/* clmode.cc */#ifdef sgi    #include <stdio.h>    #include <stdlib.h>    #include <string.h>    #include <ctype.h>    #include <time.h>    #include <sys/types.h>    #include <sys/times.h>    #include "clmode.h"#else    extern "C"    {        #include <stdio.h>        #include <stdlib.h>        #include <string.h>        #include <ctype.h>        #include <time.h>        #include <sys/types.h>        #include <sys/times.h>        #include "clmode.h"    }#endifextern FILE *logFile;extern char *programname;void  clmode( char  atm_typ_str[ATOM_MAPS],              int   num_atm_maps,              float clus_rms_tol,              char  hostnm[MAX_CHARS],              Clock jobStart,              struct tms tms_jobStart,              Boole B_write_all_clusmem,              char  clusFN[MAX_CHARS],              float crdpdb[MAX_ATOMS][SPACE],              float sml_center[SPACE],              Boole B_symmetry_flag,              char  rms_ref_crds[MAX_CHARS] ){    FILE *clusFile;    register int XYZ = 0;    int   anum = 0;    char  atomstuff[MAX_ATOMS][MAX_CHARS];    float crdSave[MAX_RUNS][MAX_ATOMS][SPACE];    float econf[MAX_RUNS];    float eSave[2];    Boole B_haveAtoms = FALSE;    Boole B_haveTypes = FALSE;    int   ii = 0;    int   lastanum = -1;    char  line[LINE_LEN];    int   nat = 0;    int   natom = 0;    int   natom_1 = -1;    int   nconf = 0;    int   ntype[MAX_ATOMS];    char  pdbaname[MAX_ATOMS][5];    float q = 0.;    char  rec5[5];    int   ss = 0;    char  anumStr[5];    int   type[MAX_ATOMS];    float clu_rms[MAX_RUNS][MAX_RUNS];    int   cluster[MAX_RUNS][MAX_RUNS];    register int i = 0;    register int j = 0;    int   irunmax = -1;    int   isort[MAX_RUNS];    int   ncluster = 0;    int   num_in_clu[MAX_RUNS];    float ref_crds[MAX_ATOMS][SPACE];    int   ref_natoms = -1;    float ref_rms[MAX_RUNS];    for (j = 0; j < MAX_RUNS; j++) {        num_in_clu[j] = 0;        isort[j] = j;        econf[j] = 0.;    }/***  Open file containing coordinates to be clustered...*/    if ( openFile( clusFN , "r", &clusFile, jobStart, tms_jobStart, TRUE ) ) {        pr( logFile, "Conformations to be clustered are in this file: \"%s\"\n\n", clusFN );    }/*    Read in the conformations    All we need are the xyz's of each conformation,    and their Energies, plus the Run number/parent dlg file.*/    while ( fgets( line, LINE_LEN, clusFile) != NULL ) {        pr( logFile, "INPUT-PDBQ: %s", line);        for (ii = 0; ii < 4; ii++) {             rec5[ii] = tolower( (int)line[ii] );        }        if (( strindex( line, "USER    Total Interaction Energy of Complex") >= 0 )         || ( strindex( line, "REMARK  Total Interaction Energy of Complex") >= 0 )) {/*            Read in the energy of this conformation*/            if ( B_haveAtoms ) {                econf[nconf] = 0.;                sscanf( line, "%*s %*s %*s %*s %*s %*s %*s %f", &econf[nconf]);            } else {                eSave[ss]=0.;                sscanf( line, "%*s %*s %*s %*s %*s %*s %*s %f", &eSave[ss] );                ++ss;            }        } else if (( strindex( line, "USER    Docked Energy") >= 0 )                 || ( strindex( line, "REMARK  Docked Energy") >= 0 )) {/*            Read in the energy of this conformation*/            if ( B_haveAtoms ) {                econf[nconf] = 0.;                sscanf( line, "%*s %*s %*s %*s %f", &econf[nconf]);            } else {                eSave[ss]=0.;                sscanf( line, "%*s %*s %*s %*s %f", &eSave[ss] );                ++ss;            }        } else if (equal( rec5,"atom", 4) || equal( rec5,"heta", 4)) {            readPDBQLine( line, crdSave[nconf][nat], &q );            if ( ! B_haveAtoms ) {                sscanf( &line[6], "%s", anumStr );                if ( ( anum = atoi( anumStr )) < lastanum ) {/*                    Start of next conformation,*/                    B_haveAtoms = TRUE;                    B_haveTypes = TRUE;                    ++nconf;                    for (XYZ = 0;  XYZ < SPACE;  