main.cc-new

c++编写的并行拉马克遗传算法的程序。实现分析对接程序

	    nval = retval;
	}
        for ( i=0; i<nval; i++ ) {
	    pr( logFile, "\tInitial torsion %2d = %7.2f deg\n", (i+1), sInit.tor[i] ); /* sInit.tor is in degrees */
	    /* Convert sInit.tor[i] into radians */
	    mol.S.tor[i] = sInit.tor[i] = Rad( sInit.tor[i] ); /* sInit.tor is now in radians  Added:05-01-95 */
        }
        (void) fflush(logFile);
        break;

/*____________________________________________________________________________*/

    case DPF_TSTEP:
        /*
        **  tstep
        **  Translation_step,
        */
        retval = (int)sscanf( line, "%*s %f %f", &trnStep0, &trnStepFinal );
        if (retval == 0) {
	    pr( logFile, "Could not read any arguments!\n" );
        } else if (retval == EOF) {
	    pr( logFile, "End of file encountered!\n");
        } else if (retval > 0) {
	    pr( logFile, "Initial cycle, maximum translation step = +/- %-.1f Angstroms\n", trnStep0);
        }
        if (retval == 2) {
	    B_CalcTrnRF = TRUE;
	    pr( logFile, "Final cycle,   maximum translation step = +/- %-.1f Angstroms\n", trnStepFinal);
	    pr( logFile, "Reduction factor will be calculated when number of cycles has been read in.\n");
        }
        (void) fflush(logFile);
        break;

/*____________________________________________________________________________*/

    case DPF_QSTEP:
        /*
        **  qstep
        **  Quaternion_step,
        */
        retval = (int)sscanf( line, "%*s %f %f", &qtwStep0, &qtwStepFinal );
        if (retval == 0) {
	    pr( logFile, "Could not read any arguments!\n" );
        } else if (retval == EOF) {
	    pr( logFile, "End of file encountered!\n");
        } else if (retval > 0) {
	    pr( logFile, "Initial cycle, maximum quaternion angle step = +/- %-.1f deg\n", qtwStep0);
	    /* convert to radians */
	    qtwStep0 = Rad( qtwStep0 );
        }
	if (retval == 2) {
	    B_CalcQtwRF = TRUE;
	    pr( logFile, "Final cycle,   maximum quaternion angle step = +/- %-.1f deg\n", qtwStepFinal);
	    pr( logFile, "Reduction factor will be calculated when number of cycles has been read in.\n");
	    /* convert to radians */
	    qtwStepFinal = Rad( qtwStepFinal );
	}
        (void) fflush(logFile);
        break;

/*____________________________________________________________________________*/

    case DPF_DSTEP:
        /*  
        **  dstep
        **  Torsion_step,
        */
        retval = (int)sscanf( line, "%*s %f %f", &torStep0, &torStepFinal );
        if (retval == 0) {
	    pr( logFile, "Could not read any arguments!\n" );
        } else if (retval == EOF) {
	    pr( logFile, "End of file encountered!\n");
        } else if (retval > 0) {
	    pr( logFile, "Initial cycle, maximum torsion angle step = +/- %-.1f deg\n", torStep0);
	    /* convert to radians */
	    torStep0 = Rad( torStep0 );
        }
	if (retval == 2) {
	    B_CalcTorRF = TRUE;
	    pr( logFile, "Final cycle,   maximum torsion angle step = +/- %-.1f deg\n", torStepFinal);
	    pr( logFile, "Reduction factor will be calculated when number of cycles has been read in.\n");
	    /* convert to radians */
	    torStepFinal = Rad( torStepFinal );
	}
        (void) fflush(logFile);
        break;

/*____________________________________________________________________________*/

    case DPF_TRNRF:
        /*
        **  trnrf
        **  Translation reduction factor,
        */
        (void) sscanf( line, "%*s %f", &trnFac );
        pr( logFile, "Reduction factor for translations =\t%-.3f /cycle\n", trnFac );
        B_trnReduc = (trnFac != 1.);       
        (void) fflush(logFile);
        break;

/*____________________________________________________________________________*/

    case DPF_QUARF:
        /*
        **  quarf
        **  Quaternion reduction factor,
        */
        (void) sscanf( line, "%*s %f", &qtwFac );
        pr( logFile, "Reduction factor for quaternion angle =\t%-.3f /cycle\n", qtwFac );
        B_qtwReduc = (qtwFac != 1.);
        (void) fflush(logFile);
        break;

/*____________________________________________________________________________*/

    case DPF_DIHRF:
        /*
        **  dihrf
        **  Torsion reduction factor,
        */
        (void) sscanf( line, "%*s %f", &torFac );
        pr( logFile, "Reduction factor for torsion angles =\t%-.3f /cycle\n", torFac );
        B_torReduc = (torFac != 1.);
        (void) fflush(logFile);
        break;

/*____________________________________________________________________________*/

    case DPF_FLEX:
        /*
        **  flex
        **  Flexible side-chains, cannot translate:
        */
        nmol++;
        nres++;
        (void) fflush(logFile);
        break;

