest
data() - Static method in class ffx.potential.bonded.LoopClosureTest
data() - Static method in class ffx.potential.groovy.EnergyTest
data() - Static method in class ffx.potential.groovy.GKEnergyTest
data() - Static method in class ffx.potential.groovy.OPLSAAEnergyTest
data() - Static method in class ffx.potential.groovy.PhGradientTest
data() - Static method in class ffx.potential.groovy.SolvatorTest
data() - Static method in class ffx.xray.FiniteDifferenceTest
data() - Static method in class ffx.xray.XRayMinimizeTest
dipoleFiniteDifferenceTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
dipoleFiniteDifferenceTest() - Method in class ffx.numerics.multipole.GKTensorQITest
dipoleTensorTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
dipoleTensorTest() - Method in class ffx.numerics.multipole.GKTensorQITest
DynamicsBeemanBerendsenTest - Class in ffx.algorithms.groovy
DynamicsBeemanBerendsenTest(String, String, double, double, double, double) - Constructor for class ffx.algorithms.groovy.DynamicsBeemanBerendsenTest
DynamicsInitVelocitiesTest - Class in ffx.algorithms.groovy
DynamicsInitVelocitiesTest(String, String, double, double, double) - Constructor for class ffx.algorithms.groovy.DynamicsInitVelocitiesTest
DynamicsNVETest - Class in ffx.algorithms.groovy
DynamicsNVETest(String, String, double, double, double, double) - Constructor for class ffx.algorithms.groovy.DynamicsNVETest
DynamicsNVTTest - Class in ffx.algorithms.groovy: Test NVT dynamics on a waterbox.
DynamicsNVTTest(String, String, double, double) - Constructor for class ffx.algorithms.groovy.DynamicsNVTTest
DynamicsOpenMMRESPANVETest - Class in ffx.algorithms.groovy
DynamicsOpenMMRESPANVETest(String, String, double) - Constructor for class ffx.algorithms.groovy.DynamicsOpenMMRESPANVETest
DynamicsOpenMMStochasticTest - Class in ffx.algorithms.groovy
DynamicsOpenMMStochasticTest(String, String, double, double, double) - Constructor for class ffx.algorithms.groovy.DynamicsOpenMMStochasticTest
DynamicsRESPANVETest - Class in ffx.algorithms.groovy
DynamicsRESPANVETest(String, String, double) - Constructor for class ffx.algorithms.groovy.DynamicsRESPANVETest
DynamicsStochasticTest - Class in ffx.algorithms.groovy
DynamicsStochasticTest(String, String, double, double, double, boolean, boolean, boolean) - Constructor for class ffx.algorithms.groovy.DynamicsStochasticTest

E

EnergyTest - Class in ffx.potential.groovy: Test the Energy script.
EnergyTest(String, String, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, boolean) - Constructor for class ffx.potential.groovy.EnergyTest
ErfTest - Class in ffx.numerics.special
ErfTest(String, double, double) - Constructor for class ffx.numerics.special.ErfTest
ExportQETest - Class in ffx.potential.groovy: Tests test.XYZtoQE command to test saving an XYZ file to QE format.
ExportQETest() - Constructor for class ffx.potential.groovy.ExportQETest

F

FFtoXMLTest - Class in ffx.potential.groovy: Test the FFtoXML script.
FFtoXMLTest() - Constructor for class ffx.potential.groovy.FFtoXMLTest
FFTTestSuite - Class in ffx.numerics.fft: FFTTestSuite collects all Unit tests from the ffx.numerics.fft package.
FFTTestSuite() - Constructor for class ffx.numerics.fft.FFTTestSuite
ffx.algorithms.groovy - package ffx.algorithms.groovy
ffx.algorithms.optimize - package ffx.algorithms.optimize
ffx.crystal - package ffx.crystal
ffx.numerics - package ffx.numerics
ffx.numerics.estimator - package ffx.numerics.estimator
ffx.numerics.fft - package ffx.numerics.fft
ffx.numerics.func1d - package ffx.numerics.func1d
ffx.numerics.integrate - package ffx.numerics.integrate
ffx.numerics.math - package ffx.numerics.math
ffx.numerics.multipole - package ffx.numerics.multipole
ffx.numerics.special - package ffx.numerics.special
ffx.numerics.spline - package ffx.numerics.spline
ffx.potential.bonded - package ffx.potential.bonded
ffx.potential.groovy - package ffx.potential.groovy
ffx.potential.nonbonded - package ffx.potential.nonbonded
ffx.potential.parsers - package ffx.potential.parsers
ffx.potential.utils - package ffx.potential.utils
ffx.realspace - package ffx.realspace
ffx.utilities - package ffx.utilities
ffx.xray - package ffx.xray
ffx.xray.parsers - package ffx.xray.parsers
finiteDifferenceTest() - Method in class ffx.crystal.CrystalVolumeDerivativeTest
finiteDifferenceTest() - Method in class ffx.numerics.multipole.MultipoleTensorGlobalTest
finiteDifferenceTest() - Method in class ffx.numerics.multipole.MultipoleTensorQITest
FiniteDifferenceTest - Class in ffx.xray
FiniteDifferenceTest(boolean, String, CrystalReciprocalSpace.SolventModel, int[], String, String) - Constructor for class ffx.xray.FiniteDifferenceTest
ForceFieldFilterTest - Class in ffx.potential.parsers: Test creation of a Force Field object from a CompositeConfiguration.
ForceFieldFilterTest() - Constructor for class ffx.potential.parsers.ForceFieldFilterTest
FormFactorTest - Class in ffx.xray
FormFactorTest() - Constructor for class ffx.xray.FormFactorTest
Frac2CartTest - Class in ffx.potential.groovy: Test the Cart2Frac script.
Frac2CartTest() - Constructor for class ffx.potential.groovy.Frac2CartTest

