/* main.cc */#include <iostream.h>#include <math.h>#include "hybrids.h"#include "ranlib.h"#include "gs.h"#include "ls.h"#include "rep.h"#include "support.h"#ifdef sgi    #include "main.h"    #include "autoglobal.h"    #include <sys/types.h> 	/*time_t time(time_t *tloc); */    #include <time.h> 		/*time_t time(time_t *tloc); */    #include <sys/times.h>    #include <stdlib.h>    #include <string.h>    #include <sys/param.h>    #include <ctype.h> /* tolower */    #include <unistd.h> /* sysconf */    #include "printdate.h"    #include "parse_dpf_line.h"    #include "print_2x.h"    #include "strindex.h"    #include "stop.h"    #include "stateLibrary.h"    #include "timesyshms.h"    #include "cnv_state_to_coords.h"    #include "structs.h"    #include "assert.h"#else    extern "C"    {	#include "main.h"	#include "autoglobal.h"        #include <sys/types.h> 	/*time_t time(time_t *tloc); */        #include <time.h> 		/*time_t time(time_t *tloc); */	#include <sys/times.h>	#include <stdlib.h>	#include <string.h>	#include <sys/param.h>	#include <ctype.h> /* tolower */	#include <unistd.h> /* sysconf */	#include "printdate.h"	#include "parse_dpf_line.h"	#include "print_2x.h"	#include "strindex.h"	#include "stop.h"	#include "stateLibrary.h"	#include "timesyshms.h"	#include "cnv_state_to_coords.h"	#include "structs.h"	#include "assert.h"#ifndef HPPA	/* Causes error with gcc on HP */	/* Needed on Sun */	int gethostname(char *name,int namelen);#endif    }#endif#define RIJ_MIN 1.0#define RIJ_MAX 6.0#define EPSIJ_MIN 0.0#define EPSIJ_MAX 10.0extern int   debug;extern int   keepresnum;extern float idct;int sel_prop_count = 0;extern Eval evaluate;int main( int argc, char **argv, char **envp )/*********************************************************************************      Name: main  (AutoDock)                                                ****  Function: Performs Automated Docking of Small Molecule into Macromolecule **** Copyright: (C) 1994-1999 TSRI, Arthur J. Olson's Labortatory.              ****____________________________________________________________________________****   Authors: Garrett Matthew Morris, Current C/C++ version 3.0               ****                                       e-mail: garrett@scripps.edu          ****                                                                            ****            David Goodsell, Orignal FORTRAN version 1.0                     ****                                       e-mail: goodsell@scripps.edu         ****                                                                            ****            The Scripps Research Institute                                  ****            Department of Molecular Biology, MB5                            ****            10550 North Torrey Pines Road                                   ****            La Jolla, CA 92037.                                             ****                                                                            ****      Date: 03/04/99                                                        ****____________________________________________________________________________****    Inputs: Control file, Small Molecule PDBQ file, macromolecular grid map ****            files.                                                          ****   Returns: Autodock Log File, includes docked conformation clusters (PDBQ).****   Globals: X, Y, Z, SPACE, MAX_GRID_PTS, NEINT, MAX_ATOMS,                 ****            MAX_MAPS, ATOM_MAPS, A_DIVISOR, LINE_LEN,TRUE,FALSE             ****            programname, command_mode,                                      ****            command_in_fp, command_out_fp, parFile, logFile.                ****____________________________________________________________________________**** Modification Record                                                        **** Date     Inits   Comments                                                  **** 09/06/95 RSH     Added code to handle GA/LS stuff                          ****          DSG     Quaternion rotations                                      ****          DSG     Generates torsions from annotated pdb list                ****          DSG     Generates internal energies                               ****          DSG     Performs a limited Cluster analysis of conformations      **** 05/07/92 GMM     C translation                                             **** 05/14/92 GMM     Time-dependent seed in random-number generation           **** 10/29/92 GMM     Application Visualization System (AVS) readable grid      ****                  display file input.                                       ****                  [AVS is a trademark of Stardent Computer Inc.]            **** 04/17/93 GMM     '-o' oldpdbq flag for q in columns 55-61;                 ****                  the default PDBQ format is now columns 71-76;             ****                  Also added the 'total_charge' check.                      **** 11/19/93 GMM     #ifdef NOSQRT, with non-square-rooting acceleration.      **** 09/26/94 GMM     Cluster analysis now outputs RMS deviations.              **** 09/28/94 GMM     Modularized code.                                         **** 10/02/94 GMM     Distance constraints added, for Ed Moret. Accelerated.    *********************************************************************************/{char atm_typ_str[ATOM_MAPS];char atomstuff[MAX_ATOMS][MAX_CHARS];char error_message[LINE_LEN];char FN_clus[MAX_CHARS];char FN_watch[MAX_CHARS];char FN_gdfld[MAX_CHARS];char FN_gpf[MAX_CHARS];char FN_ligand[MAX_CHARS];char FN_trj[MAX_CHARS];char FN_receptor[MAX_CHARS];char hostnm[MAX_CHARS];char line[LINE_LEN];char out_acc_rej = '?';char param[2][MAX_CHARS];char timeSeedIsSet[2];char pdbaname[MAX_ATOMS][5];char FN_rms_ref_crds[MAX_CHARS];char selminpar = 'm';char S_contype[8]; char torfmt[LINE_LEN];float crdpdb[MAX_ATOMS][SPACE];float crd[MAX_ATOMS][SPACE];float lig_center[SPACE];float map_center[SPACE];float vt[MAX_TORS][SPACE];float c=0.;float cA;float cB;float charge[MAX_ATOMS];float clus_rms_tol = 0.;float e0max = BIG;float eintra = 0.0;float einter = 0.0;float econf[MAX_RUNS];float elec[MAX_ATOMS];float emap[MAX_ATOMS];float epsij;float F_A;float F_Aova;float F_tor;float F_TorConRange[MAX_TORS][MAX_TOR_CON][2];float F_torPref;float F_torHWdth;float inv_spacing = 0.;float qtwFac = 1.0;float qtwStep0 = 5.;float qtwStepFinal = 5.0;float mapmax[MAX_MAPS];float mapmin[MAX_MAPS];float maxrad = -1.;float q1q2[MAX_NONBONDS];float r2sum=0.;float Rij;float RJ = 8.31441;     // in J/K/mol, Gas Constant, Atkins Phys.Chem., 2/efloat Rcal = 1.9871917; // in cal/K/mol, Gas Constant, RJ/4.184float T0K = 273.15;	// 0 degrees Celsius, in K// float TK = 298.15;	// Room temperature, in K// float deltaG = 0.0;// float Ki = 1.0;float RTreduc = 1.;float spacing = 0.;float sqlower;float squpper;float RT0 = 616.;float RTFac = 0.95;float tmpconst;float torsdoffac = 0.3113;float torFac = 1.0;float torsFreeEnergy = 0.0;float torStep0 = 5.;float torStepFinal = 5.0;float trnFac = 1.0;float trnStep0 = 0.2;float trnStepFinal = 0.2;float WallEnergy = 1.0e8; /* Energy barrier beyond walls of gridmaps. */float xhi;float xlo;float yhi;float ylo;float zhi;float zlo;unsigned short US_TorE[MAX_TORS];Boole B_isGaussTorCon = FALSE;Boole B_constrain_dist;Boole B_either = FALSE;Boole B_calcIntElec = FALSE;Boole B_write_trj = FALSE;Boole B_watch = FALSE;Boole B_acconly = FALSE;Boole B_cluster_mode = FALSE;Boole B_havemap = FALSE;Boole B_havenbp = FALSE;Boole B_haveCharges;Boole B_linear_schedule = FALSE;Boole B_qtwReduc = FALSE;Boole B_selectmin = FALSE;Boole B_symmetry_flag = TRUE;Boole B_tempChange = TRUE;Boole B_torReduc = FALSE;Boole B_trnReduc = FALSE;Boole B_write_all_clusmem = FALSE;Boole B_isTorConstrained[MAX_TORS];Boole B_ShowTorE = FALSE;Boole B_RandomTran0 = FALSE;Boole B_RandomQuat0 = FALSE;Boole B_RandomDihe0 = FALSE;Boole B_CalcTrnRF = FALSE;Boole B_CalcQtwRF = FALSE;Boole B_CalcTorRF = FALSE;Boole B_charMap = FALSE;int ntorsdof = 0;int atm1=0;int atm2=0;int a1=0;int a2=0;int atomC1;int atomC2;int dpf_keyword = -1;int gridpts1[SPACE];int gridpts[SPACE];int Htype = 0;int ncycles = -1;int iCon=0;int imap=0;int indcom = 0;int ltorfmt = 4;int nruns = 0;int nstepmax = -1;int naccmax = 0;int natom = 0;int nonbondlist[MAX_NONBONDS][2];int nconf = 0;int ncycm1 = 1;int ndihed = 0;int nlig = 0;int nres = 0;int nmol = 0;int Nnb = 0;int Nnbonds[MAX_ATOMS]; /* num. non-bonded interactions for each atom */int nrejmax = 0;int ntor;int ntor1;int num_all_maps = 0;int num_atm_maps = 0;int nval = 0;int outlev = -1;int retval = 0;int status = 0;int tlist[MAX_TORS][MAX_ATOMS];int trj_end_cyc = 0;int trj_begin_cyc = 0;int trj_freq = 0;int type[MAX_ATOMS];int xA;int xB;int I_tor;int I_torBarrier;int N_con[MAX_TORS];int MaxRetries = 1000; /* Default maximum number of retries for ligand init. */int   OutputEveryNTests = 1000;int   NumLocalTests = 10;int   maxTests = 10000;/* int beg; *//* int end; *//* int imol = 0; */unsigned short US_energy;unsigned short US_tD;unsigned short US_torBarrier = TORBARMAX;unsigned short US_torProfile[MAX_TORS][NTORDIVS];unsigned short US_min = TORBARMAX;register int i = 0;register int j = 0;int j1 = 1;register int k = 0;register int XYZ = 0;State sInit;                             /* float qtn0[QUAT], tor0[MAX_TORS]; */State sHist[MAX_RUNS];  /*qtnHist[MAX_RUNS][QUAT],torHist[MAX_RUNS][MAX_TORS];*/Molecule mol;	/* ligand */static float e_internal[NEINT][ATOM_MAPS][ATOM_MAPS];static float ELECSCALE = 83.015909;      /* relative dielectric epsilon = 4*r *//* static float ELECSCALE = 332.06363;   // relative dielectric epsilon = r   */static float F_A_from;static float F_A_to;static float F_lnH;static float F_W;static float F_hW;static float map[MAX_GRID_PTS][MAX_GRID_PTS][MAX_GRID_PTS][MAX_MAPS];static float version = 3.0;static FourByteLong clktck = 0;struct tms tms_jobStart;struct tms tms_gaStart;struct tms tms_gaEnd;Clock  jobStart;Clock  gaStart;Clock  gaEnd;time_t time_seed;//  The GA StuffFourByteLong seed[2];unsigned int pop_size = 50;unsigned int num_generations = 0;  //  Don't terminate on the basis of number of generationsunsigned int num_evals = 150000;unsigned int max_its = 30;unsigned int max_succ = 4;unsigned int max_fail = 4;int window_size = 10;int low = 0;int high = 100;int elitism = 1;float m_rate = 0.02;float c_rate = 0.80;float alpha = 0;float beta = 1;float search_freq = 0.06;float rho = 1.0;float lb_rho = 0.01;float *rho_ptr = NULL;float *lb_rho_ptr = NULL;Selection_Mode s_mode = Proportional;Xover_Mode c_mode = TwoPt;Worst_Mode w_mode = AverageOfN;EvalMode e_mode = Normal_Eval;Global_Search *GlobalSearchMethod = NULL;Local_Search *LocalSearchMethod = NULL;/*____________________________________________________________________________*//*** Get the time at the start of the run...*/jobStart = times( &tms_jobStart );/*____________________________________________________________________________*//*** Parse the arguments in the command line...*/if ( setflags(argc,argv) == -1) {    exit(-1);} /* END PROGRAM */