def test_substituent(self):
try:
import rdkit
sub = Substituent.from_string(
"acetyl", form="iupac", strict_use_rdkit=True
)
self.is_COCH3(sub)
with self.assertLogs(Substituent.LOG, level="WARNING"):
sub = Substituent.from_string(
"nitro", form="iupac", strict_use_rdkit=True
)
self.is_NO2(sub)
sub = Substituent.from_string(
"O=[N.]=O", form="smiles", strict_use_rdkit=True
)
self.is_NO2(sub)
sub = Substituent.from_string(
"O=[N]=O", form="smiles", strict_use_rdkit=True
)
self.is_NO2(sub)
except (ImportError, ModuleNotFoundError):
# I still want to test CACTVS things because sometimes they change stuff
# that breaks our stuff
if any(
user == os.getenv("USER", os.getenv("USERNAME", False))
for user in ["ajs99778", "normn"]
):
sub = Substituent.from_string("acetyl", form="iupac")
print(sub.write(outfile=False))
self.is_COCH3(sub, thresh=0.3)
sub = Substituent.from_string("nitro", form="iupac")
print(sub.write(outfile=False))
self.is_NO2(sub)
sub = Substituent.from_string("O=[N.]=O", form="smiles")
print(sub.write(outfile=False))
self.is_NO2(sub)
sub = Substituent.from_string("O=[N]=O", form="smiles")
print(sub.write(outfile=False))
self.is_NO2(sub)
else:
self.skipTest("RDKit not installed, CACTVS is not tested")
geom = Geometry(f)
target_list = []
for sub in args.substitutions:
ndx_targets = sub.split("=")[0]
target_list.append(geom.find(ndx_targets))
for i, sub in enumerate(args.substitutions):
ndx_target = target_list[i]
sub_name = "=".join(sub.split("=")[1:])
for target in ndx_target:
if sub_name.lower().startswith("iupac:"):
sub_name = ":".join(sub_name.split(":")[1:])
sub = Substituent.from_string(sub_name, form="iupac")
elif sub_name.lower().startswith("smiles:"):
sub_name = ":".join(sub_name.split(":")[1:])
sub = Substituent.from_string(sub_name, form="smiles")
else:
sub = Substituent(sub_name)
# replace old substituent with new substituent
geom.substitute(sub, target, minimize=args.mini)
geom.refresh_connected()
if args.outfile:
outfile = args.outfile
if "INFILE" in outfile:
outfile = outfile.replace("$INFILE", get_filename(infile))
geom.write(
"when no input file is given, stdin is read and a format must be specified"
)
geom = Geometry(f)
target_list = []
for sub in args.substitutions:
ndx_targets = sub.split('=')[0]
target_list.append(geom.find(ndx_targets))
for i, sub in enumerate(args.substitutions):
ndx_target = target_list[i]
sub_name = '='.join(sub.split('=')[1:])
for target in ndx_target:
if args.form[0] == 'from_library':
sub = Substituent(sub_name)
elif args.form[0] in ['iupac', 'smiles']:
sub = Substituent.from_string(sub_name, args.form[0])
#replace old substituent with new substituent
geom.substitute(sub, target)
geom.refresh_connected()
if args.outfile:
FileWriter.write_xyz(geom, append=False, outfile=args.outfile[0])
else:
s = FileWriter.write_xyz(geom, append=False, outfile=False)
print(s)