G

GKEnergyTest - Class in ffx.potential.groovy: Test the Energy script with Generalized Kirkwood parameters.
GKEnergyTest(String, String, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, boolean) - Constructor for class ffx.potential.groovy.GKEnergyTest
GKTensorGlobalTest - Class in ffx.numerics.multipole: Test the GK tensor evaluated in the global coordinate frame.
GKTensorGlobalTest() - Constructor for class ffx.numerics.multipole.GKTensorGlobalTest
GKTensorQITest - Class in ffx.numerics.multipole: Test the GK tensor evaluated in the quasi-internal coordinate frame.
GKTensorQITest() - Constructor for class ffx.numerics.multipole.GKTensorQITest

H

Hybrid36Test - Class in ffx.utilities
Hybrid36Test() - Constructor for class ffx.utilities.Hybrid36Test

I

ImportCIFTest - Class in ffx.potential.groovy: Tests ImportCIF command to determine that files are being translated correctly.
ImportCIFTest() - Constructor for class ffx.potential.groovy.ImportCIFTest
inducedDipoleEnergyAndGradient() - Method in class ffx.numerics.multipole.AMOEBAPlusMultipoleTensorGlobalTest
Integrate1DTest - Class in ffx.numerics.integrate: The IntegrationTest is a JUnit test for the Integration program that ensures that the integrals are calculated correctly.
Integrate1DTest() - Constructor for class ffx.numerics.integrate.Integrate1DTest
integrationTest() - Method in class ffx.numerics.integrate.IntegrationTest: Compares the calculated integrals with the known values.
IntegrationTest - Class in ffx.numerics.integrate: The IntegrationTest is a JUnit test for the Integration program that ensures that the integrals are calculated correctly.
IntegrationTest() - Constructor for class ffx.numerics.integrate.IntegrationTest

L

LambdaGradientTest - Class in ffx.potential.groovy: Tests test.LambdaGradient command to determine that the end state potentials and derivatives are correct.
LambdaGradientTest() - Constructor for class ffx.potential.groovy.LambdaGradientTest
LoopClosureTest - Class in ffx.potential.bonded
LoopClosureTest(double[][], double[][], double[][], double[][]) - Constructor for class ffx.potential.bonded.LoopClosureTest
loopTest() - Method in class ffx.potential.bonded.LoopClosureTest

M

ManyBodyTest - Class in ffx.algorithms.groovy: Tests many body optimization and the many body groovy script under global, box and monte carlo parameter conditions.
ManyBodyTest() - Constructor for class ffx.algorithms.groovy.ManyBodyTest
MBARFilesTest - Class in ffx.algorithms.groovy
MBARFilesTest() - Constructor for class ffx.algorithms.groovy.MBARFilesTest
MBARHarmonicOscillatorsTest - Class in ffx.numerics.estimator
MBARHarmonicOscillatorsTest() - Constructor for class ffx.numerics.estimator.MBARHarmonicOscillatorsTest
MinimizeCrystalsTest - Class in ffx.algorithms.groovy: Tests CrystalMin and CrystalMin.groovy scripts for -e -I -f and -c flags.
MinimizeCrystalsTest() - Constructor for class ffx.algorithms.groovy.MinimizeCrystalsTest
MinimizeTest - Class in ffx.algorithms.groovy: Tests Minimize command to determine if the resulting potential energies with the -e and -I flags works properly.
MinimizeTest() - Constructor for class ffx.algorithms.groovy.MinimizeTest
ModifiedBesselTest - Class in ffx.numerics.special
ModifiedBesselTest(String, double, double, double) - Constructor for class ffx.numerics.special.ModifiedBesselTest
MoveIntoUnitCellTest - Class in ffx.potential.groovy: Test the Cart2Frac script.
MoveIntoUnitCellTest() - Constructor for class ffx.potential.groovy.MoveIntoUnitCellTest
MSNode_constructor() - Method in class ffx.potential.bonded.MSNodeTest
MSNode_destroy() - Method in class ffx.potential.bonded.MSNodeTest
MSNode_equals() - Method in class ffx.potential.bonded.MSNodeTest
MSNodeTest - Class in ffx.potential.bonded: Unit tests for the MSNode class.
MSNodeTest() - Constructor for class ffx.potential.bonded.MSNodeTest
MTZFilterTest - Class in ffx.xray.parsers: Test the MTZ Filter.
MTZFilterTest() - Constructor for class ffx.xray.parsers.MTZFilterTest
multI - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
MultipoleTensorGlobalSIMDTest - Class in ffx.numerics.multipole: Parameterized Test of the MultipoleTensorSIMD class based on previous MultipoleTensorSIMD tests.
MultipoleTensorGlobalSIMDTest(String, int, Operator) - Constructor for class ffx.numerics.multipole.MultipoleTensorGlobalSIMDTest
MultipoleTensorGlobalTest - Class in ffx.numerics.multipole: Parameterized Test of the MultipoleTensor class.
MultipoleTensorGlobalTest(String, int, Operator) - Constructor for class ffx.numerics.multipole.MultipoleTensorGlobalTest
MultipoleTensorQISIMDTest - Class in ffx.numerics.multipole: Parameterized Test of the MultipoleTensorSIMD class based on previous MultipoleTensorSIMD tests.
MultipoleTensorQISIMDTest(String, int, Operator) - Constructor for class ffx.numerics.multipole.MultipoleTensorQISIMDTest
MultipoleTensorQITest - Class in ffx.numerics.multipole: Parameterized Test of the MultipoleTensor class.
MultipoleTensorQITest(String, int, Operator) - Constructor for class ffx.numerics.multipole.MultipoleTensorQITest
multipoleTensorTest() - Method in class ffx.numerics.multipole.MultipoleTensorGlobalTest: Test of recursion and noStorageRecursion methods, of class MultipoleTensor.
multipoleTensorTest() - Method in class ffx.numerics.multipole.MultipoleTensorQITest
MultipoleTensorTest - Class in ffx.numerics.multipole: Parameterized Test of the MultipoleTensor class.
MultipoleTensorTest(String, int) - Constructor for class ffx.numerics.multipole.MultipoleTensorTest
MultipoleTestSuite - Class in ffx.numerics.multipole: MultipoleTestSuite collects all Unit tests from the ffx.numerics.multipole package.
MultipoleTestSuite() - Constructor for class ffx.numerics.multipole.MultipoleTestSuite
multK - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
multSwitchTest() - Method in class ffx.potential.utils.SwitchFunctionTest: Tests multiplicative switch functions.

