atomTyper.h

Go to the documentation of this file.

#ifndef ATOMTYPER_H
#define ATOMTYPER_H

#include <iostream>
#include <string>
#include <vector>
#include <algorithm>

namespace MTKpp
{

class collection;
class molecule;
class submolecule;
class atom;

class stdLibrary;
class stdGroup;
class stdFrag;
struct stdAtom;

class parameters;
struct atomType;

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

    atomTyper();

    atomTyper(int b);

    virtual ~atomTyper();

    void atomTypeByLib(collection* c);

    void atomTypeByLib(molecule* m);

    void atomTypeByCon(collection* c);

    void assignStdProperties(molecule* m);

protected:

    void perceiveHistidines();

    void perceiveCysteines();

    void assignStdRings(molecule* pMolecule);

    void assignStdFunctionalGroups(molecule* pMolecule);

    void assignStdHydrophobicGroups(molecule* pMolecule);

    typedef std::vector<molecule*>::iterator moleculeIterator;

    typedef std::vector<submolecule*>::iterator subMoleculeIterator;

    typedef std::vector<atom*>::iterator atomIterator;

    std::vector<molecule*>    moleculeList;

    std::vector<submolecule*> subMoleculeList;

    std::vector<atom*>        atomList;

    collection*  pCollection;

    molecule*    pMolecule;

    submolecule* pSubMolecule;

    atom*        pAtom;

    stdLibrary* pStdLibrary;

    stdGroup*   pStdGroup;

    stdFrag*    pStdFrag;

    stdAtom*    pStdAtom;

    parameters*  pParameters;

    int bPerceiveHistidines;

    int bPerceiveCysteines;
};

} // MTKpp namespace

#endif // ATOMTYPER_H