ReferenceCalculationsIO.cpp File Reference

#include "ReferenceCalculationsIO.h"
#include "../ParametrizationData.h"
#include <Core/Log.h>
#include <Swoose/MMParametrization/MMParametrizationSettings.h>
#include <Swoose/MMParametrization/ParametrizationUtils/TitrationHelper.h>
#include <Swoose/StructurePreparation/ProteinStructures.h>
#include <Swoose/StructurePreparation/Protonation/TitrationData.h>
#include <Swoose/Utilities/ConnectivityFileHandler.h>
#include <Swoose/Utilities/FragmentationHelper.h>
#include <Swoose/Utilities/TopologyUtils.h>
#include <Utils/Bonds/BondOrderCollection.h>
#include <Utils/ExternalQC/Gaussian/GaussianOutputParser.h>
#include <Utils/ExternalQC/Orca/OrcaHessianOutputParser.h>
#include <Utils/ExternalQC/Orca/OrcaMainOutputParser.h>
#include <Utils/ExternalQC/Turbomole/TurbomoleMainOutputParser.h>
#include <Utils/IO/ChemicalFileFormats/ChemicalFileHandler.h>
#include <Utils/IO/FormattedIOUtils.h>
#include <Utils/IO/NativeFilenames.h>
#include <Utils/Properties/AtomicCharges/ChargeModel5.h>
#include <boost/filesystem.hpp>
#include <fstream>

Include dependency graph for ReferenceCalculationsIO.cpp:

Functions
void	Scine::MMParametrization::ReferenceCalculationsIO::writeXyzFiles (ParametrizationData &data, std::string referenceDataDir, std::shared_ptr< Utils::Settings > settings)
	This function writes the structures/fragments to disk. It also writes the information about the charge and spin multiplicity of each structure as well as (if necessary) information about constrained atoms for the fragment optimization. It is used during the "write" mode in CalculationManager.
void	Scine::MMParametrization::ReferenceCalculationsIO::writeAdditionalDataForTitration (ParametrizationData &data, int fragmentIndex, int criticalAtomIndex, std::string referenceDataDir, std::shared_ptr< Utils::Settings > settings)
	This function writes the structures/fragments for all titrable sites to disk. The additional structures correspond to the respective sites in their non-reference (i. e. charged) protonation state.
void	Scine::MMParametrization::ReferenceCalculationsIO::saveAdditionalStructuresForTitration (ParametrizationData &data, TitrationResults &results, int fragmentIndex, std::string referenceDataDir)
	This function reades the reference data for structures/fragments for all titrable sites from disk.
void	Scine::MMParametrization::ReferenceCalculationsIO::parseElectronicEnergiesForTitration (ParametrizationData &data, TitrationResults &results, int fragmentIndex, std::string referenceDataDir, bool parseTurbomoleOutput, std::shared_ptr< Utils::Settings > settings)
	This function reades the reference data for structures/fragments for all titrable sites from disk.
void	Scine::MMParametrization::ReferenceCalculationsIO::readReferenceDataFromFiles (ParametrizationData &data, TitrationResults &titrationResults, std::string referenceDataDir, std::shared_ptr< Utils::Settings > settings, Core::Log &log)
	This function reads the reference data from disk. It is used during the "read" mode in CalculationManager.
Utils::ExternalQC::TurbomoleMainOutputParser	Scine::MMParametrization::ReferenceCalculationsIO::getPreparedTurbomoleParser (const std::string &referenceDataDir, int fragmentIndex)
	Constructs Turbomole parser and returns it. This parser will already contain the correct output files directory.
void	Scine::MMParametrization::ReferenceCalculationsIO::writeConstrainedAtomsFile (const std::vector< int > &constrainedAtoms, std::string &constrainedAtomsFile)
	Writes a file with atom indices that should be constrained during the optimization. More...

Detailed Description

Copyright

This code is licensed under the 3-clause BSD license.
Copyright ETH Zurich, Department of Chemistry and Applied Biosciences, Reiher Group.
See LICENSE.txt for details.