/usr/share/EMBOSS/acd/domainrep.acd is in embassy-domalign 0.1.650-1build1.
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 | application: domainrep [
documentation: "Reorder DCF file to identify representative
structures."
groups: "Protein:3D Structure, Protein:Domains, Alignment:Local"
gui: "yes"
batch: "yes"
cpu: "medium"
embassy: "domalign"
external: "stamp Modified stamp - contact Jon Ison jison@ebi.ac.uk"
relations: "EDAM_topic:0182 Sequence alignment"
relations: "EDAM_topic:0164 Sequence clustering"
relations: "EDAM_topic:0736 Protein domains and folds"
relations: "EDAM_operation:2233 Representative sequence identification"
]
section: input [
information: "Input section"
type: "page"
]
infile: dcfinfile [
parameter: "Y"
information: "Domain classification file"
help: "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."
knowntype: "Domain classification"
relations: "EDAM_data:0900 Protein domain classification"
]
endsection: input
section: required [
information: "Required section"
type: "page"
]
list: node [
standard: "Y"
default: "1"
minimum: "1"
maximum: "1"
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)"
help: "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."
delimiter: ","
codedelimiter: ":"
header: "Node at which to reorder"
information: "Select number."
relations: "EDAM_data:2527 Parameter"
]
endsection: required
section: output [
information: "Output section"
type: "page"
]
outfile: dcfoutfile [
parameter: "Y"
information: "Domain classification output file"
help: "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."
default: "test.scop"
knowntype: "domain classification"
relations: "EDAM_data:0900 Protein domain classification"
]
endsection: output
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