1application: psiphi [
2  documentation: "Calculates phi and psi torsion angles from
3                  protein coordinates"
4  groups: "protein:3D structure"
5    relations: "EDAM_topic:2814 Protein structure analysis"
6    relations: "EDAM_operation:0249 Torsion angle calculation"
7]
8
9section: input [
10  information: "Input section"
11  type: "page"
12]
13
14  infile: infile [
15    parameter: "Y"
16    information: "Clean protein structure coordinates file"
17    knowntype: "protein clean coordinates"
18    relations: "EDAM_data:1460 Protein structure"
19  ]
20
21endsection: input
22
23section: required [
24  information: "Required section"
25  type: "page"
26]
27
28  integer: chainnumber [
29    standard: "Y"
30    information: "Number of the chain for which torsion angles
31                  should be calculated"
32    default: "1"
33    minimum: "1"
34    relations: "EDAM_identifier:1008 Polypeptide chain ID"
35  ]
36
37  integer: startresiduenumber [
38    standard: "Y"
39    information: "First residue in chain for which torsion
40                  angles should be calculated"
41    default: "1"
42    minimum: "1"
43    relations: "EDAM_data:1016 Sequence position"
44  ]
45
46  integer: finishresiduenumber [
47    standard: "Y"
48    information: "Last residue in chain for which torsion
49                  angles should be calculated (1 = last residue)"
50    default: "1"
51    relations: "EDAM_data:1016 Sequence position"
52  ]
53
54endsection: required
55
56section: advanced [
57  information: "Advanced section"
58  type: "page"
59]
60
61endsection: advanced
62
63section: output [
64  information: "Output section"
65  type: "page"
66]
67
68  report: outfile [
69    parameter: "Y"
70    rformat: "table"
71    multiple: "N"
72    precision: "1"
73    taglist: "float:phi float:psi"
74    relations: "EDAM_data:1544 Ramachandran plot"
75  ]
76
77endsection: output
78