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)

SettingsPopulator (Scine::SwooseUtilities)

AminoAcidCategorizer (Scine::StructurePreparation)

DihedralParameters (Scine::MolecularMechanics)

ImproperDihedralTerm (Scine::MolecularMechanics)

P

SfamAtomTypeIdentifier (Scine::MolecularMechanics)

AMolecularMachineLearningTest (Scine::Tests)

DihedralsEvaluator (Scine::MolecularMechanics)

ImproperDihedralType (Scine::MolecularMechanics)

SfamCalculatorSettings (Scine::MolecularMechanics)

Angle (Scine::MolecularMechanics)

DihedralTerm (Scine::MolecularMechanics)

IndexedStructuralAngle (Scine::MolecularMechanics)

ParameterFileWriter (Scine::MMParametrization)

SfamInteractionTermEliminatorTest (Scine::Tests)

AngleParameters (Scine::MolecularMechanics)

DihedralType (Scine::MolecularMechanics)

IndexedStructuralBond (Scine::MolecularMechanics)

ParameterOptimizer (Scine::MMParametrization)

SfamMolecularMechanicsCalculator (Scine::MolecularMechanics)

AnglesEvaluator (Scine::MolecularMechanics)

Dispersion (Scine::MolecularMechanics)

IndexedStructuralDihedral (Scine::MolecularMechanics)

ParametrizationData (Scine::MMParametrization)

SfamParameterParser (Scine::MolecularMechanics)

AngleTerm (Scine::MolecularMechanics)

DispersionEvaluator (Scine::MolecularMechanics)

IndexedStructuralHydrogenBond (Scine::MolecularMechanics)

Parametrizer (Scine::MMParametrization)

SfamParameters (Scine::MolecularMechanics)

AngleType (Scine::MolecularMechanics)

DispersionTerm (Scine::MolecularMechanics)

IndexedStructuralImproperDihedral (Scine::MolecularMechanics)

PeptidBond (Scine::StructurePreparation)

SfamPotentialTermsGenerator (Scine::MolecularMechanics)

AParametrizationOfLargeSystemsTest (Scine::Tests)

E

IndexedStructuralScaledNonBonded (Scine::MolecularMechanics)

ProteinAtom (Scine::StructurePreparation)

StructuralExcludedNonBonded (Scine::MolecularMechanics)

AParametrizationOfSmallSystemsTest (Scine::Tests)

IndexedStructuralTopology (Scine::MolecularMechanics)

ProtonationHandler (Scine::StructurePreparation)

StructurePreparationData (Scine::StructurePreparation)

APdbPreparationTest

Electrostatic (Scine::MolecularMechanics)

IndexedStructuralTopologyCreator (Scine::MolecularMechanics)

ProtonationTypes (Scine::StructurePreparation)

StructurePreparationFiles (Scine::StructurePreparation)

AppTest (Scine::Tests)

ElectrostaticEvaluator (Scine::MolecularMechanics)

InteractionTermBase (Scine::MolecularMechanics)

Q

StructurePreparationSettings (Scine::StructurePreparation)

ASfamMolecularMechanicsTest (Scine::Tests)

ElectrostaticTerm (Scine::MolecularMechanics)

InteractionTermEliminator (Scine::Qmmm)

StructureProcessor (Scine::StructurePreparation)

AStructurePreparationTest (Scine::Tests)

ElementTypeIsNotAllowedForHydrogenBondsException (Scine::MolecularMechanics)

J

QmmmCalculator (Scine::Qmmm)

SubsystemGenerator (Scine::SwooseUtilities)

ATitrationTest (Scine::Tests)

F

QmmmCalculatorSettings (Scine::Qmmm)

SwooseModule (Scine::Swoose)

AtomicInformationFileReaderTest (Scine::Tests)

JobSubmissionHelperTest (Scine::Tests)

QmmmData (Scine::Qmmm)

T

AtomicInformationReader (Scine::SwooseUtilities)

FragmentAnalyzer (Scine::SwooseUtilities)

L

QmmmDatabaseHelper (Scine::Qmmm)

AtomTypeIdentifier

FragmentDataDistributor (Scine::MMParametrization)

QmmmDirectCalculationsHelper (Scine::Qmmm)

