StructurePreparationHelper.cpp File Reference

#include "StructurePreparationHelper.h"
#include "AminoAcidGraphRepresentations.h"
#include "ProteinStructures.h"
#include "Protonation/ProtonationHandler.h"
#include "Protonation/TitrationData.h"
#include "SpecialCaseHandler.h"
#include "StructurePreparationData.h"
#include "StructurePreparationSettings.h"
#include <Core/Log.h>
#include <Molassembler/Graph.h>
#include <Molassembler/Interpret.h>
#include <Molassembler/Subgraphs.h>
#include <Swoose/Utilities/TopologyUtils.h>
#include <Utils/Bonds/BondDetector.h>
#include <Utils/Geometry/ElementInfo.h>
#include <Utils/IO/ChemicalFileFormats/ChemicalFileHandler.h>
#include <Utils/IO/NativeFilenames.h>
#include <Utils/Solvation/SoluteSolventComplex.h>
#include <algorithm>
#include <utility>

Include dependency graph for StructurePreparationHelper.cpp:

Functions
void	Scine::StructurePreparation::StructurePreparationHelper::performInitialCheck (const StructurePreparationFiles &files, int mode, std::shared_ptr< Utils::Settings > settings)
	At the beginning of each step, this function evaluates if the required files are present. More...
std::string	Scine::StructurePreparation::StructurePreparationHelper::indexToAtomType (StructurePreparationData &data, int index)
void	Scine::StructurePreparation::StructurePreparationHelper::getSideChainNeighbors (StructurePreparationData &data, int atomIndex, std::list< int > &atomsToAdd)
bool	Scine::StructurePreparation::StructurePreparationHelper::compareByIndex (const ProteinAtom &a, const ProteinAtom &b)
void	Scine::StructurePreparation::StructurePreparationHelper::performGraphAnalysisOnStructure (StructurePreparationData &data, const Utils::AtomCollection &structure)
	This function separates the structure into a protein and a nonregular_container subsystem by performing a molassembler subgraph matching with all essential amino acids.
void	Scine::StructurePreparation::StructurePreparationHelper::updateNonRegContainerVector (StructurePreparationData &data)
void	Scine::StructurePreparation::StructurePreparationHelper::findTermini (StructurePreparationData &data, std::list< int > &atomsToTransferToNonRegContainer)
void	Scine::StructurePreparation::StructurePreparationHelper::moveAtomsFromProteinToNonRegContainer (StructurePreparationData &data, const std::list< int > &atomsToMove)
void	Scine::StructurePreparation::StructurePreparationHelper::reevaluateConnectivityForAminoAcids (StructurePreparationData &data)
	This function constructs each amino acid residue by recursively following the bonds along each side chain and subsequently performs a subgraph matching with the amino acid that is expected.
void	Scine::StructurePreparation::StructurePreparationHelper::updatePdbPreparationData (StructurePreparationData &data, Utils::AtomCollection &structure)
	A method that updates several objects in the StructurePreparationData object.
void	Scine::StructurePreparation::StructurePreparationHelper::removeAtomsFromStructure (Utils::AtomCollection &structure, std::list< int > atomsToRemove)
	Removes atoms from a structure (required, if protonation state is changed).
void	Scine::StructurePreparation::StructurePreparationHelper::mapSubsystemIndicesToFullStructure (const Utils::AtomCollection &fullStructure, const Utils::AtomCollection &structure, std::vector< int > &indicesInStructure, std::vector< std::vector< int >> &subsystemMapping)
void	Scine::StructurePreparation::StructurePreparationHelper::handleBoundariesBetweenProteinAndNonRegContainer (StructurePreparationData &data)
	After combination of (modified) substructures, the covalent bonds at the subsystem boundaries must be fixed (superfluous hydrogens must be removed).
Utils::AtomCollection	Scine::StructurePreparation::StructurePreparationHelper::addSolvation (StructurePreparationData &data, std::shared_ptr< Utils::Settings > settings)
	Solvates the structure with a number of solvent shells that can be set as a setting.
void	Scine::StructurePreparation::StructurePreparationHelper::mergeProteinAndNonRegContainer (StructurePreparationData &data, const StructurePreparationFiles &files)
	Merges the substructures.
std::vector< TitrableSite >	Scine::StructurePreparation::StructurePreparationHelper::collectTitrableSites (StructurePreparationData &data)
	Searches for titrable amino acids in the structure.
void	Scine::StructurePreparation::StructurePreparationHelper::determineChargedSites (std::vector< int > &listOfNegatives, std::vector< int > &listOfPositives, const StructurePreparationData &data)
	Evaluates, which sites are charged, and appends the corresponding atom indices to the vectors listOfPositives, and listOfNegatives,.

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.