/* EGAD: MC.h
   
Navin Pokala and Tracy Handel
Dept. of Molecular and Cell Biology
University of California, Berkeley
Copyright (C) 2003 Regents of the University of California
GNU Public License
Aug 12 2003

Absolutely no warranties are made or are implied with the use of this program or its parts.

This file is the header for MC.cpp

*/


#ifndef MC_header_flag
#define MC_header_flag

#include <stdio.h>
#include <string.h>
#include <stdlib.h>
#include <time.h>
#include <float.h>
#include <limits.h>
#include <math.h>

#include "structure_types.h"
#include "GA_utilities.h"
#include "CHROMOSOME_to_lookupEnergy.h"
#include "search_and_sort.h"
#include "HQM_rotamers.h"
#include "output_stuff.h"
#include "GA.h"


/* controls MC_rotamers. assumes that protein has been initialized by input_stuff and generate_lookup_table.
	Final structures etc generated by final_chr_to_final_pdb_final_energy; ready for output_PROTEIN. 
*/
void MC_rotamer_control(PROTEIN *protein);

/* chr is used as a starting point for simulated annealing rotamer/resimer optimization.
	if solubility is a criterion, chr must be soluble.
	num_cycles = number of consecutive moves that do not result in a decrease in the best energy.
	The best soln is returned in chr  
*/
void MC_rotamers(PARAMETERS *parameters, CHROMOSOME *chr, VARIABLE_POSITION *var_pos);


#endif