dssp.yaml

!mobyle/program
name: dssp
title: DSSP
description: Definition of secondary structure of proteins given a set of 3D coordinates
authors: W.Kabsch, C. Sander
inputs: !mobyle/inputparagraph
    children:
    - !mobyle/inputprogramparameter {prompt: PDB File, format: '( " -- " , " " + str(value)
            )[ value is not None ]', simple: true, argpos: 10, name: pdbfile, command: false}
    - !mobyle/inputprogramparameter
        prompt: or you can instead enter a PDB id.
        format: ( "" , "cat /path/to/Pdb/databank/dir/pdb" + str( value ).lower()
            + ".ent | " )[ value is not None ]
        simple: true
        argpos: -1
        name: pdbid
        command: false
        type: !mobyle/stringtype {}
    - !mobyle/inputprogramparagraph
        prompt: Output parameters
        name: output
        children:
        - !mobyle/inputprogramparameter
            prompt: Disables the calculation of accessible surface (-na)
            format: ( "" , " -na " )[ value ]
            argpos: 1
            name: surface
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Classic (pre-July 1995) format (-c)
            format: ( "" , " -c " )[ value ]
            argpos: 1
            name: classic
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Adds information about disulfide bonds to output file (-ssa)
            format: ( "" , " -ssa " )[ value ]
            argpos: 1
            name: disulfide
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Renames residues with incomplete sidechains to 'X' (-x)
            format: ( "" , " -x " )[ value ]
            argpos: 1
            name: sidechains2X
            command: false
            type: !mobyle/booleantype {default: false}
        - !mobyle/inputprogramparameter
            prompt: Keeps an additional AltLoc indicator at the line ends (-alt2)
            format: ( "" , " -alt2 " )[ value ]
            argpos: 1
            name: altLoc
            command: false
            type: !mobyle/booleantype {default: false}
outputs: !mobyle/outputparagraph
    children:
    - !mobyle/outputprogramparameter
        prompt: Standard output
        filenames: '"dssp.out"'
        name: outfile
        output_type: stdout
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
    - !mobyle/outputprogramparameter
        prompt: Standard error
        filenames: '"dssp.err"'
        name: stderr
        type: !mobyle/formattedtype
            data_terms: ['EDAM_data:2048']
references:
- {doi: null, label: 'Kabsch,W. and Sander,C. (1983) Biopolymers 22, 2577-2637.',
    url: null}
homepage_links: ['http://swift.cmbi.ru.nl/gv/dssp/']
command: dssp
env: {}
source_links: ['ftp://ftp.cmbi.ru.nl/pub/molbio/software/']