Collaboration diagram for Scine::StructurePreparation::StructureProcessor:

Public Member Functions
	StructureProcessor ()
	Constructor.

void	prepare (const std::string &structureFile, const std::string &mode)
	Main function of this class. It prepares the protein input structure. More...

Utils::Settings &	settings ()
	Accessor for the settings.

const Utils::Settings &	settings () const
	Constant accessor for the settings.

std::string	name () const
	Getter for the name of the Parametrizer.

void	analyzeStructure (const std::string &structureFile)
	Analyzes the input structure.

void	protonate ()
	Protonates protein and nonRegContainer separately.

void	finalize ()
	This function merges protein and nonRegContainer, corrects the boundaries, adds optional solvation and generates atomic info file and connectivity file.

void	setLog (Core::Log &log)

void	setFiles (StructurePreparationFiles files)

Member Function Documentation

void Scine::StructurePreparation::StructureProcessor::prepare	(	const std::string &	structureFile,
		const std::string &	mode
	)

Main function of this class. It prepares the protein input structure.

Parameters

structure	The input file.
mode	The mode. Valid modes are: prepare-analyze, prepare-protonate and prepare-finalize.

The documentation for this class was generated from the following files:

Public Member Functions