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icagg-contacts_mean_cost_function_modification_n-clashes_energy_hydrophobicity+electrostatics+hydrogen-bonds.c
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icagg-contacts_mean_cost_function_modification_n-clashes_energy_hydrophobicity+electrostatics+hydrogen-bonds.c
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#include <stdio.h>
#include <stdlib.h>
#include <math.h>
#include <string.h>
#include <unistd.h>
#include <sys/stat.h>
#include <time.h>
//=============Parameters you might want to change===============
#define MCSTEPS (2000)
#define PROTSTEP (100)
#define STRUCTS (4005)
#define PAIRS (1000)
#define CONTACT_PAIR (2)
#define SCALE (1.) //d(CM1-CM2)=SCALE*(Rg1+Rg2)
#define SCALE_1 (1.2) //scale for adjusting CM-distance in the initial pose/orientation sampling
#define SCALE_2 (0.9) //scale for adjusting CM-distance in the initial pose/orientation sampling
#define SCALE_CLASHES (0.5)
#define HARDCORE_R (1.)
#define CONTACT_R (2.33)
#define Tm (0.15)
//Tm = temperature at which structures were sampled
//ensemble sizes: NAT(WT)pH5.2=4005
//ensemble sizes: NAT(WT)pH6.2=4005
//ensemble sizes: NAT(WT)pH7.2=4005
//ensemble sizes: NAT(D76N)pH5.2=4005
//ensemble sizes: NAT(D76N)pH6.2=4005
//ensemble sizes: NAT(D76N)pH7.2=4005
//ensemble sizes: I1(D76N)pH5.2=4005
//ensemble sizes: I1(D76N)pH6.2=4005
//ensemble sizes: I1(D76N)pH7.2=4005
//ensemble sizes: I2(D76N)pH5.2=4005
//ensemble sizes: I2(D76N)pH6.2=4005
//ensemble sizes: I2(D76N)pH7.2=4005
//end to parameters you might want to change=====================
#define MAXLENLINE (256)
#define LENCHARGESFILE (287)
#define MAXRESIDUE (99)
#define MAXATOMNUM (1100)
#define MAXCONTACT (50000)
#define HIS_TYPE_HIS (0)
#define HIS_TYPE_HSD (1)
#define HIS_TYPE_HSC (2)
#define NUM_AA_TYPE (26)
#define NUM_Atom_TYPE (32)
#define PI (3.14159265358979323846)
//==============Directories you might want to change========================================================================================
char workingdir[]="/home/rjloureiro/DOCKING/B2M-D76N-I1-PH5p2-newcf/";
char writingdir[]="/home/rjloureiro/DOCKING/DOCKING_B2M_D76N-I1-PH5p2_newcf_n-clashes_0.5_energy_hydropathy+electrostatics+hydrogen-bonds_new/";
char rootdir[]="/home/rjloureiro";
char ss[]="DOCKING_B2M_D76N-I1-PH5p2_newcf_n-clashes_0.5_energy_hydropathy+electrostatics+hydrogen-bonds_new";
//==========================================================================================================================================
int ResNum[2];
int nAtom[2];
typedef struct {
int Res_Type;
char AtmName[5];
char Atm_Type[5];
float Atm_Charge;
}MYCHARGES,*PMYCHARGES;
typedef struct {
double x,y,z;
double r0;
int NodeIndex;
int Res_Type;
int AtomIndex;
int Atom_Type;
int ASP_Type;
char AtmName[5];
char AtmHBlabel[5];
}MYATOM,*PMYATOM;
typedef struct {
double Rg;
double RMSD;
int contEn;
}MYCONF, *PMYCONF;
typedef struct {
double r01;
double r02;
double rsq;
}MYDISTANCES, *PMYDISTANCES;
double radii[]={1.61, 1.76, 1.88, 1.88, 1.88, 1.64, 1.64, 1.64, 1.64, 1.42, 1.46, 1.77, 1.77, 1.05, 0.58};
char AA_Name[NUM_AA_TYPE][5]={"METN","ILE","ILEN","VAL","LEU","PHE","CYS","MET","METC","ALA","GLY","THR","SER","TRP","TYR","PRO","HIS","HISH","GLN",
"ASN","GLU","GLUH","ASP","ASPH","LYS","ARG"};/*check*/
float atomic_solvation_parameters[6]={18.0, -7.0, 18.0, -20.0, -34.0, 0.0};
char atom_name[NUM_Atom_TYPE][4]={"CB","CG","CG1","CG2","CD","CD1","CD2","CE","CE1","CE2","CE3","CH2","CZ","CZ2","CZ3","ND1","ND2","NE","NE1","NE2",
"NH1","NH2","NZ","OD1","OD2","OE1","OE2","OG","OG1","OH","SG","SD"};
float atomic_SASA[NUM_AA_TYPE][NUM_Atom_TYPE]={
{24.0, 29.6, 0.0, 0.0, 0.0, 0.0, 0.0, 74.8, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 36.4},