N

NeckIntegralTest - Class in ffx.potential.nonbonded
NeckIntegralTest() - Constructor for class ffx.potential.nonbonded.NeckIntegralTest
NumericsTestSuite - Class in ffx.numerics: NumericsTestSuite collects all Unit tests from the ffx.numerics package.
NumericsTestSuite() - Constructor for class ffx.numerics.NumericsTestSuite

O

OPLSAAEnergyTest - Class in ffx.potential.groovy: Test OPLS-AA energy and gradient.
OPLSAAEnergyTest(String, String, int, double, int, double, int, double, int, double, int, double, int, double, int) - Constructor for class ffx.potential.groovy.OPLSAAEnergyTest
OSTGradientTest - Class in ffx.algorithms.groovy
OSTGradientTest(String, String, int) - Constructor for class ffx.algorithms.groovy.OSTGradientTest

P

parallelTest() - Method in class ffx.numerics.integrate.Integrate1DTest: Tests the parallelized versions of the integration methods.
ParentEnergyTest - Class in ffx.potential.groovy: Test the Energy script.
ParentEnergyTest(String, String, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, boolean) - Constructor for class ffx.potential.groovy.ParentEnergyTest
permanentEnergy - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
permanentEnergyAndGradientTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
permanentEnergyAndGradientTest() - Method in class ffx.numerics.multipole.GKTensorQITest
permanentEnergyEwald - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
permanentEnergyTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
permanentEnergyTest() - Method in class ffx.numerics.multipole.GKTensorQITest
permanentMultipoleEnergyAndGradTest() - Method in class ffx.numerics.multipole.AMOEBAPlusMultipoleTensorGlobalTest
permanentMultipoleEnergyAndGradTest() - Method in class ffx.numerics.multipole.CombinedTensorTest
permanentMultipoleEnergyAndGradTest() - Method in class ffx.numerics.multipole.MultipoleTensorGlobalSIMDTest
permanentMultipoleEnergyAndGradTest() - Method in class ffx.numerics.multipole.MultipoleTensorGlobalTest
permanentMultipoleEnergyAndGradTest() - Method in class ffx.numerics.multipole.MultipoleTensorQISIMDTest
permanentMultipoleEnergyAndGradTest() - Method in class ffx.numerics.multipole.MultipoleTensorQITest
permGradBorn - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
permGradI - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
permTorqueI - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
permTorqueI - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
permTorqueIEwald - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
permTorqueK - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
permTorqueK - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
permTorqueKEwald - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
PhGradientTest - Class in ffx.potential.groovy: JUnit Tests for the PhGradient Script
PhGradientTest(String, String, String, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, int, double, double) - Constructor for class ffx.potential.groovy.PhGradientTest
PhRepexTest - Class in ffx.algorithms.optimize
PhRepexTest() - Constructor for class ffx.algorithms.optimize.PhRepexTest
polarGradICoulomb - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polarGradIEwald - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polarGradIThole - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polarizationEnergyAndGradientDirectTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
polarizationEnergyAndGradientDirectTest() - Method in class ffx.numerics.multipole.GKTensorQITest
polarizationEnergyAndGradientTest() - Method in class ffx.numerics.multipole.CombinedTensorTest
polarizationEnergyAndGradientTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
polarizationEnergyAndGradientTest() - Method in class ffx.numerics.multipole.GKTensorQITest
polarizationEnergyAndGradientTest() - Method in class ffx.numerics.multipole.MultipoleTensorGlobalSIMDTest
polarizationEnergyAndGradientTest() - Method in class ffx.numerics.multipole.MultipoleTensorQISIMDTest
polarizationEnergyAndGradTest() - Method in class ffx.numerics.multipole.MultipoleTensorGlobalTest
polarizationEnergyAndGradTest() - Method in class ffx.numerics.multipole.MultipoleTensorQITest
polarizationEnergyCoulomb - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polarizationEnergyDirectTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
polarizationEnergyDirectTest() - Method in class ffx.numerics.multipole.GKTensorQITest
polarizationEnergyEwald - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polarizationEnergyTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
polarizationEnergyTest() - Method in class ffx.numerics.multipole.GKTensorQITest
polarizationEnergyThole - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polarTorqueICoulomb - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polarTorqueIEwald - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polarTorqueIThole - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polarTorqueKCoulomb - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polarTorqueKEwald - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polarTorqueKThole - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
polGradBorn - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
polGradBornDirect - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
polGradI - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
polGradIDirect - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
polTorqueI - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
polTorqueIDirect - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
polTorqueK - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
polTorqueKDirect - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
polynomialGrinderTest() - Method in class ffx.numerics.integrate.Integrate1DTest: A more difficult test on polynomials, with just five points and larger coefficients; intended to test stability in extreme cases.
polynomialTest() - Method in class ffx.numerics.integrate.Integrate1DTest: Basic test for polynomial functions; checks to ensure that each integration method is behaving as expected, and returns the exact value (to within machine precision) when the method should be exact.
PrepareSpaceGroupsTest - Class in ffx.potential.groovy: Test the Energy script.
PrepareSpaceGroupsTest() - Constructor for class ffx.potential.groovy.PrepareSpaceGroupsTest

Q

Qi - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
QiAmoebaP - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
QiInduced - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
QiXYZ - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
QjAmoebaP - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
QjInduced - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
QjXYZ - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
Qk - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
QkAmoebaP - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
QkInduced - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
QkXYZ - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
QlAPlusEwal - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
QmAplusEwal - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
quadrupoleTensorTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
quadrupoleTensorTest() - Method in class ffx.numerics.multipole.GKTensorQITest
QuasiLinearSwitchTest - Class in ffx.numerics.func1d
QuasiLinearSwitchTest(String, OptionalDouble, double[], double[][], QuasiLinearThetaMap.Branch[], QuasiLinearThetaMap.Branch[]) - Constructor for class ffx.numerics.func1d.QuasiLinearSwitchTest

