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/**********************************************************************
Copyright (C) 1998-2000 by OpenEye Scientific Software, Inc.
Some portions Copyright (c) 2001-2002 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_BINARY_H
#define OB_BINARY_H
#include <map>
#include "mol.h"
#include "rotor.h"
#include "binary_io.h"
#include "generic.h"
namespace OpenBabel
{
class OBRotamerList : public OBGenericData
{
unsigned int _NBaseCoords;
std::vector<float*> _c;
std::vector<std::vector<float> > _vres;
std::vector<unsigned char*> _vrotamer;
std::vector<std::pair<OBAtom**,std::vector<int> > > _vrotor;
//Invoking the default copy constructor or
//assignment operator would cause a serious
//memory leak. MM 4/20/01
OBRotamerList(const OBRotamerList &cp) {};
OBRotamerList& operator=(const OBRotamerList& cp) {return *this;}
public:
OBRotamerList() {_NBaseCoords=0; _type=obRotamerList; _attr="RotamerList";}
~OBRotamerList();
void Setup(OBMol&,OBRotorList&);
void Setup(OBMol&,unsigned char*,int);
int NumRotors() {return((_vrotor.empty())?0:_vrotor.size());}
int NumRotamers() {return((_vrotamer.empty())?0:_vrotamer.size());}
void AddRotamer(float*);
void AddRotamer(int *arr);
void AddRotamer(unsigned char *arr);
void AddRotamers(unsigned char*,int);
void GetReferenceArray(unsigned char*);
void ExpandConformerList(OBMol&,std::vector<float*>&);
std::vector<unsigned char*>::iterator BeginRotamer() {return(_vrotamer.begin());}
std::vector<unsigned char*>::iterator EndRotamer() {return(_vrotamer.end());}
//Support for internal storage of base coordinate sets that rotamers operate on
//Added by MM 4/19/01
//I cannot find any reference to _c in any of the member functions of OBRotamerList
//I'm canibalizing it for internal storage of the base coordinate sets, which I'm
//assuming was the original intent that was simply never coded.
//Create a conformer list using the internal base set of coordinates
std::vector<float*> CreateConformerList(OBMol& mol);
//Copies the mol's conformers (the coordinates, NOT the pointers) into the object as base coordinates
void SetBaseCoordinateSets(OBMol& mol) {SetBaseCoordinateSets(mol.GetConformers(),mol.NumAtoms());}
//Copies the coordinates in bc, NOT the pointers, into the object
void SetBaseCoordinateSets(std::vector<float*> bc, unsigned int N);
//Returns true if the internal base coordinates are set
unsigned int NumBaseCoordinateSets() {return _c.size();}
//Get a pointer to a specific base pointer
float *GetBaseCoordinateSet(unsigned int i) {return (i<_c.size()) ? _c[i] : NULL;}
unsigned int NumAtoms() {return _NBaseCoords;}
};
class OBBinaryDBase
{
std::ifstream _ifs;
std::vector<std::streampos> _vpos;
public:
OBBinaryDBase(char*);
OBBinaryDBase(std::string&);
int Size();
void GetMolecule(OBMol&,int);
};
int Swab(int);
}
#endif // OB_BINARY_H
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