src/gromacs/gmxpreprocess/xlate.cpp

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