R

Real3DParallelTest - Class in ffx.numerics.fft
Real3DParallelTest(String, int, int, int, int) - Constructor for class ffx.numerics.fft.Real3DParallelTest
Real3DTest - Class in ffx.numerics.fft
Real3DTest(String, int, int, int) - Constructor for class ffx.numerics.fft.Real3DTest
RealspaceManyBodyTest - Class in ffx.realspace: Tests Real-space many-body optimization.
RealspaceManyBodyTest() - Constructor for class ffx.realspace.RealspaceManyBodyTest
RealTest - Class in ffx.numerics.fft
RealTest(String, int) - Constructor for class ffx.numerics.fft.RealTest
ReflectionListTest - Class in ffx.crystal: Test the ReflectionList class.
ReflectionListTest(boolean, String, double, double, double, double, double, double, String, double, int, HKL, HKL, int, int) - Constructor for class ffx.crystal.ReflectionListTest
RotamerOptimizationTest - Class in ffx.algorithms.optimize: Test the Goldstein elimination criteria for both self and pair eliminations.
RotamerOptimizationTest(String, String, String, int, int, int, boolean, boolean, boolean, boolean, double, boolean, double, boolean, int, double, boolean, int, int, double, double) - Constructor for class ffx.algorithms.optimize.RotamerOptimizationTest
rWater - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest

S

SaveAsP1Test - Class in ffx.potential.groovy: Test the Energy script.
SaveAsP1Test() - Constructor for class ffx.potential.groovy.SaveAsP1Test
SaveAsPDBTest - Class in ffx.potential.groovy: Test the SaveAsPDB script.
SaveAsPDBTest() - Constructor for class ffx.potential.groovy.SaveAsPDBTest
SaveAsXYZTest - Class in ffx.potential.groovy: Test the SaveAsXYZ script.
SaveAsXYZTest() - Constructor for class ffx.potential.groovy.SaveAsXYZTest
scaleMutual - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
setUp() - Method in class ffx.numerics.fft.Complex2DTest
setUp() - Method in class ffx.numerics.fft.Complex3DParallelTest
setUp() - Method in class ffx.numerics.fft.Complex3DTest
setUp() - Method in class ffx.numerics.fft.Real3DParallelTest
setUp() - Method in class ffx.numerics.fft.Real3DTest
setUp() - Method in class ffx.numerics.integrate.IntegrationTest: Initializes the array before testing.
setUp() - Method in class ffx.potential.bonded.AngleTest
setUp() - Method in class ffx.potential.bonded.AtomTest
setUp() - Method in class ffx.potential.bonded.BondTest
setUp() - Method in class ffx.potential.bonded.MSNodeTest
setUp() - Method in class ffx.potential.bonded.TorsionTest
setUp() - Method in class ffx.xray.FormFactorTest
SimulatedAnnealingTest - Class in ffx.algorithms.groovy
SimulatedAnnealingTest(String, String, double, double, double, double) - Constructor for class ffx.algorithms.groovy.SimulatedAnnealingTest
SolvatorTest - Class in ffx.potential.groovy
SolvatorTest(String, SolvatorTest.SolvatorTestMode, String, String, String, String, String[], String[], String[]) - Constructor for class ffx.potential.groovy.SolvatorTest
SquareRootTest - Class in ffx.numerics.math
SquareRootTest(String, double) - Constructor for class ffx.numerics.math.SquareRootTest
SuperposeCrystalsTest - Class in ffx.algorithms.groovy: Tests SuperposeCrystals command to verify crystals are being aligned and compared.
SuperposeCrystalsTest() - Constructor for class ffx.algorithms.groovy.SuperposeCrystalsTest
SwitchFunctionTest - Class in ffx.potential.utils: Test the various switching functions.
SwitchFunctionTest() - Constructor for class ffx.potential.utils.SwitchFunctionTest

