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• GaffAtomTypeIdentifier() : Scine::MolecularMechanics::GaffAtomTypeIdentifier
• GaffCalculatorSettings() : Scine::MolecularMechanics::GaffCalculatorSettings
• GaffMolecularMechanicsCalculator() : Scine::MolecularMechanics::GaffMolecularMechanicsCalculator
• GaffParameterParser() : Scine::MolecularMechanics::GaffParameterParser
• GaffPotentialTermsGenerator() : Scine::MolecularMechanics::GaffPotentialTermsGenerator
• generateBondOrderMatrixFromListsOfNeighbors() : Scine::SwooseUtilities::TopologyUtils
• generateInitialListsOfNeighbors() : Scine::MMParametrization::ConnectivityGenerator
• generateInitialParameters() : Scine::MMParametrization::OptimizationSetup
• generateListsOfNeighborsFromBondOrderMatrix() : Scine::SwooseUtilities::TopologyUtils
• generateQmRegion() : Scine::Qmmm::QmRegionSelector
• generateSfamAtomTypeLevelFromString() : Scine::MolecularMechanics::SfamAtomTypeIdentifier
• generateSubsystem() : Scine::SwooseUtilities::SubsystemGenerator
• getA1() : Scine::MolecularMechanics::DispersionEvaluator
• getA2() : Scine::MolecularMechanics::DispersionEvaluator
• getAcceptorAtom() : Scine::MolecularMechanics::HydrogenBondTerm
• getAngleTerms() : Scine::MolecularMechanics::GaffPotentialTermsGenerator , Scine::MolecularMechanics::SfamPotentialTermsGenerator
• getAtomicCharges() : Scine::MolecularMechanics::ElectrostaticEvaluator
• getAtomType() : Scine::MolecularMechanics::AtomTypesHolder
• getAtomTypes() : Scine::MolecularMechanics::GaffAtomTypeIdentifier , Scine::MolecularMechanics::SfamAtomTypeIdentifier
• getBetaRepulsion() : Scine::MolecularMechanics::RepulsionParameters
• getBondedTerms() : Scine::MolecularMechanics::GaffPotentialTermsGenerator , Scine::MolecularMechanics::SfamPotentialTermsGenerator
• getC6() : Scine::MolecularMechanics::Dispersion , Scine::MolecularMechanics::SfamParameters
• getC6IndicesMap() : Scine::MolecularMechanics::SfamParameters
• getCalculationDirectory() : Scine::Swoose::MockQmCalculator
• getCandidateFragments() : Scine::MMParametrization::FragmentDataDistributor
• getCentralAtom() : Scine::MolecularMechanics::ImproperDihedralTerm
• getChargesForEachAtom() : Scine::MolecularMechanics::SfamParameters
• getDihedralTerms() : Scine::MolecularMechanics::GaffPotentialTermsGenerator , Scine::MolecularMechanics::SfamPotentialTermsGenerator
• getDispersion() : Scine::MolecularMechanics::DispersionTerm
• getDispersionTerms() : Scine::MolecularMechanics::SfamPotentialTermsGenerator
• getDonorAtom() : Scine::MolecularMechanics::HydrogenBondTerm
• getEffectiveCharge() : Scine::MolecularMechanics::RepulsionParameters
• getEquilibriumAngle() : Scine::MolecularMechanics::AngleParameters , Scine::MolecularMechanics::ImproperDihedralParameters
• getEquilibriumBondLength() : Scine::MolecularMechanics::BondParameters
• getExclusions() : Scine::MolecularMechanics::InteractionExclusion
• getFileNameBase() : Scine::Swoose::MockQmCalculator
• getFirstAtom() : Scine::MolecularMechanics::AngleTerm , Scine::MolecularMechanics::BondedTerm , Scine::MolecularMechanics::DihedralTerm , Scine::MolecularMechanics::DispersionTerm , Scine::MolecularMechanics::ImproperDihedralTerm , Scine::MolecularMechanics::RepulsionTerm
• getForceConstant() : Scine::MolecularMechanics::AngleParameters , Scine::MolecularMechanics::BondParameters , Scine::MolecularMechanics::ImproperDihedralParameters
• getFourthAtom() : Scine::MolecularMechanics::DihedralTerm , Scine::MolecularMechanics::ImproperDihedralTerm
• getHalfBarrierHeight() : Scine::MolecularMechanics::DihedralParameters
• getHydrogenAtom() : Scine::MolecularMechanics::HydrogenBondTerm
• getHydrogenBondTerms() : Scine::MolecularMechanics::SfamPotentialTermsGenerator
• getImproperDihedralForceConstantForPlanarGroups() : Scine::MMParametrization::OptimizationSetup
• getImproperDihedralTerms() : Scine::MolecularMechanics::GaffPotentialTermsGenerator , Scine::MolecularMechanics::SfamPotentialTermsGenerator
• getIndexOfOptimalModel() : Scine::Qmmm::QmmmModelAnalyzer