{11.0, 0.0, 37.0, 58.4, 0.0, 43.7, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{11.0, 0.0, 37.0, 58.4, 0.0, 43.7, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{11.1, 0.0, 57.4, 59.9, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{23.1, 9.6, 0.0, 0.0, 0.0, 63.4, 61.7, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{29.3, 0.6, 0.0, 0.0, 0.0, 22.1, 21.9, 0.0, 36.7, 36.1, 0.0, 0.0, 37.7, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{38.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 65.0, 0.0},
{24.0, 29.6, 0.0, 0.0, 0.0, 0.0, 0.0, 74.8, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 36.4},
{24.0, 29.6, 0.0, 0.0, 0.0, 0.0, 0.0, 74.8, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 36.4},
{71.9, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{18.0, 0.0, 0.0, 63.1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 33.5, 0.0, 0.0, 0.0},
{44.3, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 41.5, 0.0, 0.0, 0.0, 0.0},
{30.1, 1.3, 0.0, 0.0, 0.0, 30.2, 2.2, 0.0, 0.0, 3.3, 21.5, 37.9, 0.0, 38.5, 34.1, 0.0, 0.0, 0.0, 29.8, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{29.2, 0.4, 0.0, 0.0, 0.0, 22.6, 21.5, 0.0, 34.8, 34.1, 0.0, 0.0, 2.6, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 52.9, 0.0, 0.0},
{39.1, 44.3, 0.0, 0.0, 27.6, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{34.0, 1.6, 0.0, 0.0, 0.0, 0.0, 33.0, 0.0, 51.6, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 11.4, 0.0, 0.0, 0.0, 30.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{34.0, 1.6, 0.0, 0.0, 0.0, 0.0, 33.0, 0.0, 51.6, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 11.4, 0.0, 0.0, 0.0, 30.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{26.6, 30.9, 0.0, 0.0, 3.7, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 60.0, 0.0, 0.0, 0.0, 0.0, 0.0, 34.2, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{32.1, 3.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 59.1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 31.1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{26.8, 33.2, 0.0, 0.0, 5.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 41.4, 41.5, 0.0, 0.0, 0.0, 0.0, 0.0},
{26.8, 33.2, 0.0, 0.0, 5.5, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 41.4, 41.5, 0.0, 0.0, 0.0, 0.0, 0.0},
{33.5, 5.1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 38.7, 40.9, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{33.5, 5.1, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 38.7, 40.9, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{25.9, 22.6, 0.0, 0.0, 28.0, 0.0, 0.0, 36.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 74.6, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
{25.9, 23.9, 0.0, 0.0, 29.6, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 2.2, 0.0, 0.0, 0.0, 0.0, 13.3, 0.0, 0.0, 58.6, 63.4, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0, 0.0},
};/*atomic solvent accessible surface area*/
/*float hydropathic_inter_residue_potentials[NUM_AA_TYPE][NUM_AA_TYPE]={
{-1.0000, -1.0000, -0.9700, -0.9200, -0.8100, -0.7800, -0.7100, -0.7100, -0.7000, +0.0000, +0.0000, -0.0000, +0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000},
{-1.0000, -1.0000, -0.9700, -0.9200, -0.8100, -0.7800, -0.7100, -0.7100, -0.7000, +0.0000, +0.0000, -0.0000, +0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000},
{-0.9700, -0.9700, -0.9300, -0.8900, -0.7800, -0.7500, -0.6800, -0.6800, -0.6700, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000},
{-0.9200, -0.9200, -0.8900, -0.8400, -0.7300, -0.7000, -0.6300, -0.6300, -0.6200, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000},
{-0.8100, -0.8100, -0.7800, -0.7300, -0.6200, -0.5900, -0.5200, -0.5200, -0.5100, +0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000},
{-0.7800, -0.7800, -0.7500, -0.7000, -0.5900, -0.5600, -0.4900, -0.4900, -0.4800, +0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000},
