/usr/include/BALL/DOCKING/COMMON/structurePreparer.h is in libball1.4-dev 1.4.3~beta1-3.
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#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);
/** tries to assign the exact atom types, as defined in 'iniFile', to all atoms of 'at' */
void assignAtomTypes(AtomContainer* at, String iniFile, String AtomType_file="");
/** tries to assign simplied atom types based mainly on element symbols. \n @param 'iniFile' is needed to obtain the corresponding IDs (force field dependend AtomType of type int) for each of these simple type names */
void assignSimpleAtomTypes(AtomContainer* at, String iniFile);
/** assign Piecewise Linear Potential AtomTypes to all atoms of the given AtomContainer */
void assignPLPAtomTypes(AtomContainer* at);
void assignMMFF94AtomTypes(AtomContainer* at);
void setScoringType(String type);
/** assign all partial charges#
@param 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 assignCharges(AtomContainer* at, int overwrite_mode);
/** assigns charges to a protein based on the charges template section of the specified parameter file
@param 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) */
bool assignProteinCharges(AtomContainer* at, String parameterFile, int overwrite_mode);
void buildBonds(AtomContainer* at);
void saturate(AtomContainer* at);
void selectHeavyAtoms(AtomContainer* at);
/** run all of the above */
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_;
/** if == 1, unassigned atom types are ignored.\n
else an exception is thrown if an atom type could not be assigned for at least one atom. */
bool ignore_unassigned_;
/** determines whether Piecewise Linear Potential AtomTypes are to be used */
bool use_PLP_;
std::set<String> simple_atom_types_;
};
}
#endif // BALL_DOCKING_COMMON_STRUCTUREPREPARER_H
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