/*____________________________________________________________________________*/

    case DPF_INTNBP_REQM_EPS:
        /*
        **  intnbp_r_eps
        **  Read internal energy parameters: 
        **  Lennard-Jones and Hydrogen Bond Potentials,
        **  Using epsilon and r-equilibrium values...
        */
        (void) sscanf( line, "%*s %f %f %d %d", &Rij, &epsij, &xA, &xB );
	/* check that the Rij is reasonable */
	if ((Rij < RIJ_MIN) || (Rij > RIJ_MAX)) {
	    (void) fprintf( logFile,
	    "WARNING: pairwise distance, Rij, %.2f, is not a very reasonable value for the equilibrium separation of two atoms! (%.2f Angstroms <= Rij <= %.2f Angstroms)\n\n", Rij, RIJ_MIN, RIJ_MAX);
	    (void) fprintf( logFile, "Perhaps you meant to use \"intnbp_coeffs\" instead of \"intnbp_r_eps\"?\n\n");
	    exit(-1);
	}
	/* check that the epsij is reasonable */
	if ((epsij < EPSIJ_MIN) || (epsij > EPSIJ_MAX)) {
	    (void) fprintf( logFile,
	    "WARNING: well-depth, epsilon_ij, %.2f, is not a very reasonable value for the equilibrium potential energy of two atoms! (%.2f kcal/mol <= epsilon_ij <= %.2f kcal/mol)\n\n", epsij, EPSIJ_MIN, EPSIJ_MAX);
	    (void) fprintf( logFile, "Perhaps you meant to use \"intnbp_coeffs\" instead of \"intnbp_r_eps\"?\n\n");
	    exit(-1);
	}
        /* Defend against division by zero... */
        if (xA != xB) {
	    cA = (tmpconst = epsij / (float)(xA - xB)) * pow( (double)Rij, (double)xA ) * (float)xB;
	    cB = tmpconst * pow( (double)Rij, (double)xB ) * (float)xA;
            intnbtable( &B_havenbp, &a1, &a2, num_atm_maps, atm_typ_str, cA, cB, xA, xB, e_internal );
        } else {
            pr(logFile,"WARNING: Exponents must be different, to avoid division by zero!\n\tAborting...\n");
            exit(-1);
        }
        (void) fflush(logFile);
        break;

/*____________________________________________________________________________*/

    case DPF_INTNBP_COEFFS:
        /*
        **  intnbp_coeffs
        **  Read internal energy parameters: 
        **  Lennard-Jones and Hydrogen Bond Potentials,
        **  Using coefficients...
        */
        (void) sscanf( line, "%*s %f %f %d %d", &cA, &cB, &xA, &xB );

        /* Defend against division by zero... */
        if (xA != xB) {
            intnbtable( &B_havenbp, &a1, &a2, num_atm_maps, atm_typ_str, cA, cB, xA, xB, e_internal );
        } else {
            pr(logFile,"WARNING: Exponents must be different. Aborting...\n");
            exit(-1);
        }

        (void) fflush(logFile);
        break; 

/*____________________________________________________________________________*/

    case DPF_RT0:
        /*
        **  rt0
        **  Initial Temperature,
        */
        (void) sscanf( line, "%*s %f", &RT0 );
        if (RT0 <= 0.) {
	    pr( logFile, "\nWARNING!  Negative temperatures not allowed! Will default to RT = 616 cal mol.\n" );
	    RT0 = 616.;
        }
        pr( logFile, "\n\t\tTEMPERATURE SCHEDULE INFORMATION\n" );
        pr( logFile, "\t\t________________________________\n\n" );
        pr( logFile, "               -1 -1                 -1 -1\n" );
        pr( logFile, "R = %5.3f J mol  K    = %5.3f cal mol  K  \n\n", RJ, Rcal );
        pr( logFile, "                                        -1\n" );
        pr( logFile, "Initial R*Temperature = %8.2f cal mol\n", RT0 );
        pr( logFile, "      (=> Temperature = %8.2f K\n", RT0/Rcal );
        pr( logFile, "                   or = %8.2f C)\n\n", RT0/Rcal - T0K );
        (void) fflush(logFile);
        break;

/*____________________________________________________________________________*/

    case DPF_RTRF:
        /*
        **  rtrf
        **  Temperature reduction factor,
        */
        (void) sscanf( line, "%*s %f", &RTFac);
        pr( logFile, "R*Temperature reduction factor = %8.2f\t/cycle\n", RTFac );
        if (RTFac >= 1.) {
	    stop("Cooling is impossible with a reduction\n\tfactor greater than or equal to 1.0!" );
	    exit( -1 );
        } else if (RTFac == 0.0 ) {
	    stop("Cooling is impossible with a ZERO reduction factor!" );
	    exit( -1 );
        } else if (RTFac < 0.0 ) {
	    stop("Cooling is impossible with a NEGATIVE reduction factor!" );
	    exit( -1 );
        }
        (void) fflush(logFile);
        B_tempChange = ( RTFac != 1. );
        break; 