{-0.7100, -0.7100, -0.6800, -0.6300, -0.5200, -0.4900, -0.4200, -0.4200, -0.4100, +0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000},
{-0.7100, -0.7100, -0.6800, -0.6300, -0.5200, -0.4900, -0.4200, -0.4200, -0.4100, +0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000},
{-0.7000, -0.7000, -0.6700, -0.6200, -0.5100, -0.4800, -0.4100, -0.4100, -0.4000, -0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, +0.0000, -0.0000},
{+0.0000, +0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000},
{+0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000},
{-0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, +0.0000, -0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.0000, -0.0000},
{+0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000},
{-0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, +0.0000, +0.0000, -0.0000, +0.0000},
{+0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, +0.0000, -0.0000, -0.0000, -0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000, -0.0000},
{+0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, +0.7100, +0.7100, +0.7500, +0.7500, +0.7500, +0.7500, +0.7500, +0.7500, +0.7900, +0.8600},
{+0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, +0.7100, +0.7100, +0.7500, +0.7500, +0.7500, +0.7500, +0.7500, +0.7500, +0.7900, +0.8600},
{+0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.7500, +0.7500, +0.7800, +0.7800, +0.7800, +0.7800, +0.7800, +0.7800, +0.8300, +0.8900},
{+0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, -0.0000, -0.0000, +0.7500, +0.7500, +0.7800, +0.7800, +0.7800, +0.7800, +0.7800, +0.7800, +0.8300, +0.8900},
{-0.0000, -0.0000, +0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.0000, +0.0000, -0.0000, -0.0000, -0.0000, +0.7500, +0.7500, +0.7800, +0.7800, -0.0000, -0.0000, -0.0000, -0.0000, +0.0000, -0.0000},
{-0.0000, -0.0000, +0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.0000, +0.0000, -0.0000, -0.0000, -0.0000, +0.7500, +0.7500, +0.7800, +0.7800, -0.0000, -0.0000, -0.0000, -0.0000, +0.0000, -0.0000},
{+0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.0000, -0.0000, -0.0000, +0.0000, -0.0000, +0.7500, +0.7500, +0.7800, +0.7800, -0.0000, -0.0000, +0.0000, +0.0000, +0.0000, -0.0000},
{+0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.0000, -0.0000, -0.0000, +0.0000, -0.0000, +0.7500, +0.7500, +0.7800, +0.7800, -0.0000, -0.0000, +0.0000, +0.0000, +0.0000, -0.0000},
{+0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, +0.0000, +0.0000, -0.0000, -0.0000, -0.0000, +0.7900, +0.7900, +0.8300, +0.8300, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000},
{+0.0000, +0.0000, -0.0000, +0.0000, +0.0000, +0.0000, +0.0000, +0.0000, -0.0000, -0.0000, +0.0000, -0.0000, -0.0000, +0.0000, -0.0000, +0.8600, +0.8600, +0.8900, +0.8900, -0.0000, -0.0000, -0.0000, -0.0000, +0.0000, +0.0000},
};/*hydropathic inter-residue contact potentials between the 20 amino acids*/
/*double SASA_AA[MAXRESIDUE];*/
MYCHARGES Charges[LENCHARGESFILE];
MYATOM Atoms[MAXATOMNUM][2];
MYATOM Moved[MAXATOMNUM];
MYATOM RotMoved[MAXATOMNUM];
MYATOM stack1[MAXATOMNUM];
MYATOM stack2[MAXATOMNUM];
MYCONF Conf[2];
MYDISTANCES dist;
double MEAN_R[3][2];
float q0[MAXCONTACT];
float q1[MAXCONTACT];
/*double sasa_aa[MAXCONTACT][CONTACT_PAIR];*/
int it[MAXCONTACT];
double rd[MAXCONTACT];
int ct0[MAXCONTACT];
int ct1[MAXCONTACT];
int at0[MAXCONTACT];
int at1[MAXCONTACT];
int ri0[MAXCONTACT];
int ri1[MAXCONTACT];
double ro0[MAXCONTACT];
double ro1[MAXCONTACT];
int asp0[MAXCONTACT];
int asp1[MAXCONTACT];
double sum_vdW[MAXCONTACT];
double hidropathy_0[MAXCONTACT];
double hidropathy_1[MAXCONTACT];
double hp[MAXCONTACT];
double ep[MAXCONTACT];
double hbp[MAXCONTACT];
double ip[MAXCONTACT];
//CODE PARTS
int main(void);
void READER(int a, int b);
void CENTRALIZER(double a);
void INITIALORIENTATOR(void);
