def test_can_get_all_external_pdbs(self, mock_xml_retriever, mock_simple_retriever, mock_json_retriever):
mock_json_retriever.return_value = {"smiles": "CCC", "inchi": "CCC", "oneLetterSeq": "CCC"}
mock_simple_retriever.return_value = ElementTree.fromstring('''<?xml version='1.0' standalone='no' ?>
<smilesQueryResult smiles="NC(=O)C1=CC=CC=C1" search_type="4">
<ligandInfo>
<ligand structureId="2XG3" chemicalID="UNU" type="non-polymer" molecularWeight="121.137">
<chemicalName>BENZAMIDE</chemicalName>
<formula>C7 H7 N O</formula>
<InChIKey>KXDAEFPNCMNJSK-UHFFFAOYSA-N</InChIKey>
<InChI>InChI=1S/C7H7NO/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H2,8,9)</InChI>
<smiles>c1ccc(cc1)C(=O)N</smiles>
</ligand>
<ligand structureId="3A1I" chemicalID="UNU" type="non-polymer" molecularWeight="121.137">
<chemicalName>BENZAMIDE</chemicalName>
<formula>C7 H7 N O</formula>
<InChIKey>KXDAEFPNCMNJSK-UHFFFAOYSA-N</InChIKey>
<InChI>InChI=1S/C7H7NO/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H2,8,9)</InChI>
<smiles>c1ccc(cc1)C(=O)N</smiles>
</ligand>
</ligandInfo>
</smilesQueryResult>''')
mock_xml_retriever.side_effect = [["1xxx", "3A1I"], ["2xxx"], ["2xxx"]]
ligand = Ligand(self.ligand_json)
pdbs = ligand.all_external_pdbs()
self.assertEqual(len(pdbs), 4)
for code in ["2XG3", "3A1I", "1xxx", "2xxx"]:
self.assertIn(code, pdbs)
def test_can_get_sequence_pdbs(self, mock_xml_retriever,
mock_json_retriever):
mock_json_retriever.return_value = {"oneLetterSeq": "CCC"}
mock_xml_retriever.return_value = ["2XG3", "3A1I"]
ligand = Ligand(self.ligand_json)
pdbs = ligand.sequence_pdbs()
self.assertEqual(pdbs, ["2XG3", "3A1I"])
def test_structural_properties(self, mock_json_retriever):
mock_json_retriever.return_value = {
"iupacName": "2,3-dihydro-1,4-benzodioxin",
"smiles": "OC[C@H]1COc2c(O1)cccc2N1CCN(CC1)CCNC(=O)c1ccc(cc1)F",
"inchi":
"InChI=1S/C22H26FN3O4/c23-17-6-4-16(5-7-17)22(28)24-8-9-25-10",
"inchiKey": "NYSDRDDQELAVKP-SFHVURJKSA-N",
"oneLetterSeq": "ILK",
"threeLetterSeq": "Ile-Leu-Lys",
"postTranslationalModifications": "Glycosylation",
"chemicalModifications": "Methylation"
}
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.iupac_name(), "2,3-dihydro-1,4-benzodioxin")
self.assertEqual(
ligand.smiles(),
"OC[C@H]1COc2c(O1)cccc2N1CCN(CC1)CCNC(=O)c1ccc(cc1)F")
self.assertEqual(
ligand.inchi(),
"InChI=1S/C22H26FN3O4/c23-17-6-4-16(5-7-17)22(28)24-8-9-25-10")
self.assertEqual(ligand.inchi_key(), "NYSDRDDQELAVKP-SFHVURJKSA-N")
self.assertEqual(ligand.one_letter_sequence(), "ILK")
self.assertEqual(ligand.three_letter_sequence(), "Ile-Leu-Lys")
self.assertEqual(ligand.post_translational_modifications(),
"Glycosylation")
self.assertEqual(ligand.chemical_modifications(), "Methylation")
def test_can_get_smiles_pdbs(self, mock_xml_retriever,
mock_json_retriever):
mock_json_retriever.return_value = {"smiles": "CCC"}
mock_xml_retriever.return_value = ElementTree.fromstring(
'''<?xml version='1.0' standalone='no' ?>
<smilesQueryResult smiles="NC(=O)C1=CC=CC=C1" search_type="4">
<ligandInfo>
<ligand structureId="2XG3" chemicalID="UNU" type="non-polymer" molecularWeight="121.137">
<chemicalName>BENZAMIDE</chemicalName>
