I’ve created a web API to DSSR and SNAP, and fiber models. The overall help message is available via http://api.x3dna.org. Individually, each program is accessed as below.
Help message on x3dna-dssr (DSSR): http://api.x3dna.org/dssr/help
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): http://api.x3dna.org/snap/help
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 56 fiber models: http://api.x3dna.org/fiber/help
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.
