def test_filter_pdbs_by_ligand_name(self):
# Match
codes = pdbsearch.search(ligand_name="ZN", sort="-deposited")
self.assertEqual(codes, [
"2SOD", "1PPT", "4TLN", "5TLN", "3CPA", "4CPA", "2ATC", "5CPA",
"2INS", "7TLN"
])
# List
codes = pdbsearch.search(ligand_name__in=["FE", "ZN"],
sort="-deposited")
self.assertEqual(codes, [
"1HRB", "2SOD", "1PPT", "4TLN", "5TLN", "3CPA", "4CPA", "2ATC",
"5CPA", "2INS"
])
# Full
codes = pdbsearch.search(
rcsb_nonpolymer_instance_feature_summary__comp_id="ZN",
sort="-deposited")
self.assertEqual(codes, [
"2SOD", "1PPT", "4TLN", "5TLN", "3CPA", "4CPA", "2ATC", "5CPA",
"2INS", "7TLN"
])
# Full List
codes = pdbsearch.search(
rcsb_nonpolymer_instance_feature_summary__comp_id__in=["FE", "ZN"],
sort="-deposited")
self.assertEqual(codes, [
"1HRB", "2SOD", "1PPT", "4TLN", "5TLN", "3CPA", "4CPA", "2ATC",
"5CPA", "2INS"
])
def test_pagination_starting(self):
codes0 = pdbsearch.search(limit=10)
codes10 = pdbsearch.search(start=10, limit=10)
self.assertEqual(len(set(codes0) & set(codes10)), 0)
codes5 = pdbsearch.search(start=5, limit=10)
self.assertEqual(len(set(codes5) & set(codes0)), 5)
self.assertEqual(len(set(codes5) & set(codes10)), 5)
self.assertEqual(codes5[0], codes0[5])
def test_sorting_full_property(self):
codes = pdbsearch.search(sort="-rcsb_accession_info.deposit_date")
self.assertEqual(codes, [
"1SBT", "1MBN", "2DHB", "3LDH", "2CHA", "3LYZ", "4LYZ", "6LYZ",
"5LYZ", "2LYZ"
])
codes = pdbsearch.search(
sort="-rcsb_accession_info.initial_release_date")
self.assertEqual(codes, [
"1SRX", "1REI", "1MBN", "1EST", "1FDH", "155C", "2PGK", "2SBT",
"1CYC", "3CNA"
])
def test_sorting_shorthand(self):
codes = pdbsearch.search(sort="-deposited")
self.assertEqual(codes, [
"1SBT", "1MBN", "2DHB", "3LDH", "2CHA", "3LYZ", "4LYZ", "6LYZ",
"5LYZ", "2LYZ"
])
codes = pdbsearch.search(sort="-released")
self.assertEqual(codes, [
"1SRX", "1REI", "1MBN", "1EST", "1FDH", "155C", "2PGK", "2SBT",
"1CYC", "3CNA"
])
codes = pdbsearch.search(sort=["code", "released"])
self.assertEqual(codes[0][0], "9")
def test_multiple_criteria_searching(self):
codes = pdbsearch.search(ligand_name="ZN",
ligand_distance__within=[2.7, 2.9],
sort="-deposited")
self.assertEqual(codes, [
"4TLN", "5TLN", "4CPA", "5ADH", "6ADH", "1TLP", "8ATC", "3AT1",
"8AT1", "7AT1"
])
def test_filter_pdbs_by_ligand_distance(self):
# Match
codes = pdbsearch.search(ligand_distance=5, sort="-deposited")
self.assertEqual(codes, [
"1C1P", "1EM6", "3DN0", "3G0T", "3A0H", "2WSE", "3KZI", "4V6M",
"3SEQ", "4IXQ"
])
# Less than
codes = pdbsearch.search(ligand_distance__lt=5, sort="-deposited")
self.assertEqual(codes, [
"1MBN", "2DHB", "3LDH", "2CHA", "2CNA", "1HIP", "1GPD", "1EST",
"1CYC", "155C"
])
# Less than equal
codes = pdbsearch.search(ligand_distance__lte=5, sort="-deposited")
self.assertEqual(codes, [
"1MBN", "2DHB", "3LDH", "2CHA", "2CNA", "1HIP", "1GPD", "1EST",
"1CYC", "155C"
])
# More than
codes = pdbsearch.search(ligand_distance__gt=5, sort="-deposited")
self.assertEqual(codes, ["6IY5", "6T52", "6T54", "6T53", "6T58"])
# More than equal
codes = pdbsearch.search(ligand_distance__gte=5, sort="-deposited")
self.assertEqual(codes, [
"1C1P", "1EM6", "3DN0", "3G0T", "3A0H", "2WSE", "3KZI", "4V6M",
"3SEQ", "4IXQ"
])
# Range
codes = pdbsearch.search(ligand_distance__within=[4, 5],
sort="-deposited")
self.assertEqual(codes, [
"1GPD", "1EST", "2YHX", "1C4S", "1MBS", "1HDS", "5LDH", "1BP2",
"1FC2", "1HBS"
])
# Full
codes = pdbsearch.search(rcsb_ligand_neighbors__distance=5,
sort="-deposited")
self.assertEqual(codes, [
"1C1P", "1EM6", "3DN0", "3G0T", "3A0H", "2WSE", "3KZI", "4V6M",
"3SEQ", "4IXQ"
])
def test_default_codes(self):
codes = pdbsearch.search()
self.assertEqual(len(codes), 10)
self.assertTrue(all(len(code) == 4 for code in codes))
def test_all_codes(self):
codes = pdbsearch.search(limit=None)
self.assertGreater(len(codes), 150_000)
def test_limited_codes(self):
codes = pdbsearch.search(limit=50)
self.assertEqual(len(codes), 50)
codes = pdbsearch.search(limit=2)
self.assertEqual(len(codes), 2)