<formula>C7 H7 N O</formula>
<InChIKey>KXDAEFPNCMNJSK-UHFFFAOYSA-N</InChIKey>
<InChI>InChI=1S/C7H7NO/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H2,8,9)</InChI>
<smiles>c1ccc(cc1)C(=O)N</smiles>
</ligand>
<ligand structureId="3A1I" chemicalID="UNU" type="non-polymer" molecularWeight="121.137">
<chemicalName>BENZAMIDE</chemicalName>
<formula>C7 H7 N O</formula>
<InChIKey>KXDAEFPNCMNJSK-UHFFFAOYSA-N</InChIKey>
<InChI>InChI=1S/C7H7NO/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H2,8,9)</InChI>
<smiles>c1ccc(cc1)C(=O)N</smiles>
</ligand>
</ligandInfo>
</smilesQueryResult>''')
ligand = Ligand(self.ligand_json)
pdbs = ligand.smiles_pdbs()
self.assertEqual(pdbs, ["2XG3", "3A1I"])
def test_can_get_gtop_pdbs(self, mock_json_retriever):
self.interaction_json["ligandId"] = 149
mock_json_retriever.side_effect = [[self.interaction_json],
self.pdb_json]
ligand = Ligand(self.ligand_json)
pdbs = ligand.gtop_pdbs()
self.assertEqual(pdbs, ["4IAR"])
def test_interaction_id_id_must_be_int(self, mock_json_retriever):
mock_json_retriever.return_value = [
self.interaction_json, self.interaction_json
]
ligand = Ligand(self.ligand_json)
with self.assertRaises(TypeError):
ligand.get_interaction_by_id("1")
def test_can_get_inchi_pdbs_when_no_results(self, mock_xml_retriever,
mock_json_retriever):
mock_json_retriever.return_value = {"inchi": "CCC"}
mock_xml_retriever.return_value = None
ligand = Ligand(self.ligand_json)
pdbs = ligand.inchi_pdbs()
self.assertEqual(pdbs, [])
def test_can_get_sequence_pdbs_when_no_results(self, mock_xml_retriever,
mock_json_retriever):
mock_json_retriever.return_value = {"oneLetterSeq": "CCC"}
mock_xml_retriever.return_value = None
ligand = Ligand(self.ligand_json)
pdbs = ligand.sequence_pdbs()
self.assertEqual(pdbs, [])
def test_can_get_all_external_pdbs(self, mock_xml_retriever,
mock_simple_retriever,
mock_json_retriever):
mock_json_retriever.return_value = {
"smiles": "CCC",
"inchi": "CCC",
"oneLetterSeq": "CCC"
}
mock_simple_retriever.return_value = ElementTree.fromstring(
'''<?xml version='1.0' standalone='no' ?>
<smilesQueryResult smiles="NC(=O)C1=CC=CC=C1" search_type="4">
<ligandInfo>
<ligand structureId="2XG3" chemicalID="UNU" type="non-polymer" molecularWeight="121.137">
<chemicalName>BENZAMIDE</chemicalName>
<formula>C7 H7 N O</formula>
<InChIKey>KXDAEFPNCMNJSK-UHFFFAOYSA-N</InChIKey>
<InChI>InChI=1S/C7H7NO/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H2,8,9)</InChI>
<smiles>c1ccc(cc1)C(=O)N</smiles>
</ligand>
<ligand structureId="3A1I" chemicalID="UNU" type="non-polymer" molecularWeight="121.137">
<chemicalName>BENZAMIDE</chemicalName>
<formula>C7 H7 N O</formula>
<InChIKey>KXDAEFPNCMNJSK-UHFFFAOYSA-N</InChIKey>
<InChI>InChI=1S/C7H7NO/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H2,8,9)</InChI>
<smiles>c1ccc(cc1)C(=O)N</smiles>
</ligand>
</ligandInfo>
</smilesQueryResult>''')
mock_xml_retriever.side_effect = [["1xxx", "3A1I"], ["2xxx"], ["2xxx"]]
ligand = Ligand(self.ligand_json)
pdbs = ligand.all_external_pdbs()
self.assertEqual(len(pdbs), 4)
for code in ["2XG3", "3A1I", "1xxx", "2xxx"]:
self.assertIn(code, pdbs)
