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37 /* This file is completely threadsafe - keep it that way! */
41 #include "gromacs/utility/cstringutil.h"
44 #include "gromacs/utility/fatalerror.h"
47 static void atom_not_found(int fatal_errno, const char *file, int line,
48 const char *atomname, int resind,
50 const char *bondtype, gmx_bool bAllowMissing)
52 char message_buffer[BUFSIZE];
53 if (strcmp(bondtype, "check") != 0)
55 if (0 != strcmp(bondtype, "atom"))
57 snprintf(message_buffer, 1024,
58 "Residue %d named %s of a molecule in the input file was mapped\n"
59 "to an entry in the topology database, but the atom %s used in\n"
60 "an interaction of type %s in that entry is not found in the\n"
61 "input file. Perhaps your atom and/or residue naming needs to be\n"
63 resind+1, resname, atomname, bondtype);
67 snprintf(message_buffer, 1024,
68 "Residue %d named %s of a molecule in the input file was mapped\n"
69 "to an entry in the topology database, but the atom %s used in\n"
70 "that entry is not found in the input file. Perhaps your atom\n"
71 "and/or residue naming needs to be fixed.\n",
72 resind+1, resname, atomname);
76 gmx_warning("WARNING: %s", message_buffer);
80 gmx_fatal(fatal_errno, file, line, message_buffer);
85 atom_id search_atom(const char *type, int start,
87 const char *bondtype, gmx_bool bAllowMissing)
90 gmx_bool bPrevious, bNext;
91 int natoms = atoms->nr;
92 t_atom *at = atoms->atom;
93 char ** const * anm = atoms->atomname;
95 bPrevious = (strchr(type, '-') != NULL);
96 bNext = (strchr(type, '+') != NULL);
100 resind = at[start].resind;
103 /* The next residue */
105 while ((start < natoms) && (at[start].resind == resind))
111 resind = at[start].resind;
115 for (i = start; (i < natoms) && (bNext || (at[i].resind == resind)); i++)
117 if (anm[i] && gmx_strcasecmp(type, *(anm[i])) == 0)
122 if (!(bNext && at[start].resind == at[natoms-1].resind))
124 atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype, bAllowMissing);
129 /* The previous residue */
133 resind = at[start-1].resind;
135 for (i = start-1; (i >= 0) /*&& (at[i].resind == resind)*/; i--)
137 if (gmx_strcasecmp(type, *(anm[i])) == 0)
144 atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype, bAllowMissing);
151 search_res_atom(const char *type, int resind,
153 const char *bondtype, gmx_bool bAllowMissing)
157 for (i = 0; (i < atoms->nr); i++)
159 if (atoms->atom[i].resind == resind)
161 return search_atom(type, i, atoms, bondtype, bAllowMissing);
169 void set_at(t_atom *at, real m, real q, int type, int resind)