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structurePreparer.h
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// -*- Mode: C++; tab-width: 2; -*-
// vi: set ts=2:
//
#ifndef BALL_DOCKING_COMMON_STRUCTUREPREPARER_H
#define BALL_DOCKING_COMMON_STRUCTUREPREPARER_H
#ifndef BALL_KERNEL_ATOMCONTAINER_H
#include <BALL/KERNEL/atomContainer.h>
#endif
#ifndef BALL_STRUCTURE_ADDHYDROGENSPROCESSOR_H
#include <BALL/STRUCTURE/addHydrogenProcessor.h>
#endif
#include <set>
namespace BALL
{
class BALL_EXPORT StructurePreparer
{
public:
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();
private:
bool setIonStandardCharge(Atom* atom);
bool use_mmff94_;
bool ignore_unassigned_;
bool use_PLP_;
std::set<String> simple_atom_types_;
};
}
#endif // BALL_DOCKING_COMMON_STRUCTUREPREPARER_H
BALL_EXPORT
#define BALL_EXPORT
Definition COMMON/global.h:50
addHydrogenProcessor.h
atomContainer.h
BALL::AtomContainer
Definition atomContainer.h:32
BALL::Atom
Definition atom.h:90
BALL::String
Definition string.h:57
BALL::StructurePreparer::setScoringType
void setScoringType(String type)
BALL::StructurePreparer::setSimpleAtomTypes
void setSimpleAtomTypes(std::set< String > &new_types)
BALL::StructurePreparer::assignCharges
void assignCharges(AtomContainer *at, int overwrite_mode)
BALL::StructurePreparer::assignPLPAtomTypes
void assignPLPAtomTypes(AtomContainer *at)
BALL::StructurePreparer::prepare
void prepare(AtomContainer *at, String parameterFile, String AtomType_file="")
BALL::StructurePreparer::assignProteinCharges
bool assignProteinCharges(AtomContainer *at, String parameterFile, int overwrite_mode)
BALL::StructurePreparer::StructurePreparer
StructurePreparer(String type="", bool ignore=0)
BALL::StructurePreparer::getSimpleAtomTypes
const std::set< String > * getSimpleAtomTypes()
BALL::StructurePreparer::buildBonds
void buildBonds(AtomContainer *at)
BALL::StructurePreparer::selectHeavyAtoms
void selectHeavyAtoms(AtomContainer *at)
BALL::StructurePreparer::assignSimpleAtomTypes
void assignSimpleAtomTypes(AtomContainer *at, String iniFile)
BALL::StructurePreparer::assignMMFF94AtomTypes
void assignMMFF94AtomTypes(AtomContainer *at)
BALL::StructurePreparer::saturate
void saturate(AtomContainer *at)
BALL::StructurePreparer::assignAtomTypes
void assignAtomTypes(AtomContainer *at, String iniFile, String AtomType_file="")
BALL
Definition constants.h:13