src/gromacs/gmxpreprocess/xlate.cpp

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  38 #include "gmxpre.h"
  39
  40 #include "xlate.h"
  41
  42 #include <cctype>
  43 #include <cstring>
  44
  45 #include <string>
  46 #include <vector>
  47
  48 #include "gromacs/gmxpreprocess/fflibutil.h"
  49 #include "gromacs/gmxpreprocess/grompp_impl.h"
  50 #include "gromacs/topology/residuetypes.h"
  51 #include "gromacs/topology/symtab.h"
  52 #include "gromacs/utility/cstringutil.h"
  53 #include "gromacs/utility/fatalerror.h"
  54 #include "gromacs/utility/futil.h"
  55 #include "gromacs/utility/smalloc.h"
  56 #include "gromacs/utility/strdb.h"
  57
  58 #include "hackblock.h"
  59
  60 typedef struct
  61 {
  62     char* filebase;
  63     char* res;
  64     char* atom;
  65     char* replace;
  66 } t_xlate_atom;
  67
  68 static void get_xlatoms(const std::string& filename, FILE* fp, int* nptr, t_xlate_atom** xlptr)
  69 {
  70     char          filebase[STRLEN];
  71     char          line[STRLEN];
  72     char          abuf[1024], rbuf[1024], repbuf[1024], dumbuf[1024];
  73     char*         _ptr;
  74     int           n, na, idum;
  75     t_xlate_atom* xl;
  76
  77     fflib_filename_base(filename.c_str(), filebase, STRLEN);
  78
  79     n  = *nptr;
  80     xl = *xlptr;
  81
  82     while (get_a_line(fp, line, STRLEN))
  83     {
  84         na = sscanf(line, "%s%s%s%s", rbuf, abuf, repbuf, dumbuf);
  85         /* Check if we are reading an old format file with the number of items
  86          * on the first line.
  87          */
  88         if (na == 1 && n == *nptr && sscanf(rbuf, "%d", &idum) == 1)
  89         {
  90             continue;
  91         }
  92         if (na != 3)
  93         {
  94             gmx_fatal(FARGS, "Expected a residue name and two atom names in file '%s', not '%s'",
  95                       filename.c_str(), line);
  96         }
  97
  98         srenew(xl, n + 1);
  99         xl[n].filebase = gmx_strdup(filebase);
 100
 101         /* Use wildcards... */
 102         if (strcmp(rbuf, "*") != 0)
 103         {
 104             xl[n].res = gmx_strdup(rbuf);
 105         }
 106         else
 107         {
 108             xl[n].res = nullptr;
 109         }
 110
 111         /* Replace underscores in the string by spaces */
 112         while ((_ptr = strchr(abuf, '_')) != nullptr)
 113         {
 114             *_ptr = ' ';
 115         }
 116
 117         xl[n].atom    = gmx_strdup(abuf);
 118         xl[n].replace = gmx_strdup(repbuf);
 119         n++;
 120     }
 121
 122     *nptr  = n;
 123     *xlptr = xl;
 124 }
 125
 126 static void done_xlatom(int nxlate, t_xlate_atom* xlatom)
 127 {
 128     int i;
 129
 130     for (i = 0; (i < nxlate); i++)
 131     {
 132         sfree(xlatom[i].filebase);
 133         if (xlatom[i].res != nullptr)
 134         {
 135             sfree(xlatom[i].res);
 136         }
 137         sfree(xlatom[i].atom);
 138         sfree(xlatom[i].replace);
 139     }
 140     sfree(xlatom);
 141 }
 142
 143 void rename_atoms(const char*                            xlfile,
 144                   const char*                            ffdir,
 145                   t_atoms*                               atoms,
 146                   t_symtab*                              symtab,
 147                   gmx::ArrayRef<const PreprocessResidue> localPpResidue,
 148                   bool                                   bResname,
 149                   ResidueType*                           rt,
 150                   bool                                   bReorderNum,
 151                   bool                                   bVerbose)
 152 {
 153     int           nxlate, a, i, resind;
 154     t_xlate_atom* xlatom;
 155     char          c, *rnm, atombuf[32];
 156     bool          bReorderedNum, bRenamed, bMatch;
 157     bool          bStartTerm, bEndTerm;
 158
 159     nxlate = 0;
 160     xlatom = nullptr;
 161     if (xlfile != nullptr)
 162     {
 163         gmx::FilePtr fp = gmx::openLibraryFile(xlfile);
 164         get_xlatoms(xlfile, fp.get(), &nxlate, &xlatom);
 165     }
 166     else
 167     {
 168         std::vector<std::string> fns = fflib_search_file_end(ffdir, ".arn", FALSE);
