BALL::StructurePreparer Class Reference

#include <BALL/DOCKING/COMMON/structurePreparer.h>

Public Member Functions
	StructurePreparer (String type="", bool ignore=0)
void	assignAtomTypes (AtomContainer *at, String iniFile, String AtomType_file="")
void	assignSimpleAtomTypes (AtomContainer *at, String iniFile)
void	assignPLPAtomTypes (AtomContainer *at)
void	assignMMFF94AtomTypes (AtomContainer *at)
void	setScoringType (String type)
void	assignCharges (AtomContainer *at, int overwrite_mode)
bool	assignProteinCharges (AtomContainer *at, String parameterFile, int overwrite_mode)
void	buildBonds (AtomContainer *at)
void	saturate (AtomContainer *at)
void	selectHeavyAtoms (AtomContainer *at)
void	prepare (AtomContainer *at, String parameterFile, String AtomType_file="")
void	setSimpleAtomTypes (std::set< String > &new_types)
const std::set< String > *	getSimpleAtomTypes ()

Detailed Description

Definition at line 21 of file structurePreparer.h.

Constructor & Destructor Documentation

BALL::StructurePreparer::StructurePreparer	(	String	type = "",
		bool	ignore = 0
	)

Member Function Documentation

void BALL::StructurePreparer::assignAtomTypes	(	AtomContainer *	at,
		String	iniFile,
		String	AtomType_file = ""
	)

tries to assign the exact atom types, as defined in 'iniFile', to all atoms of 'at'

void BALL::StructurePreparer::assignCharges	(	AtomContainer *	at,
		int	overwrite_mode
	)

assign all partial charges#

Parameters

overwrite_mode

0 = no overwriting of charges, 1 = overwrite all charges, 2 = automatic (overwrite all charges only if most atoms do not have a charge yet)

void BALL::StructurePreparer::assignMMFF94AtomTypes

(

AtomContainer *

at

)

void BALL::StructurePreparer::assignPLPAtomTypes

(

AtomContainer *

at

)

assign Piecewise Linear Potential AtomTypes to all atoms of the given AtomContainer

bool BALL::StructurePreparer::assignProteinCharges	(	AtomContainer *	at,
		String	parameterFile,
		int	overwrite_mode
	)

assigns charges to a protein based on the charges template section of the specified parameter file

Parameters

overwrite_mode

0 = no overwriting of charges, 1 = overwrite all charges, 2 = automatic (overwrite all charges only if most atoms do not have a charge yet)

void BALL::StructurePreparer::assignSimpleAtomTypes	(	AtomContainer *	at,
		String	iniFile
	)

tries to assign simplied atom types based mainly on element symbols.

Parameters

'iniFile'

is needed to obtain the corresponding IDs (force field dependend AtomType of type int) for each of these simple type names

void BALL::StructurePreparer::buildBonds

(

AtomContainer *

at

)

const std::set<String>* BALL::StructurePreparer::getSimpleAtomTypes

(

)

void BALL::StructurePreparer::prepare	(	AtomContainer *	at,
		String	parameterFile,
		String	AtomType_file = ""
	)

run all of the above

void BALL::StructurePreparer::saturate

(

AtomContainer *

at

)

void BALL::StructurePreparer::selectHeavyAtoms

(

AtomContainer *

at

)

void BALL::StructurePreparer::setScoringType

(

String

type

)

void BALL::StructurePreparer::setSimpleAtomTypes

(

std::set< String > &

new_types

)