1 /*
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38 #include "gmxpre.h"
39
40 #include "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
ftp2ext(int ftp)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
ftp2ext_generic(int ftp)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
ftp2ext_with_dot(int ftp)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
ftp2generic_count(int ftp)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
ftp2generic_list(int ftp)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
ftp2desc(int ftp)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
ftp_is_text(int ftp)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
ftp_is_xdr(int ftp)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
ftp2defnm(int ftp)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
ftp2defopt(int ftp)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
fn2ftp(const char * fn)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 }
301