src/gromacs/fileio/filetypes.cpp

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  38 #include "gmxpre.h"
  39
  40 #include "gromacs/fileio/filetypes.h"
  41
  42 #include <cstring>
  43
  44 #include "gromacs/utility/arraysize.h"
  45 #include "gromacs/utility/cstringutil.h"
  46
  47 enum
  48 {
  49     eftASC,
  50     eftXDR,
  51     eftTNG,
  52     eftGEN,
  53     eftNR
  54 };
  55
  56 /* To support multiple file types with one general (eg TRX) we have
  57  * these arrays.
  58  */
  59 static const int trxs[] = { efXTC, efTRR, efCPT, efGRO, efG96, efPDB, efTNG };
  60 #define NTRXS asize(trxs)
  61
  62 static const int trcompressed[] = { efXTC, efTNG };
  63 #define NTRCOMPRESSED asize(trcompressed)
  64
  65 static const int tros[] = { efXTC, efTRR, efGRO, efG96, efPDB, efTNG };
  66 #define NTROS asize(tros)
  67
  68 static const int trns[] = { efTRR, efCPT, efTNG };
  69 #define NTRNS asize(trns)
  70
  71 static const int stos[] = { efGRO, efG96, efPDB, efBRK, efENT, efESP };
  72 #define NSTOS asize(stos)
  73
  74 static const int stxs[] = { efGRO, efG96, efPDB, efBRK, efENT, efESP, efTPR };
  75 #define NSTXS asize(stxs)
  76
  77 static const int tpss[] = { efTPR, efGRO, efG96, efPDB, efBRK, efENT };
  78 #define NTPSS asize(tpss)
  79
  80 typedef struct // NOLINT(clang-analyzer-optin.performance.Padding)
  81 {
  82     int         ftype;
  83     const char* ext;
  84     const char* defnm;
  85     const char* defopt;
  86     const char* descr;
  87     int         ntps;
  88     const int*  tps;
  89 } t_deffile;
  90
  91 /* this array should correspond to the enum in filetypes.h */
  92 static const t_deffile deffile[efNR] = {
  93     { eftASC, ".mdp", "grompp", "-f", "grompp input file with MD parameters" },
  94     { eftGEN, ".???", "traj", "-f", "Trajectory", NTRXS, trxs },
  95     { eftGEN, ".???", "trajout", "-f", "Trajectory", NTROS, tros },
  96     { eftGEN, ".???", "traj", nullptr, "Full precision trajectory", NTRNS, trns },
  97     { eftXDR, ".trr", "traj", nullptr, "Trajectory in portable xdr format" },
  98     { eftGEN, ".???", "traj_comp", nullptr,
  99       "Compressed trajectory (tng format or portable xdr format)", NTRCOMPRESSED, trcompressed },
 100     { eftXDR, ".xtc", "traj", nullptr, "Compressed trajectory (portable xdr format): xtc" },
 101     { eftTNG, ".tng", "traj", nullptr, "Trajectory file (tng format)" },
 102     { eftXDR, ".edr", "ener", nullptr, "Energy file" },
 103     { eftGEN, ".???", "conf", "-c", "Structure file", NSTXS, stxs },
 104     { eftGEN, ".???", "out", "-o", "Structure file", NSTOS, stos },
 105     { eftASC, ".gro", "conf", "-c", "Coordinate file in Gromos-87 format" },
 106     { eftASC, ".g96", "conf", "-c", "Coordinate file in Gromos-96 format" },
 107     { eftASC, ".pdb", "eiwit", "-f", "Protein data bank file" },
 108     { eftASC, ".brk", "eiwit", "-f", "Brookhaven data bank file" },
 109     { eftASC, ".ent", "eiwit", "-f", "Entry in the protein date bank" },
 110     { eftASC, ".esp", "conf", "-f", "Coordinate file in Espresso format" },
 111     { eftASC, ".pqr", "state", "-o", "Coordinate file for MEAD" },
 112     { eftXDR, ".cpt", "state", "-cp", "Checkpoint file" },
 113     { eftASC, ".log", "run", "-l", "Log file" },
 114     { eftASC, ".xvg", "graph", "-o", "xvgr/xmgr file" },
 115     { eftASC, ".out", "hello", "-o", "Generic output file" },
 116     {
 117             eftASC,
 118             ".ndx",
 119             "index",
 120             "-n",
 121             "Index file",
 122     },
 123     { eftASC, ".top", "topol", "-p", "Topology file" },
 124     { eftASC, ".itp", "topinc", nullptr, "Include file for topology" },
 125     { eftGEN, ".???", "topol", "-s", "Structure+mass(db)", NTPSS, tpss },
 126     { eftXDR, ".tpr", "topol", "-s", "Portable xdr run input file" },
 127     { eftASC, ".tex", "doc", "-o", "LaTeX file" },
 128     { eftASC, ".rtp", "residue", nullptr, "Residue Type file used by pdb2gmx" },
 129     { eftASC, ".atp", "atomtp", nullptr, "Atomtype file used by pdb2gmx" },
 130     { eftASC, ".hdb", "polar", nullptr, "Hydrogen data base" },
 131     { eftASC, ".dat", "nnnice", nullptr, "Generic data file" },
 132     { eftASC, ".dlg", "user", nullptr, "Dialog Box data for ngmx" },
 133     { eftASC, ".map", "ss", nullptr, "File that maps matrix data to colors" },
 134     { eftASC, ".eps", "plot", nullptr, "Encapsulated PostScript (tm) file" },
 135     { eftASC, ".mat", "ss", nullptr, "Matrix Data file" },
 136     { eftASC, ".m2p", "ps", nullptr, "Input file for mat2ps" },
 137     { eftXDR, ".mtx", "hessian", "-m", "Hessian matrix" },
 138     { eftASC, ".edi", "sam", nullptr, "ED sampling input" },
 139     { eftASC, ".cub", "pot", nullptr, "Gaussian cube file" },
 140     { eftASC, ".xpm", "root", nullptr, "X PixMap compatible matrix file" },
 141     { eftASC, "", "rundir", nullptr, "Run directory" },
 142     { eftASC, ".csv", "bench", nullptr, "CSV data file" }
 143 };
 144
 145 const char* ftp2ext(int ftp)
 146 {
 147     if ((0 <= ftp) && (ftp < efNR))
 148     {
 149         return deffile[ftp].ext[0] != '\0' ? deffile[ftp].ext + 1 : "";
 150     }
 151     else
 152     {
 153         return "unknown";
 154     }
 155 }
 156
 157 const char* ftp2ext_generic(int ftp)
 158 {
 159     if ((0 <= ftp) && (ftp < efNR))
 160     {
 161         switch (ftp)
 162         {
 163             case efTRX: return "trx";
 164             case efTRN: return "trn";
 165             case efSTO: return "sto";
 166             case efSTX: return "stx";
 167             case efTPS: return "tps";
 168             default: return ftp2ext(ftp);
 169         }
 170     }
 171     else
 172     {
 173         return "unknown";
 174     }
 175 }
 176
 177 const char* ftp2ext_with_dot(int ftp)
 178 {
 179     if ((0 <= ftp) && (ftp < efNR))
 180     {
 181         return deffile[ftp].ext;
 182     }
 183     else
 184     {
 185         return "unknown";
 186     }
 187 }
 188
 189 int ftp2generic_count(int ftp)
 190 {
 191     if ((0 <= ftp) && (ftp < efNR))
 192     {
 193         return deffile[ftp].ntps;
 194     }
 195     else
 196     {
 197         return 0;
 198     }
 199 }
 200
 201 const int* ftp2generic_list(int ftp)
 202 {
 203     if ((0 <= ftp) && (ftp < efNR))
 204     {
 205         return deffile[ftp].tps;
 206     }
 207     else
 208     {
 209         return nullptr;
 210     }
 211 }
 212
 213 const char* ftp2desc(int ftp)
 214 {
 215     if ((0 <= ftp) && (ftp < efNR))
 216     {
 217         return deffile[ftp].descr;
 218     }
 219     else
 220     {
 221         return "unknown filetype";
 222     }
 223 }
 224
 225 gmx_bool ftp_is_text(int ftp)
 226 {
 227     if ((ftp >= 0) && (ftp < efNR))
 228     {
 229         return deffile[ftp].ftype == eftASC;
 230     }
 231     return FALSE;
 232 }
 233
 234 gmx_bool ftp_is_xdr(int ftp)
 235 {
 236     if ((ftp >= 0) && (ftp < efNR))
 237     {
 238         return deffile[ftp].ftype == eftXDR;
 239     }
 240     return FALSE;
 241 }
 242
 243 const char* ftp2defnm(int ftp)
 244 {
 245     if ((0 <= ftp) && (ftp < efNR))
 246     {
 247         return deffile[ftp].defnm;
 248     }
 249     else
 250     {
 251         return nullptr;
 252     }
 253 }
 254
 255 const char* ftp2defopt(int ftp)
 256 {
 257     if ((0 <= ftp) && (ftp < efNR))
 258     {
 259         return deffile[ftp].defopt;
 260     }
 261     else
 262     {
 263         return nullptr;
 264     }
 265 }
 266
 267 int fn2ftp(const char* fn)
 268 {
 269     int         i, len;
 270     const char* feptr;
 271     const char* eptr;
 272
 273     if (!fn)
 274     {
 275         return efNR;
 276     }
 277
 278     len = std::strlen(fn);
 279     if ((len >= 4) && (fn[len - 4] == '.'))
 280     {
 281         feptr = &(fn[len - 4]);
 282     }
 283     else
 284     {
 285         return efNR;
 286     }
 287
 288     for (i = 0; (i < efNR); i++)
 289     {
 290         if ((eptr = deffile[i].ext) != nullptr)
 291         {
 292             if (gmx_strcasecmp(feptr, eptr) == 0)
 293             {
 294                 break;
 295             }
 296         }
 297     }
 298
 299     return i;
 300 }