/****************************************************************************
 * Copyright (C) 2009-2015 EPAM Systems
 * 
 * This file is part of Indigo toolkit.
 * 
 * This file may be distributed and/or modified under the terms of the
 * GNU General Public License version 3 as published by the Free Software
 * Foundation and appearing in the file LICENSE.GPL included in the
 * packaging of this file.
 * 
 * This file is provided AS IS with NO WARRANTY OF ANY KIND, INCLUDING THE
 * WARRANTY OF DESIGN, MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE.
 ***************************************************************************/

#ifndef __molecule_ionize_h__
#define __molecule_ionize_h__

#include "base_cpp/tlscont.h"
#include "base_cpp/obj_array.h"
#include "base_cpp/red_black.h"

#ifdef _WIN32
#pragma warning(push)
#pragma warning(disable:4251)
#endif

namespace indigo {

class Molecule;
class QueryMolecule;

struct IonizeOptions
{
   enum PkaModel { PKA_MODEL_SIMPLE, PKA_MODEL_ADVANCED };

   PkaModel model;
   int level = 0;
   int min_level = 0;

   IonizeOptions (PkaModel model = PKA_MODEL_SIMPLE) : model(model) {}
};

class MoleculePkaModel
{
public:
   DECL_ERROR;
   static void estimate_pKa (Molecule &mol, const IonizeOptions &options, Array<int> &acid_sites,
                      Array<int> &basic_sites, Array<float> &acid_pkas, Array<float> &basic_pkas);
   static void getAtomLocalFingerprint (Molecule &mol, int idx, Array<char> &fp, int level);
   static void getAtomLocalKey (Molecule &mol, int idx, Array<char> &fp);
   static int buildPkaModel (int level, float threshold, const char * filename);

   static float getAcidPkaValue (Molecule &mol, int idx, int level, int min_level);
   static float getBasicPkaValue (Molecule &mol, int idx, int level, int min_level);

private:
   MoleculePkaModel ();
   static MoleculePkaModel _model;

   static void _loadSimplePkaModel ();
   static void _loadAdvancedPkaModel ();
   static void _estimate_pKa_Simple (Molecule &mol, const IonizeOptions &options, Array<int> &acid_sites,
                      Array<int> &basic_sites, Array<float> &acid_pkas, Array<float> &basic_pkas);

   static void _estimate_pKa_Advanced (Molecule &mol, const IonizeOptions &options, Array<int> &acid_sites,
                      Array<int> &basic_sites, Array<float> &acid_pkas, Array<float> &basic_pkas);


   static int _asc_cmp_cb (int &v1, int &v2, void *context);
   static void _checkCanonicalOrder(Molecule &mol, Molecule &can_mol, Array<int> &order);
   static void _removeExtraHydrogens (Molecule &mol);

   ObjArray<QueryMolecule> acids;
   ObjArray<QueryMolecule> basics;
   Array<float> a_pkas;
   Array<float> b_pkas;
   bool simple_model_ready = false;

   RedBlackStringObjMap<Array <float> > adv_a_pkas;
   RedBlackStringObjMap<Array <float> > adv_b_pkas;
   int level;
   Array<float> max_deviations;
   bool advanced_model_ready = false;
};

class DLLEXPORT MoleculeIonizer
{
public:
   MoleculeIonizer ();

   static bool ionize (Molecule &molecule, float ph, float ph_toll, const IonizeOptions &options);

   DECL_ERROR;
   CP_DECL;

protected:
   static void _setCharges (Molecule &mol, float ph, float ph_toll, const IonizeOptions &options, Array<int> &acid_sites,
                      Array<int> &basic_sites, Array<float> &acid_pkas, Array<float> &basic_pkas);
};

}

#ifdef _WIN32
#pragma warning(pop)
#endif

#endif