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A

DatabaseParametrizationTests (Scine::Tests)

HydrogenBondParameters (Scine::MolecularMechanics)

MMLjParametersNotAvailableException (Scine::MolecularMechanics)

QmRegionSelectorSettings (Scine::Qmmm)

Dihedral (Scine::MolecularMechanics)

HydrogenBondTerm (Scine::MolecularMechanics)

MMParameters (Scine::MolecularMechanics)

R

AGaffMolecularMechanicsTest (Scine::Tests)

DihedralParameters (Scine::MolecularMechanics)

I

MMParametrizationSettings (Scine::MMParametrization)

AMolecularMachineLearningTest (Scine::Tests)

DihedralsEvaluator (Scine::MolecularMechanics)

MockModule (Scine::Swoose)

ReparametrizationHelper (Scine::MMParametrization)

Angle (Scine::MolecularMechanics)

DihedralTerm (Scine::MolecularMechanics)

CommandLineOptions::Impl (Scine::Swoose)

MockQmCalculator (Scine::Swoose)

Repulsion (Scine::MolecularMechanics)

AngleParameters (Scine::MolecularMechanics)

DihedralType (Scine::MolecularMechanics)

ImproperDihedral (Scine::MolecularMechanics)

MockQmCalculatorSettings (Scine::Swoose)

RepulsionEvaluator (Scine::MolecularMechanics)

AnglesEvaluator (Scine::MolecularMechanics)

Dispersion (Scine::MolecularMechanics)

ImproperDihedralParameters (Scine::MolecularMechanics)

MolecularMachineLearningModel (Scine::Swoose::MachineLearning)

RepulsionParameters (Scine::MolecularMechanics)

AngleTerm (Scine::MolecularMechanics)

DispersionEvaluator (Scine::MolecularMechanics)

ImproperDihedralsEvaluator (Scine::MolecularMechanics)

MolecularMechanicsCalculator (Scine::MolecularMechanics)

RepulsionTerm (Scine::MolecularMechanics)

AngleType (Scine::MolecularMechanics)

DispersionTerm (Scine::MolecularMechanics)

ImproperDihedralTerm (Scine::MolecularMechanics)

MolecularSystemPartitioner (Scine::MMParametrization)

S

AParametrizationOfLargeSystemsTest (Scine::Tests)

E

ImproperDihedralType (Scine::MolecularMechanics)

O

AParametrizationOfSmallSystemsTest (Scine::Tests)

IndexedStructuralAngle (Scine::MolecularMechanics)

SettingsPopulator (Scine::SwooseUtilities)

AppTest (Scine::Tests)

Electrostatic (Scine::MolecularMechanics)

IndexedStructuralBond (Scine::MolecularMechanics)

OptimizationSetup (Scine::MMParametrization)

SfamAtomTypeIdentifier (Scine::MolecularMechanics)

ASfamMolecularMechanicsTest (Scine::Tests)

ElectrostaticEvaluator (Scine::MolecularMechanics)

IndexedStructuralDihedral (Scine::MolecularMechanics)

P

SfamCalculatorSettings (Scine::MolecularMechanics)

AtomicInformationFileReaderTest (Scine::Tests)

ElectrostaticTerm (Scine::MolecularMechanics)

IndexedStructuralHydrogenBond (Scine::MolecularMechanics)

SfamInteractionTermEliminatorTest (Scine::Tests)

AtomicInformationReader (Scine::SwooseUtilities)

ElementTypeIsNotAllowedForHydrogenBondsException (Scine::MolecularMechanics)

IndexedStructuralImproperDihedral (Scine::MolecularMechanics)

ParameterFileWriter (Scine::MMParametrization)

SfamMolecularMechanicsCalculator (Scine::MolecularMechanics)

AtomTypeIdentifier

EmptyListWithLength (Python.setup)

IndexedStructuralScaledNonBonded (Scine::MolecularMechanics)

ParameterOptimizer (Scine::MMParametrization)

SfamParameterParser (Scine::MolecularMechanics)

