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.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