cmdmode.cc

c++编写的并行拉马克遗传算法的程序。实现分析对接程序

/* cmdmode.cc */


#include <math.h>

#ifdef sgi
    #include <stdio.h>
    #include <stdlib.h>
    #include <sys/types.h>
    #include <sys/times.h>
    #include <time.h>
    #include <string.h>
    #include <ctype.h>
    #include "cmdmode.h"
    #include "cmdtokens.h"
    #include "trjtokens.h"
#else
    extern "C"
    {
        #include <stdio.h>
        #include <stdlib.h>
        #include <sys/types.h>
        #include <sys/times.h>
        #include <time.h>
        #include <string.h>
        #include <ctype.h>
        #include "cmdmode.h"
        #include "cmdtokens.h"
        #include "trjtokens.h"
    }
#endif


extern FILE *logFile;
extern FILE *command_in_fp;
extern FILE *command_out_fp;

extern char *programname;
extern char dock_param_fn[];
extern char AutoDockHelp[];

extern int oldpdbq;
extern int ignore_errors;
extern int keepresnum;
extern int debug;
extern int parse_tors_mode;

int cmdmode( int   natom,
             Clock jobStart,
             struct tms tms_jobStart,
             float xlo,
             float ylo,
             float zlo,
             float xhi,
             float yhi,
             float zhi,
             float inv_spacing,
             float map[MAX_GRID_PTS][MAX_GRID_PTS][MAX_GRID_PTS][MAX_MAPS],
             float e_internal[NEINT][ATOM_MAPS][ATOM_MAPS],
             float WallEnergy,
             float vt[MAX_TORS][SPACE],
             int   tlist[MAX_TORS][MAX_ATOMS],
             int   ntor,
             int   Nnb,
             int   nonbondlist[MAX_NONBONDS][2],
             char  atomstuff[MAX_ATOMS][MAX_CHARS],
             float crdpdb[MAX_ATOMS][SPACE],
             char  hostnm[MAX_CHARS],
             int   type[MAX_ATOMS],
             float charge[MAX_ATOMS],
             Boole B_calcIntElec,
             float q1q2[MAX_NONBONDS],
             char  atm_typ_str[ATOM_MAPS],
             float torsFreeEnergy)
{
    char message[LINE_LEN],
         command[LINE_LEN],
         trjline[LINE_LEN],
         filename[MAX_CHARS],
         line[LINE_LEN],
         rec5[5],
         pdbaname[MAX_ATOMS][5],
         rec8[MAX_ATOMS][9], /* rec[X] gives (X+1) elements...   */
         rec14[MAX_ATOMS][15],
         trjFileName[MAX_CHARS],
         lastmove = '?';

    int  com_id = 0,
         nframes = 0,
         indpf = 0,
         offset[VECLENMAX],
         nat = 0,
         outside = FALSE,
         ntor_old = 0,
         keyword_id = -1,
         irun = -1,
         icycle = -1,
         nstep = 0,
         veclen = 0,
         movecode = -1;

    register int   i = 0,
         ii = 0;

    Clock  jobEnd;

    struct tms tms_jobEnd;

    float eintra = 0.,
          einter = 0.,
          etotal = 0.,
          etot   = 0.,
          crd[MAX_ATOMS][SPACE],
          elec[MAX_ATOMS],
          emap[MAX_ATOMS],
          T = 0.,
          charge_total = 0.,
          emap_total = 0.,
          elec_total = 0.,
          E = 0.,
          Eint   = 0.;

    FILE *pdbFile, *trjFile;

    State S;


    for (i = 0;  i < natom;  i++) {
        strncpy( rec8[i], &atomstuff[i][13], ( size_t )8 );
        strncpy( rec14[i], &atomstuff[i][6], ( size_t )14 );
    }

/*
    Set up the command file-pointers to standard i/o,
*/
    set_cmd_io_std();

    pr_2x( logFile, stderr, UnderLine );
    prStr(  message, "%s: NOW IN COMMAND MODE.\n", programname );
    pr_2x( logFile, stderr, message );
    fflush( logFile );
    fflush( stderr );

/*
    Now read in the Commands...
*/
    while( ( fgets( command, LINE_LEN, command_in_fp ) ) != NULL ) {
/* 
        Parse the command line...
*/
        com_id = parse_com_line( command );

        if ( com_id == -1 ) {
            pr( stderr, "%s: ERROR: Unrecognized command: \"%c%c%c%c\"\n",
               programname, command[0], command[1], command[2], command[3] );
            continue;
        } /* endif */