T

tearDown() - Method in class ffx.potential.bonded.AngleTest
tearDown() - Method in class ffx.potential.bonded.AtomTest
tearDown() - Method in class ffx.potential.bonded.BondTest
tearDown() - Method in class ffx.potential.bonded.MSNodeTest
tearDown() - Method in class ffx.potential.bonded.TorsionTest
tensorAuxiliaryTest() - Method in class ffx.numerics.multipole.GKTensorGlobalTest
tensorAuxiliaryTest() - Method in class ffx.numerics.multipole.GKTensorQITest
tensorCountTest() - Method in class ffx.numerics.multipole.MultipoleTensorTest: Test of tensorCount method, of class MultipoleTensor.
tensorIndexTest() - Method in class ffx.numerics.multipole.MultipoleTensorTest: Test of ti method, of class MultipoleTensor.
test1N7SPermanent() - Method in class ffx.xray.CrystalReciprocalSpaceTest: Test of permanent method, of class CrystalReciprocalSpace.
test1NSFPermanent() - Method in class ffx.xray.CrystalReciprocalSpaceTest
testAutoSymGeneration() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Test the automatic symmetry operator generation.
testBAR() - Method in class ffx.algorithms.groovy.BARDualTopologyTest: Tests BAR script with nw input.
testBAR() - Method in class ffx.algorithms.groovy.BARSingleTopologyTest: Tests BAR script with nw input.
testBARFiles() - Method in class ffx.algorithms.groovy.BARFilesTest: Tests BAR script with tinker bar files input.
testBARHelp() - Method in class ffx.algorithms.groovy.BARDualTopologyTest
testBARHelp() - Method in class ffx.algorithms.groovy.BARFilesTest
testBARHelp() - Method in class ffx.algorithms.groovy.BARSingleTopologyTest
testBaseAverageSuperposeCrystals() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script with default settings and average linkage.
testBaseAverageSuperposeCrystalsAlchemicalAtoms() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script alchemical atoms functionality.
testBaseAverageSuperposeCrystalsHandedness() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script on tricky handedness case.
testBaseAverageSuperposeCrystalsHydrogen() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script with hydrogens.
testBaseAverageSuperposeCrystalsPrintSym() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script print symmetry operator functionality.
testBaseAverageSuperposeCrystalsSmallProtein() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script on protein crystal.
testBaseAverageSuperposeCrystalsSohnckeGroup() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script in Sohncke group.
testBaseAverageSuperposeCrystalsZPrime2() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script on asymmetric unit greater than one.
testBaseCluster() - Method in class ffx.algorithms.groovy.ClusteringTest: Tests the Cluster script.
testBaseSingleAUSuperposeCrystals() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script with RMSD size of one.
testBaseSingleMTSuperposeCrystals() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script with small symmetric molecules (can be tricky to determine conformations).
testBaseSingleMTSuperposeCrystals2() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script with small symmetric molecules (can be tricky to determine conformations).
testBaseSingleSuperposeCrystals() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script with default settings.
testBaseSingleSuperposeCrystalsHandedness() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script on tricky handedness case.
testBaseSingleSuperposeCrystalsHydrogen() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script with hydrogens.
testBaseSingleSuperposeCrystalsSmallProtein() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script on protein crystal.
testBaseSingleSuperposeCrystalsSohnckeGroup() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script in Sohncke group.
testBaseSingleSuperposeCrystalsZPrime2() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script on asymmetric unit greater than one.
testBiotype() - Method in class ffx.potential.groovy.BiotypeTest
testBiotypeHelp() - Method in class ffx.potential.groovy.BiotypeTest
testBlockedScalar() - Method in class ffx.numerics.fft.Complex2DTest: Test of the fft and ifft methods, of class Complex3D.
testBlockedScalar() - Method in class ffx.numerics.fft.ComplexTest: Test of fft method, of class Complex.
testBlockedScalarNFFT() - Method in class ffx.numerics.fft.ComplexTest: Test of fft method, of class Complex, using N FFTs packed next to each other.
testBlockedScalarPacked() - Method in class ffx.numerics.fft.Complex2DTest: Test of the fft and ifft methods, of class Complex3D.
testBlockedSIMD() - Method in class ffx.numerics.fft.Complex2DTest: Test of the fft and ifft methods, of class Complex3D.
testBlockedSIMD() - Method in class ffx.numerics.fft.ComplexTest: Test of fft method, of class Complex.
testBlockedSIMDNFFT() - Method in class ffx.numerics.fft.ComplexTest: Test of fft method, of class Complex, using N FFTs packed next to each other.
testBlockedSIMDPacked() - Method in class ffx.numerics.fft.Complex2DTest: Test of the fft and ifft methods, of class Complex3D.
testBSpline() - Method in class ffx.numerics.spline.UniformBSplineTest: Test of bSpline method, of class UniformBSpline.
testBSplineDerivatives() - Method in class ffx.numerics.spline.UniformBSplineTest: Test of bSplineDerivatives method, of class UniformBSpline.
testByBinIntegral() - Method in class ffx.numerics.integrate.Integrate1DTest: Ensures that the by-bin integration machinery matches an all-at-once integral.
testCarbonFF() - Method in class ffx.xray.FormFactorTest
testCarbonfrho() - Method in class ffx.xray.FormFactorTest
testCart2Frac() - Method in class ffx.potential.groovy.Cart2FracTest
testCart2FractHelp() - Method in class ffx.potential.groovy.Cart2FracTest
testCIFFilter2DRM() - Method in class ffx.xray.parsers.CIFFilterTest
testCIFFilter3DYC() - Method in class ffx.xray.parsers.CIFFilterTest
testClusterHelp() - Method in class ffx.algorithms.groovy.ClusteringTest
testConnollyMolecularButane() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly molecular surface area and volume without hydrogen and a 1.4 A exclude radius.
testConnollyMolecularCrambin() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly SEV invalid input: '&' SASA with a 1.4 A exclude radius.
testConnollyMolecularEthylbenzene() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly molecular surface area and volume without hydrogen and a 1.4 A exclude radius.
testConnollyMolecularHydrogenButane() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly molecular surface area and volume without hydrogen and a 1.4 A exclude radius.
testConnollyMolecularHydrogenCrambin() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly SEV invalid input: '&' SASA with a 1.4 A exclude radius and hydrogen atoms.
testConnollyMolecularHydrogenEthylbenzene() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly molecular surface area and volume with hydrogen and a 1.4 A exclude radius.
testConnollySEVButane() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly SEV invalid input: '&' SASA without hydrogen and a 1.4 A exclude radius.
testConnollySEVCrambin() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly SEV invalid input: '&' SASA with a 1.4 A exclude radius.
testConnollySEVEthylbenzene() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly SEV invalid input: '&' SASA without hydrogen and a 1.4 A exclude radius.
testConnollySEVHydrogenButane() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly SEV invalid input: '&' SASA with hydrogen and a 1.4 A exclude radius.
testConnollySEVHydrogenCrambin() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly SEV invalid input: '&' SASA with a 1.4 A exclude radius and hydrogen atoms.
