src/gromacs/gmxpreprocess/pgutil.cpp

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  38 /* This file is completely threadsafe - keep it that way! */
  39
  40 #include "gmxpre.h"
  41
  42 #include "pgutil.h"
  43
  44 #include <cstring>
  45
  46 #include <algorithm>
  47
  48 #include "gromacs/topology/atoms.h"
  49 #include "gromacs/utility/cstringutil.h"
  50 #include "gromacs/utility/fatalerror.h"
  51 #include "gromacs/utility/snprintf.h"
  52
  53 #define BUFSIZE 1024
  54 static void atom_not_found(int         fatal_errno,
  55                            const char* file,
  56                            int         line,
  57                            const char* atomname,
  58                            int         resind,
  59                            const char* resname,
  60                            const char* bondtype,
  61                            bool        bAllowMissing)
  62 {
  63     char message_buffer[BUFSIZE];
  64     if (strcmp(bondtype, "check") != 0)
  65     {
  66         if (0 != strcmp(bondtype, "atom"))
  67         {
  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                      "an interaction of type %s in that entry is not found in the\n"
  72                      "input file. Perhaps your atom and/or residue naming needs to be\n"
  73                      "fixed.\n",
  74                      resind + 1, resname, atomname, bondtype);
  75         }
  76         else
  77         {
  78             snprintf(message_buffer, 1024,
  79                      "Residue %d named %s of a molecule in the input file was mapped\n"
  80                      "to an entry in the topology database, but the atom %s used in\n"
  81                      "that entry is not found in the input file. Perhaps your atom\n"
  82                      "and/or residue naming needs to be fixed.\n",
  83                      resind + 1, resname, atomname);
  84         }
  85         if (bAllowMissing)
  86         {
  87             gmx_warning("WARNING: %s", message_buffer);
  88         }
  89         else
  90         {
  91             gmx_fatal(fatal_errno, file, line, "%s", message_buffer);
  92         }
  93     }
  94 }
  95
  96 int search_atom(const char*              type,
  97                 int                      start,
  98                 const t_atoms*           atoms,
  99                 const char*              bondtype,
 100                 bool                     bAllowMissing,
 101                 gmx::ArrayRef<const int> cyclicBondsIndex)
 102 {
 103     int                                i, resind = -1;
 104     bool                               bPrevious, bNext, bOverring;
 105     int                                natoms = atoms->nr;
 106     t_atom*                            at     = atoms->atom;
 107     char** const*                      anm    = atoms->atomname;
 108     gmx::ArrayRef<const int>::iterator cyclicBondsIterator;
 109
 110     bPrevious = (strchr(type, '-') != nullptr);
 111     bNext     = (strchr(type, '+') != nullptr);
 112
 113     if (!bPrevious)
 114     {
 115         resind = at[start].resind;
 116         if (bNext)
 117         {
 118             /* The next residue */
 119             type++;
 120             bOverring = !cyclicBondsIndex.empty()
 121                         && (cyclicBondsIterator =
 122                                     std::find(cyclicBondsIndex.begin(), cyclicBondsIndex.end(), resind))
 123                                    != cyclicBondsIndex.end();
 124             if (bOverring && ((cyclicBondsIterator - cyclicBondsIndex.begin()) & 1))
 125             {
 126                 resind = *(--cyclicBondsIterator);
 127                 return search_res_atom(type, resind, atoms, bondtype, false);
 128             }
 129             else
 130             {
 131                 while ((start < natoms) && (at[start].resind == resind))
 132                 {
 133                     start++;
 134                 }
 135                 if (start < natoms)
 136                 {
 137                     resind = at[start].resind;
 138                 }
 139             }
 140         }
 141
 142         for (i = start; (i < natoms) && (bNext || (at[i].resind == resind)); i++)
 143         {
 144             if (anm[i] && gmx_strcasecmp(type, *(anm[i])) == 0)
 145             {
 146                 return i;
 147             }
 148         }
 149         if (!(bNext && at[start].resind == at[natoms - 1].resind))
 150         {
 151             atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype,
 152                            bAllowMissing);
 153         }
 154     }
 155     else
 156     {
 157         /* The previous residue */
 158         type++;
 159         resind    = at[start].resind;
 160         bOverring = !cyclicBondsIndex.empty()
 161                     && (cyclicBondsIterator =
 162                                 std::find(cyclicBondsIndex.begin(), cyclicBondsIndex.end(), resind))
 163                                != cyclicBondsIndex.end();
 164
 165         if (bOverring && !((cyclicBondsIterator - cyclicBondsIndex.begin()) & 1))
 166         {
 167             resind = *(++cyclicBondsIterator);
 168             return search_res_atom(type, resind, atoms, bondtype, false);
 169         }
 170         else
 171         {
 172             while ((start >= 0) && (at[start].resind == resind))
 173             {
 174                 start--;
 175             }
 176             if (start >= 0)
 177             {
 178                 resind = at[start].resind;
 179                 start++;
 180             }
 181         }
 182         for (i = start - 1; (i >= 0) && (at[i].resind == resind); i--)
 183         {
 184             if (gmx_strcasecmp(type, *(anm[i])) == 0)
 185             {
 186                 return i;
 187             }
 188         }
 189         if (start > 0)
 190         {
 191             atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype,
 192                            bAllowMissing);
 193         }
 194     }
 195     return -1;
 196 }
 197
 198 int search_res_atom(const char* type, int resind, const t_atoms* atoms, const char* bondtype, bool bAllowMissing)
 199 {
 200     int i;
 201
 202     for (i = 0; (i < atoms->nr); i++)
 203     {
 204         if (atoms->atom[i].resind == resind)
 205         {
 206             return search_atom(type, i, atoms, bondtype, bAllowMissing, gmx::ArrayRef<const int>());
 207         }
 208     }
 209
 210     return -1;
 211 }