def test_appendSmallMol(self):
mol2file = os.path.join(self.dataDir, 'benzamidine.mol2')
sdffile = os.path.join(self.dataDir, 'fda_drugs_light.sdf')
lib = SmallMolLib(sdffile)
sm = SmallMol(mol2file)
lib.appendSmallMol(sm)
n_mol2_append = lib.numMols
self.assertEqual(
n_mol2_append,
SDF_N_MOLS + 1,
msg="The number of molecules in the SmallMolLib is not as expected."
"The mol2 were not correctly append. ")
def getChemblSimilarLigandsBySmile(smi, threshold=85, returnSmiles=False):
"""
Returns a SmallMolLib object of the ligands having a similarity with a smile of at least the specified
threshold.. This molecules are retrieve from Chembl. It is possible to return also the list smiles.
Parameters
----------
smi: str
The smile
threshold: int
The threshold value to apply for the similarity search
returnSmiles: bool
If True, the list smiles is returned
Returns
-------
sm: moleculekit.smallmol.smallmol.SmallMol
The SmallMol object
smiles: str
The list of smiles
Example
-------
>>> _, smile = getChemblLigandByDrugName('ibuprofen', returnSmile=True) # doctest: +SKIP
>>> lib = getChemblSimilarLigandsBySmile(smile) # doctest: +SKIP
>>> lib.numMols # doctest: +SKIP
4
>>> lib, smiles = getChemblSimilarLigandsBySmile(smile, returnSmiles=True) # doctest: +SKIP
>>> len(smiles) # doctest: +SKIP
4
"""
from moleculekit.smallmol.smallmol import SmallMol
from moleculekit.smallmol.smallmollib import SmallMolLib
try:
from chembl_webresource_client.new_client import new_client
except ImportError:
raise ImportError(
"You need to install the chembl_webresource package to use this function. Try using `conda install "
"-c chembl chembl_webresource_client`.")
smi_list = []
similarity = new_client.similarity
results = similarity.filter(smiles=smi, similarity=threshold).only(
["molecule_structures"])
results = results.all()
for r in range(len(results)):
tmp_smi = results[r]["molecule_structures"]["canonical_smiles"]
fragments = tmp_smi.split(".")
fragments_len = [len(fr) for fr in fragments]
fragment = fragments[fragments_len.index(max(fragments_len))]
if fragment not in smi_list:
smi_list.append(fragment)
lib = SmallMolLib()
for smi in smi_list:
lib.appendSmallMol(SmallMol(smi))
if returnSmiles:
return lib, smi_list
return lib