BALL 1.5.0
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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

◆ StructurePreparer()

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

Member Function Documentation

◆ assignAtomTypes()

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'

◆ assignCharges()

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

assign all partial charges#

Parameters
overwrite_mode0 = no overwriting of charges, 1 = overwrite all charges, 2 = automatic (overwrite all charges only if most atoms do not have a charge yet)

◆ assignMMFF94AtomTypes()

void BALL::StructurePreparer::assignMMFF94AtomTypes ( AtomContainer * at)

◆ assignPLPAtomTypes()

void BALL::StructurePreparer::assignPLPAtomTypes ( AtomContainer * at)

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

◆ assignProteinCharges()

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_mode0 = no overwriting of charges, 1 = overwrite all charges, 2 = automatic (overwrite all charges only if most atoms do not have a charge yet)

◆ assignSimpleAtomTypes()

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

◆ buildBonds()

void BALL::StructurePreparer::buildBonds ( AtomContainer * at)

◆ getSimpleAtomTypes()

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

◆ prepare()

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

run all of the above

◆ saturate()

void BALL::StructurePreparer::saturate ( AtomContainer * at)

◆ selectHeavyAtoms()

void BALL::StructurePreparer::selectHeavyAtoms ( AtomContainer * at)

◆ setScoringType()

void BALL::StructurePreparer::setScoringType ( String type)

◆ setSimpleAtomTypes()

void BALL::StructurePreparer::setSimpleAtomTypes ( std::set< String > & new_types)