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