/* 
        Act on that command...
*/
        switch( com_id ) {
/*
            ____________________________________________________________________
*/
            case COM_NULL:
                pr( logFile, "%s\n", command );
                break;
/*
            ____________________________________________________________________
*/
            case COM_STOP:
/*
                Write out AVS field-file suitable for "animating" a
                trajectory file.
*/
                pr( logFile, "\n\nTotal number of atoms = %d\n", natom );
                pr( logFile, "Total number of trajectory frames = %d\n\n", nframes );

                indpf = strindex( dock_param_fn, ".dpf" );
                strncpy( filename, dock_param_fn, (size_t)indpf );
                filename[ indpf ] = '\0';
                strcat( filename, ".dlg.pdb\0" );

                offset[0]=5;
                offset[1]=6;
                offset[2]=7;
                offset[3]=4;
                offset[4]=1;

                print_avsfld( logFile, 5, natom, nframes, offset, 8,
                                  "x y z ResidueNum AtomNum", filename );

                pr( logFile, "COMMAND: stop\n\n" );

                success( hostnm, jobStart, tms_jobStart );

                return 0;
/*
            ____________________________________________________________________
*/
            case COM_EPDB:
/*
                EPDB filename flag
                Return the energy of the Small Molecule.

                filename must be in PDBQ-format;

                flag can be:-
                0 = NEW, or PDBQ-71, and
                1 = OLD, or PDBQ-55 (old PDBq format).
*/
                sscanf( command, "%*s %s %d", filename, &oldpdbq );
                pr( logFile, "COMMAND: epdb %s %d\n\n", filename, oldpdbq );

                nat = 0;
                eintra = einter = etotal = 0.;
                outside = FALSE;

                if (openFile(filename,"r",&pdbFile,jobStart,tms_jobStart,FALSE)) {
                    while( ( fgets( line, LINE_LEN, pdbFile ) ) != NULL ) {

                        for ( ii = 0; ii < 4; ii++ ) {
                            rec5[ii] = (char) tolower( (int)line[ii] );
                        }

                        if ( equal( rec5, "atom", 4 ) || equal( rec5, "heta", 4 ) ) {

                            readPDBQLine( line, crd[nat], &charge[nat] );

                            strncpy( pdbaname[natom], &line[12], (size_t)4 );
                            type[nat]=get_atom_type( pdbaname[natom], atm_typ_str );

                            if ( type[nat] == -1 ) {
                                jobEnd = times( &tms_jobEnd );
                                timesys( jobEnd - jobStart, &tms_jobStart, &tms_jobEnd );
                                pr_2x( logFile, stderr, UnderLine );

                                return -1;
                            } /* endif */

                            outside = is_out_grid( crd[nat][X],
                                                   crd[nat][Y],
                                                   crd[nat][Z] );
                            nat++;
                        } /* endif atom or hetatm */
                    } /* endwhile */
                    fclose( pdbFile );
                    natom = nat;
                    if ( ntor > 0 ) {
                        eintra = eintcalPrint( nonbondlist, e_internal, crd, type, Nnb, B_calcIntElec, q1q2 );
                    } else {
                        eintra = 0.0;
                    }
                    if ( outside ) {
                        etotal = (einter = WallEnergy) + eintra;
                    } else {
                        etotal = (einter = trilinterp( crd, charge, type, natom, map, inv_spacing, elec, emap, xlo, ylo, zlo )) + eintra;
                    } /* endif */

                    pr( logFile, "\n\n\t\tIntermolecular Energy Analysis\n" );
                    pr( logFile,     "\t\t==============================\n\n\n" );
                    pr( logFile, "Atom  NB.+ Elec.  Non-bonded  Electrosta  Partial          Coordinates         \n" );
                    pr( logFile, "Type    Energy      Energy    tic Energy  Charge      x         y         z    \n" );
                    pr( logFile, "____  __________  __________  __________  _______  ________  ________  ________\n" );
                    /*            1234  0123456789  0123456789  0123456789  1234567  12345678  12345678  12345678"*/
                    /*           " ---  ----------  ----------  ----------  -------  --------  --------  --------"*/
                    emap_total = 0.;
                    elec_total = 0.;
                    charge_total = 0.;
                    for (i = 0;  i < natom;  i++) {
                        etot = emap[i] + elec[i];
                        pr( logFile, "%4d  %10.2f  %10.2f  %10.2f  %7.3f  %8.4f  %8.4f  %8.4f\n",
                                (type[i]+1), etot, emap[i], elec[i], charge[i], crd[i][X], crd[i][Y], crd[i][Z] );