A | B | C | D | E | F | G | H | I | J | L | M | O | P | Q | R | S | T | U | Y

A

DatabaseParametrizationTests (Scine::Tests)

ImproperDihedral (Scine::MolecularMechanics)

O

S

Default (Scine::StructurePreparation)

ImproperDihedralParameters (Scine::MolecularMechanics)

AGaffMolecularMechanicsTest (Scine::Tests)

Dihedral (Scine::MolecularMechanics)

ImproperDihedralsEvaluator (Scine::MolecularMechanics)

OptimizationSetup (Scine::MMParametrization)

ScaledInteractions (Scine::MolecularMechanics)

AminoAcidCategorizer (Scine::StructurePreparation)

DihedralParameters (Scine::MolecularMechanics)

ImproperDihedralTerm (Scine::MolecularMechanics)

P

SettingsPopulator (Scine::SwooseUtilities)

AMolecularMachineLearningTest (Scine::Tests)

DihedralsEvaluator (Scine::MolecularMechanics)

ImproperDihedralType (Scine::MolecularMechanics)

SfamAtomTypeIdentifier (Scine::MolecularMechanics)

Angle (Scine::MolecularMechanics)

DihedralTerm (Scine::MolecularMechanics)

IndexedStructuralAngle (Scine::MolecularMechanics)

ParameterFileWriter (Scine::MMParametrization)

SfamCalculatorSettings (Scine::MolecularMechanics)

AngleParameters (Scine::MolecularMechanics)

DihedralType (Scine::MolecularMechanics)

IndexedStructuralBond (Scine::MolecularMechanics)

ParameterOptimizer (Scine::MMParametrization)

SfamInteractionTermEliminatorTest (Scine::Tests)

AnglesEvaluator (Scine::MolecularMechanics)

Dispersion (Scine::MolecularMechanics)

IndexedStructuralDihedral (Scine::MolecularMechanics)

ParametrizationData (Scine::MMParametrization)

SfamMolecularMechanicsCalculator (Scine::MolecularMechanics)

AngleTerm (Scine::MolecularMechanics)

DispersionEvaluator (Scine::MolecularMechanics)

IndexedStructuralHydrogenBond (Scine::MolecularMechanics)

Parametrizer (Scine::MMParametrization)

SfamParameterParser (Scine::MolecularMechanics)

AngleType (Scine::MolecularMechanics)

DispersionTerm (Scine::MolecularMechanics)

IndexedStructuralImproperDihedral (Scine::MolecularMechanics)

PeptidBond (Scine::StructurePreparation)

SfamParameters (Scine::MolecularMechanics)

AParametrizationOfLargeSystemsTest (Scine::Tests)

E

IndexedStructuralScaledNonBonded (Scine::MolecularMechanics)

ProteinAtom (Scine::StructurePreparation)

SfamPotentialTermsGenerator (Scine::MolecularMechanics)

AParametrizationOfSmallSystemsTest (Scine::Tests)

IndexedStructuralTopology (Scine::MolecularMechanics)

ProtonationHandler (Scine::StructurePreparation)

StructuralExcludedNonBonded (Scine::MolecularMechanics)

APdbPreparationTest

Electrostatic (Scine::MolecularMechanics)

IndexedStructuralTopologyCreator (Scine::MolecularMechanics)

ProtonationTypes (Scine::StructurePreparation)

StructurePreparationData (Scine::StructurePreparation)

AppTest (Scine::Tests)

ElectrostaticEvaluator (Scine::MolecularMechanics)

InteractionExclusion (Scine::MolecularMechanics)

Q

StructurePreparationFiles (Scine::StructurePreparation)

ASfamMolecularMechanicsTest (Scine::Tests)

ElementTypeIsNotAllowedForHydrogenBondsException (Scine::MolecularMechanics)

InteractionTermBase (Scine::MolecularMechanics)

StructurePreparationSettings (Scine::StructurePreparation)

AStructurePreparationTest (Scine::Tests)

F

InteractionTermEliminator (Scine::Qmmm)

QmmmCalculator (Scine::Qmmm)

StructureProcessor (Scine::StructurePreparation)

ATitrationTest (Scine::Tests)

J

QmmmCalculatorSettings (Scine::Qmmm)

SubsystemGenerator (Scine::SwooseUtilities)

AtomicInformationFileReaderTest (Scine::Tests)

FragmentAnalyzer (Scine::SwooseUtilities)

QmmmData (Scine::Qmmm)

SwooseModule (Scine::Swoose)

AtomicInformationReader (Scine::SwooseUtilities)

