コード例 #1
0
int read_ter_db(char *FF,char ter,t_hackblock **tbptr,gpp_atomtype_t atype)
{
    FILE       *in;
    char       inf[STRLEN],header[STRLEN],buf[STRLEN],line[STRLEN];
    t_hackblock *tb;
    int        i,j,n,ni,kwnr,nb,maxnb,nh;

    sprintf(inf,"%s-%c.tdb",FF,ter);
    in=libopen(inf);
    if (debug)
        fprintf(debug,"Opened %s\n",inf);

    tb=NULL;
    nb=-1;
    maxnb=0;
    kwnr=NOTSET;
    get_a_line(in,line,STRLEN);
    while (!feof(in)) {
        if (get_header(line,header)) {
            /* this is a new block, or a new keyword */
            kwnr=find_kw(header);

            if (kwnr == NOTSET) {
                nb++;
                /* here starts a new block */
                if ( nb >= maxnb ) {
                    maxnb+=100;
                    srenew(tb,maxnb);
                }
                clear_t_hackblock(&tb[nb]);
                tb[nb].name=strdup(header);
            }
        } else {
            if (nb < 0)
                gmx_fatal(FARGS,"reading termini database: "
                          "directive expected before line:\n%s\n"
                          "This might be a file in an old format.",line);
            /* this is not a header, so it must be data */
            if (kwnr >= ebtsNR) {
                /* this is a hack: add/rename/delete atoms */
                /* make space for hacks */
                if (tb[nb].nhack >= tb[nb].maxhack) {
                    tb[nb].maxhack+=10;
                    srenew(tb[nb].hack, tb[nb].maxhack);
                }
                nh=tb[nb].nhack;
                clear_t_hack(&(tb[nb].hack[nh]));
                for(i=0; i<4; i++)
                    tb[nb].hack[nh].a[i]=NULL;
                tb[nb].nhack++;

                /* get data */
                n=0;
                if ( kwnr==ekwRepl || kwnr==ekwDel ) {
                    if (sscanf(line, "%s%n", buf, &n) != 1)
                        gmx_fatal(FARGS,"Reading Termini Database: "
                                  "expected atom name on line\n%s",line);
                    tb[nb].hack[nh].oname = strdup(buf);
                    /* we only replace or delete one atom at a time */
                    tb[nb].hack[nh].nr = 1;
                } else if ( kwnr==ekwAdd ) {
                    read_ab(line, inf, &(tb[nb].hack[nh]));
                    get_a_line(in, line, STRLEN);
                } else
                    gmx_fatal(FARGS,"unimplemented keyword number %d (%s:%d)",
                              kwnr,__FILE__,__LINE__);
                if ( kwnr==ekwRepl || kwnr==ekwAdd ) {
                    snew(tb[nb].hack[nh].atom, 1);
                    read_atom(line+n, tb[nb].hack[nh].atom, atype,
                              &tb[nb].hack[nh].cgnr);
                    if (!tb[nb].hack[nh].nname) {
                        if (tb[nb].hack[nh].oname)
                            tb[nb].hack[nh].nname = strdup(tb[nb].hack[nh].oname);
                        else
                            gmx_fatal(FARGS,"Don't know which name the new atom should have");
                    }
                }
            } else if (kwnr >= 0 && kwnr < ebtsNR) {
                /* this is bonded data: bonds, angles, dihedrals or impropers */
                srenew(tb[nb].rb[kwnr].b,tb[nb].rb[kwnr].nb+1);
                n=0;
                for(j=0; j<btsNiatoms[kwnr]; j++) {
                    if ( sscanf(line+n, "%s%n", buf, &ni) == 1 )
                        tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = strdup(buf);
                    else
                        gmx_fatal(FARGS,"Reading Termini Database: expected %d atom names (found %d) on line\n%s", btsNiatoms[kwnr], j-1, line);
                    n+=ni;
                }
                for(   ; j<MAXATOMLIST; j++)
                    tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = NULL;
                strcpy(buf, "");
                sscanf(line+n, "%s", buf);
                tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = strdup(buf);
                tb[nb].rb[kwnr].nb++;
            } else
                gmx_fatal(FARGS,"Reading Termini Database: Expecting a header at line\n"
                          "%s",line);
        }
        get_a_line(in,line,STRLEN);
    }
    nb++;
    srenew(tb,nb);

    fclose(in);

    if (debug)
        print_ter_db(FF,ter,nb,tb,atype);

