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