int TYPECONTACTS(int ct0[MAXCONTACT], int ct1[MAXCONTACT], int at0[MAXCONTACT], int at1[MAXCONTACT], int ri0[MAXCONTACT], int ri1[MAXCONTACT], double ro0[MAXCONTACT], double ro1[MAXCONTACT], double rd[MAXCONTACT], int it[MAXCONTACT], float q0[MAXCONTACT], float q1[MAXCONTACT], int asp0[MAXCONTACT], int asp1[MAXCONTACT]);
int CONTACTS(void);
int CLASHES(void);
int TYPECONTACTSMOVED(int ct0[MAXCONTACT], int ct1[MAXCONTACT], int at0[MAXCONTACT], int at1[MAXCONTACT], int ri0[MAXCONTACT], int ri1[MAXCONTACT], double ro0[MAXCONTACT], double ro1[MAXCONTACT], double rd[MAXCONTACT], int it[MAXCONTACT], float q0[MAXCONTACT], float q1[MAXCONTACT], int asp0[MAXCONTACT], int asp1[MAXCONTACT]);
int CONTACTSMOVED(void);
int CLASHESMOVED(void);
void MCMOVE(double a);
void READCHARGES(void);
/*void READPOTENTIALS(void);
/*double RESIDUECHARGES(int residues_index, int contacts);*/
/*void READSASA(void);*/
//PDB HANDLING
double abbs(double a);
int IsANumber(char c);
int Get_AA_Type(char SzAAName[]);
int Get_Atom_Type(char SzAtomName[]);
void AssignAtomRadii(void);
int QueryAtomType(char *s, char *res);
void ExportSnapshot(int Index1, int Index2);
//RANDOM NUMBER GENERATOR HEADER
void RandomInitialise(int ij,int kl);
double RandomUniform(void);
double RandomGaussian(double mean,double stddev);
int RandomInt(int lower,int upper);
double RandomDouble(double lower,double upper);
double restdist=0;
double currentdist=0;
double olddist=0;
double mcinternal1=0.025; //perturbation amplitude for translations
double mcinternal2=0.025; //perturbation amplitude for rotations
double TOL=0.2; //tolerance of CM-diffusion in percent of d(CM1-CM2)
double TOL0=0.2;
double x = 1.3;
int DIR;
// COMMENT on DIR
// direction of docking:
// +1 ... positive x-axis
// -1 ... negative x-axis
// +2 ... positive y-axis
// -2 ... negative y-axis
// +3 ... positive z-axis
// -3 ... negative z-axis
int ORIENTATION;
// COMMENT on ORIENTATION
// initial orientation of docking:
// 0 ... no rotation
// +1 ... +90º rotation arround x-axis
// -1 ... -90º rotation arround x-axis
// +2 ... +90º rotation arround y-axis
// -2 ... -90º rotation arround y-axis
// +3 ... +90º rotation arround z-axis
// -3 ... -90º rotation arround z-axis
int main(void)
{
FILE *output1;
FILE *output2;
/*FILE *output3;
FILE *output4;
FILE *output5;
FILE *output6;
FILE *output7;
FILE *output8;*/
int i,j,k,l,m,o,p,e,mc,helper1,helper2,index,ncontacts,N,contact_flag,restdistchange1,restdistchange2;
int newrestdist1,newrestdist2;
int n = 2;
int cc,clashinit[6][7][3],contactinit[6][7][3],hitwall;
int hydropathic_flag;
int residue_index_0;
int residue_index_1;
int accepted, rejected;
int initial_counter;
int final_counter;
int counter_before_mcmove;
int counter_after_mcmove;
double SASA_AA[MAXRESIDUE];
char oo[256], pp[256], qq[256], rr[256], s[256], tt[256], uu[256], vv[256];
/*double diffcontactsenergy[PAIRS][MCSTEPS],diffcontactsenergy_sum[PAIRS],diffcontactsenergy_mean[PAIRS];*/
double shapeinit[6][7][3];
double Etransl, Econtnew, Etranslold, Econtold,Eallold,Eallnew;
double contactnew, contactold;
double initclash,clashnew,clashold;
double Pacc,Pdecl;
double dummie;
double lastTOL;
int CONTACTS_SUM = 0;
double CONTACTS_MEAN;
double contacts_diff_sum = 0.0;
double VARIANCE_CONTACTS;
double VARIANCE_CONTACTS_MEAN;
int CLASHES_SUM = 0;
double CLASHES_MEAN;
double ENERGY_SUM = 0.0;
double ENERGY_MEAN;
double energy_diff_sum = 0.0;
double VARIANCE_ENERGY;
double VARIANCE_ENERGY_MEAN;
double initial_energy_sum = 0.0;
double initial_hp_energy_sum = 0.0;
double initial_ep_energy_sum = 0.0;
double initial_hbp_energy_sum = 0.0;
double energy_sum_before_mcmove = 0.0;
double energy_sum_after_mcmove = 0.0;
double final_energy_sum = 0.0;
double final_hp_energy_sum = 0.0;
double final_ep_energy_sum = 0.0;
double final_hbp_energy_sum = 0.0;
int CCONTACTS[PAIRS];
int CCLASHES[PAIRS];
double ENERGY[PAIRS];
/*float * ptq0;
float * ptq1;
int * ptct0;
int * ptct1;
int * ptri0;
int * ptri1;
double * ptro0;