FragmentDataDistributor (Scine::MMParametrization)

JobSubmissionHelperTest (Scine::Tests)

QmmmDatabaseHelper (Scine::Qmmm)

T

AtomTypeIdentifier

FullHessianAssembler (Scine::MMParametrization)

L

QmmmDirectCalculationsHelper (Scine::Qmmm)

AtomTypesHolder (Scine::MolecularMechanics)

G

QmmmGradientsEvaluator (Scine::Qmmm)

Tests

B

LennardJones (Scine::MolecularMechanics)

QmmmHelperFunctionsTest (Scine::Tests)

Tests

GaffAtomTypeIdentifier (Scine::MolecularMechanics)

LennardJonesEvaluator (Scine::MolecularMechanics)

QmmmHessianEvaluator (Scine::Qmmm)

TitrableSite (Scine::StructurePreparation)

Bond (Scine::MolecularMechanics)

GaffCalculatorSettings (Scine::MolecularMechanics)

LennardJonesParameters (Scine::MolecularMechanics)

QmmmModel (Scine::Qmmm)

TitrationFileHandler (Scine::SwooseUtilities)

BondedTerm (Scine::MolecularMechanics)

GaffInteractionTermEliminatorTest (Scine::Tests)

M

QmmmModelAnalyzer (Scine::Qmmm)

TitrationHelper (Scine::MMParametrization)

BondOrderRefinementTest (Scine::Tests)

GaffMolecularMechanicsCalculator (Scine::MolecularMechanics)

QmmmReferenceData

TitrationResults (Scine::MMParametrization)

BondParameters (Scine::MolecularMechanics)

GaffParameterDefaultsProvider (Scine::MolecularMechanics)

MMAngleParametersNotAvailableException (Scine::MolecularMechanics)

QmmmReferenceDataManager (Scine::Qmmm)

TopologyUtils (Scine::SwooseUtilities)

BondsEvaluator (Scine::MolecularMechanics)

GaffParameterParser (Scine::MolecularMechanics)

MMBondParametersNotAvailableException (Scine::MolecularMechanics)

QmmmTest (Scine::Tests)

TrainingData (Scine::MMParametrization)

BondType (Scine::MolecularMechanics)

GaffParameters (Scine::MolecularMechanics)

MMDihedralParametersNotAvailableException (Scine::MolecularMechanics)

QmRegionHasNotBeenSelectedException (Scine::Qmmm)

TwoResultsForHydrogenBondsAreNotEqualException (Scine::MolecularMechanics)

C

GaffPotentialTermsGenerator (Scine::MolecularMechanics)

MMImproperDihedralParametersNotAvailableException (Scine::MolecularMechanics)

QmRegionSelectionTests (Scine::Tests)

U

H

MMLjParametersNotAvailableException (Scine::MolecularMechanics)

QmRegionSelector (Scine::Qmmm)

CalculationManager (Scine::MMParametrization)

MMParameters (Scine::MolecularMechanics)

QmRegionSelectorSettings (Scine::Qmmm)

UpdateFunctionManager (Scine::MMParametrization)

ChargeRedistributionResult (Scine::Qmmm::QmmmHelpers)

HydrogenBond (Scine::MolecularMechanics)

MMParametrizationSettings (Scine::MMParametrization)

R

Y

Class

HydrogenBondEvaluator (Scine::MolecularMechanics)

MockModule (Scine::Swoose)

CommandLineOptions (Scine::Swoose)

HydrogenBondParameters (Scine::MolecularMechanics)

MockQmCalculator (Scine::Swoose)

ReparametrizationHelper (Scine::MMParametrization)

YamlFileHandler

ConnectivityFileHandler (Scine::SwooseUtilities)

HydrogenBondTerm (Scine::MolecularMechanics)

MockQmCalculatorSettings (Scine::Swoose)

Repulsion (Scine::MolecularMechanics)

ConnectivityGenerator (Scine::MMParametrization)

I

MolecularMachineLearningModel (Scine::Swoose::MachineLearning)

RepulsionEvaluator (Scine::MolecularMechanics)

ConstrainedAtomsIdentifier (Scine::MMParametrization)

MolecularMechanicsCalculator (Scine::MolecularMechanics)

RepulsionParameters (Scine::MolecularMechanics)

D

CommandLineOptions::Impl (Scine::Swoose)

MolecularSystemPartitioner (Scine::MMParametrization)

RepulsionTerm (Scine::MolecularMechanics)

DatabaseHelper (Scine::MMParametrization)

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