src/gromacs/gmxpreprocess/h_db.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38 #include "gmxpre.h"
  39
  40 #include "h_db.h"
  41
  42 #include <stdlib.h>
  43 #include <string.h>
  44
  45 #include "gromacs/gmxpreprocess/fflibutil.h"
  46 #include "gromacs/gmxpreprocess/notset.h"
  47 #include "gromacs/utility/arraysize.h"
  48 #include "gromacs/utility/cstringutil.h"
  49 #include "gromacs/utility/fatalerror.h"
  50 #include "gromacs/utility/futil.h"
  51 #include "gromacs/utility/smalloc.h"
  52
  53 /* Number of control atoms for each 'add' type.
  54  *
  55  * There are 11 types of adding hydrogens, numbered from 1 thru
  56  * 11. Each of these has a specific number of control atoms, that
  57  * determine how the hydrogens are added.  Here these number are
  58  * given. Because arrays start at 0, an extra dummy for index 0 is
  59  * added.
  60  */
  61 const int ncontrol[] = { -1, 3, 3, 3, 3, 4, 3, 1, 3, 3, 1, 1 };
  62 #define maxcontrol asize(ncontrol)
  63
  64 int compaddh(const void *a, const void *b)
  65 {
  66     t_hackblock *ah, *bh;
  67
  68     ah = (t_hackblock *)a;
  69     bh = (t_hackblock *)b;
  70     return gmx_strcasecmp(ah->name, bh->name);
  71 }
  72
  73 void print_ab(FILE *out, t_hack *hack, char *nname)
  74 {
  75     int i;
  76
  77     fprintf(out, "%d\t%d\t%s", hack->nr, hack->tp, nname);
  78     for (i = 0; (i < hack->nctl); i++)
  79     {
  80         fprintf(out, "\t%s", hack->a[i]);
  81     }
  82     fprintf(out, "\n");
  83 }
  84
  85
  86 void read_ab(char *line, const char *fn, t_hack *hack)
  87 {
  88     int  i, nh, tp, ns;
  89     char a[4][12];
  90     char hn[32];
  91
  92     ns = sscanf(line, "%d%d%s%s%s%s%s", &nh, &tp, hn, a[0], a[1], a[2], a[3]);
  93     if (ns < 4)
  94     {
  95         gmx_fatal(FARGS, "wrong format in input file %s on line\n%s\n", fn, line);
  96     }
  97
  98     hack->nr = nh;
  99     hack->tp = tp;
 100     if ((tp < 1) || (tp >= maxcontrol))
 101     {
 102         gmx_fatal(FARGS, "Error in hdb file %s:\nH-type should be in 1-%d. Offending line:\n%s", fn, maxcontrol-1, line);
 103     }
 104
 105     hack->nctl = ns - 3;
 106     if ((hack->nctl != ncontrol[hack->tp]) && (ncontrol[hack->tp] != -1))
 107     {
 108         gmx_fatal(FARGS, "Error in hdb file %s:\nWrong number of control atoms (%d iso %d) on line:\n%s\n", fn, hack->nctl, ncontrol[hack->tp], line);
 109     }
 110     for (i = 0; (i < hack->nctl); i++)
 111     {
 112         hack->a[i] = gmx_strdup(a[i]);
 113     }
 114     for (; i < 4; i++)
 115     {
 116         hack->a[i] = NULL;
 117     }
 118     hack->oname = NULL;
 119     hack->nname = gmx_strdup(hn);
 120     hack->atom  = NULL;
 121     hack->cgnr  = NOTSET;
 122     hack->bXSet = FALSE;
 123     for (i = 0; i < DIM; i++)
 124     {
 125         hack->newx[i] = NOTSET;
 126     }
 127 }
 128
 129 static void read_h_db_file(const char *hfn, int *nahptr, t_hackblock **ah)
 130 {
 131     FILE        *in;
 132     char         filebase[STRLEN], line[STRLEN], buf[STRLEN];
 133     int          i, n, nab, nah;
 134     t_hackblock *aah;
 135
 136     if (debug)
 137     {
 138         fprintf(debug, "Hydrogen Database (%s):\n", hfn);
 139     }
 140
 141     fflib_filename_base(hfn, filebase, STRLEN);
 142     /* Currently filebase is read and set, but not used.
 143      * hdb entries from any hdb file and be applied to rtp entries
 144      * in any rtp file.
 145      */
 146
 147     in = fflib_open(hfn);
 148
 149     nah = *nahptr;
 150     aah = *ah;
 151     while (fgets2(line, STRLEN-1, in))
 152     {
 153         if (sscanf(line, "%s%n", buf, &n) != 1)
 154         {
 155             fprintf(stderr, "Error in hdb file: nah = %d\nline = '%s'\n",
 156                     nah, line);
 157             break;
 158         }
 159         if (debug)
 160         {
 161             fprintf(debug, "%s", buf);
 162         }
 163         srenew(aah, nah+1);
 164         clear_t_hackblock(&aah[nah]);
 165         aah[nah].name     = gmx_strdup(buf);
 166         aah[nah].filebase = gmx_strdup(filebase);
 167
 168         if (sscanf(line+n, "%d", &nab) == 1)
 169         {
 170             if (debug)
 171             {
 172                 fprintf(debug, "  %d\n", nab);
 173             }
 174             snew(aah[nah].hack, nab);
 175             aah[nah].nhack = nab;
 176             for (i = 0; (i < nab); i++)
 177             {
 178                 if (feof(in))
 179                 {
 180                     gmx_fatal(FARGS, "Expected %d lines of hydrogens, found only %d "
 181                               "while reading Hydrogen Database %s residue %s",
 182                               nab, i-1, aah[nah].name, hfn);
 183                 }
 184                 if (NULL == fgets(buf, STRLEN, in))
 185                 {
 186                     gmx_fatal(FARGS, "Error reading from file %s", hfn);
 187                 }
 188                 read_ab(buf, hfn, &(aah[nah].hack[i]));
 189             }
 190         }
 191         nah++;
 192     }
 193     gmx_ffclose(in);
 194
 195     if (nah > 0)
 196     {
 197         /* Sort the list (necessary to be able to use bsearch */
 198         qsort(aah, nah, (size_t)sizeof(**ah), compaddh);
 199     }
 200
 201     /*
 202        if (debug)
 203        dump_h_db(hfn,nah,aah);
 204      */
 205
 206     *nahptr = nah;
 207     *ah     = aah;
 208 }
 209
 210 int read_h_db(const char *ffdir, t_hackblock **ah)
 211 {
 212     int    nhdbf, f;
 213     char **hdbf;
 214     int    nah;
 215
 216     /* Read the hydrogen database file(s).
 217      * Do not generate an error when no files are found.
 218      */
 219     nhdbf = fflib_search_file_end(ffdir, ".hdb", FALSE, &hdbf);
 220     nah   = 0;
 221     *ah   = NULL;
 222     for (f = 0; f < nhdbf; f++)
 223     {
 224         read_h_db_file(hdbf[f], &nah, ah);
 225         sfree(hdbf[f]);
 226     }
 227     sfree(hdbf);
 228
 229     return nah;
 230 }
 231
 232 t_hackblock *search_h_db(int nh, t_hackblock ah[], char *key)
 233 {
 234     t_hackblock ahkey, *result;
 235
 236     if (nh <= 0)
 237     {
 238         return NULL;
 239     }
 240
 241     ahkey.name = key;
 242
 243     result = (t_hackblock *)bsearch(&ahkey, ah, nh, (size_t)sizeof(ah[0]), compaddh);
 244
 245     return result;
 246 }