def test_can_get_interactions(self, mock_json_retriever):
mock_json_retriever.return_value = [self.interaction_json, self.interaction_json]
ligand = Ligand(self.ligand_json)
interactions = ligand.interactions()
self.assertIsInstance(interactions, list)
self.assertEqual(len(interactions), 2)
for interaction in interactions:
self.assertIsInstance(interaction, Interaction)
def test_can_get_prodrugs(self, mock_json_retriever):
mock_json_retriever.return_value = self.ligand_json
ligand = Ligand(self.ligand_json)
prodrugs = ligand.prodrugs()
self.assertIsInstance(prodrugs, list)
self.assertEqual(len(prodrugs), len(self.ligand_json["prodrugIds"]))
for prodrug in prodrugs:
self.assertIsInstance(prodrug, Ligand)
def test_can_get_complexes(self, mock_json_retriever):
mock_json_retriever.return_value = self.ligand_json
ligand = Ligand(self.ligand_json)
complexes = ligand.complexes()
self.assertIsInstance(complexes, list)
self.assertEqual(len(complexes), len(self.ligand_json["complexIds"]))
for complex_ in complexes:
self.assertIsInstance(complex_, Ligand)
def test_can_get_subunits(self, mock_json_retriever):
mock_json_retriever.return_value = self.ligand_json
ligand = Ligand(self.ligand_json)
subunits = ligand.subunits()
self.assertIsInstance(subunits, list)
self.assertEqual(len(subunits), len(self.ligand_json["subunitIds"]))
for subunit in subunits:
self.assertIsInstance(subunit, Ligand)
def test_can_get_active_drugs(self, mock_json_retriever):
mock_json_retriever.return_value = self.ligand_json
ligand = Ligand(self.ligand_json)
active_drugs = ligand.active_drugs()
self.assertIsInstance(active_drugs, list)
self.assertEqual(len(active_drugs), len(self.ligand_json["activeDrugIds"]))
for active_drug in active_drugs:
self.assertIsInstance(active_drug, Ligand)
def test_can_get_complexes(self, mock_json_retriever):
mock_json_retriever.return_value = self.ligand_json
ligand = Ligand(self.ligand_json)
complexes = ligand.complexes()
self.assertIsInstance(complexes, list)
self.assertEqual(len(complexes), len(self.ligand_json["complexIds"]))
for complex_ in complexes:
self.assertIsInstance(complex_, Ligand)
def test_can_get_prodrugs(self, mock_json_retriever):
mock_json_retriever.return_value = self.ligand_json
ligand = Ligand(self.ligand_json)
prodrugs = ligand.prodrugs()
self.assertIsInstance(prodrugs, list)
self.assertEqual(len(prodrugs), len(self.ligand_json["prodrugIds"]))
for prodrug in prodrugs:
self.assertIsInstance(prodrug, Ligand)
def test_can_get_interaction_by_id(self, mock_json_retriever):
mock_json_retriever.return_value = [
self.interaction_json, self.interaction_json
]
ligand = Ligand(self.ligand_json)
interaction = ligand.get_interaction_by_id(
self.interaction_json["interactionId"])
self.assertIsInstance(interaction, Interaction)
def test_synonym_properties(self, mock_json_retriever):
mock_json_retriever.return_value = [
{"name": "DU-29,373", "refs": []},
{"name": "(+)-flesinoxan", "refs": []}
]
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.synonyms(), ["DU-29,373", "(+)-flesinoxan"])
def test_can_get_subunits(self, mock_json_retriever):
mock_json_retriever.return_value = self.ligand_json