double * ptro1;
double * ptrd;
int * ptit;
double * ptsvdw;
double * ptep;
double * pthp;
double * pthbp;
double * ptip;*/
mkdir(ss,457);
cc=time(NULL);
RandomInitialise(cc%20000,cc%10000);
//READPOTENTIALS();
READCHARGES();
accepted=0;
rejected=0;
chdir(writingdir);
sprintf(oo,"B2M_D76N-I1-PH5p2_2000_T-0.15_newcf_n-clashes_0.5_energy_hydropathy+electrostatics+hydrogen-bonds_new.dat");
output1=fopen(oo,"a");
sprintf(pp,"B2M_D76N-I1-PH5p2_contacts_energy_mean_2000_T-0.15_newcf_n-clashes_0.5_energy_hydropathy+electrostatics+hydrogen-bonds_new.dat");
output2=fopen(pp,"a");
/*sprintf(qq,"B2M_D76N_I2_pH6p2_contacts_energy_mean_10000_T-0.7_n-clashes_energy_hidropathy+electrostatics_5_test_potentials.dat");
output3=fopen(qq,"a");
sprintf(qq,"B2M_D76N_I2_pH6p2_contacts_energy_mean_10000_T-0.7_n-clashes_energy_hidropathy+electrostatics_5_residues_distance-mean.dat");
output3=fopen(qq,"a");
sprintf(rr,"B2M_D76N_I2_pH6p2_contacts_energy_mean_10000_T-0.7_n-clashes_energy_hidropathy+electrostatics_5_sum_vdW-mean.dat");
output4=fopen(rr,"a");
sprintf(s,"B2M_D76N_I2_pH6p2_contacts_energy_mean_10000_T-0.7_n-clashes_energy_hidropathy+electrostatics_5_1.4_sum_vdW-mean.dat");
output5=fopen(s,"a");
sprintf(tt,"B2M_D76N_I2_pH6p2_contacts_energy_mean_10000_T-0.7_n-clashes_energy_hidropathy+electrostatics_5_2.3_sum_vdW-mean.dat");
output6=fopen(tt,"a");
sprintf(uu,"B2M_D76N_I2_pH6p2_contacts_energy_mean_10000_T-0.7_n-clashes_energy_hidropathy+electrostatics_5_clashes_cutoff-mean.dat");
output7=fopen(uu,"a");
sprintf(vv,"B2M_D76N_I2_pH6p2_contacts_energy_mean_10000_T-0.7_n-clashes_energy_hidropathy+electrostatics_5_contacts_cutoff-mean.dat");
output8=fopen(vv,"a");*/
/*sprintf(uu,"Total_energy_mc-step_10000_T-0.7_n-clashes_energy_hidropathy+electrostatics_5.dat");
output3=fopen(uu,"a");
/*sprintf(vv,"B2M_D76N_I2_pH6p2_diffcontactsenergy_mean_10000_T-0.7_n-clashes_energy_hidropathy+electrostatics_5.dat");
output8=fopen(vv,"a");*/
/*for (e=0; e < PAIRS; e++)
{
diffcontactsenergy_sum[e] = 0.0;
}*/
chdir(workingdir);
/*READSASA();*/
for (k=1;k<=PAIRS;k++)
{
chdir(workingdir);
//PICKING TWO STRUCTURE INDICES
i=RandomInt(1,STRUCTS);
j=RandomInt(1,STRUCTS);
READER(i,j);
chdir(writingdir);
index=0;
//restdist=SCALE*(Conf[0].Rg + Conf[1].Rg);
restdist=31.95; //SCALE*(2*Rg(D76N-I1))
hitwall=0;
//BEGINNING of INITIAL DIRECTION/ORIENTATION sampling
for (DIR=-3;DIR<=-1;DIR++)
{
for(ORIENTATION=-3;ORIENTATION<=-1;ORIENTATION++)
{
CENTRALIZER(restdist);
clashinit[DIR+3][ORIENTATION+3][0] = CLASHES();
contactinit[DIR+3][ORIENTATION+3][0] = -CONTACTS();
clashinit[DIR+3][ORIENTATION+3][1]=DIR;
contactinit[DIR+3][ORIENTATION+3][1]=DIR;
clashinit[DIR+3][ORIENTATION+3][2]=ORIENTATION;
contactinit[DIR+3][ORIENTATION+3][2]=ORIENTATION;
chdir(workingdir);
READER(i,j);
chdir(writingdir);
}
for(ORIENTATION=1;ORIENTATION<=4;ORIENTATION++)
{
CENTRALIZER(restdist);
clashinit[DIR+3][ORIENTATION+2][0] = CLASHES();
contactinit[DIR+3][ORIENTATION+2][0] = -CONTACTS();
clashinit[DIR+3][ORIENTATION+2][1]=DIR;
contactinit[DIR+3][ORIENTATION+2][1]=DIR;
clashinit[DIR+3][ORIENTATION+2][2]=ORIENTATION;
contactinit[DIR+3][ORIENTATION+2][2]=ORIENTATION;
chdir(workingdir);
READER(i,j);
chdir(writingdir);
}
}
for (DIR=1;DIR<=3;DIR++)
{
for(ORIENTATION=-3;ORIENTATION<=-1;ORIENTATION++)
{
CENTRALIZER(restdist);
clashinit[DIR+2][ORIENTATION+3][0] = CLASHES();
contactinit[DIR+2][ORIENTATION+3][0] = -CONTACTS();
clashinit[DIR+2][ORIENTATION+3][1]=DIR;
contactinit[DIR+2][ORIENTATION+3][1]=DIR;
clashinit[DIR+2][ORIENTATION+3][2]=ORIENTATION;
contactinit[DIR+2][ORIENTATION+3][2]=ORIENTATION;
chdir(workingdir);
READER(i,j);
chdir(writingdir);
}
for(ORIENTATION=1;ORIENTATION<=4;ORIENTATION++)
{
CENTRALIZER(restdist);
clashinit[DIR+2][ORIENTATION+2][0] = CLASHES();
contactinit[DIR+2][ORIENTATION+2][0] = -CONTACTS();
clashinit[DIR+2][ORIENTATION+2][1]=DIR;
contactinit[DIR+2][ORIENTATION+2][1]=DIR;
