def testRemoveEntry(self):
params = FilterCatalog.FilterCatalogParams(
FilterCatalogParams.FilterCatalogs.ZINC)
catalog = FilterCatalog.FilterCatalog(params)
entry = catalog.GetEntryWithIdx(10)
desc = entry.GetDescription()
count = 0
descs = set([
catalog.GetEntryWithIdx(i).GetDescription()
for i in range(catalog.GetNumEntries())
])
for i in range(catalog.GetNumEntries()):
if catalog.GetEntryWithIdx(i).GetDescription() == desc:
count += 1
print("Count", count)
sz = catalog.GetNumEntries()
print("*" * 44)
self.assertTrue(catalog.RemoveEntry(entry))
del entry
self.assertTrue(catalog.GetNumEntries() == sz - 1)
descs2 = set([
catalog.GetEntryWithIdx(i).GetDescription()
for i in range(catalog.GetNumEntries())
])
print(descs - descs2)
newcount = 0
for i in range(catalog.GetNumEntries()):
if catalog.GetEntryWithIdx(i).GetDescription() == desc:
newcount += 1
self.assertEquals(count, newcount + 1)
def testThreadedRunner(self):
path = os.path.join(os.environ['RDBASE'], 'Code', 'GraphMol',
'test_data', 'pains.smi')
with open(path) as f:
smiles = [f.strip() for f in f.readlines()][1:]
self.assertEquals(len(smiles), 3)
params = FilterCatalog.FilterCatalogParams()
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_A)
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_B)
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_C)
fc = FilterCatalog.FilterCatalog(params)
results = FilterCatalog.RunFilterCatalog(fc, smiles)
self.assertEquals(len(results), 3)
descriptions = [
"hzone_phenol_A(479)", "cyano_imine_B(17)", "keto_keto_gamma(5)"
]
for i, res in enumerate(results):
self.assertTrue(len(res) > 0)
self.assertEquals(res[0].GetDescription(), descriptions[i])
# Test with some bad input
smiles = ['mydoghasfleas']
results = FilterCatalog.RunFilterCatalog(fc, smiles, numThreads=3)
self.assertEquals(len(results[0]), 1)
self.assertEquals(results[0][0].GetDescription(),
"no valid RDKit molecule")
def testZinc(self):
params = FilterCatalog.FilterCatalogParams(FilterCatalogParams.FilterCatalogs.ZINC)
catalog = FilterCatalog.FilterCatalog(params)
self.assertTrue(catalog.GetNumEntries())
m = Chem.MolFromSmiles("C" * 41)
entry = catalog.GetFirstMatch(m)
self.assertTrue(entry.GetDescription(), "Non-Hydrogen_atoms")
m = Chem.MolFromSmiles("CN" * 20)
entry = catalog.GetFirstMatch(m)
self.assertEquals(catalog.GetFirstMatch(m), None)
def pains(self):
"""
Baell and Holloway (2010) New Substructure Filters for Removal of Pan
Assay Interference Compounds (PAINS) from Screening Libraries and for
Their Exclusion in Bioassays
This filter finds promiscuous compounds that are likely to show activity
regardless of the target.
Returns:
Boolean of whether the molecule triggers the PAINS filter.
"""
params = FilterCatalog.FilterCatalogParams()
params.AddCatalog(
FilterCatalog.FilterCatalogParams.FilterCatalogs.PAINS)
catalog = FilterCatalog.FilterCatalog(params)
return catalog.HasMatch(self.mol)
def brenk(self):
"""
Brenk (2008) Lessons Learnt from Assembling Screening Libraries for
Drug Discovery for Neglected Diseases
Brenk's Structural Alert filter finds fragments "putatively toxic,
chemically reactive, metabolically unstable or to bear properties
responsible for poor pharmacokinetics."
Returns:
Boolean of whether the molecule triggers the Brenk filter.
