Overall syntax

http://api.x3dna.org/index.html
http://api.x3dna.org/dssr/help
http://api.x3dna.org/snap/help
http://api.x3dna.org/fiber/help

Help message on x3dna-dssr (DSSR)

Usage with 'http' (HTTPie):
    http -f http://api.x3dna.org/dssr [options] url=|model@
    http http://api.x3dna.org/dssr/help   -- display this help message

Options:
    json=true-or-FALSE(default)    [e.g., json=true # JSON output]
    pair=true-or-FALSE(default)    [e.g., pair=1    # base-pair only]
    hbond=true-or-FALSE(default)   [e.g., hbond=t   # H-bonding info]
    more=true-or-FALSE(default)    [e.g., more=y    # further details]

Required parameter:
    url=URL-to-coordinate-file [e.g., url=https://files.rcsb.org/download/1ehz.pdb.gz]
    model@coordinate-file      [e.g., model@1ehz.cif]
    # Only one must be specified. 'url' precedes 'model' when both are specified.
    # The coordinate file must be in PDB or PDBx/mmCIF format, optionally gzipped.

Examples:
    http -f http://api.x3dna.org/dssr url=https://files.rcsb.org/download/1ehz.pdb.gz
    http -f http://api.x3dna.org/dssr model@1ehz.cif pair=1
    # with 'curl'
    curl http://api.x3dna.org/dssr -F 'url=https://files.rcsb.org/download/1ehz.pdb.gz'
    curl http://api.x3dna.org/dssr -F 'model=@1msy.pdb' -F 'pair=1'

Note:
    The web API has an upper limit on coordinate file size (gzipped): < 6 MB

Help message on x3dna-snap (SNAP)

Usage with 'http' (HTTPie):
    http -f http://api.x3dna.org/snap [options] url=|model@
    http http://api.x3dna.org/snap/help   -- display this help message

Options:
    json=true-or-FALSE(default)    [e.g., json=true # JSON output]
    hbond=true-or-FALSE(default)   [e.g., hbond=t   # H-bonding info]

Required parameter:
    url=URL-to-coordinate-file [e.g., url=https://files.rcsb.org/download/1oct.pdb.gz]
    model@coordinate-file      [e.g., model@1oct.cif]
    # Only one must be specified. 'url' precedes 'model' when both are specified.
    # The coordinate file must be in PDB or PDBx/mmCIF format, optionally gzipped.

Examples:
    http -f http://api.x3dna.org/snap url=https://files.rcsb.org/download/1oct.pdb.gz
    http -f http://api.x3dna.org/snap model@1oct.cif json=1
    # with 'curl'
    curl http://api.x3dna.org/snap -F 'url=https://files.rcsb.org/download/1oct.pdb.gz'
    curl http://api.x3dna.org/snap -F 'model=@1oct.cif' -F 'json=1'

Note:
    The web API has an upper limit on coordinate file size (gzipped): < 6 MB

Help message on x3dna-fiber (56 fiber models)

Usage with 'http' (HTTPie):
    http http://api.x3dna.org/fiber/help    # display this help message
    http http://api.x3dna.org/fiber/list    # show a list of available fiber models (56 in total)
    http http://api.x3dna.org/fiber/str_id  # build model 'str_id' in the range of [1, 56]
    http http://api.x3dna.org/fiber/name    # generate a model with common names as shown below:
              A-DNA, B-dna, C_DNA, D-DNA, ZDNA, RNA, RNAduplex, PaulingTriplex, G4
              Case does not matter, and the separator can be '-' or '_' or omitted.
              So a-dna, A-dNA, a_DNA, or ADNA is valid for building an A-DNA model.

Options (via query strings, or form fields):
    seq=base-sequence # A, C, G, T, U for generic model
    repeat=number     # number of repeats of the sequence
    cif=1             # output file in mmCIF format

Examples with 'http' (HTTPie):
    http http://api.x3dna.org/fiber/1       # model no. 1 (i.e., calf thymus A-DNA model)
    http -f http://api.x3dna.org/fiber/1 seq=A3TTT repeat=2  # specific sequence, repeated twice
    http http://api.x3dna.org/fiber/rna     # single-stranded RNA model
    http http://api.x3dna.org/fiber/rna-ds  # double-stranded RNA model
    http http://api.x3dna.org/fiber/pauling # the triplex model of Pauling & Corey
    http http://api.x3dna.org/fiber/g4      # G-quadruplex model
    # with 'curl'
    curl http://api.x3dna.org/fiber/1
    curl http://api.x3dna.org/fiber/1 -d 'seq=A3TTT' -d 'repeat=2'
    curl http://api.x3dna.org/fiber/rna
    curl http://api.x3dna.org/fiber/rna-ds
    curl http://api.x3dna.org/fiber/pauling
    curl http://api.x3dna.org/fiber/g4

Note:
    The web API has two upper limits: repeats < 1,000, and nucleotides < 10,000.