clashinit[DIR+2][ORIENTATION+2][2]=ORIENTATION;
contactinit[DIR+2][ORIENTATION+2][2]=ORIENTATION;
chdir(workingdir);
READER(i,j);
chdir(writingdir);
}
}
DIR=0;
ORIENTATION=0;
dummie=0;
for (o=0;o<6;o++)
{
for (p=0;p<7;p++)
{
restdistchange1=0;
restdistchange2=0;
//INITIAL OPTIMIZATION OF CLASHES AND CONTACTS
if (clashinit[o][p][0]>=200)
{
DIR=contactinit[o][p][1];
ORIENTATION=contactinit[o][p][2];
restdist=SCALE_1*restdist;
CENTRALIZER(restdist);
restdistchange1=1;
contactinit[o][p][0] = -CONTACTS();
clashinit[o][p][0] = CLASHES();
chdir(workingdir);
READER(i,j);
chdir(writingdir);
restdist=32.59;
}
else if (contactinit[o][p][0]>=-3000)
{
DIR=contactinit[o][p][1];
ORIENTATION=contactinit[o][p][2];
restdist=SCALE_2*restdist;
CENTRALIZER(restdist);
restdistchange2=1;
contactinit[o][p][0] = -CONTACTS();
clashinit[o][p][0] = CLASHES();
chdir(workingdir);
READER(i,j);
chdir(writingdir);
restdist=32.59;
}
printf("%d %d %d\n",contactinit[o][p][1],contactinit[o][p][2],contactinit[o][p][0]);
/*if(clashinit[o][p][0]==0)
{
shapeinit[o][p][0]=0;
continue;
}
else
{
shapeinit[o][p][0]=(0.99*contactinit[o][p][0])/(0.01*clashinit[o][p][0]);
if (shapeinit[o][p][0]<dummie)
{
dummie=shapeinit[o][p][0];
}
}*/
if (contactinit[o][p][0]<dummie)
{
dummie=contactinit[o][p][0];
if(restdistchange1)
{
newrestdist1=1;
}
else
{
newrestdist1=0;
}
if(restdistchange2)
{
newrestdist2=1;
}
else
{
newrestdist2=0;
}
}
}
}
printf("\n\n");
for (o=0;o<6;o++)
{
for (p=0;p<7;p++)
{
if (dummie==contactinit[o][p][0])
{
DIR=contactinit[o][p][1];
ORIENTATION=contactinit[o][p][2];
break;
}
}
}
if(newrestdist1==1)
{
restdist=SCALE_1*restdist;
}
if(newrestdist2==1)
{
restdist=SCALE_2*restdist;
}
CENTRALIZER(restdist);
currentdist=restdist;
//ExportSnapshot(i,j);
//sprintf(oo,"MCRUN_I_H_BETA2M_%d_%d_DIR=%d.dat",i,j,(int)DIR);
//output1=fopen(oo,"w");
//END of INITIAL DIRECTION/ORIENTATION sampling
//BEGINNING of the computation of the INITIAL nº of CONTACTS, CLASHES and INTERMOLECULAR ENERGY
ncontacts = CONTACTS();
if (ncontacts > MAXCONTACT)
{
contact_flag=1;
continue;
}
for (N=0; N<ncontacts; N++)
{
it[N]=0;
}
for (N=0; N<MAXATOMNUM; N++)
{
strcpy(Atoms[N][0].AtmHBlabel,"NoHB");
strcpy(Atoms[N][1].AtmHBlabel,"NoHB");
}
/*ptq0 = (float *) malloc(nmalloc * sizeof(float));
ptq1 = (float *) malloc(nmalloc * sizeof(float));
ptct0 = (int *) malloc(nmalloc * sizeof(int));
ptct1 = (int *) malloc(nmalloc * sizeof(int));
ptri0 = (int *) malloc(nmalloc * sizeof(int));
ptri1 = (int *) malloc(nmalloc * sizeof(int));
ptro0 = (double *) malloc(nmalloc * sizeof(double));
ptro1 = (double *) malloc(nmalloc * sizeof(double));
ptrd = (double *) malloc(nmalloc * sizeof(double));
ptit = (int *) malloc(nmalloc * sizeof(int));
ptsvdw = (double *) malloc(nmalloc * sizeof(double));
ptep = (double *) malloc(nmalloc * sizeof(double));
pthp = (double *) malloc(nmalloc * sizeof(double));
pthbp = (double *) malloc(nmalloc * sizeof(double));
ptip = (double *) malloc(nmalloc * sizeof(double));*/
initial_counter = TYPECONTACTS(ct0, ct1, at0, at1, ri0, ri1, ro0, ro1, rd, it, q0, q1, asp0, asp1);
initial_energy_sum = 0.0;
initial_hp_energy_sum = 0.0;
initial_ep_energy_sum = 0.0;
initial_hbp_energy_sum = 0.0;
hydropathic_flag = 0;
for (m=0; m<initial_counter; m++)
{
sum_vdW[m] = HARDCORE_R*(ro0[m] + ro1[m]);
/*ct0 = ptct0;
ct1 = ptct1;
ri0 = ptri0;
ri1 = ptri1;
/*q[m][0] = RESIDUECHARGES(ri0, ct0);
q[m][1] = RESIDUECHARGES(ri1, ct1);
/*sasa_aa[m][0] = SASA_AA[ri0-1];
sasa_aa[m][1] = SASA_AA[ri1-1];
/*fprintf(output3, "%lf\n", residues_distance[m]);
fprintf(output4, "%lf\n", sum_vdW[m]);
fprintf(output5, "%lf\n", 1.4*sum_vdW[m]);
fprintf(output6, "%lf\n", 2.3*sum_vdW[m]);
fprintf(output7, "%lf\n", clashes_cutoff[m]);
fprintf(output8, "%lf\n", contacts_cutoff[m]);*/
if (it[m] == 1 || it[m] == 3 || it[m] == 4) //TYPE OF INTERACTION: 1=electro;3=electro+hidro;4=electro+HB.