"""
params = FilterCatalog.FilterCatalogParams()
params.AddCatalog(
FilterCatalog.FilterCatalogParams.FilterCatalogs.BRENK)
catalog = FilterCatalog.FilterCatalog(params)
return catalog.HasMatch(self.mol)
def test2FilterCatalogTest(self):
tests = ((FilterCatalogParams.FilterCatalogs.PAINS_A,
16), (FilterCatalogParams.FilterCatalogs.PAINS_B,
55), (FilterCatalogParams.FilterCatalogs.PAINS_C, 409),
(FilterCatalogParams.FilterCatalogs.PAINS, 409 + 16 + 55))
for catalog_idx, num in tests:
params = FilterCatalog.FilterCatalogParams()
print("*" * 44)
print("Testing:", catalog_idx, int(catalog_idx))
self.assertTrue(params.AddCatalog(catalog_idx))
catalog1 = FilterCatalog.FilterCatalog(params)
if FilterCatalog.FilterCatalogCanSerialize():
pickle = catalog1.Serialize()
catalog2 = FilterCatalog.FilterCatalog(pickle)
catalogs = [catalog1, catalog2]
else:
catalogs = [catalog1]
catalogs.append(FilterCatalog.FilterCatalog(catalog_idx))
for index, catalog in enumerate(catalogs):
self.assertEqual(catalog.GetNumEntries(), num)
if catalog_idx in [
FilterCatalogParams.FilterCatalogs.PAINS_A,
FilterCatalogParams.FilterCatalogs.PAINS
]:
# http://chemistrycompass.com/chemsearch/58909/
mol = Chem.MolFromSmiles(
"O=C(Cn1cnc2c1c(=O)n(C)c(=O)n2C)N/N=C/c1c(O)ccc2c1cccc2"
)
entry = catalog.GetFirstMatch(mol)
for key in entry.GetPropList():
if key == "Reference":
self.assertEquals(
entry.GetProp(key),
"Baell JB, Holloway GA. New Substructure Filters for "
"Removal of Pan Assay Interference Compounds (PAINS) "
"from Screening Libraries and for Their Exclusion in "
"Bioassays. J Med Chem 53 (2010) 2719D40. "
"doi:10.1021/jm901137j.")
elif key == "Scope":
self.assertEquals(entry.GetProp(key),
"PAINS filters (family A)")
self.assertEqual(entry.GetDescription(),
"hzone_phenol_A(479)")
result = catalog.GetMatches(mol)
self.assertEquals(len(result), 1)
for entry in result:
for filtermatch in entry.GetFilterMatches(mol):
self.assertEquals(str(filtermatch.filterMatch),
"hzone_phenol_A(479)")
atomPairs = [
tuple(x) for x in filtermatch.atomPairs
]
self.assertEquals(atomPairs, [(0, 23), (1, 22),
(2, 20), (3, 19),
(4, 25), (5, 24),
(6, 18), (7, 17),
(8, 16), (9, 21)])
elif catalog_idx == FilterCatalogParams.FilterCatalogs.PAINS_B:
mol = Chem.MolFromSmiles(
"FC(F)(F)Oc1ccc(NN=C(C#N)C#N)cc1") # CHEMBL457504
entry = catalog.GetFirstMatch(mol)
self.assertTrue(entry)
self.assertEquals(entry.GetDescription(),
"cyano_imine_B(17)")
elif catalog_idx == FilterCatalogParams.FilterCatalogs.PAINS_C:
mol = Chem.MolFromSmiles(
"O=C1C2OC2C(=O)c3cc4CCCCc4cc13") # CHEMBL476649
entry = catalog.GetFirstMatch(mol)
self.assertTrue(entry)
self.assertEquals(entry.GetDescription(),
"keto_keto_gamma(5)")
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import FilterCatalog
from rdkit.Chem.FilterCatalog import FilterCatalogParams
import json, gzip
from ijson import items
from django.core.exceptions import ValidationError
from threading import Thread
import CloseableQueue
#from multiprocessing.dummy import Pool
from mol_parsing.functions import find_lib_type, read_input, write_json_results, write_results
from mol_parsing.rdkit_parse import parse_mol_json, generate_mols_from_json
from StringIO import StringIO
params = FilterCatalog.FilterCatalogParams()
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_A)
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_B)
params.AddCatalog(FilterCatalogParams.FilterCatalogs.PAINS_C)
catalog = FilterCatalog.FilterCatalog(params)
def request_params(request):
"""Function to handle the request parameters"""
#screen_lib, mol_type = find_lib_type(request)
screen_lib, mol_type = read_input(request)
if "filter" in request.GET:
filter = request.GET["filter"]
if not (filter == "INCLUDE_MATCHING" or filter
== "INCLUDE_NON_MATCHING" or filter == "INCLUDE_ALL"):
raise ValidationError("Invalid filter value " + filter)
def __init__(self, n_cores=-1):
params = FilterCatalog.FilterCatalogParams()
params.AddCatalog(FilterCatalog.FilterCatalogParams.FilterCatalogs.PAINS)
self.filter = FilterCatalog.FilterCatalog(params)
self.n_cores = n_cores
