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37 /* This file is completely threadsafe - keep it that way! */
42 #include "gromacs/utility/cstringutil.h"
45 #include "gmx_fatal.h"
48 static void atom_not_found(int fatal_errno, const char *file, int line,
49 const char *atomname, int resind,
51 const char *bondtype, gmx_bool bAllowMissing)
53 char message_buffer[BUFSIZE];
54 if (strcmp(bondtype, "check") != 0)
56 if (0 != strcmp(bondtype, "atom"))
58 snprintf(message_buffer, 1024,
59 "Residue %d named %s of a molecule in the input file was mapped\n"
60 "to an entry in the topology database, but the atom %s used in\n"
61 "an interaction of type %s in that entry is not found in the\n"
62 "input file. Perhaps your atom and/or residue naming needs to be\n"
64 resind+1, resname, atomname, bondtype);
68 snprintf(message_buffer, 1024,
69 "Residue %d named %s of a molecule in the input file was mapped\n"
70 "to an entry in the topology database, but the atom %s used in\n"
71 "that entry is not found in the input file. Perhaps your atom\n"
72 "and/or residue naming needs to be fixed.\n",
73 resind+1, resname, atomname);
77 gmx_warning("WARNING: %s", message_buffer);
81 gmx_fatal(fatal_errno, file, line, message_buffer);
86 atom_id search_atom(const char *type, int start,
88 const char *bondtype, gmx_bool bAllowMissing)
91 gmx_bool bPrevious, bNext;
92 int natoms = atoms->nr;
93 t_atom *at = atoms->atom;
94 char ** const * anm = atoms->atomname;
96 bPrevious = (strchr(type, '-') != NULL);
97 bNext = (strchr(type, '+') != NULL);
101 resind = at[start].resind;
104 /* The next residue */
106 while ((start < natoms) && (at[start].resind == resind))
112 resind = at[start].resind;
116 for (i = start; (i < natoms) && (bNext || (at[i].resind == resind)); i++)
118 if (anm[i] && gmx_strcasecmp(type, *(anm[i])) == 0)
123 if (!(bNext && at[start].resind == at[natoms-1].resind))
125 atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype, bAllowMissing);
130 /* The previous residue */
134 resind = at[start-1].resind;
136 for (i = start-1; (i >= 0) /*&& (at[i].resind == resind)*/; i--)
138 if (gmx_strcasecmp(type, *(anm[i])) == 0)
145 atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype, bAllowMissing);
152 search_res_atom(const char *type, int resind,
154 const char *bondtype, gmx_bool bAllowMissing)
158 for (i = 0; (i < atoms->nr); i++)
160 if (atoms->atom[i].resind == resind)
162 return search_atom(type, i, atoms, bondtype, bAllowMissing);
170 void set_at(t_atom *at, real m, real q, int type, int resind)