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Scine::Swoose
2.1.0
This is the SCINE module Swoose.
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Scine::Swoose
2.1.0
This is the SCINE module Swoose.
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  Scine | |
  MMParametrization | |
  CalculationManager | This class handles the reference calculations |
| MMParametrizationSettings | Settings for the MM model parametrizer |
| MolecularSystemPartitioner | Divides the full system into subsystems |
| OptimizationSetup | This class sets up the initial MM parameters. The force constants will be optimized after that |
| ParameterOptimizer | The class optimizes the force constants of the MM model in a least squares manner |
| ParametrizationData | This struct holds all objects used inside the MM parametrization algorithm |
| TrainingData | |
| TitrationResults | |
| ConnectivityGenerator | This class handles the generation of the connectivity of the molecular system |
| ConstrainedAtomsIdentifier | |
| 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 |
| FullHessianAssembler | Assembles the full system's Hessian matrix from the subsystem's Hessians |
| ParameterFileWriter | This class writes the results of a SFAM parametrization (parameters) to file |
| 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 |
| TitrationHelper | |
| UpdateFunctionManager | |
| Parametrizer | This class manages the parametrization of an MM model from quantum-chemical reference data |
 DatabaseHelper | |
| MolecularMechanics | |
| AtomTypesHolder | Class containing the MM atom types of the atoms in a molecular system |
| GaffAtomTypeIdentifier | Class determining the GAFF atom types of a system given its connectivity, its element types and an atom type level |
| GaffCalculatorSettings | Settings for GAFF molecular mechanics calculations |
| GaffMolecularMechanicsCalculator | Calculator for the GAFF Molecular Mechanics method |
| GaffParameterDefaultsProvider | This class processes the default GAFF parameters from the file 'GaffDefaultParameters.h' and returns the result when the getParameters() function is called |
| 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" |
| 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 |
| 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 |
| 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 |
| Angle | Class treating an angle interaction,based solely on the angle (in rad), i.e. in 1 dimension |
| AnglesEvaluator | |
| AngleTerm | Class evaluating angle interaction for three given atoms |
| Bond | Class treating a bonded interaction, based solely on the bond length. (i.e. in 1 dimension) |
| BondedTerm | Class evaluating harmonic bonded interaction between two atoms |
| BondsEvaluator | BondsEvaluator BondsEvaluator.h |
| Dihedral | Class treating a dihedral interaction, based solely on the angle (in rad), i.e. in 1 dimension |
| DihedralsEvaluator | This class calculates the total energy with its derivatives for all dihedral terms of the force field |
| DihedralTerm | Class evaluating dihedral interaction for four given atoms |
| Dispersion | Class treating a dispersion (D3-BJ) interaction, based solely on the bond length. (i.e. in 1 dimension) |
| DispersionEvaluator | DispersionEvaluator DispersionEvaluator.h |
| DispersionTerm | Class evaluating dispersion (D3-BJ) interaction between two atoms |
| Electrostatic | Class treating non-bonded electrostatic interaction, based solely on the bond length. (i.e. in 1 dimension) |
| ElectrostaticEvaluator | Class evaluating the total energy and derivatives from the electrostatic interactions |
| 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 |
| HydrogenBondEvaluator | This class evaluates the total energy and its derivative from all hydrogen bonds |
| HydrogenBondParameters | |
| HydrogenBondTerm | This class evaluates the energy and its derivatives for one hydrogen bond term |
| ImproperDihedral | Class treating an improper dihedral interaction, based solely on the angle (in rad), i.e. in 1 dimension |
| ImproperDihedralsEvaluator | This class calculates the total energy and its derivatives for all improper dihedral terms |
| ImproperDihedralTerm | Class evaluating improper dihedral interaction for four given atoms |
| InteractionTermBase | Base class for all interaction terms |
| 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) |
| LennardJonesEvaluator | LennardJonesEvaluator LennardJonesEvaluator.h |
| Repulsion | Class treating a repulsive non-bonded interaction, based solely on the bond length. (i.e. in 1 dimension) |
| RepulsionEvaluator | This class evaluates the Pauli repulsion part of the MM model |
| RepulsionParameters | Class handling the parameters needed for the repulsive non-bonded interaction term |
| RepulsionTerm | Class evaluating repulsive non-bonded interaction between two atoms |
| MMBondParametersNotAvailableException | |
| MMAngleParametersNotAvailableException | |
| MMDihedralParametersNotAvailableException | |
| MMImproperDihedralParametersNotAvailableException | |
| MMLjParametersNotAvailableException | |
| ElementTypeIsNotAllowedForHydrogenBondsException | |
| TwoResultsForHydrogenBondsAreNotEqualException | |
| 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 |
| MolecularMechanicsCalculator | Base class for the MM methods (currently: SFAM and GAFF) |
| AngleParameters | Class containing the parameters for an MM angle |
| BondParameters | Class containing the parameters for an MM bond |
| DihedralParameters | Class containing the parameters for an MM dihedral |
| ImproperDihedralParameters | |
| LennardJonesParameters | Class containing the parameters for a van der Waals LJ-type interaction |
| 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 |
| SfamAtomTypeIdentifier | |
| SfamCalculatorSettings | Settings for SFAM molecular mechanics calculations |