testConnollySEVHydrogenEthylbenzene() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly SEV invalid input: '&' SASA with hydrogen and a 1.4 A exclude radius.
testConnollySEVHydrogenEthylbenzeneDerivatives() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly SEV invalid input: '&' SASA with hydrogen and a 1.4 A exclude radius.
testConnollyVDWCrambin() - Method in class ffx.potential.groovy.VolumeTest: Test Connolly vdW volume and surface area (probe radius = 0.0).
testConvolution() - Method in class ffx.numerics.fft.Complex3DParallelTest: Test of convolution method, of class Complex3D.
testConvolution() - Method in class ffx.numerics.fft.Complex3DTest: Test of convolution method, of class Complex3D.
testConvolution() - Method in class ffx.numerics.fft.Real3DParallelTest: Test of convolution method, of class Real3DParallel.
testConvolution() - Method in class ffx.numerics.fft.Real3DTest: Test of convolution method, of class Real3D.
testCrystalMinConvergenceCriteria() - Method in class ffx.algorithms.groovy.MinimizeCrystalsTest: Tests convergence criteria flag of the CrystalMin class.
testCrystalMinCoords() - Method in class ffx.algorithms.groovy.MinimizeCrystalsTest: Tests the fractional flag of the CrystalMin class.
testCrystalMinFractional() - Method in class ffx.algorithms.groovy.MinimizeCrystalsTest: Tests the fractional flag of the CrystalMin class.
testCrystalMinHelp() - Method in class ffx.algorithms.groovy.MinimizeCrystalsTest
testCrystalMinIterations() - Method in class ffx.algorithms.groovy.MinimizeCrystalsTest: Tests the iterations flag of the CrystalMin class.
testCrystalStats() - Method in class ffx.xray.XRayMinimizeTest
testDecode() - Method in class ffx.utilities.Hybrid36Test: Test of decode method, of class Hybrid36.
testDynamicsBeemanBerendsen() - Method in class ffx.algorithms.groovy.DynamicsBeemanBerendsenTest
testDynamicsHelp() - Method in class ffx.algorithms.groovy.DynamicsNVETest
testDynamicsInitVelocities() - Method in class ffx.algorithms.groovy.DynamicsInitVelocitiesTest
testDynamicsNVE() - Method in class ffx.algorithms.groovy.DynamicsNVETest
testDynamicsNVT() - Method in class ffx.algorithms.groovy.DynamicsNVTTest
testDynamicsOpenMMRESPANVE() - Method in class ffx.algorithms.groovy.DynamicsOpenMMRESPANVETest
testDynamicsOpenMMStochastic() - Method in class ffx.algorithms.groovy.DynamicsOpenMMStochasticTest
testDynamicsStochasticRandomSeed() - Method in class ffx.algorithms.groovy.DynamicsStochasticTest
testDynamicsStochasticRandomSeedFriction0() - Method in class ffx.algorithms.groovy.DynamicsStochasticTest
testDynamicsStochasticRandomSeedFriction01() - Method in class ffx.algorithms.groovy.DynamicsStochasticTest
testEncode() - Method in class ffx.utilities.Hybrid36Test: Test of encode method, of class Hybrid36.
testEndStateEnergyAndGradient() - Method in class ffx.potential.groovy.PhGradientTest
testEnergy() - Method in class ffx.potential.groovy.OPLSAAEnergyTest
testEnergy() - Method in class ffx.potential.groovy.ParentEnergyTest
testErf() - Method in class ffx.numerics.special.ErfTest: Test of erf method, of class Erf.
testErfc() - Method in class ffx.numerics.special.ErfTest: Test of erfc method, of class Erf.
testErfcSpecialCases() - Method in class ffx.numerics.special.ErfTest: Test of erfc method with special values.
testErfSpecialCases() - Method in class ffx.numerics.special.ErfTest: Test of erf method with special values.
testFft() - Method in class ffx.numerics.fft.Complex3DParallelTest: Test of the fft and ifft methods, of class Complex3D.
testFft() - Method in class ffx.numerics.fft.Complex3DTest: Test of the fft and ifft methods, of class Complex3D.
testFft() - Method in class ffx.numerics.fft.Real3DParallelTest: Test of the fft and ifft methods, of class Real3DParallel.
testFft() - Method in class ffx.numerics.fft.Real3DTest: Test of the fft and ifft methods, of class Real3D.
testFft() - Method in class ffx.numerics.fft.RealTest: Test of fft method, of class Complex.
testFFtoXML() - Method in class ffx.potential.groovy.FFtoXMLTest
testFFtoXMLHelp() - Method in class ffx.potential.groovy.FFtoXMLTest
testFiniteDifferences() - Method in class ffx.xray.FiniteDifferenceTest
testFirstOrderModifiedBessel() - Method in class ffx.numerics.special.ModifiedBesselTest: Test of i1 method, of class ModifiedBessel.
testFrac2Cart() - Method in class ffx.potential.groovy.Frac2CartTest
testFrac2CartHelp() - Method in class ffx.potential.groovy.Frac2CartTest
testGaussVolButane() - Method in class ffx.potential.groovy.VolumeTest: Test GaussVol without hydrogen and a 0.4 A radii offset.
testGaussVolCrambin() - Method in class ffx.potential.groovy.VolumeTest: Test GaussVol without hydrogen and a 0.0 A radii offset.
testGaussVolCrambinDerivatives() - Method in class ffx.potential.groovy.VolumeTest: Test GaussVol derivatives.
testGaussVolEthylbenzene() - Method in class ffx.potential.groovy.VolumeTest: Test GaussVol without hydrogen and a 0.4 A radii offset.
testGaussVolHydrogenEthylbenzeneDerivatives() - Method in class ffx.potential.groovy.VolumeTest: Test GaussVol derivatives.
testGradient() - Method in class ffx.potential.groovy.OPLSAAEnergyTest
testGradient() - Method in class ffx.potential.groovy.ParentEnergyTest
testi1OverI0() - Method in class ffx.numerics.special.ModifiedBesselTest: Test utility methods i1OverI0.
testImportCIF() - Method in class ffx.potential.groovy.ImportCIFTest: Test a basic CIF to XYZ conversion.
testImportCIFarc() - Method in class ffx.potential.groovy.ImportCIFTest: Test ImportCIF on concatenated CIF files (produces multiple ARC files).
testImportCIFdisulfide() - Method in class ffx.potential.groovy.ImportCIFTest: Test ImportCIF across a molecular disulfide bond.
testImportCIFHelp() - Method in class ffx.potential.groovy.ImportCIFTest: Print out help message.
testImportCIFMultipleMolecules() - Method in class ffx.potential.groovy.ImportCIFTest: Test ImportCIF when several molecules are included in asymmetric unit.
testImportCIFNoHydrogen() - Method in class ffx.potential.groovy.ImportCIFTest: Test ImportCIF when the CIF file is missing hydrogen atoms.
testImportCIFpdb() - Method in class ffx.potential.groovy.ImportCIFTest: Test ImportCIF conversion to PDB.
testImportCIFWriteAsCIF() - Method in class ffx.potential.groovy.ImportCIFTest: Test writing out a CIF file (XYZ to CIF).
testImportCIFzPrimeChallenge() - Method in class ffx.potential.groovy.ImportCIFTest: Test ImportCIF when similar (but different) molecules are in asymmetric unit.
testInterleavedScalar() - Method in class ffx.numerics.fft.Complex2DTest: Test of the fft and ifft methods, of class Complex3D.
testInterleavedScalar() - Method in class ffx.numerics.fft.ComplexTest: Test of fft method, of class Complex.
testInterleavedScalarNFFT() - Method in class ffx.numerics.fft.ComplexTest: Test of fft method, of class Complex, using N FFTs packed next to each other.
testInterleavedScalarPacked() - Method in class ffx.numerics.fft.Complex2DTest: Test of the fft and ifft methods, of class Complex3D.
testInterleavedSIMD() - Method in class ffx.numerics.fft.Complex2DTest: Test of the fft and ifft methods, of class Complex3D.
testInterleavedSIMD() - Method in class ffx.numerics.fft.ComplexTest: Test of fft method, of class Complex.
testInterleavedSIMDNFFT() - Method in class ffx.numerics.fft.ComplexTest: Test of fft method, of class Complex, using N FFTs packed next to each other.
testInterleavedSIMDPacked() - Method in class ffx.numerics.fft.Complex2DTest: Test of the fft and ifft methods, of class Complex3D.
testInverseSqrt() - Method in class ffx.numerics.math.SquareRootTest: Test inverse sqrt method, of class InverseSqrt.
testLambdaGradient() - Method in class ffx.potential.groovy.LambdaGradientTest: Tests the End States of the LambdaGradient class.
