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     char *filebase;
  61     char *res;
  62     char *atom;
  63     char *replace;
  64 } t_xlate_atom;
  65
  66 static void get_xlatoms(const std::string &filename, FILE *fp,
  67                         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'", filename.c_str(), line);
  94         }
  95
  96         srenew(xl, n+1);
  97         xl[n].filebase = gmx_strdup(filebase);
  98
  99         /* Use wildcards... */
 100         if (strcmp(rbuf, "*") != 0)
 101         {
 102             xl[n].res = gmx_strdup(rbuf);
 103         }
 104         else
 105         {
 106             xl[n].res = nullptr;
 107         }
 108
 109         /* Replace underscores in the string by spaces */
 110         while ((_ptr = strchr(abuf, '_')) != nullptr)
 111         {
 112             *_ptr = ' ';
 113         }
 114
 115         xl[n].atom    = gmx_strdup(abuf);
 116         xl[n].replace = gmx_strdup(repbuf);
 117         n++;
 118     }
 119
 120     *nptr  = n;
 121     *xlptr = xl;
 122 }
 123
 124 static void done_xlatom(int nxlate, t_xlate_atom *xlatom)
 125 {
 126     int i;
 127
 128     for (i = 0; (i < nxlate); i++)
 129     {
 130         sfree(xlatom[i].filebase);
 131         if (xlatom[i].res != nullptr)
 132         {
 133             sfree(xlatom[i].res);
 134         }
 135         sfree(xlatom[i].atom);
 136         sfree(xlatom[i].replace);
 137     }
 138     sfree(xlatom);
 139 }
 140
 141 void rename_atoms(const char* xlfile, const char *ffdir,
 142                   t_atoms *atoms, t_symtab *symtab, gmx::ArrayRef<const PreprocessResidue> localPpResidue,
 143                   bool bResname, ResidueType *rt, bool bReorderNum,
 144                   bool bVerbose)
 145 {
 146     int           nxlate, a, i, resind;
 147     t_xlate_atom *xlatom;
 148     char          c, *rnm, atombuf[32];
 149     bool          bReorderedNum, bRenamed, bMatch;
 150     bool          bStartTerm, bEndTerm;
 151
 152     nxlate = 0;
 153     xlatom = nullptr;
 154     if (xlfile != nullptr)
 155     {
 156         gmx::FilePtr fp = gmx::openLibraryFile(xlfile);
 157         get_xlatoms(xlfile, fp.get(), &nxlate, &xlatom);
 158     }
 159     else
 160     {
 161         std::vector<std::string> fns = fflib_search_file_end(ffdir, ".arn", FALSE);
 162         for (const auto &filename : fns)
 163         {
 164             FILE * fp = fflib_open(filename);
 165             get_xlatoms(filename, fp, &nxlate, &xlatom);
 166             gmx_ffclose(fp);
 167         }
 168     }
 169
 170     for (a = 0; (a < atoms->nr); a++)
 171     {
 172         resind = atoms->atom[a].resind;
 173
 174         bStartTerm = (resind == 0) || atoms->resinfo[resind].chainnum != atoms->resinfo[resind-1].chainnum;
 175         bEndTerm   = (resind >= atoms->nres-1) || atoms->resinfo[resind].chainnum != atoms->resinfo[resind+1].chainnum;
 176
 177         if (bResname)
 178         {
 179             rnm = *(atoms->resinfo[resind].name);
 180         }
 181         else
 182         {
 183             rnm = *(atoms->resinfo[resind].rtp);
 184         }
 185
 186         strcpy(atombuf, *(atoms->atomname[a]));
 187         bReorderedNum = FALSE;
 188         if (bReorderNum)
 189         {
 190             if (isdigit(atombuf[0]))
 191             {
 192                 c = atombuf[0];
 193                 for (i = 0; (static_cast<size_t>(i) < strlen(atombuf)-1); i++)
 194                 {
 195                     atombuf[i] = atombuf[i+1];
 196                 }
 197                 atombuf[i]    = c;
 198                 bReorderedNum = TRUE;
 199             }
 200         }
 201         bRenamed = FALSE;
 202         for (i = 0; (i < nxlate) && !bRenamed; i++)
 203         {
 204             /* Check if the base file name of the rtp and arn entry match */
 205             if (localPpResidue.empty() ||
 206                 gmx::equalCaseInsensitive(localPpResidue[resind].filebase, xlatom[i].filebase))
 207             {
 208                 /* Match the residue name */
 209                 bMatch = (xlatom[i].res == nullptr ||
 210                           (gmx_strcasecmp("protein-nterm", xlatom[i].res) == 0 &&
 211                            rt->namedResidueHasType(rnm, "Protein") && bStartTerm) ||
 212                           (gmx_strcasecmp("protein-cterm", xlatom[i].res) == 0 &&
 213                            rt->namedResidueHasType(rnm, "Protein") && bEndTerm) ||
 214                           (gmx_strcasecmp("protein", xlatom[i].res) == 0 &&
 215                            rt->namedResidueHasType(rnm, "Protein")) ||
 216                           (gmx_strcasecmp("DNA", xlatom[i].res) == 0 &&
 217                            rt->namedResidueHasType(rnm, "DNA")) ||
 218                           (gmx_strcasecmp("RNA", xlatom[i].res) == 0 &&
 219                            rt->namedResidueHasType(rnm, "RNA")));
 220                 if (!bMatch)
 221                 {
 222                     const char *ptr0 = rnm;
 223                     const char *ptr1 = xlatom[i].res;
 224                     while (ptr0[0] != '\0' && ptr1[0] != '\0' &&
 225                            (ptr0[0] == ptr1[0] || ptr1[0] == '?'))
 226                     {
 227                         ptr0++;
 228                         ptr1++;
 229                     }
 230                     bMatch = (ptr0[0] == '\0' && ptr1[0] == '\0');
 231                 }
 232                 if (bMatch && strcmp(atombuf, xlatom[i].atom) == 0)
 233                 {
 234                     /* We have a match. */
 235                     /* Don't free the old atomname,
 236                      * since it might be in the symtab.
 237                      */
 238                     const char *ptr0 = xlatom[i].replace;
 239                     if (bVerbose)
 240                     {
 241                         printf("Renaming atom '%s' in residue %d %s to '%s'\n",
 242                                *atoms->atomname[a],
 243                                atoms->resinfo[resind].nr,
 244                                *atoms->resinfo[resind].name,
 245                                ptr0);
 246                     }
 247                     atoms->atomname[a] = put_symtab(symtab, ptr0);
 248                     bRenamed           = TRUE;
 249                 }
 250             }
 251         }
 252         if (bReorderedNum && !bRenamed)
 253         {
 254             atoms->atomname[a] = put_symtab(symtab, atombuf);
 255         }
 256     }
 257
 258     done_xlatom(nxlate, xlatom);
 259 }