Here is a list of all documented class members with links to the class documentation for each member:
- g -
- 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