    *tbptr=tb;
    return nb;
}
コード例 #2
0
ファイル: ter_db.cpp プロジェクト: friforever/gromacs
static void read_ter_db_file(const char *fn,
                             int *ntbptr, t_hackblock **tbptr,
                             gpp_atomtype_t atype)
{
    char         filebase[STRLEN], *ptr;
    FILE        *in;
    char         header[STRLEN], buf[STRLEN], line[STRLEN];
    t_hackblock *tb;
    int          i, j, n, ni, kwnr, nb, maxnb, nh;

    fflib_filename_base(fn, filebase, STRLEN);
    /* Remove the C/N termini extension */
    ptr = strrchr(filebase, '.');
    if (ptr != nullptr)
    {
        ptr[0] = '\0';
    }

    in = fflib_open(fn);

    tb    = *tbptr;
    nb    = *ntbptr - 1;
    maxnb = 0;
    kwnr  = NOTSET;
    get_a_line(in, line, STRLEN);
    while (!feof(in))
    {
        if (get_header(line, header))
        {
            /* this is a new block, or a new keyword */
            kwnr = find_kw(header);

            if (kwnr == NOTSET)
            {
                nb++;
                /* here starts a new block */
                if (nb >= maxnb)
                {
                    maxnb = nb + 100;
                    srenew(tb, maxnb);
                }
                clear_t_hackblock(&tb[nb]);
                tb[nb].name     = gmx_strdup(header);
                tb[nb].filebase = gmx_strdup(filebase);
            }
        }
        else
        {
            if (nb < 0)
            {
                gmx_fatal(FARGS, "reading termini database: "
                          "directive expected before line:\n%s\n"
                          "This might be a file in an old format.", line);
            }
            /* this is not a header, so it must be data */
            if (kwnr >= ebtsNR)
            {
                /* this is a hack: add/rename/delete atoms */
                /* make space for hacks */
                if (tb[nb].nhack >= tb[nb].maxhack)
                {
                    tb[nb].maxhack += 10;
                    srenew(tb[nb].hack, tb[nb].maxhack);
                }
                nh = tb[nb].nhack;
                clear_t_hack(&(tb[nb].hack[nh]));
                for (i = 0; i < 4; i++)
                {
                    tb[nb].hack[nh].a[i] = nullptr;
                }
                tb[nb].nhack++;

                /* get data */
                n = 0;
                if (kwnr == ekwRepl || kwnr == ekwDel)
                {
                    if (sscanf(line, "%s%n", buf, &n) != 1)
                    {
                        gmx_fatal(FARGS, "Reading Termini Database '%s': "
                                  "expected atom name on line\n%s", fn, line);
                    }
                    tb[nb].hack[nh].oname = gmx_strdup(buf);
                    /* we only replace or delete one atom at a time */
                    tb[nb].hack[nh].nr = 1;
                }
                else if (kwnr == ekwAdd)
                {
                    read_ab(line, fn, &(tb[nb].hack[nh]));
                    get_a_line(in, line, STRLEN);
                }
                else
                {
                    gmx_fatal(FARGS, "unimplemented keyword number %d (%s:%d)",
                              kwnr, __FILE__, __LINE__);
                }
                if (kwnr == ekwRepl || kwnr == ekwAdd)
                {
                    snew(tb[nb].hack[nh].atom, 1);
                    read_atom(line+n, kwnr == ekwAdd,
                              &tb[nb].hack[nh].nname, tb[nb].hack[nh].atom, atype,
                              &tb[nb].hack[nh].cgnr);
                    if (tb[nb].hack[nh].nname == nullptr)
                    {
                        if (tb[nb].hack[nh].oname != nullptr)
                        {
                            tb[nb].hack[nh].nname = gmx_strdup(tb[nb].hack[nh].oname);
                        }
                        else
                        {
                            gmx_fatal(FARGS, "Reading Termini Database '%s': don't know which name the new atom should have on line\n%s", fn, line);
                        }
                    }
                }
            }
            else if (kwnr >= 0 && kwnr < ebtsNR)
            {
                /* this is bonded data: bonds, angles, dihedrals or impropers */
                srenew(tb[nb].rb[kwnr].b, tb[nb].rb[kwnr].nb+1);
                n = 0;
                for (j = 0; j < btsNiatoms[kwnr]; j++)
                {
                    if (sscanf(line+n, "%s%n", buf, &ni) == 1)
                    {
                        tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = gmx_strdup(buf);
                    }
                    else
                    {
                        gmx_fatal(FARGS, "Reading Termini Database '%s': expected %d atom names (found %d) on line\n%s", fn, btsNiatoms[kwnr], j-1, line);
                    }
                    n += ni;
                }
                for (; j < MAXATOMLIST; j++)
                {
                    tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].a[j] = nullptr;
                }
                strcpy(buf, "");
                sscanf(line+n, "%s", buf);
                tb[nb].rb[kwnr].b[tb[nb].rb[kwnr].nb].s = gmx_strdup(buf);
                tb[nb].rb[kwnr].nb++;
            }
            else
            {
                gmx_fatal(FARGS, "Reading Termini Database: Expecting a header at line\n"
                          "%s", line);
            }
        }
        get_a_line(in, line, STRLEN);
    }
    nb++;
    srenew(tb, nb);

    gmx_ffclose(in);

    *ntbptr = nb;
    *tbptr  = tb;
}