/usr/share/EMBOSS/doc/programs/text/domainrep.txt is in embassy-domalign 0.1.660-2.
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 | DOMAINREP documentation
CONTENTS
1.0 SUMMARY
2.0 INPUTS & OUTPUTS
3.0 INPUT FILE FORMAT
4.0 OUTPUT FILE FORMAT
5.0 DATA FILES
6.0 USAGE
7.0 KNOWN BUGS & WARNINGS
8.0 NOTES
9.0 DESCRIPTION
10.0 ALGORITHM
11.0 RELATED APPLICATIONS
12.0 DIAGNOSTIC ERROR MESSAGES
13.0 AUTHORS
14.0 REFERENCES
1.0 SUMMARY
Reorder DCF file to identify representative structures
2.0 INPUTS & OUTPUTS
DOMAINREP reads a DCF file (domain classification file) and writes a
DCF file containing the same data except that the order of domains
within each user-specified node (e.g. family) in the hierarchy may be
changed so that the representative structure of each node is given
first. The representative structure is found by using stamp and this
application must be installed on the system that is running DOMAINREP
and correctly configured (see 'Notes' below). A 'domain PDB file' for
each domain in the DCF file must exist in a directory specified in the
stamp "pdb.directories" file (see 'Notes' below). The domain PDB file
contains coordinate data for a single domain from SCOP or CATH, in PDB
format. The input and output files are specified by the user.
3.0 INPUT FILE FORMAT
The format of the DCF file is described in the SCOPPARSE documentation.
Input files for usage example
File: all.scop2
ID D1CS4A_
XX
EN 1CS4
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Adenylyl and guanylyl cyclase catalytic domain
XX
FA Adenylyl and guanylyl cyclase catalytic domain
XX
DO Adenylyl cyclase VC1, domain C1a
XX
OS Dog (Canis familiaris)
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
ID D1FX2A_
XX
EN 1FX2
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Adenylyl and guanylyl cyclase catalytic domain
XX
FA Adenylyl and guanylyl cyclase catalytic domain
XX
DO Receptor-type monomeric adenylyl cyclase
XX
OS Trypanosome (Trypanosoma brucei), different isoform
XX
NC 1
XX
CN [1]
XX
[Part of this file has been deleted for brevity]
XX
EN 4AT1
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO Aspartate carbamoyltransferase
XX
OS Escherichia coli
XX
NC 1
XX
CN [1]
XX
CH B CHAIN; 8 START; 100 END;
//
ID D4AT1D1
XX
EN 4AT1
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO Aspartate carbamoyltransferase
XX
OS Escherichia coli
XX
NC 1
XX
CN [1]
XX
CH D CHAIN; 8 START; 100 END;
//
4.0 OUTPUT FILE FORMAT
The format of the DCF file is described in the SCOPPARSE documentation.
Output files for usage example
File: all_rep1st.scop
ID D4AT1B1
XX
EN 4AT1
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39019 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO Aspartate carbamoyltransferase
XX
OS Escherichia coli
XX
NC 1
XX
CN [1]
XX
CH B CHAIN; 8 START; 100 END;
//
ID D1CS4A_
XX
EN 1CS4
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55077 DO; 55078 SO; 39418 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Adenylyl and guanylyl cyclase catalytic domain
XX
FA Adenylyl and guanylyl cyclase catalytic domain
XX
DO Adenylyl cyclase VC1, domain C1a
XX
OS Dog (Canis familiaris)
XX
NC 1
XX
CN [1]
XX
[Part of this file has been deleted for brevity]
XX
EN 1FX2
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 55073 SF; 55074 FA; 55081 DO; 55082 SO; 39430 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Adenylyl and guanylyl cyclase catalytic domain
XX
FA Adenylyl and guanylyl cyclase catalytic domain
XX
DO Receptor-type monomeric adenylyl cyclase
XX
OS Trypanosome (Trypanosoma brucei), different isoform
XX
NC 1
XX
CN [1]
XX
CH A CHAIN; . START; . END;
//
ID D4AT1D1
XX
EN 4AT1
XX
TY SCOP
XX
SI 53931 CL; 54861 FO; 54893 SF; 54894 FA; 54895 DO; 54896 SO; 39020 DD;
XX
CL Alpha and beta proteins (a+b)
XX
FO Ferredoxin-like
XX
SF Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
FA Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain
XX
DO Aspartate carbamoyltransferase
XX
OS Escherichia coli
XX
NC 1
XX
CN [1]
XX
CH D CHAIN; 8 START; 100 END;
//
5.0 DATA FILES
DOMAINREP does not use any data files but does make use of the stamp
"pdb.directories" file (see 'Notes').
6.0 USAGE
6.1 COMMAND LINE ARGUMENTS
Reorder DCF file to identify representative structures.
Version: EMBOSS:6.6.0.0
Standard (Mandatory) qualifiers:
[-dcfinfile] infile This option specifies the name of DCF file
(domain classification file) (input). A
'domain classification file' contains
classification and other data for domains
from SCOP or CATH, in DCF format
(EMBL-like). The files are generated by
using SCOPPARSE and CATHPARSE. Domain
sequence information can be added to the
file by using DOMAINSEQS.
-node menu [1] This option specifies the node fore
reordering the file. Reordering can be done
for any specified node in the SCOP or CATH
hierarchies. For example by selecting
'Class' entries belonging to the same Class
will be reordered in turn. (Values: 1 (Class
(SCOP)); 2 (Fold (SCOP)); 3 (Superfamily
(SCOP)); 4 (Family (SCOP)); 5 (Class
(CATH)); 6 (Architecture (CATH)); 7
(Topology (CATH)); 8 (Homologous Superfamily
(CATH)); 9 (Family (CATH)))
[-dcfoutfile] outfile [test.scop] This option specifies the name
of DCF file (domain classification file)
(output). A 'domain classification file'
contains classification and other data for
domains from SCOP or CATH, in DCF format
(EMBL-like). The files are generated by
using SCOPPARSE and CATHPARSE. Domain
sequence information can be added to the
file by using DOMAINSEQS.
Additional (Optional) qualifiers: (none)
Advanced (Unprompted) qualifiers: (none)
Associated qualifiers:
"-dcfoutfile" associated qualifiers
-odirectory2 string Output directory
General qualifiers:
-auto boolean Turn off prompts
-stdout boolean Write first file to standard output
-filter boolean Read first file from standard input, write
first file to standard output
-options boolean Prompt for standard and additional values
-debug boolean Write debug output to program.dbg
-verbose boolean Report some/full command line options
-help boolean Report command line options and exit. More
information on associated and general
qualifiers can be found with -help -verbose
-warning boolean Report warnings
-error boolean Report errors
-fatal boolean Report fatal errors
-die boolean Report dying program messages
-version boolean Report version number and exit
|