/usr/share/EMBOSS/acd/scopparse.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 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 | application: scopparse [
documentation: "Generate DCF file from raw SCOP files."
groups: "Utils:Database creation, Protein:Domains"
gui: "yes"
batch: "yes"
cpu: "low"
embassy: "domainatrix"
relations: "EDAM_topic:0091 Data handling"
relations: "EDAM_topic:0736 Protein domains and folds"
relations: "EDAM_operation:0335 File reformatting"
relations: "EDAM_operation:2234 Structure file processing"
]
section: input [
information: "Input section"
type: "page"
]
infile: classfile [
information: "Raw scop classification file"
help: "This option specifies the name of raw SCOP classification
file dir.cla.scop.txt_X.XX (input). This is the raw SCOP
classification file available at
http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.cla.scop.txt_1.57."
knowntype: "Raw scop classification"
parameter: "Y"
relations: "EDAM_data:0900 Protein domain classification"
]
infile: desinfile [
information: "Raw scop description file"
help: "This option specifies the name of raw SCOP description file
dir.des.scop.txt_X.XX (input). This is the raw SCOP description
file available at
http://scop.mrc-lmb.cam.ac.uk/scop/parse/dir.des.scop.txt_1.57."
knowntype: "raw scop description"
parameter: "Y"
relations: "EDAM_data:0900 Protein domain classification"
]
endsection: input
section: required [
information: "Required section"
type: "page"
]
boolean: nosegments [
standard: "Y"
information: "Omit domains comprising of more than one
segment."
help: "This option specifies whether to omit domains comprising of
more than one segment. This is necessary if a continuous residue
sequence is required."
default: "N"
relations: "EDAM_data:2527 Parameter"
]
boolean: nomultichain [
standard: "Y"
information: "Omit domains comprising segments from more
than one chain."
help: "This option specifies whether to omit domains comprising
segments from more than one chain. This is necessary if a
continuous residue sequence is required."
default: "N"
relations: "EDAM_data:2527 Parameter"
]
endsection: required
section: additional [
information: "Additional section"
type: "page"
]
boolean: nominor [
additional: "Y"
information: "Omit domains from minor classes. This is
defined as anything not in class 'All alpha proteins', 'All
beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha
and beta proteins (a+b)'."
help: "This option specifies whether to omit domains from minor
classes (defined as anything not in class 'All alpha proteins',
'All beta proteins', 'Alpha and beta proteins (a/b)' or 'Alpha and
beta proteins (a+b)'). This is necessary or appropriate for many
analyses."
default: "N"
relations: "EDAM_data:2527 Parameter"
]
endsection: additional
section: output [
information: "Output section"
type: "page"
]
outfile: dcffile [
information: "Domain classification output file"
help: "This option specifies the name of SCOP DCF file (domain
classification file) (output). A 'domain classification file'
contains classification and other data for domains from the SCOP
or CATH databases. The file is generated by using DOMAINER and is
in DCF format (EMBL-like). Domain sequence information can be
added to the file by using DOMAINSEQS."
default: "test.scop"
knowntype: "domain classification"
parameter: "Y"
relations: "EDAM_data:0900 Protein domain classification"
]
endsection: output
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