rotamer.h

Go to the documentation of this file.

/**********************************************************************
rotamer.h - Handle rotamer list data.

Copyright (C) 1998-2000 by OpenEye Scientific Software, Inc.
Some portions Copyright (C) 2001-2006 by Geoffrey R. Hutchison

This file is part of the Open Babel project.
For more information, see <http://openbabel.org/>

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation version 2 of the License.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.
***********************************************************************/

#ifndef OB_ROTAMER_H
#define OB_ROTAMER_H

#include <vector>
#include <map>

#include <openbabel/rotor.h>
#include <openbabel/generic.h>

namespace OpenBabel
{
  class OBMol;

  // Further class introduction in rotamer.cpp
 class OBAPI OBRotamerList : public OBGenericData
  {
    unsigned int                         _NBaseCoords;
    std::vector<double*>                 _c;
    std::vector<std::pair<OBAtom**,std::vector<int> > > _vrotor;
    std::vector<std::vector<double> >    _vres;
    std::vector<unsigned char*>          _vrotamer;
    std::vector<std::vector<int> >       _vrings;
    std::vector<std::vector<double> >    _vringTors;

  public:
    OBRotamerList()
      {
        _NBaseCoords=0;
        _type= OBGenericDataType::RotamerList;
        _attr="RotamerList";
      }
                virtual OBGenericData* Clone(OBBase* parent) const;

    ~OBRotamerList();
    void Setup(OBMol&,OBRotorList&);
    void Setup(OBMol &mol,unsigned char*ref,int nrotors);
    unsigned int NumRotors()   const
    {
      return (unsigned int)_vrotor.size();
    }
    unsigned int NumRotamers() const
    {
      return (unsigned int)_vrotamer.size();
    }
    void AddRotamer(double*);
    void AddRotamer(int *key);
    void AddRotamer(std::vector<int> key);
    void AddRotamer(unsigned char *key);
    void AddRotamers(unsigned char *arr,int nconf);
    void GetReferenceArray(unsigned char*) const;


    std::vector<unsigned char*>::iterator BeginRotamer()
      {
        return _vrotamer.begin();
      }
    std::vector<unsigned char*>::iterator EndRotamer()
      {
        return _vrotamer.end();
      }

    std::vector<double*> CreateConformerList(OBMol& mol);

    void ExpandConformerList(OBMol&mol,std::vector<double*>& confs);

    bool SetCurrentCoordinates(OBMol &mol, std::vector<int> arr);

    void SetBaseCoordinateSets(OBMol& mol);


    void SetBaseCoordinateSets(std::vector<double*> bc, unsigned int N);

    unsigned int NumBaseCoordinateSets() const
    {
      return static_cast<unsigned int> (_c.size());
    }

    double *GetBaseCoordinateSet(unsigned int i) const
    {
      return (i<_c.size()) ? _c[i] : NULL;
    }

    unsigned int NumAtoms() const
    {
      return _NBaseCoords;
    }
  };

  int Swab(int);

}

#endif // OB_ROTAMER_H