def test_tranche_with_filters_url_list():
client = ZincClient()
col_list = ["C"]
row_list = ["B"]
url_list = client._tranche_with_filters_url_list(col_list, row_list,
availability="for-sale",
bioactive=None,
biogenic=None,
reactivity=None,
fileformat="smi")
assert len(url_list) == 16
assert url_list[0] == "https://zinc.docking.org/substances/subsets/for-sale.smi?count=all&tranche_name=CBAA"
assert url_list[-1] == "https://zinc.docking.org/substances/subsets/for-sale.smi?count=all&tranche_name=CBED"
col_list = ["E", "F"]
row_list = ["B"]
url_list = client._tranche_with_filters_url_list(col_list, row_list,
availability="now",
bioactive=None,
biogenic=None,
reactivity="anodyne",
fileformat="mol2")
assert len(url_list) == 32
assert url_list[0] == "https://zinc.docking.org/substances/subsets/now+anodyne.mol2?count=all&tranche_name=EBAA"
assert url_list[-1] == "https://zinc.docking.org/substances/subsets/now+anodyne.mol2?count=all&tranche_name=FBED"
def test_urls_for_tranches_2d():
client = ZincClient()
col_list = ["A", "B", "C"]
row_list = ["A", "B", "C"]
url_list = client._urls_for_tranches_2d(col_list, row_list)
assert len(url_list) == 144
# Test the first four
assert url_list[0] == "http://files.docking.org/2D/AA/AAAA.smi"
assert url_list[1] == "http://files.docking.org/2D/AA/AAAB.smi"
assert url_list[2] == "http://files.docking.org/2D/AA/AAAC.smi"
assert url_list[3] == "http://files.docking.org/2D/AA/AAAD.smi"
# Test the last four
assert url_list[-1] == "http://files.docking.org/2D/CC/CCED.smi"
assert url_list[-2] == "http://files.docking.org/2D/CC/CCEC.smi"
assert url_list[-3] == "http://files.docking.org/2D/CC/CCEB.smi"
assert url_list[-4] == "http://files.docking.org/2D/CC/CCEA.smi"
col_list = ["A", "B", "C", "D"]
row_list = ["A", "B", "C", "D"]
url_list = client._urls_for_tranches_2d(col_list, row_list)
assert len(url_list) == 256 # len(col_list) * len(row_list) * 16
col_list = ["B", "C"]
row_list = ["A", "B", "C", "D"]
url_list = client._urls_for_tranches_2d(col_list, row_list)
assert len(url_list) == 128 # len(col_list) * len(row_list) * 16
def test_append_filters_to_url():
client = ZincClient()
catalog_url = client._catalog_url + "/chembl27/substances"
full_url = client._append_filters_to_url(catalog_url, "smi", count=1000)
assert full_url == "https://zinc.docking.org/catalogs/chembl27/substances.smi?count=1000"
full_url = client._append_filters_to_url(catalog_url, "smi", count=1000, availability="for-sale")
assert full_url == "https://zinc.docking.org/catalogs/chembl27/substances/subsets/for-sale.smi?count=1000"
full_url = client._append_filters_to_url(catalog_url, "smi", count=1000, availability="for-sale", reactivity="anodyne")
assert full_url == "https://zinc.docking.org/catalogs/chembl27/substances/subsets/for-sale+anodyne.smi?count=1000"
full_url = client._append_filters_to_url(catalog_url, "smi", count=1000, bioactive="fda")
assert full_url == "https://zinc.docking.org/catalogs/chembl27/substances/subsets/fda.smi?count=1000"
full_url = client._append_filters_to_url(catalog_url, "smi", count=1000, biogenic="metabolites")
assert full_url == "https://zinc.docking.org/catalogs/chembl27/substances/subsets/metabolites.smi?count=1000"
substances_url = client._substances_url
full_url = client._append_filters_to_url(substances_url, "smi", count=1000)
assert full_url == "https://zinc.docking.org/substances.smi?count=1000"
full_url = client._append_filters_to_url(substances_url, "smi", count=1000, availability="for-sale", reactivity="anodyne")
assert full_url == "https://zinc.docking.org/substances/subsets/for-sale+anodyne.smi?count=1000"
def test_discretize_values(value, lower):
bins = [200, 250, 300, 325, 350, 375, 400, 425, 450, 500, 550]
new_value = ZincClient.discretize_values(value=value, bins=bins, name="Test", lower=lower)
if value == 230:
assert new_value == 200
elif value == 484:
assert new_value == 500
else:
assert new_value == 550
def test_get_catalog_url():
client = ZincClient()
file_name = "./temp.smi"
# First we test for errors
catalog_name = "hello"
with pytest.raises(exc.InvalidCatalogError, match="is not a valid catalog name"):
client._get_catalog_url(file_name, catalog_name)
catalog_name = "Asinex"
assert client._get_catalog_url(file_name, catalog_name, count="all") == "https://zinc.docking.org/catalogs/asin/substances.smi?count=all"
catalog_name = "Apollo Scientific"
catalog_url = client._get_catalog_url(file_name, catalog_name, availability="for-sale")
assert catalog_url == "https://zinc.docking.org/catalogs/apollo/substances/subsets/for-sale.smi?count=1000"
catalog_name = "ChemBridge Economical"
catalog_url = client._get_catalog_url(file_name, catalog_name, availability="wait-ok", reactivity="clean")
assert catalog_url == "https://zinc.docking.org/catalogs/chbre/substances/subsets/wait-ok+clean.smi?count=1000"
def test_tranch_url_with_filters():
client = ZincClient()
url = client._tranch_url_with_filters(tranch="AAAA",
availability=None,
