/usr/share/EMBOSS/acd/domainsse.acd is in embassy-domainatrix 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 | application: domainsse [
documentation: "Add secondary structure records to a DCF
file."
groups: "Utils:Database creation, Protein:Domains"
gui: "yes"
batch: "yes"
cpu: "medium"
embassy: "domainatrix"
relations: "EDAM_topic:0091 Data handling"
relations: "EDAM_topic:0736 Protein domains and folds"
relations: "EDAM_operation:2234 Structure file processing"
]
section: input [
information: "Input section"
type: "page"
]
infile: dcfinfile [
parameter: "Y"
information: "Domain classification file"
help: "This option specifies the name of the 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"
]
directory: dccfdir [
parameter: "Y"
information: "Clean domain coordinates directory"
help: "This option specifies the location of the domain CCF file
(clean coordinate files) (input). A 'clean cordinate file'
contains protein coordinate and derived data for a single PDB file
('protein clean coordinate file') or a single domain from SCOP or
CATH ('domain clean coordinate file'), in CCF format (EMBL-like).
The files, generated by using PDBPARSE (PDB files) or DOMAINER
(domains), contain 'cleaned-up' data that is self-consistent and
error-corrected. Records for residue solvent accessibility and
secondary structure are added to the file by using PDBPLUS."
default: "./"
extension: "ccf"
knowntype: "domain clean coordinates"
relations: "EDAM_identifier:1049 Directory name"
relations: "EDAM_data:1468 Protein domain"
]
endsection: input
section: required [
information: "Required section"
type: "page"
]
endsection: required
section: advanced [
information: "Advanced section"
type: "page"
]
endsection: advanced
section: output [
information: "Output section"
type: "page"
]
outfile: dcfoutfile [
parameter: "Y"
help: "This option specifies the name of the DCF file (domain
classification file) with secondary structure records (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."
knowntype: "domain classification"
information: "Domain classification output file"
relations: "EDAM_data:0900 Protein domain classification"
]
outfile: logfile [
parameter: "Y"
help: "This option specifies the name of the DOMAINSSE log file."
default: "domainsse.log"
knowntype: "domainatrix log"
information: "Domainatrix log output file"
relations: "EDAM_data:1678 Tool log"
]
endsection: output
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