testLambdaGradient() - Method in class ffx.potential.groovy.OPLSAAEnergyTest
testLambdaGradient() - Method in class ffx.potential.groovy.ParentEnergyTest
testLambdaGradientHelp() - Method in class ffx.potential.groovy.LambdaGradientTest
testLambdaGradientIntermolecularSoftcore() - Method in class ffx.potential.groovy.LambdaGradientTest: Tests the End States of the LambdaGradient class when softcore is active.
testLambdaGradientSymOp() - Method in class ffx.potential.groovy.LambdaGradientTest: Tests the End States of the LambdaGradient class when mapped via sym op.
testlnI0() - Method in class ffx.numerics.special.ModifiedBesselTest: Test utility methods lnI0.
testManyBodyBoxOptimization() - Method in class ffx.algorithms.groovy.ManyBodyTest: Tests ManyBody.groovy and RotamerOptimization.java by running a box optimization simulation on a small pdb file.
testManyBodyBoxRestart() - Method in class ffx.algorithms.groovy.ManyBodyTest: Tests the restart file functionality for box optimization.
testManyBodyGlobal() - Method in class ffx.algorithms.groovy.ManyBodyTest
testManyBodyGlobal() - Method in class ffx.realspace.RealspaceManyBodyTest
testManyBodyGlobal() - Method in class ffx.xray.XRayManyBodyTest
testManyBodyHelp() - Method in class ffx.algorithms.groovy.ManyBodyTest
testManyBodyHelp() - Method in class ffx.realspace.RealspaceManyBodyTest
testManyBodyHelp() - Method in class ffx.xray.XRayManyBodyTest
testManyBodyMonteCarlo() - Method in class ffx.algorithms.groovy.ManyBodyTest: Tests ManyBody.groovy and RotamerOptimization.java by running a monte carlo optimization simulation on a small pdb file.
testManyBodyRestart() - Method in class ffx.algorithms.groovy.ManyBodyTest: Tests the restart file functionality.
testManyBodyTitration() - Method in class ffx.algorithms.groovy.ManyBodyTest
testMBARFiles() - Method in class ffx.algorithms.groovy.MBARFilesTest: Tests MBAR groovy script that reads in MBAR files.
testMBAROscillators() - Method in class ffx.numerics.estimator.MBARHarmonicOscillatorsTest: Test the MBAR estimator numerics with harmonic oscillators.
testMetaDynamicsGradient() - Method in class ffx.algorithms.groovy.OSTGradientTest
testMinimizeConvergenceCriteria() - Method in class ffx.algorithms.groovy.MinimizeTest: Tests convergence criteria flag of the minimize class.
testMinimizeHelp() - Method in class ffx.algorithms.groovy.MinimizeTest
testMinimizeIterations() - Method in class ffx.algorithms.groovy.MinimizeTest: Tests the iterations flag of the minimize class.
testMoveIntoUnitCell() - Method in class ffx.potential.groovy.MoveIntoUnitCellTest
testMoveIntoUnitCellHelp() - Method in class ffx.potential.groovy.MoveIntoUnitCellTest
testMTZHKL() - Method in class ffx.xray.parsers.MTZFilterTest
testMTZParams() - Method in class ffx.xray.parsers.MTZFilterTest
testMTZReadFile() - Method in class ffx.xray.parsers.MTZFilterTest
testMTZReflectionList() - Method in class ffx.xray.parsers.MTZFilterTest
testOpenMMEnergy() - Method in class ffx.potential.groovy.ParentEnergyTest
testOSTBiasHelp() - Method in class ffx.algorithms.groovy.OSTGradientTest
testOSTGradient() - Method in class ffx.algorithms.groovy.OSTGradientTest
testPairEnergyElimination() - Method in class ffx.algorithms.optimize.RotamerOptimizationTest
testParse() - Method in class ffx.potential.parsers.ForceFieldFilterTest: Test of parse method, of class ForceFieldFilter.
testPhRepexExchangeValidity() - Method in class ffx.algorithms.optimize.PhRepexTest
testPhRepexRestarts() - Method in class ffx.algorithms.optimize.PhRepexTest
testPoints() - Method in class ffx.numerics.func1d.QuasiLinearSwitchTest
testPowerInterpolation() - Method in class ffx.potential.utils.SwitchFunctionTest: Tests interpolation via the PowerSwitch class.
testPreferredDimension() - Method in class ffx.numerics.fft.ComplexTest: Test of preferredDimension method, of class Complex.
testPrepareSpaceGroupHelp() - Method in class ffx.potential.groovy.PrepareSpaceGroupsTest
testPrepareSpaceGroups() - Method in class ffx.potential.groovy.PrepareSpaceGroupsTest
testPrepareSpaceGroupsAChiral() - Method in class ffx.potential.groovy.PrepareSpaceGroupsTest
testPrepareSpaceGroupsChiral() - Method in class ffx.potential.groovy.PrepareSpaceGroupsTest
testreflections() - Method in class ffx.crystal.ReflectionListTest
testRESPANVE() - Method in class ffx.algorithms.groovy.DynamicsRESPANVETest
testSaveAsP1() - Method in class ffx.potential.groovy.SaveAsP1Test
testSaveAsP1Help() - Method in class ffx.potential.groovy.SaveAsP1Test
testSaveAsPDB() - Method in class ffx.potential.groovy.SaveAsPDBTest
testSaveAsPDBHelp() - Method in class ffx.potential.groovy.SaveAsPDBTest
testSaveAsXYZ() - Method in class ffx.potential.groovy.SaveAsXYZTest
testSaveAsXYZHelp() - Method in class ffx.potential.groovy.SaveAsXYZTest
testScaleBulk() - Method in class ffx.xray.XRayMinimizeTest
testSelfEnergyElimination() - Method in class ffx.algorithms.optimize.RotamerOptimizationTest
testSettingConstants() - Method in class ffx.potential.nonbonded.NeckIntegralTest
testSigmaA() - Method in class ffx.xray.XRayMinimizeTest
testSimulatedAnnealing() - Method in class ffx.algorithms.groovy.SimulatedAnnealingTest
testSinCosine() - Method in class ffx.numerics.integrate.Integrate1DTest
testsize() - Method in class ffx.crystal.ReflectionListTest
testSolvator() - Method in class ffx.potential.groovy.SolvatorTest
testSpecialValues() - Method in class ffx.numerics.special.ModifiedBesselTest: Test special values for i0 and i1 methods.
testSplineF1F2() - Method in class ffx.xray.XRayMinimizeTest
testSplineFCTOESQ() - Method in class ffx.xray.XRayMinimizeTest
testSplineFOFC() - Method in class ffx.xray.XRayMinimizeTest
testSplineFOTOESQ() - Method in class ffx.xray.XRayMinimizeTest
testSqrt() - Method in class ffx.numerics.math.SquareRootTest: Test sqrt method, of class InverseSqrt.
testSuperposeCrystalsHelp() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest
testSuperposeCrystalsLongMolecule() - Method in class ffx.algorithms.groovy.SuperposeCrystalsTest: Tests the SuperposeCrystals script on long molecule (potential issue with inflation factor).
testThermodynamics() - Method in class ffx.algorithms.groovy.ThermodynamicsTest
testTimer() - Method in class ffx.potential.groovy.TimerTest
testTimerHelp() - Method in class ffx.potential.groovy.TimerTest
testXYZtoQE() - Method in class ffx.potential.groovy.ExportQETest: Tests the XYZtoQE script.
testXYZtoQEHelp() - Method in class ffx.potential.groovy.ExportQETest
testZeroOrderModifiedBessel() - Method in class ffx.numerics.special.ModifiedBesselTest: Test of i0 method, of class ModifiedBessel.
ThermodynamicsTest - Class in ffx.algorithms.groovy: Tests the functionality of the OST algorithm in Force Field X, both by running a very simple and quick OST run, and setting up a number of systems, comparing output energies and gradients from the starting algorithmConfig.
ThermodynamicsTest(String, String[], ThermodynamicsTest.ThermoTestMode, boolean, double, double, int[], double[], double[], double[], double[][][], double[][][], String[], String[], String[]) - Constructor for class ffx.algorithms.groovy.ThermodynamicsTest
TimerTest - Class in ffx.potential.groovy: Test the Energy script.
TimerTest() - Constructor for class ffx.potential.groovy.TimerTest
Torsion_constructor() - Method in class ffx.potential.bonded.TorsionTest
TorsionTest - Class in ffx.potential.bonded: Unit tests for the Torsion class.
TorsionTest() - Constructor for class ffx.potential.bonded.TorsionTest
toString() - Method in class ffx.numerics.func1d.QuasiLinearSwitchTest
toString() - Method in class ffx.potential.groovy.SolvatorTest
trigTest() - Method in class ffx.potential.utils.SwitchFunctionTest

