File List

Here is a list of all documented files with brief descriptions:

[detail level 123456]

src
Swoose
App
AppUtils
CommandLineOptions.cpp
CommandLineOptions.h
TaskManagement.h
Tasks.cpp
Tasks.h
SwooseApp.cpp
Python
ParametrizerPython.cpp
PythonModule.cpp
QmRegionSelectorPython.cpp
SwooseUtilitiesPython.cpp
TaskHandlerPython.cpp
Swoose
MachineLearning
MolecularMachineLearningModel.cpp
MolecularMachineLearningModel.h
MMParametrization
ParametrizationUtils
AtomicChargesAssembler.cpp
AtomicChargesAssembler.h
ConnectivityGenerator.cpp
ConnectivityGenerator.h
ConstrainedAtomsIdentifier.cpp
ConstrainedAtomsIdentifier.h
FragmentDataDistributor.cpp
FragmentDataDistributor.h
FullHessianAssembler.cpp
FullHessianAssembler.h
ParameterFileWriter.cpp
ParameterFileWriter.h
ReparametrizationHelper.cpp
ReparametrizationHelper.h
SuperfluousFragmentIdentifier.cpp
SuperfluousFragmentIdentifier.h
TitrationHelper.cpp
TitrationHelper.h
UpdateFunctionManager.cpp
UpdateFunctionManager.h
ReferenceCalculationHelpers
DatabaseHelper.cpp
DatabaseHelper.h
DatabaseJobSubmissionHelper.cpp
DatabaseJobSubmissionHelper.h
DatabaseOrderNames.h
DirectCalculationsHelper.cpp
DirectCalculationsHelper.h
ReferenceCalculationsIO.cpp
ReferenceCalculationsIO.h
CalculationManager.cpp
CalculationManager.h
MMParametrizationSettings.h
MolecularSystemPartitioner.cpp
MolecularSystemPartitioner.h
OptimizationSetup.cpp
OptimizationSetup.h
ParameterOptimizer.cpp
ParameterOptimizer.h
ParametrizationData.h
Parametrizer.cpp
Parametrizer.h
MolecularMechanics
GAFF
GaffAtomTypeIdentifier.cpp
GaffAtomTypeIdentifier.h
GaffCalculatorSettings.h
GaffDefaultParameters.h
GaffMolecularMechanicsCalculator.cpp
GaffMolecularMechanicsCalculator.h
GaffParameterDefaultsProvider.cpp
GaffParameterDefaultsProvider.h
GaffParameterParser.cpp
GaffParameterParser.h
GaffParameters.cpp
GaffParameters.h
GaffPotentialTermsGenerator.cpp
GaffPotentialTermsGenerator.h
Interactions
Angle.cpp
Angle.h
AnglesEvaluator.cpp
AnglesEvaluator.h
AngleTerm.cpp
AngleTerm.h
Bond.cpp
Bond.h
BondedTerm.cpp
BondedTerm.h
BondsEvaluator.cpp
BondsEvaluator.h
Dihedral.cpp
Dihedral.h
DihedralsEvaluator.cpp
DihedralsEvaluator.h
DihedralTerm.cpp
DihedralTerm.h
Dispersion.cpp
Dispersion.h
DispersionEvaluator.cpp
DispersionEvaluator.h
DispersionTerm.cpp
DispersionTerm.h
Electrostatic.cpp
Electrostatic.h
ElectrostaticEvaluator.cpp
ElectrostaticEvaluator.h
HydrogenBond.cpp
HydrogenBond.h
HydrogenBondEvaluator.cpp
HydrogenBondEvaluator.h
HydrogenBondParameters.h
HydrogenBondTerm.cpp
HydrogenBondTerm.h
ImproperDihedral.cpp
ImproperDihedral.h
ImproperDihedralsEvaluator.cpp
ImproperDihedralsEvaluator.h
ImproperDihedralTerm.cpp
ImproperDihedralTerm.h
InteractionTermBase.h
LennardJones.cpp
LennardJones.h
LennardJonesEvaluator.cpp
LennardJonesEvaluator.h
Repulsion.cpp
Repulsion.h
RepulsionEvaluator.cpp
RepulsionEvaluator.h
RepulsionParameters.cpp
RepulsionParameters.h
RepulsionTerm.cpp
RepulsionTerm.h
Parameters
AngleParameters.cpp
AngleParameters.h
BondParameters.cpp
BondParameters.h
DihedralParameters.cpp
DihedralParameters.h
DispersionC6Parameters.cpp
DispersionC6Parameters.h