{
if (rd[m] > sum_vdW[m] & rd[m] < 1.4*sum_vdW[m]) //1st well of the electrostatic potential
{
if (q0[m] < 0.0 & q1[m] < 0.0)
{
ep[m] = 0.4;
}
else if (q0[m] > 0.0 & q1[m] > 0.0)
{
ep[m] = 0.4;
}
else if (q0[m] < 0.0 & q1[m] > 0.0)
{
ep[m] = -0.4;
}
else if (q0[m] > 0.0 & q1[m] < 0.0)
{
ep[m] = -0.4;
}
else
{
ep[m] = 0.0;
}
}
else if (rd[m] > 1.4*sum_vdW[m] & rd[m] < 2.33*sum_vdW[m]) //2nd well of the electrostatic potential
{
if (q0[m] < 0.0 & q1[m] < 0.0)
{
ep[m] = 0.3*0.4;
}
else if (q0[m] > 0.0 & q1[m] > 0.0)
{
ep[m] = 0.3*0.4;
}
else if (q0[m] < 0.0 & q1[m] > 0.0)
{
ep[m] = -0.3*0.4;
}
else if (q0[m] > 0.0 & q1[m] < 0.0)
{
ep[m] = -0.3*0.4;
}
else
{
ep[m] = 0.0;
}
}
else
{
ep[m] = 0.0;
}
hp[m] = 0.0;
hbp[m] = 0.0;
if ((it[m] == 3) && (rd[m] < 1.6*sum_vdW[m])) //TYPE OF INTERACTION: 3=electro+hidro;
{
hidropathy_0[m] = -((atomic_solvation_parameters[asp0[m]]*atomic_SASA[ct0[m]][at0[m]])/n)/3000;
hidropathy_1[m] = -((atomic_solvation_parameters[asp1[m]]*atomic_SASA[ct1[m]][at1[m]])/n)/3000;
if (hidropathy_0[m] <= -0.0539995)
{
hidropathy_0[m] = -0.1;
}
else if ((hidropathy_0[m] >= -0.0332997) && (hidropathy_0[m] <= 0.0484162))
{
hidropathy_0[m] = 0.0;
}
else if ((hidropathy_0[m] >= 0.0617161) && (hidropathy_0[m] <= 0.138332))
{
hidropathy_0[m] = 0.1;
}
else if (hidropathy_0[m] >= 0.332063)
{
hidropathy_0[m] = 0.4;
}
if (hidropathy_1[m] <= -0.0539995)
{
hidropathy_1[m] = -0.1;
}
else if ((hidropathy_1[m] >= -0.0332997) && (hidropathy_1[m] <= 0.0484162))
{
hidropathy_1[m] = 0.0;
}
else if ((hidropathy_1[m] >= 0.0617161) && (hidropathy_1[m] <= 0.138332))
{
hidropathy_1[m] = 0.1;
}
else if (hidropathy_1[m] >= 0.332063)
{
hidropathy_1[m] = 0.4;
}
hp[m] = hidropathy_0[m]+hidropathy_1[m];
}
if (it[m] == 4) //TYPE OF INTERACTION: 4=electro+HB;
{
hbp[m] = -1.0;
}
else
{
hbp[m] = 0.0;
}
}
else if ((it[m] == 2) && (rd[m] < 1.6*sum_vdW[m])) //TYPE OF INTERACTION: 2=hidro.
{
hidropathy_0[m] = -((atomic_solvation_parameters[asp0[m]]*atomic_SASA[ct0[m]][at0[m]])/n)/3000;
hidropathy_1[m] = -((atomic_solvation_parameters[asp1[m]]*atomic_SASA[ct1[m]][at1[m]])/n)/3000;
if (hidropathy_0[m] <= -0.0539995)
{
hidropathy_0[m] = -0.1;
}
else if ((hidropathy_0[m] >= -0.0332997) && (hidropathy_0[m] <= 0.0484162))
{
hidropathy_0[m] = 0.0;
}
else if ((hidropathy_0[m] >= 0.0617161) && (hidropathy_0[m] <= 0.138332))
{
hidropathy_0[m] = 0.1;
}
else if (hidropathy_0[m] >= 0.332063)
{
hidropathy_0[m] = 0.4;
}
if (hidropathy_1[m] <= -0.0539995)
{
hidropathy_1[m] = -0.1;
}
else if ((hidropathy_1[m] >= -0.0332997) && (hidropathy_1[m] <= 0.0484162))
{
hidropathy_1[m] = 0.0;
}
else if ((hidropathy_1[m] >= 0.0617161) && (hidropathy_1[m] <= 0.138332))
{
hidropathy_1[m] = 0.1;
}
else if (hidropathy_1[m] >= 0.332063)
{
hidropathy_1[m] = 0.4;
}
hp[m] = hidropathy_0[m]+hidropathy_1[m];
ep[m] = 0.0;
hbp[m] = 0.0;
}
/*else if ((it[m] == 2) && ((ri0[m] != residue_index_0) || (ri1[m] != residue_index_1)))
{
hp[m] = 0.3*hydropathic_inter_residue_potentials[ct0[m]][ct1[m]];
ep[m] = 0.0;
hbp[m] = 0.0;
residue_index_0 = ri0[m];
residue_index_1 = ri1[m];
hydropathic_flag = 1;
}*/
else
{
ep[m] = 0.0;
hp[m] = 0.0;
hbp[m] = 0.0;
}
/*fprintf(output3,"electrostatic potential: %lf\n", electrostatic_potential[m]);
fprintf(output3,"hydropathic inter-residue potential: %lf\n", hydropathic_inter_residue_potentials[contact_type[m][0]][contact_type[m][1]]);*/
ip[m] = ep[m] + hp[m] + hbp[m];
/*fprintf(output3,"interaction potential: %lf\n", interaction_potential[m]);*/
/*f[m][0] = tanh(5*tan(PI*sasa_aa[m][0]/2));
f[m][1] = tanh(5*tan(PI*sasa_aa[m][1]/2));*/
initial_energy_sum = initial_energy_sum + /*f[m][0]*f[m][1]**/ip[m];
initial_hp_energy_sum = initial_hp_energy_sum + hp[m];
initial_ep_energy_sum = initial_ep_energy_sum + ep[m];
initial_hbp_energy_sum = initial_hbp_energy_sum + hbp[m];
/*fprintf(output8,"%d %d %d-%d %lf %lf\n",m+1, initial_counter, contact_type_initial[m][0], contact_type_initial[m][1],hydropathic_inter_residue_potentials[contact_type_initial[m][0]][contact_type_initial[m][1]], initial_energy_sum);