U

uI - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
Ui - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
uIDirect - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
UiEwald - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
uK - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
Uk - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
uKDirect - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
UkEwald - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
UniformBSplineTest - Class in ffx.numerics.spline: Parameterized test of the UniformBSpline class.
UniformBSplineTest(String, int, double, double[], double[]) - Constructor for class ffx.numerics.spline.UniformBSplineTest: Parameterized test of the UniformBSpline class.

V

VolumeTest - Class in ffx.potential.groovy: JUnit Tests for the Volume Script
VolumeTest() - Constructor for class ffx.potential.groovy.VolumeTest

W

watPermEnergy - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
watPolDirect - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
watPolEnergy - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
watTotalDirect - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest
watTotalEnergy - Static variable in class ffx.numerics.multipole.GKTensorGlobalTest

X

XRayManyBodyTest - Class in ffx.xray: Tests X-Ray many body optimization and the X-Ray many body groovy script under varying parameters.
XRayManyBodyTest() - Constructor for class ffx.xray.XRayManyBodyTest
XRayMinimizeTest - Class in ffx.xray
XRayMinimizeTest(boolean, String, String, String, String, double, double, double, double) - Constructor for class ffx.xray.XRayMinimizeTest
xyz - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
xyzEwaldAPlus - Static variable in class ffx.numerics.multipole.MultipoleTensorTest

Z

Zi - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
Zj - Static variable in class ffx.numerics.multipole.MultipoleTensorTest
Zk - Static variable in class ffx.numerics.multipole.MultipoleTensorTest

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