rotamer.h

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/**********************************************************************
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.sourceforge.net/>
 
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/mol.h>
#include <openbabel/rotor.h>
#include <openbabel/generic.h>

namespace OpenBabel
{

  // 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;

    /*Because contains OBAtom*, these aren't meaningful without knowing the parent molecule
      OBRotamerList(const OBRotamerList &cpy) : OBGenericData(cpy)
      {}
      OBRotamerList& operator =(const OBRotamerList &)
      {
      return *this;
      }
                */

  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);

    void SetBaseCoordinateSets(OBMol& mol)
    {
      SetBaseCoordinateSets(mol.GetConformers(), mol.NumAtoms());
    }


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

    unsigned int NumBaseCoordinateSets() const
    {
      return _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

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This file is part of the documentation for Open Babel, version 2.1.0.

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