This inheritance list is sorted roughly, but not completely, alphabetically:

[detail level 123]

Scine::StructurePreparation::AminoAcidCategorizer
Scine::MolecularMechanics::Angle	Class treating an angle interaction,based solely on the angle (in rad), i.e. in 1 dimension
Scine::MolecularMechanics::AngleParameters	Class containing the parameters for an MM angle
Scine::MolecularMechanics::AnglesEvaluator
Scine::MolecularMechanics::AngleType	Describes a bond uniquely for given atom types. (useful for maps/unordered_maps)
APdbPreparationTest
Scine::SwooseUtilities::AtomicInformationReader
AtomTypeIdentifier	Class determining the atom types of a system given its connectivity, its element types and an atom type level
Scine::MolecularMechanics::AtomTypesHolder	Class containing the MM atom types of the atoms in a molecular system
Scine::MolecularMechanics::Bond	Class treating a bonded interaction, based solely on the bond length. (i.e. in 1 dimension)
Scine::MolecularMechanics::BondParameters	Class containing the parameters for an MM bond
Scine::MolecularMechanics::BondsEvaluator	BondsEvaluator BondsEvaluator.h
Scine::MolecularMechanics::BondType	Describes a bond uniquely for given atom types. (useful for maps/unordered_maps)
Scine::MMParametrization::CalculationManager	This class handles the reference calculations
Scine::Qmmm::QmmmHelpers::ChargeRedistributionResult	A small container for the result of a charge redistribution, containing the new atomic charges, the auxiliary virtual charges that are not placed on atoms as well as their positions
Class
Scine::Utils::CloneInterface< GaffMolecularMechanicsCalculator, MolecularMechanicsCalculator, Core::Calculator > [external]
Scine::MolecularMechanics::GaffMolecularMechanicsCalculator	Calculator for the GAFF Molecular Mechanics method
Scine::Utils::CloneInterface< MockQmCalculator, Core::Calculator, Core::Calculator > [external]
Scine::Swoose::MockQmCalculator	Mock class for a QM calculator to use in QM/MM tests
Scine::Utils::CloneInterface< QmmmCalculator, Core::EmbeddingCalculator, Core::Calculator > [external]
Scine::Qmmm::QmmmCalculator	Calculator implementing the QM/MM method
Scine::Utils::CloneInterface< SfamMolecularMechanicsCalculator, MolecularMechanicsCalculator, Core::Calculator > [external]
Scine::MolecularMechanics::SfamMolecularMechanicsCalculator	Calculator for the SFAM Molecular Mechanics method
Scine::Utils::CloneInterface< Utils::Abstract< MolecularMechanicsCalculator >, Core::Calculator > [external]
Scine::MolecularMechanics::MolecularMechanicsCalculator	Base class for the MM methods (currently: SFAM and GAFF)
Scine::Swoose::CommandLineOptions	Class to parse the command line options for non-default options and pass them to a Utils::Settings class
Scine::SwooseUtilities::ConnectivityFileHandler	Method for reading and writing the connectivity of atoms (list of neighbors for each atom)
Scine::MMParametrization::ConnectivityGenerator	This class handles the generation of the connectivity of the molecular system
Scine::MMParametrization::ConstrainedAtomsIdentifier
Scine::MMParametrization::DatabaseHelper
Scine::StructurePreparation::Default
Scine::MolecularMechanics::Dihedral	Class treating a dihedral interaction, based solely on the angle (in rad), i.e. in 1 dimension
Scine::MolecularMechanics::DihedralParameters	Class containing the parameters for an MM dihedral
Scine::MolecularMechanics::DihedralsEvaluator	This class calculates the total energy with its derivatives for all dihedral terms of the force field
Scine::MolecularMechanics::DihedralType	Unique descriptor a dihedral for given atom types. (useful for maps/unordered_maps)
Scine::MolecularMechanics::Dispersion	Class treating a dispersion (D3-BJ) interaction, based solely on the bond length. (i.e. in 1 dimension)
Scine::MolecularMechanics::DispersionEvaluator	DispersionEvaluator DispersionEvaluator.h
Scine::MolecularMechanics::Electrostatic	Class treating non-bonded electrostatic interaction, based solely on the bond length. (i.e. in 1 dimension)
std::exception	STL class
Scine::MolecularMechanics::MMAngleParametersNotAvailableException
Scine::MolecularMechanics::MMBondParametersNotAvailableException
Scine::MolecularMechanics::MMDihedralParametersNotAvailableException
Scine::MolecularMechanics::MMImproperDihedralParametersNotAvailableException
Scine::MolecularMechanics::MMLjParametersNotAvailableException
