/usr/share/EMBOSS/acd/cathparse.acd is in embassy-domainatrix 0.1.0+20100721-3build1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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documentation: "Generates DCF file from raw CATH files."
groups: "Utils:Database creation"
gui: "yes"
batch: "yes"
cpu: "low"
embassy: "domainatrix"
]
section: input [
information: "Input section"
type: "page"
]
infile: listfile [
parameter: "Y"
information: "Raw cath list file"
help: "This option specifies the name of raw CATH classification
file (caths.list.vX.X) (input). The raw CATH parsable files
(classification and description files) available from
ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4)."
default: "caths.list.v2.4"
knowntype: "Raw cath list"
relations: "EDAM: Free text file"
]
infile: domfile [
parameter: "Y"
information: "Raw cath domlist file"
help: "This option specifies the name of raw CATH classification
file (domlist.vX.X) (input). The raw CATH parsable files
(classification and description files) available from
ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4)."
default: "domlist.v2.4"
knowntype: "Raw cath domlist"
relations: "EDAM: Free text file"
]
infile: namesfile [
parameter: "Y"
information: "Raw cath names file"
help: "This option specifies the name of raw CATH classification
file (CAT.names.all.vX.X) (input). The raw CATH parsable files
(classification and description files) available from
ftp.biochem.ucl.ac.uk (/pub/cathdata/v2.4)."
default: "CAT.names.all.v2.4"
knowntype: "Raw cath names"
relations: "EDAM: Free text file"
]
endsection: input
section: output [
information: "Output section"
type: "page"
]
outfile: outfile [
parameter: "Y"
information: "Domain classification output file"
help: "This option specifies the name of CATH 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: "Ecath.dat"
knowntype: "domain classification"
relations: "EDAM: EMBASSY domain classification record"
]
outfile: logfile [
standard: "Y"
information: "Domainatrix log output file"
help: "This option specifies the name of the CATHPARSE log file."
default: "cathparse.log"
knowntype: "domainatrix log"
relations: "EDAM: Domainatrix log file"
]
endsection: output
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