/*____________________________________________________________________________*//*** Initialize torsion arrays and constants.*/(void) strcpy( torfmt, "%*s\0" ); /* len(torfmt) is 4 chars */for (j = 0;  j < MAX_ATOMS;  j++ ) {    Nnbonds[j] = type[j] = 0;} for (i = 0; i  < MAX_TORS;  i++ ) {    for (j = 0;  j < MAX_ATOMS;  j++ ) {	tlist[i][j] = 0;    }}for (i = 0; i  < MAX_TORS;  i++ ) {    B_isTorConstrained[i] = 0;    US_torProfile[i][0] = 0;    N_con[i] = 0;}initialiseState( &sInit );initialiseState( &(mol.S) );F_W      =  360. / NTORDIVS;F_hW     =  F_W  / 2.;F_A_from = -360. + F_hW;F_A_to   =  360. + F_hW;for (k = 0; k < MAX_RUNS; k++) {    for (i = 0; i  < MAX_TORS;  i++ ) {        sHist[k].tor[i] = 0.;    }}for (i = 0; i < MAX_TORS;  i++ ) {    if ( (ltorfmt += 3) > LINE_LEN ) {	prStr( error_message, "ERROR: MAX_TORS = %d torsions declared in \"constants.h\";\n\t LINE_LEN = %d, Therefore you must change \"LINE_LEN\" to exceed %d...\n", MAX_TORS, LINE_LEN, 4+3*MAX_TORS );	stop( error_message );	exit( -1 );    } else {	(void) strcat( torfmt, " %f\0" );  /* add on 3 chars  for each new torsion... */    }} /* len(torfmt) is 4+3*MAX_TORS chars */for (j = 0; j < MAX_NONBONDS; j++) {    nonbondlist[j][ATM1] = nonbondlist[j][ATM2] = 0;}for (j = 0; j < MAX_RUNS; j++) {    // isort[j] = j;    econf[j] = 0.;}B_constrain_dist = B_haveCharges = FALSE;ntor1 = ntor = atomC1 = atomC2 = 0;sqlower = squpper = 0.;timeSeedIsSet[0] = 'F';timeSeedIsSet[1] = 'F';if (clktck == 0) {        /* fetch clock ticks per second first time */    if ( (clktck = sysconf(_SC_CLK_TCK)) < (FourByteLong)0L) {	stop("\"sysconf(_SC_CLK_TCK)\" command failed in \"main.c\"\n");	exit( -1 );    } else {	idct = (float)1. / (float)clktck;    }}(void) strcpy(FN_rms_ref_crds,"unspecified filename\0");/*____________________________________________________________________________*//*** log(x): compute the natural (base e) logarithm of x,*/F_lnH = ((float)log(0.5));/*____________________________________________________________________________*//*** Output banner...*/banner( version );/*____________________________________________________________________________*//*** Print the time and date when the file was created...*/pr( logFile, "This file was created at:\t\t\t" );printdate( logFile, 1 );(void) strcpy(hostnm, "unknown host\0");if (gethostname( hostnm, MAX_CHARS ) == 0) {    pr( logFile, "                   using:\t\t\t\"%s\"\n", hostnm );}pr( logFile, "\nNOTE: \"rus\" stands for:\n\n      r = Real, wall-clock or elapsed time;\n      u = User or cpu-usage time;\n      s = System time\n\nAll timings are in seconds, unless otherwise stated.\n\n\n" );/*____________________________________________________________________________*//*** (Note: "dock_param_fn" set in "setflags.c"...)*/pr( logFile, "Parameter file used for this docking:\t\t%s\n\n", dock_param_fn );/*____________________________________________________________________________*//*** Start reading in the parameter/run-control file,*/while( fgets(line, LINE_LEN, parFile) != NULL ) { /* PARSING-DPF parFile */    dpf_keyword = parse_dpf_line( line );    switch( dpf_keyword ) {    case -1:        pr( logFile, "DPF> %s", line );        prStr( error_message,"%s: WARNING: Unrecognized keyword in docking parameter file.\n", programname );        pr_2x( logFile, stderr, error_message );        continue;        /* break; */    case DPF_NULL:    case DPF_COMMENT:        pr( logFile, "DPF> %s", line );        (void) fflush(logFile);        break;    default:        pr( logFile, "\n\nDPF> %s\n", line );        indcom = strindex( line, "#" );        if (indcom != -1) {	    line[ indcom ] = '\0'; /* Truncate "line" at the comment */        }        (void) fflush(logFile);        break;    } /* switch */    switch( dpf_keyword ) {/*____________________________________________________________________________*/    