Tests

AtomTypesHolder (Scine::MolecularMechanics)

FullHessianAssembler (Scine::MMParametrization)

LennardJones (Scine::MolecularMechanics)

QmmmGradientsEvaluator (Scine::Qmmm)

Tests

B

G

LennardJonesEvaluator (Scine::MolecularMechanics)

QmmmHelperFunctionsTest (Scine::Tests)

TitrableSite (Scine::StructurePreparation)

LennardJonesParameters (Scine::MolecularMechanics)

QmmmHessianEvaluator (Scine::Qmmm)

TitrationFileHandler (Scine::SwooseUtilities)

Bond (Scine::MolecularMechanics)

GaffAtomTypeIdentifier (Scine::MolecularMechanics)

LennardJonesTerm (Scine::MolecularMechanics)

QmmmModel (Scine::Qmmm)

TitrationHelper (Scine::MMParametrization)

BondedTerm (Scine::MolecularMechanics)

GaffCalculatorSettings (Scine::MolecularMechanics)

M

QmmmModelAnalyzer (Scine::Qmmm)

TitrationResults (Scine::MMParametrization)

BondOrderRefinementTest (Scine::Tests)

GaffInteractionTermEliminatorTest (Scine::Tests)

QmmmReferenceData

TopologyUtils (Scine::SwooseUtilities)

BondParameters (Scine::MolecularMechanics)

GaffMolecularMechanicsCalculator (Scine::MolecularMechanics)

MMAngleParametersNotAvailableException (Scine::MolecularMechanics)

QmmmReferenceDataManager (Scine::Qmmm)

TrainingData (Scine::MMParametrization)

BondsEvaluator (Scine::MolecularMechanics)

GaffParameterDefaultsProvider (Scine::MolecularMechanics)

MMBondParametersNotAvailableException (Scine::MolecularMechanics)

QmmmTest (Scine::Tests)

TwoResultsForHydrogenBondsAreNotEqualException (Scine::MolecularMechanics)

BondType (Scine::MolecularMechanics)

GaffParameterParser (Scine::MolecularMechanics)

MMDihedralParametersNotAvailableException (Scine::MolecularMechanics)

QmRegionHasNotBeenSelectedException (Scine::Qmmm)

U

C

GaffParameters (Scine::MolecularMechanics)

MMImproperDihedralParametersNotAvailableException (Scine::MolecularMechanics)

QmRegionSelectionTests (Scine::Tests)

GaffPotentialTermsGenerator (Scine::MolecularMechanics)

MMLjParametersNotAvailableException (Scine::MolecularMechanics)

QmRegionSelector (Scine::Qmmm)

UpdateFunctionManager (Scine::MMParametrization)

CalculationManager (Scine::MMParametrization)

H

MMParameters (Scine::MolecularMechanics)

QmRegionSelectorSettings (Scine::Qmmm)

Y

ChargeRedistributionResult (Scine::Qmmm::QmmmHelpers)

MMParametrizationSettings (Scine::MMParametrization)

R

Class

HydrogenBond (Scine::MolecularMechanics)

MockModule (Scine::Swoose)

YamlFileHandler

CommandLineOptions (Scine::Swoose)

HydrogenBondEvaluator (Scine::MolecularMechanics)

MockQmCalculator (Scine::Swoose)

ReparametrizationHelper (Scine::MMParametrization)

ConnectivityFileHandler (Scine::SwooseUtilities)

HydrogenBondParameters (Scine::MolecularMechanics)

MockQmCalculatorSettings (Scine::Swoose)

Repulsion (Scine::MolecularMechanics)

ConnectivityGenerator (Scine::MMParametrization)

HydrogenBondTerm (Scine::MolecularMechanics)

MolecularMachineLearningModel (Scine::Swoose::MachineLearning)

RepulsionEvaluator (Scine::MolecularMechanics)

ConstrainedAtomsIdentifier (Scine::MMParametrization)

I

MolecularMechanicsCalculator (Scine::MolecularMechanics)

RepulsionParameters (Scine::MolecularMechanics)

D

MolecularSystemPartitioner (Scine::MMParametrization)

RepulsionTerm (Scine::MolecularMechanics)

CommandLineOptions::Impl (Scine::Swoose)

DatabaseHelper (Scine::MMParametrization)

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