/*printf("%d %d %d-%d %lf %lf\n",m+1, initial_counter, contact_type_initial[m][0],contact_type_initial[m][1],hydropathic_inter_residue_potentials[contact_type_initial[m][0]][contact_type_initial[m][1]], initial_energy_sum);*/
}
/*free(ptq0);
free(ptq1);
free(ptct0);
free(ptct1);
free(ptri0);
free(ptri1);
free(ptro0);
free(ptro1);
free(ptrd);
free(ptit);
free(ptsvdw);
free(ptep);
free(pthp);
free(pthbp);
free(ptip);*/
printf("%d %d %d %d %4.3lf %4.3lf %4.3lf %4.3lf %4.3lf %4.3lf %4.3lf %d %d %d %d\n",k,i,j,0,(1-TOL)*restdist,currentdist,(1+TOL0)*restdist,initial_energy_sum,initial_hp_energy_sum,initial_ep_energy_sum,initial_hbp_energy_sum,CONTACTS(),initial_counter,CLASHES(),DIR);
/*fprintf(output7,"%d %d %d %d %4.3lf %4.3lf %4.3lf %4.3lf %d %d %d\n",k,i,j,0,(1-TOL)*restdist,currentdist,(1+TOL0)*restdist,initial_energy_sum,CONTACTS(),CLASHES(),DIR);*/
//fprintf(output1,"%d %d %d %4.3lf %4.3lf %4.3lf %d %d %4.3lf\n",i,j,index,currentdist,restdist,initial_energy_sum,CONTACTS(),CLASHES(),Pacc);
//fflush(output1);
//END of the computation of the INITIAL nº of CONTACTS, CLASHES and INTERMOLECULAR ENERGY
//BEGINNING OF MONTE CARLO
initclash=(double)CLASHES();
accepted=0;
rejected=0;
Pacc=0;
Pdecl=0;
for (index=1;index<=MCSTEPS;index++)
{
if (currentdist<=(1+0.01)*(1-TOL)*restdist)
{
lastTOL=TOL;
TOL=TOL+0.01;
hitwall++;
if ((1-TOL)*restdist <= 0)
TOL=lastTOL;
}
//copying information of structure 2 to a stack variable which will be
//subjected to a MC move
for (m=0;m<nAtom[1];m++)
{
Moved[m]=Atoms[m][1];
}
olddist=currentdist;
//total energy for l-th Markov state
//=== translating + rotating ====================================
dummie=RandomUniform();
MCMOVE(dummie);
//===============================================================
//total energy for possible (l+1)-th Markov state
//BEGINNING of the computation of the nº of CONTACTS, CLASHES and INTERMOLECULAR ENERGY BEFORE THE MOVE
ncontacts = CONTACTS();
if (ncontacts > MAXCONTACT)
{
contact_flag=1;
break;
}
for (N=0; N<ncontacts; N++)
{
it[N]=0;
}
for (N=0; N<MAXATOMNUM; N++)
{
strcpy(Atoms[N][0].AtmHBlabel,"NoHB");
strcpy(Atoms[N][1].AtmHBlabel,"NoHB");
}
/*ptq0 = (float *) malloc(nmalloc * sizeof(float));
ptq1 = (float *) malloc(nmalloc * sizeof(float));
ptct0 = (int *) malloc(nmalloc * sizeof(int));
ptct1 = (int *) malloc(nmalloc * sizeof(int));
ptri0 = (int *) malloc(nmalloc * sizeof(int));
ptri1 = (int *) malloc(nmalloc * sizeof(int));
ptro0 = (double *) malloc(nmalloc * sizeof(double));
ptro1 = (double *) malloc(nmalloc * sizeof(double));
ptrd = (double *) malloc(nmalloc * sizeof(double));
ptit = (int *) malloc(nmalloc * sizeof(int));
ptsvdw = (double *) malloc(nmalloc * sizeof(double));
ptep = (double *) malloc(nmalloc * sizeof(double));
pthp = (double *) malloc(nmalloc * sizeof(double));
pthbp = (double *) malloc(nmalloc * sizeof(double));
ptip = (double *) malloc(nmalloc * sizeof(double));*/
counter_before_mcmove = TYPECONTACTS(ct0, ct1, at0, at1, ri0, ri1, ro0, ro1, rd, it, q0, q1, asp0, asp1);
energy_sum_before_mcmove = 0.0;
hydropathic_flag = 0;
for (m=0; m<counter_before_mcmove; m++)
{
sum_vdW[m] = HARDCORE_R*(ro0[m] + ro1[m]);
/*ct0 = ptct0;
ct1 = ptct1;
ri0 = ptri0;
ri1 = ptri1;
/*q[m][0] = RESIDUECHARGES(ri0, ct0);
q[m][1] = RESIDUECHARGES(ri1, ct1);
/*sasa_aa[m][0] = SASA_AA[ri0-1];
sasa_aa[m][1] = SASA_AA[ri1-1];
/*fprintf(output3, "%lf\n", residues_distance[m]);
fprintf(output4, "%lf\n", sum_vdW[m]);
fprintf(output5, "%lf\n", 1.4*sum_vdW[m]);
fprintf(output6, "%lf\n", 2.3*sum_vdW[m]);
fprintf(output7, "%lf\n", clashes_cutoff[m]);
fprintf(output8, "%lf\n", contacts_cutoff[m]);*/
if (it[m] == 1 || it[m] == 3 || it[m] == 4) //TYPE OF INTERACTION: 1=electro;3=electro+hidro;4=electro+HB.
{
if (rd[m] > sum_vdW[m] & rd[m] < 1.4*sum_vdW[m]) //1st well of the electrostatic potential
{
if (q0[m] < 0.0 & q1[m] < 0.0)
{
ep[m] = 0.4;
}
else if (q0[m] > 0.0 & q1[m] > 0.0)
{
ep[m] = 0.4;