case DPF_NULL:    case DPF_COMMENT:        break;/*____________________________________________________________________________*/    case DPF_TYPES:        /*        ** types        ** ATOM_TYPE_NAMES        */        (void) strncpy( atm_typ_str, "????????", (size_t)ATOM_MAPS);        dpftypes( &Htype,&num_all_maps,&num_atm_maps,atm_typ_str,line );        (void) fflush(logFile);        break;/*____________________________________________________________________________*/    case DPF_FLD:        /*        ** fld        ** GRID_DATA_FILE        ** Read the (AVS-format) grid data file, .fld        */        readfield( &inv_spacing, &spacing, FN_gdfld,             FN_gpf, gridpts1, gridpts, &xhi,&yhi,&zhi,             jobStart, line, &xlo,&ylo,&zlo, FN_receptor,             map_center, tms_jobStart );        (void) fflush(logFile);        break;/*____________________________________________________________________________*/     case DPF_MAP:        /*        ** map        ** ATOMIC AFFINITY or ELECTROSTATIC GRID MAP        ** Read in active site grid map...        */        B_charMap = FALSE;        readmap( &B_havemap, &imap, &num_atm_maps, &spacing,             atm_typ_str, FN_gdfld, gridpts1, gridpts,             jobStart, line, FN_receptor, map, map_center,             mapmax, mapmin, tms_jobStart, B_charMap );        (void) fflush(logFile);        break;/*____________________________________________________________________________*/     case DPF_CHARMAP:        /*        ** charmap        ** ATOMIC AFFINITY or ELECTROSTATIC GRID MAP        ** Read in active site grid map...        */        B_charMap = TRUE;        readmap( &B_havemap, &imap, &num_atm_maps, &spacing,             atm_typ_str, FN_gdfld, gridpts1, gridpts,             jobStart, line, FN_receptor, map, map_center,             mapmax, mapmin, tms_jobStart, B_charMap );        (void) fflush(logFile);        break;/*____________________________________________________________________________*/    case DPF_MOVE:        /*        ** move        ** Movable ligand,        */        mol = readPDBQ( line,             atm_typ_str, num_atm_maps,             &natom,              crdpdb, charge, &B_haveCharges, type,             pdbaname, FN_ligand, atomstuff, Htype,             &B_constrain_dist, &atomC1, &atomC2,              &sqlower, &squpper,             &ntor1, &ntor, tlist, vt,              &Nnb, Nnbonds, nonbondlist,             jobStart, tms_jobStart, hostnm);        sInit.ntor = mol.S.ntor;        ++nmol;        ++nlig;        (void) fflush(logFile);        break;/*____________________________________________________________________________*/    case DPF_ABOUT:        /*        **  about        **  Rotation center for current ligand,        */        (void) sscanf( line, "%*s %f %f %f", &lig_center[X], &lig_center[Y], &lig_center[Z]);        pr( logFile, "Small molecule center of rotation =\t" );        pr( logFile, "(%+.3f, %+.3f, %+.3f)\n\n", lig_center[X], lig_center[Y], lig_center[Z]);        /*        **  Center the ligand,        */        if ( nmol == 0 ) {	    pr( logFile, "Must specify a ligand PDBQ file, using the \"move\" command.\n");	} else {	    pr( logFile, "Translating small molecule by:\t" );	    pr( logFile, "(%+.3f, %+.3f, %+.3f)\n\n", -lig_center[X], -lig_center[Y], -lig_center[Z]);	    /*	    **  Zero-out on central point...	    */	    maxrad = -1.;	    	    for ( i=0; i<natom; i++ ) {		r2sum=0.;		for (XYZ = 0;  XYZ < SPACE;  XYZ++) {		    c = crd[i][XYZ] = (crdpdb[i][XYZ] -= lig_center[XYZ]);		    r2sum += c*c;		} /* XYZ */		maxrad = max(maxrad,sqrt(r2sum));	    } /* i */	    pr( logFile, "Furthest ligand atom from \"about\" center is %.3f Angstroms (maxrad).