ligand = Ligand(self.ligand_json)
subunits = ligand.subunits()
self.assertIsInstance(subunits, list)
self.assertEqual(len(subunits), len(self.ligand_json["subunitIds"]))
for subunit in subunits:
self.assertIsInstance(subunit, Ligand)
def test_can_get_active_drugs(self, mock_json_retriever):
mock_json_retriever.return_value = self.ligand_json
ligand = Ligand(self.ligand_json)
active_drugs = ligand.active_drugs()
self.assertIsInstance(active_drugs, list)
self.assertEqual(len(active_drugs),
len(self.ligand_json["activeDrugIds"]))
for active_drug in active_drugs:
self.assertIsInstance(active_drug, Ligand)
def test_can_get_targets(self, mock_json_retriever):
mock_json_retriever.side_effect = [
[self.interaction_json, self.interaction_json], self.target_json, self.target_json
]
ligand = Ligand(self.ligand_json)
targets = ligand.targets()
self.assertIsInstance(targets, list)
self.assertEqual(len(targets), 2)
for target in targets:
self.assertIsInstance(target, Target)
def test_can_get_interactions(self, mock_json_retriever):
mock_json_retriever.return_value = [
self.interaction_json, self.interaction_json
]
ligand = Ligand(self.ligand_json)
interactions = ligand.interactions()
self.assertIsInstance(interactions, list)
self.assertEqual(len(interactions), 2)
for interaction in interactions:
self.assertIsInstance(interaction, Interaction)
def test_can_get_targets(self, mock_json_retriever):
mock_json_retriever.side_effect = [[
self.interaction_json, self.interaction_json
], self.target_json, self.target_json]
ligand = Ligand(self.ligand_json)
targets = ligand.targets()
self.assertIsInstance(targets, list)
self.assertEqual(len(targets), 2)
for target in targets:
self.assertIsInstance(target, Target)
def test_structural_properties(self, mock_json_retriever):
mock_json_retriever.return_value = {
"iupacName": "2,3-dihydro-1,4-benzodioxin",
"smiles": "OC[C@H]1COc2c(O1)cccc2N1CCN(CC1)CCNC(=O)c1ccc(cc1)F",
"inchi": "InChI=1S/C22H26FN3O4/c23-17-6-4-16(5-7-17)22(28)24-8-9-25-10",
"inchiKey": "NYSDRDDQELAVKP-SFHVURJKSA-N",
"oneLetterSeq": "ILK",
"threeLetterSeq": "Ile-Leu-Lys",
"postTranslationalModifications": "Glycosylation",
"chemicalModifications": "Methylation"
}
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.iupac_name(), "2,3-dihydro-1,4-benzodioxin")
self.assertEqual(
ligand.smiles(),
"OC[C@H]1COc2c(O1)cccc2N1CCN(CC1)CCNC(=O)c1ccc(cc1)F"
)
self.assertEqual(
ligand.inchi(),
"InChI=1S/C22H26FN3O4/c23-17-6-4-16(5-7-17)22(28)24-8-9-25-10"
)
self.assertEqual(ligand.inchi_key(), "NYSDRDDQELAVKP-SFHVURJKSA-N")
self.assertEqual(ligand.one_letter_sequence(), "ILK")
self.assertEqual(ligand.three_letter_sequence(), "Ile-Leu-Lys")
self.assertEqual(
ligand.post_translational_modifications(),
"Glycosylation"
)
self.assertEqual(ligand.chemical_modifications(), "Methylation")
def test_structural_properties_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
ligand = Ligand(self.ligand_json)
self.assertIs(ligand.iupac_name(), None)
self.assertIs(ligand.smiles(), None)
self.assertIs(ligand.inchi(), None)
self.assertIs(ligand.inchi_key(), None)
self.assertIs(ligand.one_letter_sequence(), None)
self.assertIs(ligand.three_letter_sequence(), None)