std::runtime_error	STL class
Scine::MolecularMechanics::ElementTypeIsNotAllowedForHydrogenBondsException
Scine::MolecularMechanics::TwoResultsForHydrogenBondsAreNotEqualException
Scine::Qmmm::QmRegionHasNotBeenSelectedException
Scine::SwooseUtilities::FragmentAnalyzer
Scine::MMParametrization::FragmentDataDistributor	This class handles the distribution of the available data for the parameter optimization. This mainly includes the task of providing a list of candidate fragments from which to take reference data for the parameters associated with a given atom
Scine::MMParametrization::FullHessianAssembler	Assembles the full system's Hessian matrix from the subsystem's Hessians
Scine::MolecularMechanics::GaffAtomTypeIdentifier	Class determining the GAFF atom types of a system given its connectivity, its element types and an atom type level
Scine::MolecularMechanics::GaffParameterDefaultsProvider	This class processes the default GAFF parameters from the file 'GaffDefaultParameters.h' and returns the result when the `getParameters()` function is called
Scine::MolecularMechanics::GaffParameterParser	This class reads in the GAFF parameters from the parameter file. The parsing relies on Qt and the conversion to doubles works also when numbers in the current locale are of the form "x,xxx"
Scine::MolecularMechanics::GaffPotentialTermsGenerator	This class creates the actual potential terms that are employed during a GAFF molecular mechanics calculation. It combines information about structure (bonds, angles, etc), atom types and parameters in order to do so
Scine::MolecularMechanics::HydrogenBond	Class calculating the energy and derivatives for a hydrogen bond based solely on the distance or on the angle, i.e. in 1 dimension, respectively
Scine::MolecularMechanics::HydrogenBondEvaluator	This class evaluates the total energy and its derivative from all hydrogen bonds
Scine::MolecularMechanics::HydrogenBondParameters
Scine::Swoose::CommandLineOptions::Impl
Scine::MolecularMechanics::ImproperDihedral	Class treating an improper dihedral interaction, based solely on the angle (in rad), i.e. in 1 dimension
Scine::MolecularMechanics::ImproperDihedralParameters
Scine::MolecularMechanics::ImproperDihedralsEvaluator	This class calculates the total energy and its derivatives for all improper dihedral terms
Scine::MolecularMechanics::ImproperDihedralType	Unique descriptor an improper dihedral for given atom types. (useful for maps/unordered_maps)
Scine::MolecularMechanics::IndexedStructuralAngle	Holds indexes for an angle. The connectivity is atom1 – atom2 – atom3
Scine::MolecularMechanics::IndexedStructuralBond	Holds indexes for a bond
Scine::MolecularMechanics::IndexedStructuralDihedral	Holds indexes for a dihedral. The connectivity is atom1 – atom2 – atom3 – atom4
Scine::MolecularMechanics::IndexedStructuralHydrogenBond	Holds indexes for a hydrogen-bond interaction
Scine::MolecularMechanics::IndexedStructuralImproperDihedral	Holds indexes for an improper dihedral
Scine::MolecularMechanics::IndexedStructuralScaledNonBonded	Holds indexes for a potentially scaled non-bonded interaction. (1-4 neighbors)
Scine::MolecularMechanics::IndexedStructuralTopology	Class containing the structural information about the connectivity of a system
Scine::MolecularMechanics::IndexedStructuralTopologyCreator	Class that creates an IndexedStructuralTopology based on the connectivity of a molecular system
Scine::MolecularMechanics::InteractionExclusion	This class provides a framework to store exclusions of interactions between atoms. Such exclusions are required for the non-covalent interactions between bonded atoms or to eliminate contributions to the energy for the interaction between QM atoms in QM/MM
Scine::MolecularMechanics::ElectrostaticEvaluator	Class evaluating the total energy and derivatives from the electrostatic interactions
Scine::MolecularMechanics::LennardJonesEvaluator	LennardJonesEvaluator LennardJonesEvaluator.h
Scine::MolecularMechanics::InteractionTermBase	Base class for all interaction terms
Scine::MolecularMechanics::AngleTerm	Class evaluating angle interaction for three given atoms
Scine::MolecularMechanics::BondedTerm	Class evaluating harmonic bonded interaction between two atoms
Scine::MolecularMechanics::DihedralTerm	Class evaluating dihedral interaction for four given atoms
Scine::MolecularMechanics::DispersionTerm	Class evaluating dispersion (D3-BJ) interaction between two atoms
