GetEnergy.h
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/** \file GetEnergy.h
* GetEnergy.h by Robert Dirks.
* This program determines the energies of
* substructures, mirroring the loops of Fold.out
* and includes the function for determining energies. 03/15/2001
*/
#ifndef __GETENERGY_H__
#define __GETENERGY_H__
#include "ene.h"
#ifdef __cplusplus
extern "C" {
#endif
//These functions are used to calculate the energy of a structure (linear time algorithm)
//compute the energy of the structure described in *thefold
DBL_TYPE GetEnergy( fold *thefold);
//Calculate the energy of an exterior loop substructure
DBL_TYPE EnergyF( int start, int stop, fold *thefold);
//Energy of Paired substructure
DBL_TYPE EnergyFb( int start, int stop, fold *thefold);
//Energy of pseudoknotted substructure
DBL_TYPE EnergyPk( int i, int j, fold *thefold);
//Energy of gap spanning region
DBL_TYPE EnergyFg( int i, int d, int e, int j, fold *thefold);
//Energy of pseudoknot interior
DBL_TYPE EnergyFz( int start, int stop, fold *thefold);
#ifdef __cplusplus
}
#endif /* __cplusplus */
#endif