self.assertIs(ligand.post_translational_modifications(), None)
self.assertIs(ligand.chemical_modifications(), None)
def test_synonym_properties(self, mock_json_retriever):
mock_json_retriever.return_value = [{
"name": "DU-29,373",
"refs": []
}, {
"name": "(+)-flesinoxan",
"refs": []
}]
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.synonyms(),
["DU-29,373", "(+)-flesinoxan"])
def test_molecular_properties_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.hydrogen_bond_acceptors(), None)
self.assertEqual(ligand.hydrogen_bond_donors(), None)
self.assertEqual(ligand.rotatable_bonds(), None)
self.assertEqual(ligand.topological_polar_surface_area(), None)
self.assertEqual(ligand.molecular_weight(), None)
self.assertEqual(ligand.log_p(), None)
self.assertEqual(ligand.lipinski_rules_broken(), None)
def test_structural_properties_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
ligand = Ligand(self.ligand_json)
self.assertIs(ligand.iupac_name(), None)
self.assertIs(ligand.smiles(), None)
self.assertIs(ligand.inchi(), None)
self.assertIs(ligand.inchi_key(), None)
self.assertIs(ligand.one_letter_sequence(), None)
self.assertIs(ligand.three_letter_sequence(), None)
self.assertIs(ligand.post_translational_modifications(), None)
self.assertIs(ligand.chemical_modifications(), None)
def test_molecular_properties_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.hydrogen_bond_acceptors(), None)
self.assertEqual(ligand.hydrogen_bond_donors(), None)
self.assertEqual(ligand.rotatable_bonds(), None)
self.assertEqual(ligand.topological_polar_surface_area(), None)
self.assertEqual(ligand.molecular_weight(), None)
self.assertEqual(ligand.log_p(), None)
self.assertEqual(ligand.lipinski_rules_broken(), None)
def test_database_properties(self, mock_json_retriever):
mock_json_retriever.return_value = [
{
"accession": "CHEMBL1742477",
"database": "ChEMBL Ligand",
"url": "http://www.ebi.ac.uk/chembldb/index.php/compound/inspect/CHEMBL1742477",
"species": "None"
},
{
"accession": "57347",
"database": "PubChem CID",
"url": "http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=57347",
"species": "None"
}
]
ligand = Ligand(self.ligand_json)
self.assertEqual(len(ligand.database_links()), 2)
self.assertIsInstance(ligand.database_links()[0], DatabaseLink)
self.assertIsInstance(ligand.database_links()[1], DatabaseLink)
self.assertEqual(ligand.database_links()[0].accession(), "CHEMBL1742477")
self.assertEqual(ligand.database_links()[1].accession(), "57347")
def test_molecular_properties(self, mock_json_retriever):
mock_json_retriever.return_value = {
"hydrogenBondAcceptors": 5,
"hydrogenBondDonors": 2,
"rotatableBonds": 7,
"topologicalPolarSurfaceArea": 74.27,
"molecularWeight": 415.19073474,
"logP": 1.84,
"lipinskisRuleOfFive": 0
}
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.hydrogen_bond_acceptors(), 5)
self.assertEqual(ligand.hydrogen_bond_donors(), 2)
self.assertEqual(ligand.rotatable_bonds(), 7)
self.assertEqual(ligand.topological_polar_surface_area(), 74.27)
self.assertEqual(ligand.molecular_weight(), 415.19073474)
self.assertEqual(ligand.log_p(), 1.84)