Scine::MolecularMechanics::HydrogenBondTerm	This class evaluates the energy and its derivatives for one hydrogen bond term
Scine::MolecularMechanics::ImproperDihedralTerm	Class evaluating improper dihedral interaction for four given atoms
Scine::MolecularMechanics::RepulsionTerm	Class evaluating repulsive non-bonded interaction between two atoms
Scine::Qmmm::InteractionTermEliminator	This class handles the elimination of MM interaction terms, which are already covered by the QM calculation in QM/MM
Scine::MolecularMechanics::LennardJones	Class treating a non-bonded van der Waals interaction with a LJ potential, based solely on the bond length. (i.e. in 1 dimension)
Scine::MolecularMechanics::LennardJonesParameters	Class containing the parameters for a van der Waals LJ-type interaction
Scine::MolecularMechanics::MMParameters	Base class for the MM parameters classes, which holds and manages the bond and angle parameters as these are identically handled for SFAM and GAFF. Functions are still labeled as virtual such that these can be overwritten
Scine::MolecularMechanics::GaffParameters	Class containing the parameters for the GAFF model obtained after parsing a GAFF parameter file. The angle and bond parameters are handled by the base class MMParameters
Scine::MolecularMechanics::SfamParameters	Class containing the parameters for SFAM's MM model obtained after parsing a SFAM parameter file. The angle and bond parameters are handled by the base class MMParameters
Scine::Core::Module [external]
Scine::Swoose::MockModule	Mock module for QM/MM tests
Scine::Swoose::SwooseModule	This module provides all features regarding methods that are intended to be applicable to nanoscale systems
Scine::Swoose::MachineLearning::MolecularMachineLearningModel	The combination of the machine learning models for molecular energies and atomic forces
Scine::MMParametrization::MolecularSystemPartitioner	Divides the full system into subsystems
Scine::Core::ObjectWithLog [external]
Scine::Core::MMParametrizer [external]
Scine::MMParametrization::Parametrizer	This class manages the parametrization of an MM model from quantum-chemical reference data
Scine::Qmmm::QmRegionSelector	Automated selection of the QM region given a central atom around which it should be constructed and other settings
Scine::MMParametrization::OptimizationSetup	This class sets up the initial MM parameters. The force constants will be optimized after that
Scine::MMParametrization::ParameterFileWriter	This class writes the results of a SFAM parametrization (parameters) to file
Scine::MMParametrization::ParameterOptimizer	The class optimizes the force constants of the MM model in a least squares manner
Scine::MMParametrization::ParametrizationData	This struct holds all objects used inside the MM parametrization algorithm
Scine::StructurePreparation::PeptidBond
Scine::StructurePreparation::ProteinAtom
Scine::StructurePreparation::ProtonationHandler
Scine::StructurePreparation::ProtonationTypes
Scine::Qmmm::QmmmData
Scine::Qmmm::QmmmDatabaseHelper	This class handles the submission and collection of results for QM/MM calculations via the database
Scine::Qmmm::QmmmDirectCalculationsHelper	This class handles QM/MM calculations in the direct mode
Scine::Qmmm::QmmmGradientsEvaluator
Scine::Qmmm::QmmmHessianEvaluator
Scine::Qmmm::QmmmModel	Holds the information about one QM/MM model: its structure, its QM atom indices, and its charge and spin multiplicity
Scine::Qmmm::QmmmModelAnalyzer	TODO
QmmmReferenceData	Container for the reference data for all of the QM/MM models
Scine::Qmmm::QmmmReferenceDataManager	Manages the calculation of all data contained in the QmmmData struct
Scine::MMParametrization::ReparametrizationHelper	This class provides functionalities for the re-parametrization of a system, which has only slightly been modified. The most of the parameters can be re-used without new reference data generation or parameter optimization
Scine::MolecularMechanics::Repulsion	Class treating a repulsive non-bonded interaction, based solely on the bond length. (i.e. in 1 dimension)
Scine::MolecularMechanics::RepulsionEvaluator	This class evaluates the Pauli repulsion part of the MM model
Scine::MolecularMechanics::RepulsionParameters	Class handling the parameters needed for the repulsive non-bonded interaction term