• getInitialAngleForceConstant() : Scine::MMParametrization::OptimizationSetup
• getInitialBondForceConstant() : Scine::MMParametrization::OptimizationSetup
• getInitialDihedralHalfBarrierHeight() : Scine::MMParametrization::OptimizationSetup
• getInitialImproperDihedralForceConstantForNonPlanarGroups() : Scine::MMParametrization::OptimizationSetup
• getInteraction() : Scine::MolecularMechanics::Angle , Scine::MolecularMechanics::Bond , Scine::MolecularMechanics::Dihedral , Scine::MolecularMechanics::Electrostatic , Scine::MolecularMechanics::LennardJones , Scine::MolecularMechanics::ImproperDihedral
• getInteractionAngleVariable() : Scine::MolecularMechanics::HydrogenBond
• getInteractionDistanceVariable() : Scine::MolecularMechanics::HydrogenBond
• getInteractionScalingFactor() : Scine::MolecularMechanics::ScaledInteractions
• getMMAngle() : Scine::MolecularMechanics::MMParameters
• getMMBond() : Scine::MolecularMechanics::MMParameters
• getMMDihedrals() : Scine::MolecularMechanics::GaffParameters , Scine::MolecularMechanics::SfamParameters
• getMMImproperDihedral() : Scine::MolecularMechanics::SfamParameters
• getMMImproperDihedrals() : Scine::MolecularMechanics::GaffParameters
• getMMLennardJones() : Scine::MolecularMechanics::GaffParameters
• getMode() : Scine::Swoose::CommandLineOptions
• getMolecularCharge() : Scine::SwooseUtilities::FragmentAnalyzer
• getMolecularMechanicsCalculator() : Scine::Qmmm::QmmmCalculator
• getNonCovalentParameters() : Scine::MolecularMechanics::SfamParameters
• getNumberOfDataPoints() : Scine::MMParametrization::UpdateFunctionManager
• getParameters() : Scine::MolecularMechanics::GaffParameterDefaultsProvider
• getPeriodicity() : Scine::MolecularMechanics::DihedralParameters
• getPhaseShift() : Scine::MolecularMechanics::DihedralParameters
• getPlanarGroupThreshold() : Scine::MolecularMechanics::ImproperDihedral
• getPositions() : Scine::Swoose::MockQmCalculator , Scine::MolecularMechanics::MolecularMechanicsCalculator , Scine::Qmmm::QmmmCalculator
• getQmRegionChargeAndMultiplicity() : Scine::Qmmm::QmRegionSelector
• getQmRegionIndices() : Scine::Qmmm::QmRegionSelector
• getQmRegionIndicesWithoutLinkAtoms() : Scine::Qmmm::QmRegionSelector
• getQmRegionStructure() : Scine::Qmmm::QmRegionSelector
• getQuantumMechanicsCalculator() : Scine::Qmmm::QmmmCalculator
• getR0() : Scine::MolecularMechanics::RepulsionParameters
• getRepulsionTerms() : Scine::MolecularMechanics::SfamPotentialTermsGenerator
• getRequiredProperties() : Scine::MolecularMechanics::MolecularMechanicsCalculator , Scine::Swoose::MockQmCalculator , Scine::Qmmm::QmmmCalculator
• getS8() : Scine::MolecularMechanics::DispersionEvaluator
• getScaledInteractionPairs() : Scine::MolecularMechanics::ScaledInteractions
• getScalingFactor() : Scine::MolecularMechanics::Dispersion
• getSecondAtom() : Scine::MolecularMechanics::DihedralTerm , Scine::MolecularMechanics::AngleTerm , Scine::MolecularMechanics::RepulsionTerm , Scine::MolecularMechanics::BondedTerm , Scine::MolecularMechanics::DispersionTerm , Scine::MolecularMechanics::ImproperDihedralTerm
• getSettingsFile() : Scine::Swoose::CommandLineOptions
• getSpinMultiplicity() : Scine::SwooseUtilities::FragmentAnalyzer
• getState() : Scine::Qmmm::QmmmCalculator , Scine::Swoose::MockQmCalculator , Scine::MolecularMechanics::MolecularMechanicsCalculator
• getStructure() : Scine::Qmmm::QmmmCalculator , Scine::MolecularMechanics::MolecularMechanicsCalculator , Scine::Swoose::MockQmCalculator
• getStructureFile() : Scine::Swoose::CommandLineOptions
• getTheta() : Scine::MolecularMechanics::ImproperDihedralTerm , Scine::MolecularMechanics::DihedralTerm
• getThirdAtom() : Scine::MolecularMechanics::AngleTerm , Scine::MolecularMechanics::DihedralTerm
• getTypeOfAngle() : Scine::MolecularMechanics::AngleTerm
• getTypeOfBond() : Scine::MolecularMechanics::BondedTerm
• getTypeOfDihedral() : Scine::MolecularMechanics::DihedralTerm
• getTypeOfImproperDihedral() : Scine::MolecularMechanics::ImproperDihedralTerm
• getUnderlyingCalculators() : Scine::Qmmm::QmmmCalculator