src/gromacs/gmxpreprocess/pgutil.cpp

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  37 /* This file is completely threadsafe - keep it that way! */
  38
  39 #include "gmxpre.h"
  40
  41 #include "pgutil.h"
  42
  43 #include <cstring>
  44
  45 #include "gromacs/topology/atoms.h"
  46 #include "gromacs/utility/cstringutil.h"
  47 #include "gromacs/utility/fatalerror.h"
  48 #include "gromacs/utility/snprintf.h"
  49
  50 #define BUFSIZE 1024
  51 static void atom_not_found(int fatal_errno, const char *file, int line,
  52                            const char *atomname, int resind,
  53                            const char *resname,
  54                            const char *bondtype, bool bAllowMissing)
  55 {
  56     char message_buffer[BUFSIZE];
  57     if (strcmp(bondtype, "check") != 0)
  58     {
  59         if (0 != strcmp(bondtype, "atom"))
  60         {
  61             snprintf(message_buffer, 1024,
  62                      "Residue %d named %s of a molecule in the input file was mapped\n"
  63                      "to an entry in the topology database, but the atom %s used in\n"
  64                      "an interaction of type %s in that entry is not found in the\n"
  65                      "input file. Perhaps your atom and/or residue naming needs to be\n"
  66                      "fixed.\n",
  67                      resind+1, resname, atomname, bondtype);
  68         }
  69         else
  70         {
  71             snprintf(message_buffer, 1024,
  72                      "Residue %d named %s of a molecule in the input file was mapped\n"
  73                      "to an entry in the topology database, but the atom %s used in\n"
  74                      "that entry is not found in the input file. Perhaps your atom\n"
  75                      "and/or residue naming needs to be fixed.\n",
  76                      resind+1, resname, atomname);
  77         }
  78         if (bAllowMissing)
  79         {
  80             gmx_warning("WARNING: %s", message_buffer);
  81         }
  82         else
  83         {
  84             gmx_fatal(fatal_errno, file, line, "%s", message_buffer);
  85         }
  86     }
  87 }
  88
  89 int search_atom(const char *type, int start,
  90                 const t_atoms *atoms,
  91                 const char *bondtype, bool bAllowMissing)
  92 {
  93     int             i, resind = -1;
  94     bool            bPrevious, bNext;
  95     int             natoms = atoms->nr;
  96     t_atom         *at     = atoms->atom;
  97     char ** const * anm    = atoms->atomname;
  98
  99     bPrevious = (strchr(type, '-') != nullptr);
 100     bNext     = (strchr(type, '+') != nullptr);
 101
 102     if (!bPrevious)
 103     {
 104         resind = at[start].resind;
 105         if (bNext)
 106         {
 107             /* The next residue */
 108             type++;
 109             while ((start < natoms) && (at[start].resind == resind))
 110             {
 111                 start++;
 112             }
 113             if (start < natoms)
 114             {
 115                 resind = at[start].resind;
 116             }
 117         }
 118
 119         for (i = start; (i < natoms) && (bNext || (at[i].resind == resind)); i++)
 120         {
 121             if (anm[i] && gmx_strcasecmp(type, *(anm[i])) == 0)
 122             {
 123                 return i;
 124             }
 125         }
 126         if (!(bNext && at[start].resind == at[natoms-1].resind))
 127         {
 128             atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype, bAllowMissing);
 129         }
 130     }
 131     else
 132     {
 133         /* The previous residue */
 134         type++;
 135         if (start > 0)
 136         {
 137             resind = at[start-1].resind;
 138         }
 139         for (i = start-1; (i >= 0) /*&& (at[i].resind == resind)*/; i--)
 140         {
 141             if (gmx_strcasecmp(type, *(anm[i])) == 0)
 142             {
 143                 return i;
 144             }
 145         }
 146         if (start > 0)
 147         {
 148             atom_not_found(FARGS, type, at[start].resind, *atoms->resinfo[resind].name, bondtype, bAllowMissing);
 149         }
 150     }
 151     return -1;
 152 }
 153
 154 int
 155 search_res_atom(const char *type, int resind,
 156                 const t_atoms *atoms,
 157                 const char *bondtype, bool bAllowMissing)
 158 {
 159     int i;
 160
 161     for (i = 0; (i < atoms->nr); i++)
 162     {
 163         if (atoms->atom[i].resind == resind)
 164         {
 165             return search_atom(type, i, atoms, bondtype, bAllowMissing);
 166         }
 167     }
 168
 169     return -1;
 170 }
 171
 172
 173 void set_at(t_atom *at, real m, real q, int type, int resind)
 174 {
 175     at->m      = m;
 176     at->q      = q;
 177     at->type   = type;
 178     at->resind = resind;
 179 }