protonate.h

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#ifndef PROTONATE_H
#define PROTONATE_H

#include <iostream>
#include <string>
#include <vector>
#include <algorithm>
#include <cmath>
#include "Utils/constants.h"

namespace MTKpp
{

class collection;
class molecule;
class submolecule;
class atom;
struct Bond;

class vector3d;

class stdLibrary;
class stdGroup;
class stdFrag;
struct stdAtom;
struct stdBond;
struct stdImproper;
struct stdLoop;
struct stdAlias;

class parameters;
struct bondParam;
struct angleParam;
struct torsionParam;

class proProtonate;
class ligProtonate;
class watProtonate;

// ============================================================
// Class : protonate()
// ------------------------------------------------------------
// ============================================================
class protonate
{
public:

    protonate(collection *col = 0);

    protonate(molecule *mol = 0);

    virtual ~protonate();

    void run();

    void optimizePolarHs();

protected: // FUNCTIONS

    void initialize();

    void runCol();

    void runMol(molecule* pMolecule);

    /*
      \brief Attempt to build the missing heavy atoms of a fragment
      \param pSubMolecule submolcule pointer
    */
    int buildMissingHeavyAtoms(submolecule* pSubMolecule);

protected: // DATA
    proProtonate*  pPro;

    ligProtonate*  pLig;

    watProtonate*  pWat;

    collection*    pCol;

    bool           bCol;

    molecule*      pMol;

    bool           bMol;

    std::vector<submolecule*> subMoleculeList;

    std::vector<atom*> atomList;

    submolecule*   pSubMolecule;

    submolecule*   pSubMoleculeMinus1;

    stdLibrary*    pStdLibrary;

    stdGroup*      pStdGroup;

    stdFrag*       pStdFrag;

    stdFrag*       pStdFragMinus1;

    parameters*    pParam;

    std::vector<atom*> prev3Atoms;
};

} // MTKpp namespace

#endif // PROTONATE_H