self.assertEqual(ligand.lipinski_rules_broken(), 0)
def test_can_get_smiles_pdbs(self, mock_xml_retriever, mock_json_retriever):
mock_json_retriever.return_value = {"smiles": "CCC"}
mock_xml_retriever.return_value = ElementTree.fromstring('''<?xml version='1.0' standalone='no' ?>
<smilesQueryResult smiles="NC(=O)C1=CC=CC=C1" search_type="4">
<ligandInfo>
<ligand structureId="2XG3" chemicalID="UNU" type="non-polymer" molecularWeight="121.137">
<chemicalName>BENZAMIDE</chemicalName>
<formula>C7 H7 N O</formula>
<InChIKey>KXDAEFPNCMNJSK-UHFFFAOYSA-N</InChIKey>
<InChI>InChI=1S/C7H7NO/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H2,8,9)</InChI>
<smiles>c1ccc(cc1)C(=O)N</smiles>
</ligand>
<ligand structureId="3A1I" chemicalID="UNU" type="non-polymer" molecularWeight="121.137">
<chemicalName>BENZAMIDE</chemicalName>
<formula>C7 H7 N O</formula>
<InChIKey>KXDAEFPNCMNJSK-UHFFFAOYSA-N</InChIKey>
<InChI>InChI=1S/C7H7NO/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H2,8,9)</InChI>
<smiles>c1ccc(cc1)C(=O)N</smiles>
</ligand>
</ligandInfo>
</smilesQueryResult>''')
ligand = Ligand(self.ligand_json)
pdbs = ligand.smiles_pdbs()
self.assertEqual(pdbs, ["2XG3", "3A1I"])
def test_molecular_properties(self, mock_json_retriever):
mock_json_retriever.return_value = {
"hydrogenBondAcceptors": 5,
"hydrogenBondDonors": 2,
"rotatableBonds": 7,
"topologicalPolarSurfaceArea": 74.27,
"molecularWeight": 415.19073474,
"logP": 1.84,
"lipinskisRuleOfFive": 0
}
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.hydrogen_bond_acceptors(), 5)
self.assertEqual(ligand.hydrogen_bond_donors(), 2)
self.assertEqual(ligand.rotatable_bonds(), 7)
self.assertEqual(ligand.topological_polar_surface_area(), 74.27)
self.assertEqual(ligand.molecular_weight(), 415.19073474)
self.assertEqual(ligand.log_p(), 1.84)
self.assertEqual(ligand.lipinski_rules_broken(), 0)
def test_can_create_ligand(self):
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.json_data, self.ligand_json)
self.assertEqual(ligand._ligand_id, 1)
self.assertEqual(ligand._name, "flesinoxan")
self.assertEqual(ligand._abbreviation, "flexo")
self.assertEqual(ligand._inn, "flesinoxan")
self.assertEqual(ligand._ligand_type, "Synthetic organic")
self.assertEqual(ligand._species, None)
self.assertEqual(ligand._radioactive, False)
self.assertEqual(ligand._labelled, True)
self.assertEqual(ligand._approved, True)
self.assertEqual(ligand._withdrawn, False)
self.assertEqual(ligand._approval_source, "FDA (1997)")
self.assertEqual(ligand._subunit_ids, [2, 3])
self.assertEqual(ligand._complex_ids, [5])
self.assertEqual(ligand._prodrug_ids, [7])
self.assertEqual(ligand._active_drug_ids, [9, 10])
def test_database_properties(self, mock_json_retriever):
mock_json_retriever.return_value = [{
"accession": "CHEMBL1742477",
"database": "ChEMBL Ligand",
"url":
"http://www.ebi.ac.uk/chembldb/index.php/compound/inspect/CHEMBL1742477",
"species": "None"
}, {
"accession": "57347",
"database": "PubChem CID",
"url":
"http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=57347",
"species": "None"
}]
ligand = Ligand(self.ligand_json)
self.assertEqual(len(ligand.database_links()), 2)
