one of:
File Type Valid FORMATs
--------- -------------
SMILES smi, can, ism, smiles
SDF sdf, mol, sd, mdl
RDF rdf
CML cml
Indigo will automatically handle gzip'ed input data if the filename
ends with".gz". You may optionally include that suffix in the format name.
"""
parser = argparse.ArgumentParser(
description="Generate FPS fingerprints from a structure file using Indigo",
)
group = parser.add_mutually_exclusive_group()
group.add_argument("--sim",
action="store_true",
help="similarity fingerprints")
group.add_argument("--sub",
action="store_true",
help="substructure fingerprints")
group.add_argument("--sub-res",
action="store_true",
help="resonance substructure fingerprints")
group.add_argument("--sub-tau",
action="store_true",
help="tautomer substructure fingerprints")
group.add_argument("--full", action="store_true", help="full fingerprints")
(t2 - t1, t3 - t2, t3 - t1))
####
def int_or_all(s):
if s == "all":
return s
return int(s)
# the "2fps" options need a way to say "get the options from --reference"
# ob2fps --reference targets.fps | simsearch -k 5 --threshold 0.5 targets.fps
parser = argparse.ArgumentParser(
description="Search an FPS file for similar fingerprints")
parser.add_argument(
"-k",
"--k-nearest",
help="select the k nearest neighbors (use 'all' for all neighbors)",
default=None,
type=int_or_all)
parser.add_argument("-t",
"--threshold",
help="minimum similarity score threshold",
default=None,
type=float)
parser.add_argument("-q",
"--queries",
help="filename containing the query fingerprints")
parser.add_argument(