def main(args=None):
args = parser.parse_args(args)
outfile = sys.stdout
cmdsupport.mutual_exclusion(
parser, args, "sim",
("sim", "sub", "sub_res", "sub_tau", "full", "substruct", "rdmaccs"))
if args.sim:
opener = types.get_fingerprint_family("Indigo-Similarity")()
elif args.sub:
opener = types.get_fingerprint_family("Indigo-Substructure")()
elif args.sub_res:
opener = types.get_fingerprint_family("Indigo-ResonanceSubstructure")()
elif args.sub_tau:
opener = types.get_fingerprint_family("Indigo-TautomerSubstructure")()
elif args.full:
opener = types.get_fingerprint_family("Indigo-Full")()
elif args.substruct:
opener = types.get_fingerprint_family("ChemFP-Substruct-Indigo")()
elif args.rdmaccs:
opener = types.get_fingerprint_family("RDMACCS-Indigo")()
else:
parser.error("should not get here")
# Ready the input reader/iterator
try:
reader = opener.read_structure_fingerprints(args.filename, args.format)
except IOError, err:
sys.stderr.write("Cannot read structures: %s" % (err, ))
raise SystemExit(1)
def main(args=None):
args = parser.parse_args(args)
outfile = sys.stdout
cmdsupport.mutual_exclusion(parser, args, "sim",
("sim", "sub", "sub_res", "sub_tau", "full",
"substruct", "rdmaccs"
))
if args.sim:
opener = types.get_fingerprint_family("Indigo-Similarity")()
elif args.sub:
opener = types.get_fingerprint_family("Indigo-Substructure")()
elif args.sub_res:
opener = types.get_fingerprint_family("Indigo-ResonanceSubstructure")()
elif args.sub_tau:
opener = types.get_fingerprint_family("Indigo-TautomerSubstructure")()
elif args.full:
opener = types.get_fingerprint_family("Indigo-Full")()
elif args.substruct:
opener = types.get_fingerprint_family("ChemFP-Substruct-Indigo")()
elif args.rdmaccs:
opener = types.get_fingerprint_family("RDMACCS-Indigo")()
else:
parser.error("should not get here")
# Ready the input reader/iterator
try:
reader = opener.read_structure_fingerprints(args.filename, args.format)
except IOError, err:
sys.stderr.write("Cannot read structures: %s" % (err,))
raise SystemExit(1)
def main(args=None):
args = parser.parse_args(args)
outfile = sys.stdout
cmdsupport.mutual_exclusion(
parser, args, "FP2",
("FP2", "FP3", "FP4", "MACCS", "substruct", "rdmaccs"))
if args.FP2:
opener = types.get_fingerprint_family("OpenBabel-FP2")()
elif args.FP3:
opener = types.get_fingerprint_family("OpenBabel-FP3")()
elif args.FP4:
opener = types.get_fingerprint_family("OpenBabel-FP4")()
elif args.MACCS:
if not ob.HAS_MACCS:
parser.error(
"--MACCS is not supported in your OpenBabel installation (%s)"
% (ob.GetReleaseVersion(), ))
opener = types.get_fingerprint_family("OpenBabel-MACCS")()
elif args.substruct:
opener = types.get_fingerprint_family("ChemFP-Substruct-OpenBabel")()
elif args.rdmaccs:
opener = types.get_fingerprint_family("RDMACCS-OpenBabel")()
else:
parser.error("should not get here")
if not ob.is_valid_format(args.format):
parser.error("Unsupported format specifier: %r" % (args.format, ))
if not cmdsupport.is_valid_tag(args.id_tag):
parser.error("Invalid id tag: %r" % (args.id_tag, ))
missing = cmdsupport.check_filenames(args.filenames)
if missing:
parser.error("Structure file %r does not exist" % (missing, ))
# Ready the input reader/iterator
metadata, reader = cmdsupport.read_multifile_structure_fingerprints(
opener,
args.filenames,
format=args.format,
id_tag=args.id_tag,
aromaticity=None,
errors=args.errors)
try:
io.write_fps1_output(reader, args.output, metadata)
except ParseError, err:
sys.stderr.write("ERROR: %s. Exiting." % (err, ))
raise SystemExit(1)
def main(args=None):
args = parser.parse_args(args)
outfile = sys.stdout
cmdsupport.mutual_exclusion(parser, args, "FP2",
("FP2", "FP3", "FP4", "MACCS", "substruct", "rdmaccs"))
if args.FP2:
opener = types.get_fingerprint_family("OpenBabel-FP2")()
elif args.FP3:
opener = types.get_fingerprint_family("OpenBabel-FP3")()
elif args.FP4:
opener = types.get_fingerprint_family("OpenBabel-FP4")()
elif args.MACCS:
if not ob.HAS_MACCS:
parser.error(
"--MACCS is not supported in your OpenBabel installation (%s)" % (
ob.GetReleaseVersion(),))
opener = types.get_fingerprint_family("OpenBabel-MACCS")()
elif args.substruct:
opener = types.get_fingerprint_family("ChemFP-Substruct-OpenBabel")()
elif args.rdmaccs:
opener = types.get_fingerprint_family("RDMACCS-OpenBabel")()
else:
parser.error("should not get here")
if not ob.is_valid_format(args.format):
parser.error("Unsupported format specifier: %r" % (args.format,))
if not cmdsupport.is_valid_tag(args.id_tag):
parser.error("Invalid id tag: %r" % (args.id_tag,))
missing = cmdsupport.check_filenames(args.filenames)
if missing:
parser.error("Structure file %r does not exist" % (missing,))
# Ready the input reader/iterator
metadata, reader = cmdsupport.read_multifile_structure_fingerprints(
opener, args.filenames, format = args.format,
id_tag = args.id_tag, aromaticity = None, errors = args.errors)
try:
io.write_fps1_output(reader, args.output, metadata)
except ParseError, err:
sys.stderr.write("ERROR: %s. Exiting." % (err,))
raise SystemExit(1)
def test_make_fingerprinter_from_type_with_empty_string(self):
family = types.get_fingerprint_family("OpenEye-Path")
with self.assertRaisesRegexp(ValueError,
r"Empty fingerprint type \(''\)"):
family.make_fingerprinter_from_type("")
def test_make_fingerprinter_from_type_with_empty_string(self):
family = types.get_fingerprint_family("OpenEye-Path")
with self.assertRaisesRegexp(ValueError, r"Empty fingerprint type \(''\)"):
family.make_fingerprinter_from_type("")