Scine::MolecularMechanics::ScaledInteractions	This class keeps track which pair-wise interaction between atoms is scaled. The scaling information is stored as a sparse matrix atoms x atoms of booleans
Scine::MolecularMechanics::ElectrostaticEvaluator	Class evaluating the total energy and derivatives from the electrostatic interactions
Scine::MolecularMechanics::LennardJonesEvaluator	LennardJonesEvaluator LennardJonesEvaluator.h
Scine::SwooseUtilities::SettingsPopulator	Class with only static functions to populate settings
Scine::MolecularMechanics::SfamAtomTypeIdentifier
Scine::MolecularMechanics::SfamParameterParser	This class reads in the SFAM parameters from the parameter file. The parsing relies on Qt and the conversion to doubles works also when numbers in the current locale are of the form "x,xxx"
Scine::MolecularMechanics::SfamPotentialTermsGenerator	This class creates the actual potential terms that are employed during an SFAM molecular mechanics calculation. It combines information about structure (bonds, angles, etc), atom types and parameters in order to do so
Scine::MolecularMechanics::StructuralExcludedNonBonded	Holds indexes for an excluded non-bonded interaction. (1-2 and 1-3 neighbors)
Scine::StructurePreparation::StructurePreparationData	This struct holds all objects used inside the MM parametrization algorithm
Scine::StructurePreparation::StructurePreparationFiles
Scine::StructurePreparation::StructureProcessor
Scine::SwooseUtilities::SubsystemGenerator
Test
Scine::Tests::AGaffMolecularMechanicsTest	Tests concerning the GAFF molecular mechanics method in SCINE
Scine::Tests::AMolecularMachineLearningTest	Tests the molecular machine learning class to predict energies and atomic forces from reference data
Scine::Tests::AParametrizationOfLargeSystemsTest	Tests the automated parametrization for large molecular systems
Scine::Tests::AParametrizationOfSmallSystemsTest	Tests the automated parametrization for small molecular systems
Scine::Tests::AppTest	Tests the functionality of task handlers applied in the app. It basically just tests whether the tasks run through normally without throwing exceptions. The correctness of results is tested individually for the classes that do the work in other tests
Scine::Tests::ASfamMolecularMechanicsTest	Tests concerning SFAM's molecular mechanics method in SCINE
Scine::Tests::AStructurePreparationTest
Scine::Tests::ATitrationTest
Scine::Tests::AtomicInformationFileReaderTest	Tests the AtomicInformationFileReader class
Scine::Tests::BondOrderRefinementTest	Tests the refinement of bond orders by quantum-chemical data
Scine::Tests::DatabaseParametrizationTests
Scine::Tests::GaffInteractionTermEliminatorTest	Tests the functionality of the InteractionTermEliminator class applied in QM/MM with GAFF as MM
Scine::Tests::JobSubmissionHelperTest	Tests helper function for job submission in MM parametrization
Scine::Tests::QmmmHelperFunctionsTest	Tests the functionality of some helper functions which are applied in the QM/MM calculator
Scine::Tests::QmmmTest	Tests the functionality of some helper functions which are applied in the QM/MM calculator
Scine::Tests::QmRegionSelectionTests	Tests the automated QM region selection
Scine::Tests::SfamInteractionTermEliminatorTest	Tests the functionality of the InteractionTermEliminator class applied in QM/MM with SFAM as MM
Tests
Tests
Scine::StructurePreparation::TitrableSite
Scine::SwooseUtilities::TitrationFileHandler
Scine::MMParametrization::TitrationHelper
Scine::MMParametrization::TitrationResults
Scine::SwooseUtilities::TopologyUtils
Scine::MMParametrization::TrainingData
Scine::Utils::UpdateFunctionManagerBase [external]
Scine::MMParametrization::UpdateFunctionManager
Scine::Utils::UniversalSettings::ValueCollection [external]
Scine::Utils::Settings [external]
Scine::MMParametrization::MMParametrizationSettings	Settings for the MM model parametrizer
Scine::MolecularMechanics::GaffCalculatorSettings	Settings for GAFF molecular mechanics calculations
Scine::MolecularMechanics::SfamCalculatorSettings	Settings for SFAM molecular mechanics calculations
Scine::Qmmm::QmmmCalculatorSettings	Settings for QM/MM calculations
Scine::Qmmm::QmRegionSelectorSettings	Settings for automated QM region selection
Scine::StructurePreparation::StructurePreparationSettings	Settings for the PDB preparation mode
Scine::Swoose::MockQmCalculatorSettings	Mocks the settings for the mock QM calculator
YamlFileHandler