This file is indexed.

/usr/share/EMBOSS/acd/domainsse.acd is in embassy-domainatrix 0.1.650-1.

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