XYZ++) {                        crdSave[nconf][0][XYZ] = crdSave[nconf-1][nat][XYZ];                     }                    econf[0] = eSave[0];                    econf[1] = eSave[1];                    natom = nat;                    natom_1 = natom-1;                    nat = 0;                } else {                    strncpy( atomstuff[nat], line, (size_t)30 );                    atomstuff[nat][30] = '\0';                    if ( ! B_haveTypes ) {                        type[nat] = -1;                        sscanf( &line[12], "%s", pdbaname[nat] );                        type[nat] = get_atom_type( pdbaname[nat], atm_typ_str );                        if ( type[nat] == -1 ) {                            pr( logFile, "\nNOTE: Atom number %d, using default atom type 1...\n\n", nat+1);                            type[nat] = 1;                        } else {                            pr( logFile, "\nAtom number %d, recognized atom type = %d...\n\n", nat+1, type[nat]+1);                        }                        ++ntype[ type[nat] ];                    }                }                lastanum = anum;            } else if ( nat == natom_1 ) {/*                Increment total number of conformations,*/                ++nconf;                nat = -1; /*  Pre-zero out the "nat" counter... */            }            ++nat;        }     } /* end while */    irunmax = nconf;    pr( logFile, "\nNumber of conformations found = %d\n", nconf );    pr( logFile, "\nNumber of atoms per conformation = %d\n\n", natom );    for (i=0; i<num_atm_maps; i++) {        pr( logFile, "Number of atoms with type %d = %d\n", i+1, ntype[i]);    }    if (strncmp(rms_ref_crds,"unspecified filename",20) != 0) {/*        Read in reference structure, specified by the "rmsref" command...*/        if ((ref_natoms = getpdbcrds( rms_ref_crds, ref_crds)) == -1) {                 fprintf( logFile, "%s: Problems while reading \"%s\".\n", programname, rms_ref_crds);            fprintf( logFile, "Will attempt to use the input PDBQ file coordinates as reference.\n");             } else if (ref_natoms != natom) {                 pr( logFile, "%s: ERROR!  Wrong number of atoms in reference structure.\n", programname);            pr( logFile, "Input PDBQ structure has %d atoms, but reference structure has %d atoms.\n\n", natom, ref_natoms);            ref_natoms = -1;             }    }    if (nconf <= 1) {        pr( logFile, "\nSorry!  Unable to perform cluster analysis, because not enough structures were read in.\n");    } else {#ifdef DEBUG     for (i = 0;  i < nconf;  i++) {         pr( logFile, "i=%-3d\tisort[i]=%-3d\teconf[isort[i]]=%+7.2f\n",                       i, isort[i], econf[isort[i]] );    }#endif /* DEBUG */        pr( logFile, "\nSorting %d conformations by their energy.\n", irunmax);        flushLog;        sort_enrg( econf, isort, nconf );#ifdef DEBUG     for (i = 0;  i < nconf;  i++) { pr( logFile, "i=%-3d\tisort[i]=%-3d\teconf[isort[i]]=%+7.2f\n", i, isort[i], econf[isort[i]] ); }#endif /* DEBUG */        pr( logFile, "\nPerforming cluster analysis, using a cluster RMS tolerance of %.1f\n", clus_rms_tol );        flushLog;        ncluster = cluster_analysis( clus_rms_tol, cluster, num_in_clu, isort,                                      nconf, natom, type, crdSave, crdpdb,                                      sml_center, clu_rms, B_symmetry_flag,                                     ref_crds, ref_natoms, ref_rms);        pr( logFile, "\nOutputting structurally similar clusters, ranked in order of increasing energy.\n" );        flushLog;        prClusterHist( ncluster, irunmax, clus_rms_tol, num_in_clu,                        cluster, econf, clu_rms, ref_rms);        bestpdb( ncluster, num_in_clu, cluster, econf, crdSave,                  atomstuff, natom, B_write_all_clusmem, ref_rms);    }/*if we have more than 1 conformation... *//***  End cluster_mode and END PROGRAM...*/    success( hostnm, jobStart, tms_jobStart );    exit((int)0);}/* EOF */