bioactive=None,
biogenic=None,
reactivity=None)
assert url == 'https://zinc.docking.org/substances.smi?count=all&tranche_name=AAAA'
url = client._tranch_url_with_filters(tranch="BBAA",
availability="for-sale",
bioactive=None,
biogenic=None,
reactivity="anodyne")
assert url == "https://zinc.docking.org/substances/subsets/for-sale+anodyne.smi?count=all&tranche_name=BBAA"
url = client._tranch_url_with_filters(tranch="CAAB",
availability="for-sale",
bioactive=None,
biogenic="biogenic",
reactivity=None,
fileformat="sdf")
assert url == "https://zinc.docking.org/substances/subsets/for-sale+biogenic.sdf?count=all&tranche_name=CAAB"
url = client._tranch_url_with_filters(tranch="JCAA",
availability="now",
bioactive="in-vitro",
biogenic=None,
reactivity=None,
fileformat="json"
)
assert url == "https://zinc.docking.org/substances/subsets/now+in-vitro.json?count=all&tranche_name=JCAA"
def test_validate_filters():
client = ZincClient()
with pytest.raises(exc.InvalidFileFormat, match="is not a valid fileformat"):
client._validate_filters(fileformat="pdf")
with pytest.raises(exc.InvalidAvailabilityError, match="is not a valid availability"):
client._validate_filters(fileformat="smi", availability="instantaneous")
with pytest.raises(exc.InvalidBioactiveError, match="is not a valid bioactivity"):
client._validate_filters(fileformat="smi", bioactive="hello")
with pytest.raises(exc.InvalidBiogenicError, match="is not a valid biogenic"):
client._validate_filters(fileformat="smi", biogenic="hello")
with pytest.raises(exc.InvalidReactivityError, match="is not a valid reactivity"):
client._validate_filters(fileformat="smi", reactivity="explosive")
def test_molw_and_logp_tranches():
client = ZincClient()
mw = (250, 200)
logp = (0, 2)
#Test for errors first
with pytest.raises(exc.InvalidMolecularWeightRangeError, match="First number must be smaller"):
client._mw_and_logp_tranches(mw, logp)
mw = (100, 200)
with pytest.raises(exc.InvalidMolecularWeightRangeError, match="Molecular weight must be a value between"):
client._mw_and_logp_tranches(mw, logp)
mw = (300, 700)
with pytest.raises(exc.InvalidMolecularWeightRangeError, match="Molecular weight must be a value between"):
client._mw_and_logp_tranches(mw, logp)
mw = (250, 325)
logp = (3, 1)
with pytest.raises(exc.InvalidLogPRangeError, match="First number must be smaller"):
client._mw_and_logp_tranches(mw, logp)
logp = (-5, 2)
with pytest.raises(exc.InvalidLogPRangeError, match="LogP must be a value between"):
client._mw_and_logp_tranches(mw, logp)
logp = (3, 10)
with pytest.raises(exc.InvalidLogPRangeError, match="LogP must be a value between"):
client._mw_and_logp_tranches(mw, logp)
# Test that it returns the correct tranches
mw = (200, 550)
logp = (-1, 6)
col_list, row_list = client._mw_and_logp_tranches(mw, logp)
assert col_list == ["A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K"]
assert row_list == ["A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K"]
mw = (320, 500)
logp = (0.5, 3)
col_list, row_list = client._mw_and_logp_tranches(mw, logp)
assert col_list == ["C", "D", "E", "F", "G", "H", "I", "J"]
assert row_list == ["B", "C", "D", "E", "F"]
mw = (415.5, 525)
logp = (2.75, 4)
col_list, row_list = client._mw_and_logp_tranches(mw, logp)
assert col_list == ["G", "H", "I", "J", "K"]
assert row_list == ["E", "F", "G", "H"]
def test_predifined_subset_tranches():
client = ZincClient()
# Test for errors
with pytest.raises(exc.InvalidSubsetError, match="is not a valid subset"):
client._predefined_subset_tranches(subset="hello")
# Test each subset
subset="Drug-Like"
col_list, row_list = client._predefined_subset_tranches(subset)
assert col_list == ["B", "C", "D", "E", "F", "G", "H", "I", "J"]
assert row_list == ["A", "B", "C", "D", "E", "F", "G", "H", "I", "J"]
subset="Lead-Like"
col_list, row_list = client._predefined_subset_tranches(subset)
assert col_list == ["C", "D", "E"]
assert row_list == ["A", "B", "C", "D", "E", "F", "G"]
subset="Lugs"
col_list, row_list = client._predefined_subset_tranches(subset)
assert col_list == ["E", "F", "G", "H", "I"]
assert row_list == ["A", "B", "C", "D", "E", "F", "G", "H", "I"]
subset="Goldilocks"
col_list, row_list = client._predefined_subset_tranches(subset)
assert col_list == ["C", "D", "E"]
assert row_list == ["D", "E", "F"]
subset="Big-n-Greasy"
col_list, row_list = client._predefined_subset_tranches(subset)
assert col_list == ["J", "K"]
assert row_list == ["I", "J", "K"]
subset="Fragments"
col_list, row_list = client._predefined_subset_tranches(subset)
assert col_list == ["A", "B"]
assert row_list == ["A", "B", "C", "D", "E", "F", "G"]
subset="Flagments"
col_list, row_list = client._predefined_subset_tranches(subset)
assert col_list == ["B", "C", "D"]
assert row_list == ["A", "B", "C", "D", "E", "F", "G"]
subset="Shards"
col_list, row_list = client._predefined_subset_tranches(subset)
assert col_list == ["A"]
assert row_list == ["A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K"]