ImproperDihedralParameters.cpp
ImproperDihedralParameters.h
LennardJonesParameters.cpp
LennardJonesParameters.h
SFAM
SfamAtomTypeIdentifier.cpp
SfamAtomTypeIdentifier.h
SfamCalculatorSettings.h
SfamMolecularMechanicsCalculator.cpp
SfamMolecularMechanicsCalculator.h
SfamParameterParser.cpp
SfamParameterParser.h
SfamParameters.cpp
SfamParameters.h
SfamPotentialTermsGenerator.cpp
SfamPotentialTermsGenerator.h
Topology
AngleType.h
BondType.h
DihedralType.h
ImproperDihedralType.h
IndexedStructuralElements.h
IndexedStructuralTopology.cpp
IndexedStructuralTopology.h
IndexedStructuralTopologyCreator.cpp
IndexedStructuralTopologyCreator.h
AtomTypesHolder.h
InteractionExclusion.cpp
InteractionExclusion.h
MMExceptions.h
MMParameters.cpp
MMParameters.h
MolecularMechanicsCalculator.cpp
MolecularMechanicsCalculator.h
PotentialTermsHelper.cpp
PotentialTermsHelper.h
ScaledInteractions.cpp
ScaledInteractions.h
QMMM
QmRegionSelection
QmmmDatabaseHelper.cpp
QmmmDatabaseHelper.h
QmmmDirectCalculationsHelper.cpp
QmmmDirectCalculationsHelper.h
QmmmModelAnalyzer.cpp
QmmmModelAnalyzer.h
QmmmReferenceDataManager.cpp
QmmmReferenceDataManager.h
QmRegionCandidateGenerator.cpp
QmRegionCandidateGenerator.h
QmRegionSelector.cpp
QmRegionSelector.h
QmRegionSelectorSettings.h
SymmetryScores.cpp
SymmetryScores.h
InteractionTermEliminator.cpp
InteractionTermEliminator.h
QmmmCalculator.cpp
QmmmCalculator.h
QmmmCalculatorSettings.h
QmmmGradientsEvaluator.cpp
QmmmGradientsEvaluator.h
QmmmHelpers.cpp
QmmmHelpers.h
QmmmHessianEvaluator.cpp
QmmmHessianEvaluator.h
StructurePreparation
Protonation
ProtonationHandler.cpp
ProtonationHandler.h
ProtonationHelper.cpp
ProtonationHelper.h
TitrationData.h
AminoAcidGraphRepresentations.cpp
AminoAcidGraphRepresentations.h
ProteinStructures.h
SpecialCaseHandler.cpp
SpecialCaseHandler.h
StructurePreparationData.h
StructurePreparationHelper.cpp
StructurePreparationHelper.h
StructurePreparationIO.cpp
StructurePreparationIO.h
StructurePreparationSettings.h
StructureProcessor.cpp
StructureProcessor.h
Utilities
AtomicInformationReader.cpp
AtomicInformationReader.h
BasicJobSubmissionHelper.cpp
BasicJobSubmissionHelper.h
CalculatorOptions.h
ConnectivityFileHandler.cpp
ConnectivityFileHandler.h
FragmentAnalyzer.cpp
FragmentAnalyzer.h
FragmentationHelper.cpp
FragmentationHelper.h
ModuleLoader.h
OptionNames.h
SettingsNames.h
SettingsPopulator.h
SubsystemGenerator.cpp
SubsystemGenerator.h
TitrationFileHandler.cpp
TitrationFileHandler.h
TopologyUtils.cpp
TopologyUtils.h
SwooseModule.cpp
SwooseModule.h
Tests
Files
tests_file_location.h
TestUtilities
AminoAcidDataForTests.h
MockModule.cpp
MockModule.h
MockQmCalculator.cpp
MockQmCalculator.h
ReferenceDataForTests.h
AppTest.cpp
AtomicInformationReaderTest.cpp
BondOrderRefinementTest.cpp
DatabaseModeTest.cpp
GaffMolecularMechanicsTest.cpp
InteractionTermEliminatorTest.cpp
JobSubmissionHelperTest.cpp
MolecularMachineLearningTest.cpp
ParametrizationOfLargeSystemsTest.cpp
ParametrizationOfSmallSystemsTest.cpp
QmmmHelperFunctionsTest.cpp
QmmmTest.cpp
QmRegionSelectionTests.cpp
SfamMolecularMechanicsTest.cpp
StructurePreparationTest.cpp
TitrationTest.cpp