Scine::Swoose  2.1.0
This is the SCINE module Swoose.
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Scine::MMParametrization::TitrationHelper Class Reference
Collaboration diagram for Scine::MMParametrization::TitrationHelper:
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Public Member Functions

 TitrationHelper (std::shared_ptr< Utils::Settings > &settings)
 
Utils::AtomCollection changeProtonationState (const Utils::AtomCollection &refStructure, std::string residueName, bool isBase, int indexOfCriticalAtom, std::vector< int > superfluousHydrogens)
 Changes the protonation state of a pH sensitive site in a fragment during the parametrization. More...
 
void collectTrainingData (TitrationResults &results)
 
double getModelPka (const std::string &residueName)
 

Static Public Member Functions

static void calculateFreeEnergiesOfDeprotonation (TitrationResults &results)
 

Member Function Documentation

Utils::AtomCollection Scine::MMParametrization::TitrationHelper::changeProtonationState ( const Utils::AtomCollection &  refStructure,
std::string  residueName,
bool  isBase,
int  indexOfCriticalAtom,
std::vector< int >  superfluousHydrogens 
)

Changes the protonation state of a pH sensitive site in a fragment during the parametrization.

Parameters
refStructureThe input structure.
residueNameThe residue name.
isBaseWhether the amino acid is a base.
indexOfCriticalAtomThe index of the atom at which the protonation pattern should be changed.
superfluousHydrogensThe hydrogens that must be eliminated.
Returns
Utils::AtomCollection The updated structure.
The documentation for this class was generated from the following files: