/usr/share/doc/garlic-doc/commands/dum.html is in garlic-doc 1.6-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331 332 333 334 335 336 337 338 339 340 341 342 343 344 345 346 347 348 349 350 351 352 353 354 355 356 357 358 359 360 361 362 363 364 365 366 367 368 369 370 371 372 373 374 375 376 377 378 379 380 381 382 383 384 385 386 387 388 389 390 391 392 393 394 395 396 397 398 399 400 401 402 403 404 405 406 407 408 409 410 411 412 413 414 415 416 417 418 419 420 421 422 423 424 425 426 427 428 429 430 431 432 433 434 435 436 437 438 439 440 441 | <html>
<head>
<title>
DUM, DUMP
</title>
</head>
<h1 align=center>
DUM, DUMP
</h1>
<hr size="3">
<font color=#880000>
<b>
NAME
<br>
</b>
</font>
DUM, DUMP - dump selected numeric data to the console (standard output)
or the the specified file.
<br><br>
<font color=#880000>
<b>
SYNOPSIS
<br>
</b>
</font>
<table border=1 cellspacing=1 cellpading=0>
<td align="left">
<font color=#004400>
<b>
SHORT FORM
</b>
</font>
</td>
<td align="left">
<font color=#004400>
<b>
LONG FORM
</b>
</font>
</td>
<tr>
<td align="left">
DUM HYD
<br>
DUM HYD filename
<br>
DUM AVE
<br>
DUM AVE filename
<br>
DUM WEI
<br>
DUM WEI filename
<br>
DUM F1
<br>
DUM F1 filename
<br>
DUM F2
<br>
DUM F2 filename
<br>
DUM F3
<br>
DUM F3 filename
<br>
DUM F4
<br>
DUM F4 filename
<br>
DUM F5
<br>
DUM F5 filename
<br>
DUM F6
<br>
DUM F6 filename
<br>
DUM F7
<br>
DUM F7 filename
</td>
<td align="left">
DUMP HYDROPHOBICITY
<br>
DUMP HYDROPHOBICITY filename
<br>
DUMP AVERAGE
<br>
DUMP AVERAGE filename
<br>
DUMP WEIGHTED
<br>
DUMP WEIGHTED filename
<br>
DUMP F1
<br>
DUMP F1 filename
<br>
DUMP F2
<br>
DUMP F2 filename
<br>
DUMP F3
<br>
DUMP F3 filename
<br>
DUMP F4
<br>
DUMP F4 filename
<br>
DUMP F5
<br>
DUMP F5 filename
<br>
DUMP F6
<br>
DUMP F6 filename
<br>
DUMP F7
<br>
DUMP F7 filename
</td>
</table>
<br>
<font color=#880000>
<b>
DESCRIPTION
<br>
</b>
</font>
The command DUM (DUMP) may be used to dump selected numeric data to the
console (standard output) or to the specified file. At present (version 1.6),
the command DUMP may be used to dump hydrophobicity functions. Note that the
selected hydrophobicity function should be calculated first, which is forced
by executing the command PLOT (for example, PLOT AVERAGE will force the
calculation of the average hydrophobicity). The output consists of two columns:
The first column contains the residue serial number (integer) and the second
column contains the requested value (floating point value). Sample output:
<br>
<pre>
# Raw hydrophobicity
0 -3.63
1 0.46
2 -2.80
3 1.25
4 -0.46
5 -1.15
6 -3.64
7 -0.50
8 -1.81
9 0.67
10 -1.15
</pre>
The first line is just a comment.
<br><br>
The simplest hydrophobicity function are the raw hydrophobicity and
the average hydrophobicity. The weighted hydrophobicity was introduced
in version 1.6. The hydrophobicity functions F1, F2, F3, F4 and F5 were
introduced in version 1.4, and functions F6 F7 were introduced in
version 1.6. These hydrophobicity functions are described in the
following source files:
<br>
F1: hyphob_function1.c
<br>
F2: hyphob_function2.c
<br>
F3: hyphob_function3.c
<br>
F4: hyphob_function4.c
<br>
F5: hyphob_function5.c
<br>
F6: hyphob_function6.c
<br>
F7: hyphob_function7.c
<br><br>
<font color=#880000>
<b>
KEYWORDS
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
KEYWORD
<br>
(SHORT)
</td>
<td align="left">
KEYWORD
<br>
(LONG)
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
HYD
</td>
<td align="left">
HYDROPHOBICITY
</td>
<td align="left">
Dump raw hydrophobicity values.
</td>
<tr>
<td align="left">
AVE
</td>
<td align="left">
AVERAGE
</td>
<td align="left">
Dump average hydrophobicity, using
<br>
the current sliding window width.
</td>
<tr>
<td align="left">
WEI
</td>
<td align="left">
WEIGHTED
</td>
<td align="left">
Dump weighted hydrophobicity, defined in
<br>
the source file weighted_hydrophobicity.c .
</td>
<tr>
<td align="left">
F1
</td>
<td align="left">
F1
</td>
<td align="left">
Dump hydrophobicity function F1.
</td>
<tr>
<td align="left">
F2
</td>
<td align="left">
F2
</td>
<td align="left">
Dump hydrophobicity function F2.
</td>
<tr>
<td align="left">
F3
</td>
<td align="left">
F3
</td>
<td align="left">
Dump hydrophobicity function F3.
</td>
<tr>
<td align="left">
F4
</td>
<td align="left">
F4
</td>
<td align="left">
Dump hydrophobicity function F4.
</td>
<tr>
<td align="left">
F5
</td>
<td align="left">
F5
</td>
<td align="left">
Dump hydrophobicity function F5.
</td>
<tr>
<td align="left">
F6
</td>
<td align="left">
F6
</td>
<td align="left">
Dump hydrophobicity function F6.
</td>
<tr>
<td align="left">
F7
</td>
<td align="left">
F7
</td>
<td align="left">
Dump hydrophobicity function F7.
</td>
</table>
<br>
<font color=#880000>
<b>
EXAMPLES
<br>
</b>
</font>
<table border=2 cellspacing=2 cellpading=0>
<td align="left">
COMMAND
</td>
<td align="left">
DESCRIPTION
</td>
<tr>
<td align="left">
dump ave
</td>
<td align="left">
Dump average hydrophobicity to the console.
</td>
<tr>
<td align="left">
dump hyd raw.data
</td>
<td align="left">
Dump raw hydrophobicity values to the file
<br>
called raw.data (file names are case sensitive).
</td>
</table>
<br>
<font color=#880000>
<b>
NOTES
<br>
</b>
</font>
(1) A very simple output format was choosen to make it compatible with
popular drawing programs.
<br><br>
<font color=#880000>
<b>
RELATED COMMANDS
<br>
</b>
</font>
PLOT is used to draw the specified hydrophobicity function. It should be
used before the command dump, to force the calculation of the specified
hydrophobicity function. The only exception is raw hydrophobicity (keyword
HYD) - it is assigned automatically.
<br>
WINDOW is used to define the sliding window width, which affects the
average hydrophobicity function.
<br><br>
<hr size="3">
</html>
|