| SfamMolecularMechanicsCalculator | Calculator for the SFAM Molecular Mechanics method |
| 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" |
| 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 |
| 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 |
| AngleType | Describes a bond uniquely for given atom types. (useful for maps/unordered_maps) |
| BondType | Describes a bond uniquely for given atom types. (useful for maps/unordered_maps) |
| DihedralType | Unique descriptor a dihedral for given atom types. (useful for maps/unordered_maps) |
| ImproperDihedralType | Unique descriptor an improper dihedral for given atom types. (useful for maps/unordered_maps) |
| IndexedStructuralBond | Holds indexes for a bond |
| IndexedStructuralAngle | Holds indexes for an angle. The connectivity is atom1 – atom2 – atom3 |
| IndexedStructuralDihedral | Holds indexes for a dihedral. The connectivity is atom1 – atom2 – atom3 – atom4 |
| IndexedStructuralImproperDihedral | Holds indexes for an improper dihedral |
| StructuralExcludedNonBonded | Holds indexes for an excluded non-bonded interaction. (1-2 and 1-3 neighbors) |
| IndexedStructuralScaledNonBonded | Holds indexes for a potentially scaled non-bonded interaction. (1-4 neighbors) |
| IndexedStructuralHydrogenBond | Holds indexes for a hydrogen-bond interaction |
| IndexedStructuralTopology | Class containing the structural information about the connectivity of a system |
| IndexedStructuralTopologyCreator | Class that creates an IndexedStructuralTopology based on the connectivity of a molecular system |
| 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 |
| InteractionTermEliminator | This class handles the elimination of MM interaction terms, which are already covered by the QM calculation in QM/MM |
| QmmmCalculator | Calculator implementing the QM/MM method |
| QmmmCalculatorSettings | Settings for QM/MM calculations |
| QmmmGradientsEvaluator | |
| QmmmHessianEvaluator | |
| QmmmDatabaseHelper | This class handles the submission and collection of results for QM/MM calculations via the database |
| QmmmDirectCalculationsHelper | This class handles QM/MM calculations in the direct mode |
| QmmmModelAnalyzer | TODO |
| QmmmData | |
| QmmmReferenceDataManager | Manages the calculation of all data contained in the QmmmData struct |
| QmmmModel | Holds the information about one QM/MM model: its structure, its QM atom indices, and its charge and spin multiplicity |
| QmRegionSelector | Automated selection of the QM region given a central atom around which it should be constructed and other settings |
| QmRegionHasNotBeenSelectedException | |
| QmRegionSelectorSettings | Settings for automated QM region selection |
| StructurePreparation | |
| ProteinAtom | |
| PeptidBond | |
| ProtonationTypes | |
| AminoAcidCategorizer | |
| ProtonationHandler | |
| TitrableSite | |
| StructurePreparationData | This struct holds all objects used inside the MM parametrization algorithm |
| Default | |
| StructurePreparationFiles | |
| StructurePreparationSettings | Settings for the PDB preparation mode |
| StructureProcessor | |
| Swoose | |
| MachineLearning | |
| MolecularMachineLearningModel | The combination of the machine learning models for molecular energies and atomic forces |
| CommandLineOptions | Class to parse the command line options for non-default options and pass them to a Utils::Settings class |
| Impl | |
| SwooseModule | This module provides all features regarding methods that are intended to be applicable to nanoscale systems |
| MockModule | Mock module for QM/MM tests |
| MockQmCalculatorSettings | Mocks the settings for the mock QM calculator |
| MockQmCalculator | Mock class for a QM calculator to use in QM/MM tests |
| SwooseUtilities | |
| AtomicInformationReader | |
| ConnectivityFileHandler | Method for reading and writing the connectivity of atoms (list of neighbors for each atom) |
| FragmentAnalyzer | |
| SettingsPopulator | Class with only static functions to populate settings |
| SubsystemGenerator | |
| TitrationFileHandler | |
| TopologyUtils | |
| 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 |
| AtomicInformationFileReaderTest | Tests the AtomicInformationFileReader class |
| BondOrderRefinementTest | Tests the refinement of bond orders by quantum-chemical data |
| DatabaseParametrizationTests | |
| AGaffMolecularMechanicsTest | Tests concerning the GAFF molecular mechanics method in SCINE |
| SfamInteractionTermEliminatorTest | Tests the functionality of the InteractionTermEliminator class applied in QM/MM with SFAM as MM |
| GaffInteractionTermEliminatorTest | Tests the functionality of the InteractionTermEliminator class applied in QM/MM with GAFF as MM |
| JobSubmissionHelperTest | Tests helper function for job submission in MM parametrization |
| AMolecularMachineLearningTest | Tests the molecular machine learning class to predict energies and atomic forces from reference data |
| AParametrizationOfLargeSystemsTest | Tests the automated parametrization for large molecular systems |
| AParametrizationOfSmallSystemsTest | Tests the automated parametrization for small molecular systems |
| QmmmHelperFunctionsTest | Tests the functionality of some helper functions which are applied in the QM/MM calculator |
| QmmmTest | Tests the functionality of some helper functions which are applied in the QM/MM calculator |
| QmRegionSelectionTests | Tests the automated QM region selection |
| ASfamMolecularMechanicsTest | Tests concerning SFAM's molecular mechanics method in SCINE |
| AStructurePreparationTest | |
| ATitrationTest | |
 Utils | |
 BSplines | |
| ExternalQC | |
| Geometry | |
| APdbPreparationTest | |
| AtomTypeIdentifier | Class determining the atom types of a system given its connectivity, its element types and an atom type level |
| Class | |
| QmmmReferenceData | Container for the reference data for all of the QM/MM models |
| Tests | |
| Tests | |
| YamlFileHandler |
1.8.5 
