class GuessIonTests(unittest.TestCase):
geneSet = genetic.generate_geneset()
df = salty.load_data("cationInfo.csv")
parent_candidates = df['smiles'].unique()
df = salty.load_data("anionInfo.csv")
df = df['smiles'].unique()
random.seed(1234)
ohPickMe = random.sample(range(df.shape[0]), 1)
anion = Chem.MolFromSmiles(df[ohPickMe[0]])
def test_1_density(self):
target = 1250
self.guess_password(target)
def test_benchmark(self):
genetic.Benchmark.run(self.test_1_density)
def guess_password(self, target):
startTime = datetime.datetime.now()
def fnGetFitness(genes, target):
return get_fitness(self.anion, genes, target)
def fnDisplay(candidate, mutation, target):
display(candidate, mutation, startTime)
def fnShowIon(genes, target, mutation_attempts, sim_score,
molecular_relative):
show_ion(genes, target, mutation_attempts, sim_score,
molecular_relative, self.anion)
optimalFitness = 0.9
best = genetic.get_best(fnGetFitness,
optimalFitness,
self.geneSet,
fnDisplay,
fnShowIon,
target,
self.parent_candidates,
seed=123)
cation = best.Mol
anion = self.anion
# Uncomment PDB lines to wrote PDB file
# cation = Chem.AddHs(best.Mol)
# Chem.EmbedMolecule(cation, Chem.ETKDG())
# Chem.UFFOptimizeMolecule(cation)
# Chem.rdmolfiles.MolToPDBFile(cation, "cation_test.pdb")
# anion = Chem.AddHs(self.anion)
# Chem.EmbedMolecule(anion, Chem.ETKDG())
# Chem.UFFOptimizeMolecule(anion)
# Chem.rdmolfiles.MolToPDBFile(anion, "anion_test.pdb")
return cation, anion
class iupac_smiles_tests(unittest.TestCase):
data_files = ["cationInfo.csv", "anionInfo.csv"]
df = salty.load_data(data_files[0])
smiles = df.smiles
for i in range(len(smiles)):
ion = smiles[i]
salty.check_name(ion)
def test_1_check_data(self):
for i in range(len(self.data_files)):
df = salty.load_data(self.data_files[i])
self.check_data(df)
def test_2_check_wrong_ion(selfs):
ion = 'stupid_nonsense_string'
salty.check_name(ion)
def test_benchmark(self):
salty.Benchmark.run(self.test_1_check_data)
salty.Benchmark.run(self.test_2_check_wrong_ion)
def check_data(self, df):
startTime = datetime.datetime.now()
def fnDisplay(message):
display(message, startTime)
smiles = df.smiles
for i in range(len(smiles)):
ion = smiles[i]
try:
Chem.SanitizeMol(Chem.MolFromSmiles(ion))
except ValueError:
name = salty.check_name(ion)
message = "RDKit cannot interpret %s ion SMILES in datafile" \
% name
fnDisplay(message)
if "-" not in ion and "+" not in ion:
name = salty.check_name(ion)
message = "%s ion does not have a charge" % name
fnDisplay(message)
if "." in ion:
name = salty.check_name(ion)
message = "%s ion contains more than one molecular entity" \
% name
fnDisplay(message)
def test_1_check_data(self):
for i in range(len(self.data_files)):
df = salty.load_data(self.data_files[i])
self.check_data(df)
class GuessIonTests(unittest.TestCase):
geneSet = genetic.generate_geneset()
df = salty.load_data("cationInfo.csv")
df = df.loc[df["name"].str.contains("imid", case=False)]