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37 /* This file is completely threadsafe - keep it that way! */
45 #include "gromacs/utility/cstringutil.h"
46 #include "gromacs/utility/smalloc.h"
47 #include "gromacs/utility/futil.h"
49 #include "gromacs/fileio/gmxfio.h"
50 #include "fflibutil.h"
51 #include "gromacs/utility/fatalerror.h"
52 #include "gromacs/legacyheaders/macros.h"
54 /* Number of control atoms for each 'add' type.
56 * There are 11 types of adding hydrogens, numbered from 1 thru
57 * 11. Each of these has a specific number of control atoms, that
58 * determine how the hydrogens are added. Here these number are
59 * given. Because arrays start at 0, an extra dummy for index 0 is
62 const int ncontrol[] = { -1, 3, 3, 3, 3, 4, 3, 1, 3, 3, 1, 1 };
63 #define maxcontrol asize(ncontrol)
65 int compaddh(const void *a, const void *b)
69 ah = (t_hackblock *)a;
70 bh = (t_hackblock *)b;
71 return gmx_strcasecmp(ah->name, bh->name);
74 void print_ab(FILE *out, t_hack *hack, char *nname)
78 fprintf(out, "%d\t%d\t%s", hack->nr, hack->tp, nname);
79 for (i = 0; (i < hack->nctl); i++)
81 fprintf(out, "\t%s", hack->a[i]);
87 void read_ab(char *line, const char *fn, t_hack *hack)
93 ns = sscanf(line, "%d%d%s%s%s%s%s", &nh, &tp, hn, a[0], a[1], a[2], a[3]);
96 gmx_fatal(FARGS, "wrong format in input file %s on line\n%s\n", fn, line);
101 if ((tp < 1) || (tp >= maxcontrol))
103 gmx_fatal(FARGS, "Error in hdb file %s:\nH-type should be in 1-%d. Offending line:\n%s", fn, maxcontrol-1, line);
107 if ((hack->nctl != ncontrol[hack->tp]) && (ncontrol[hack->tp] != -1))
109 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);
111 for (i = 0; (i < hack->nctl); i++)
113 hack->a[i] = gmx_strdup(a[i]);
120 hack->nname = gmx_strdup(hn);
124 for (i = 0; i < DIM; i++)
126 hack->newx[i] = NOTSET;
130 static void read_h_db_file(const char *hfn, int *nahptr, t_hackblock **ah)
133 char filebase[STRLEN], line[STRLEN], buf[STRLEN];
139 fprintf(debug, "Hydrogen Database (%s):\n", hfn);
142 fflib_filename_base(hfn, filebase, STRLEN);
143 /* Currently filebase is read and set, but not used.
144 * hdb entries from any hdb file and be applied to rtp entries
148 in = fflib_open(hfn);
152 while (fgets2(line, STRLEN-1, in))
154 if (sscanf(line, "%s%n", buf, &n) != 1)
156 fprintf(stderr, "Error in hdb file: nah = %d\nline = '%s'\n",
162 fprintf(debug, "%s", buf);
165 clear_t_hackblock(&aah[nah]);
166 aah[nah].name = gmx_strdup(buf);
167 aah[nah].filebase = gmx_strdup(filebase);
169 if (sscanf(line+n, "%d", &nab) == 1)
173 fprintf(debug, " %d\n", nab);
175 snew(aah[nah].hack, nab);
176 aah[nah].nhack = nab;
177 for (i = 0; (i < nab); i++)
181 gmx_fatal(FARGS, "Expected %d lines of hydrogens, found only %d "
182 "while reading Hydrogen Database %s residue %s",
183 nab, i-1, aah[nah].name, hfn);
185 if (NULL == fgets(buf, STRLEN, in))
187 gmx_fatal(FARGS, "Error reading from file %s", hfn);
189 read_ab(buf, hfn, &(aah[nah].hack[i]));
196 /* Sort the list (necessary to be able to use bsearch */
197 qsort(aah, nah, (size_t)sizeof(**ah), compaddh);
201 dump_h_db(hfn,nah,aah);
208 int read_h_db(const char *ffdir, t_hackblock **ah)
215 /* Read the hydrogen database file(s).
216 * Do not generate an error when no files are found.
218 nhdbf = fflib_search_file_end(ffdir, ".hdb", FALSE, &hdbf);
221 for (f = 0; f < nhdbf; f++)
223 read_h_db_file(hdbf[f], &nah, ah);
231 t_hackblock *search_h_db(int nh, t_hackblock ah[], char *key)
233 t_hackblock ahkey, *result;
242 result = (t_hackblock *)bsearch(&ahkey, ah, nh, (size_t)sizeof(ah[0]), compaddh);