\n\n",maxrad);	}        (void) fflush(logFile);        break;/*____________________________________________________________________________*/    case DPF_TRAN0:        /*         **  tran0        **  Initial_translation,        */        (void) sscanf( line, "%*s %s", param[0]);        for (i=0; i<6; i++) {	    param[0][i] = (char)tolower( (int)param[0][i] );        }        if (equal(param[0],"random",6)) {	    B_RandomTran0 = TRUE;	    mol.S.T.x = sInit.T.x = random_range( xlo, xhi );	    mol.S.T.y = sInit.T.y = random_range( ylo, yhi );	    mol.S.T.z = sInit.T.z = random_range( zlo, zhi );        } else {	    B_RandomTran0 = FALSE;	    (void) sscanf( line,"%*s %lf %lf %lf", &(sInit.T.x), &(sInit.T.y), &(sInit.T.z));	    mol.S.T.x = sInit.T.x;	    mol.S.T.y = sInit.T.y;	    mol.S.T.z = sInit.T.z;	    pr( logFile, "Initial translation =\t\t\t(%.3f, %.3f, %.3f) Angstroms\n", sInit.T.x, sInit.T.y, sInit.T.z );	    (void) fflush(logFile);        }        break;/*____________________________________________________________________________*/    case DPF_QUAT0:        /*        **  quat0        **  Initial_quaternion,        */        (void) sscanf( line, "%*s %s", param[0]);        for (i=0; i<6; i++) {	    param[0][i] = (char)tolower( (int)param[0][i] );        }        if (equal(param[0],"random",6)) {	    B_RandomQuat0 = TRUE;	    sInit.Q.nx  = random_range( -1.,   1. );	    sInit.Q.ny  = random_range( -1.,   1. );	    sInit.Q.nz  = random_range( -1.,   1. );	    sInit.Q.ang = random_range(  0., 360. );	    pr( logFile, "Each run will begin with a new, random initial quaternion.\n");        } else {	    B_RandomQuat0 = FALSE;        }	(void) sscanf( line, "%*s %lf %lf %lf %lf", &sInit.Q.nx, &sInit.Q.ny, &sInit.Q.nz, &sInit.Q.ang);	pr( logFile, "Initial quaternion,  q = [(x,y,z),w] =\t[ (%.3f, %.3f, %.3f), %.1f deg ],\n", sInit.Q.nx, sInit.Q.ny, sInit.Q.nz, sInit.Q.ang);	mol.S.Q.nx  = sInit.Q.nx;	mol.S.Q.ny  = sInit.Q.ny;	mol.S.Q.nz  = sInit.Q.nz;	mol.S.Q.ang = sInit.Q.ang;	mol.S.Q.ang = sInit.Q.ang = Rad( sInit.Q.ang ); /*convert to radians*/	mkUnitQuat( &sInit.Q );	mkUnitQuat( &(mol.S.Q) );	pr( logFile, "Quaternion Vector Normalized to:  %.3f %.3f %.3f\n", sInit.Q.nx, sInit.Q.ny, sInit.Q.nz );        (void) fflush(logFile);        break;/*____________________________________________________________________________*/    case DPF_NDIHE:        /*        **  ndihe        **  Number of dihedral angles to be specified by "dihe0"        */        (void) sscanf( line, "%*s %d", &ndihed );        if ( nmol == 0 ) {	    pr( logFile, "Must specify a ligand PDBQ file, using the \"move\" command.\n");	} else {	    pr( logFile, "Number of torsions = %d\n", ndihed);	    if ( ndihed != ntor ) {		pr( logFile, "WARNING! You requested %d torsions, but I found %d in PDBQ-file specifications.\n", ndihed, ntor );	    } /* if */	}        (void) fflush(logFile);        break;/*____________________________________________________________________________*/    case DPF_DIHE0:        /*        **  dihe0        **  Initial dihedral angles, input in degrees,        */        (void) sscanf( line, "%*s %s", param[0]);        for (i=0; i<6; i++) {	    param[0][i] = (char)tolower( (int)param[0][i] );        }	if (equal(param[0],"random",6)) {	    B_RandomDihe0 = TRUE;	    sInit.ntor = nval = ndihed;	    for ( i=0; i<nval; i++ ) {		sInit.tor[i] = random_range( -180., 180. );	    }	} else {	    B_RandomDihe0 = FALSE;	    retval = (int)sscanf( line, torfmt, TOR_ARG_LIST );	    if (retval == 0) {		pr( logFile, "Could not read any torsions!\n" );	    } else if (retval == EOF) {		pr( logFile, "End of file encountered while reading dihe0 line\n");	    } else if (retval < ndihed) {		pr( logFile, "WARNING!  Only %d initial torsion angles were detected on input line.\n",retval);		pr( logFile, "I am sorry, you set 'ndihe', the number of dihedrals, to %d torsions.\n", ndihed);	    } else {		pr( logFile, "%d initial torsion angles were detected on input line.\n", retval );	    }