/*____________________________________________________________________________*/

    case DPF_RUNS:
        /*
        **  runs
        **  Number of docking runs,
        */
        (void) sscanf( line, "%*s %d", &nruns );
        if ( nruns > MAX_RUNS ) {
	    prStr( error_message, "ERROR: %d runs were requested, but AutoDock is only dimensioned for %d.\nChange \"MAX_RUNS\" in \"constants.h\".", nruns, MAX_RUNS);
	    stop( error_message );
	    exit( -1 );
        }
        pr( logFile, "Number of runs =\t\t\t\t%8d run%c\n", nruns, (nruns > 1)?'s':' ');
        (void) fflush(logFile);
        break; 

/*____________________________________________________________________________*/

    case DPF_CYCLES:
        /*
        **  cycles
        **  Number of constant temperature SA cycles,
        */
        (void) sscanf( line, "%*s %d", &ncycles );
        if (ncycles < 0) {
	    pr( logFile, "WARNING!  Negative number of cycles found!  Using default value.\n");
	    ncycles = 50;
        }
        pr( logFile, "Maximum number of cycles =\t\t\t%8d cycles\n\n", ncycles);
        if (B_linear_schedule) {
	    pr( logFile, "\nA linear temperature reduction schedule was requested...\n" );
	    RTreduc = RT0 / ncycles;
	    pr( logFile, "Annealing temperature will be reduced by %.3f cal mol per cycle.\n\n", RTreduc );
        }
        (void) fflush(logFile);
        break; 

/*____________________________________________________________________________*/

    case DPF_ACCS:
        /*
        **  accs
        **  Maximum number of steps accepted,
        */
        (void) sscanf( line, "%*s %d", &naccmax );
        if (naccmax < 0) {
	    naccmax = 100;
	    pr( logFile, "WARNING!  Negative number of accepted moves found!  Using default value.\n");
        }
        pr( logFile, "Maximum number accepted per cycle =\t\t%8d steps\n", naccmax);
        if (nrejmax != 0) {
	    nstepmax = naccmax + nrejmax;
	    pr( logFile, "                                           \t_________\n" );
	    pr( logFile, "Maximum possible number of steps per cycle =\t%8d\tsteps\n\n", nstepmax);
        }
        (void) fflush(logFile);
        break; 

/*____________________________________________________________________________*/

    case DPF_REJS:
        /*
        **  rejs
        **  Maximum number of steps rejected,
        */
        (void) sscanf( line, "%*s %d", &nrejmax );
        if (nrejmax < 0) {
	    nrejmax = 100;
	    pr( logFile, "WARNING!  Negative number of rejected moves found!  Using default value.\n");
        }
        pr( logFile, "Maximum number rejected per cycle =\t\t%8d steps\n", nrejmax);
        if (naccmax != 0) {
	    nstepmax = naccmax + nrejmax;
	    pr( logFile, "                                           \t_________\n" );
	    pr( logFile, "Maximum possible number of steps per cycle =\t%8d steps\n\n", nstepmax);
        }
        (void) fflush(logFile);
        break; 

/*____________________________________________________________________________*/

    case DPF_SELECT:
        /*
        **  select
        **  Select either minimum or last state from previous cycle,
        */
        (void) sscanf( line, "%*s %1s", &selminpar );
        B_selectmin = (selminpar == 'm');
        if ( B_selectmin ) {
	    pr( logFile, "%s will begin each new cycle\nwith the state of minimum energy from the previous annealing cycle.\n", programname);
        } else {
	    pr( logFile, "%s will begin each new cycle\nwith the last state from the previous annealing cycle.\n", programname);
        }
        (void) fflush(logFile);
        break; 

/*____________________________________________________________________________*/

    case DPF_OUTLEV:
        /*
        **  outlev
        **  Output level,
        */
        (void) sscanf( line, "%*s %d", &outlev );
        switch ( outlev ) {
        case 0:
            pr( logFile, "Output Level = 0.  NO OUTPUT DURING DOCKING.\n" );
            break;
        case 1:
            pr( logFile, "Output Level = 1.  MINIMUM OUTPUT DURING DOCKING.\n" );
            break;
        case 2:
        default:
            pr( logFile, "Output Level = 2.  FULL OUTPUT DURING DOCKING.\n" );
            break;
        }
        (void) fflush(logFile);
        break; 

/*____________________________________________________________________________*/

    case DPF_RMSTOL:
        /*
        **  rmstol
        **  Cluster tolerance,
        */
        (void) sscanf( line, "%*s %f", &clus_rms_tol);
        pr( logFile, "Maximum RMS tolerance for conformational cluster analysis = %.2f Angstroms\n", clus_rms_tol);
        (void) fflush(logFile);
        break; 

/*____________________________________________________________________________*/

    case DPF_RMSREF:
        /*
        **  rmsref
        **  RMS Reference Coordinates:
        */
        (void) sscanf( line, "%*s %s", FN_rms_ref_crds);
        pr( logFile, "RMS reference coordinates will taken from \"%s\"\n", FN_rms_ref_crds );
        (void) fflush(logFile);
        break;