 169         for (const auto& filename : fns)
 170         {
 171             FILE* fp = fflib_open(filename);
 172             get_xlatoms(filename, fp, &nxlate, &xlatom);
 173             gmx_ffclose(fp);
 174         }
 175     }
 176
 177     for (a = 0; (a < atoms->nr); a++)
 178     {
 179         resind = atoms->atom[a].resind;
 180
 181         bStartTerm = (resind == 0) || atoms->resinfo[resind].chainnum != atoms->resinfo[resind - 1].chainnum;
 182         bEndTerm = (resind >= atoms->nres - 1)
 183                    || atoms->resinfo[resind].chainnum != atoms->resinfo[resind + 1].chainnum;
 184
 185         if (bResname)
 186         {
 187             rnm = *(atoms->resinfo[resind].name);
 188         }
 189         else
 190         {
 191             rnm = *(atoms->resinfo[resind].rtp);
 192         }
 193
 194         strcpy(atombuf, *(atoms->atomname[a]));
 195         bReorderedNum = FALSE;
 196         if (bReorderNum)
 197         {
 198             if (isdigit(atombuf[0]))
 199             {
 200                 c = atombuf[0];
 201                 for (i = 0; (static_cast<size_t>(i) < strlen(atombuf) - 1); i++)
 202                 {
 203                     atombuf[i] = atombuf[i + 1];
 204                 }
 205                 atombuf[i]    = c;
 206                 bReorderedNum = TRUE;
 207             }
 208         }
 209         bRenamed = FALSE;
 210         for (i = 0; (i < nxlate) && !bRenamed; i++)
 211         {
 212             /* Check if the base file name of the rtp and arn entry match */
 213             if (localPpResidue.empty()
 214                 || gmx::equalCaseInsensitive(localPpResidue[resind].filebase, xlatom[i].filebase))
 215             {
 216                 /* Match the residue name */
 217                 bMatch = (xlatom[i].res == nullptr
 218                           || (gmx_strcasecmp("protein-nterm", xlatom[i].res) == 0
 219                               && rt->namedResidueHasType(rnm, "Protein") && bStartTerm)
 220                           || (gmx_strcasecmp("protein-cterm", xlatom[i].res) == 0
 221                               && rt->namedResidueHasType(rnm, "Protein") && bEndTerm)
 222                           || (gmx_strcasecmp("protein", xlatom[i].res) == 0
 223                               && rt->namedResidueHasType(rnm, "Protein"))
 224                           || (gmx_strcasecmp("DNA", xlatom[i].res) == 0
 225                               && rt->namedResidueHasType(rnm, "DNA"))
 226                           || (gmx_strcasecmp("RNA", xlatom[i].res) == 0
 227                               && rt->namedResidueHasType(rnm, "RNA")));
 228                 if (!bMatch)
 229                 {
 230                     const char* ptr0 = rnm;
 231                     const char* ptr1 = xlatom[i].res;
 232                     while (ptr0[0] != '\0' && ptr1[0] != '\0' && (ptr0[0] == ptr1[0] || ptr1[0] == '?'))
 233                     {
 234                         ptr0++;
 235                         ptr1++;
 236                     }
 237                     bMatch = (ptr0[0] == '\0' && ptr1[0] == '\0');
 238                 }
 239                 if (bMatch && strcmp(atombuf, xlatom[i].atom) == 0)
 240                 {
 241                     /* We have a match. */
 242                     /* Don't free the old atomname,
 243                      * since it might be in the symtab.
 244                      */
 245                     const char* ptr0 = xlatom[i].replace;
 246                     if (bVerbose)
 247                     {
 248                         printf("Renaming atom '%s' in residue %d %s to '%s'\n", *atoms->atomname[a],
 249                                atoms->resinfo[resind].nr, *atoms->resinfo[resind].name, ptr0);
 250                     }
 251                     atoms->atomname[a] = put_symtab(symtab, ptr0);
 252                     bRenamed           = TRUE;
 253                 }
 254             }
 255         }
 256         if (bReorderedNum && !bRenamed)
 257         {
 258             atoms->atomname[a] = put_symtab(symtab, atombuf);
 259         }
 260     }
 261
 262     done_xlatom(nxlate, xlatom);
 263 }