AtomTypesHolder (Scine::MolecularMechanics)

F

IndexedStructuralTopology (Scine::MolecularMechanics)

ParametrizationData (Scine::MMParametrization)

SfamParameters (Scine::MolecularMechanics)

B

IndexedStructuralTopologyCreator (Scine::MolecularMechanics)

Parametrizer (Scine::MMParametrization)

SfamPotentialTermsGenerator (Scine::MolecularMechanics)

FragmentAnalyzer (Scine::SwooseUtilities)

InteractionTermBase (Scine::MolecularMechanics)

Q

StructuralExcludedNonBonded (Scine::MolecularMechanics)

Bond (Scine::MolecularMechanics)

FragmentDataDistributor (Scine::MMParametrization)

InteractionTermEliminator (Scine::Qmmm)

SubsystemGenerator (Scine::SwooseUtilities)

BondedTerm (Scine::MolecularMechanics)

FullHessianAssembler (Scine::MMParametrization)

J

QmmmCalculator (Scine::Qmmm)

SwooseModule (Scine::Swoose)

BondOrderRefinementTest (Scine::Tests)

G

QmmmCalculatorSettings (Scine::Qmmm)

T

BondParameters (Scine::MolecularMechanics)

JobSubmissionHelperTest (Scine::Tests)

QmmmData (Scine::Qmmm)

BondsEvaluator (Scine::MolecularMechanics)

GaffAtomTypeIdentifier (Scine::MolecularMechanics)

L

QmmmDatabaseHelper (Scine::Qmmm)

TopologyUtils (Scine::SwooseUtilities)

BondType (Scine::MolecularMechanics)

GaffCalculatorSettings (Scine::MolecularMechanics)

QmmmDirectCalculationsHelper (Scine::Qmmm)

TwoResultsForHydrogenBondsAreNotEqualException (Scine::MolecularMechanics)

C

GaffInteractionTermEliminatorTest (Scine::Tests)

LennardJones (Scine::MolecularMechanics)

QmmmGradientsEvaluator (Scine::Qmmm)

U

GaffMolecularMechanicsCalculator (Scine::MolecularMechanics)

LennardJonesEvaluator (Scine::MolecularMechanics)

QmmmHelperFunctionsTest (Scine::Tests)

CalculationManager (Scine::MMParametrization)

GaffParameterDefaultsProvider (Scine::MolecularMechanics)

LennardJonesParameters (Scine::MolecularMechanics)

QmmmModel (Scine::Qmmm)

UpdateFunctionManager (Scine::MMParametrization)

ChargeRedistributionResult (Scine::Qmmm::QmmmHelpers)

GaffParameterParser (Scine::MolecularMechanics)

LennardJonesTerm (Scine::MolecularMechanics)

QmmmModelAnalyzer (Scine::Qmmm)

Y

Class

GaffParameters (Scine::MolecularMechanics)

M

QmmmReferenceData

CommandLineOptions (Scine::Swoose)

GaffPotentialTermsGenerator (Scine::MolecularMechanics)

QmmmReferenceDataManager (Scine::Qmmm)

YamlFileHandler

ConnectivityFileHandler (Scine::SwooseUtilities)

H

MMAngleParametersNotAvailableException (Scine::MolecularMechanics)

QmmmTest (Scine::Tests)

ConnectivityGenerator (Scine::MMParametrization)

MMBondParametersNotAvailableException (Scine::MolecularMechanics)

QmRegionHasNotBeenSelectedException (Scine::Qmmm)

ConstrainedAtomsIdentifier (Scine::MMParametrization)

HydrogenBond (Scine::MolecularMechanics)

MMDihedralParametersNotAvailableException (Scine::MolecularMechanics)

QmRegionSelectionTests (Scine::Tests)

D

HydrogenBondEvaluator (Scine::MolecularMechanics)

MMImproperDihedralParametersNotAvailableException (Scine::MolecularMechanics)

QmRegionSelector (Scine::Qmmm)

DatabaseHelper (Scine::MMParametrization)

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