self.assertIsInstance(ligand.database_links()[0], DatabaseLink)
self.assertIsInstance(ligand.database_links()[1], DatabaseLink)
self.assertEqual(ligand.database_links()[0].accession(),
"CHEMBL1742477")
self.assertEqual(ligand.database_links()[1].accession(), "57347")
def test_can_get_gtop_pdbs(self, mock_json_retriever):
self.interaction_json["ligandId"] = 149
mock_json_retriever.side_effect = [[self.interaction_json], self.pdb_json]
ligand = Ligand(self.ligand_json)
pdbs = ligand.gtop_pdbs()
self.assertEqual(pdbs, ["4IAR"])
def test_gtop_pdbs_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.gtop_pdbs(), [])
def test_interactions_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.interactions(), [])
def test_can_find_ligand_in_pdb_by_name(self):
ligand = Ligand(self.ligand_json)
molecule = ligand.find_in_pdb_by_name(self.pdb)
self.assertIs(molecule, self.molecule2)
def test_can_get_sequence_pdbs_when_no_results(self, mock_xml_retriever, mock_json_retriever):
mock_json_retriever.return_value = {"oneLetterSeq": "CCC"}
mock_xml_retriever.return_value = None
ligand = Ligand(self.ligand_json)
pdbs = ligand.sequence_pdbs()
self.assertEqual(pdbs, [])
def test_can_find_ligand_in_pdb_by_peptide_string(self,
mock_json_retriever):
mock_json_retriever.return_value = {"oneLetterSeq": "ABCDEFG"}
ligand = Ligand(self.ligand_json)
molecule = ligand.find_in_pdb_by_peptide_string(self.pdb)
self.assertIs(molecule, self.chain1)
def test_can_get_inchi_pdbs_when_no_results(self, mock_xml_retriever, mock_json_retriever):
mock_json_retriever.return_value = {"inchi": "CCC"}
mock_xml_retriever.return_value = None
ligand = Ligand(self.ligand_json)
pdbs = ligand.inchi_pdbs()
self.assertEqual(pdbs, [])
def test_can_get_name_pdbs_when_no_results(self, mock_xml_retriever):
mock_xml_retriever.return_value = None
ligand = Ligand(self.ligand_json)
pdbs = ligand.name_pdbs()
self.assertEqual(pdbs, [])
def test_can_get_name_pdbs(self, mock_xml_retriever):
mock_xml_retriever.return_value = ["2XG3", "3A1I"]
ligand = Ligand(self.ligand_json)
pdbs = ligand.name_pdbs()
self.assertEqual(pdbs, ["2XG3", "3A1I"])
def test_interactions_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.interactions(), [])
def test_gtop_pdbs_when_no_json(self, mock_json_retriever):
mock_json_retriever.return_value = None
ligand = Ligand(self.ligand_json)
self.assertEqual(ligand.gtop_pdbs(), [])
def test_can_get_inchi_pdbs(self, mock_xml_retriever, mock_json_retriever):
mock_json_retriever.return_value = {"inchi": "CCC"}
mock_xml_retriever.return_value = ["2XG3", "3A1I"]
ligand = Ligand(self.ligand_json)
pdbs = ligand.inchi_pdbs()
self.assertEqual(pdbs, ["2XG3", "3A1I"])
def test_can_find_ligand_in_pdb_by_mass(self, mock_json_retriever):
mock_json_retriever.return_value = {"molecularWeight": 100}
ligand = Ligand(self.ligand_json)
molecule = ligand.find_in_pdb_by_mass(self.pdb)
self.assertIs(molecule, self.molecule3)
def test_can_get_inchi_pdbs(self, mock_xml_retriever, mock_json_retriever):
mock_json_retriever.return_value = {"inchi": "CCC"}
mock_xml_retriever.return_value = ["2XG3", "3A1I"]
ligand = Ligand(self.ligand_json)
pdbs = ligand.inchi_pdbs()
self.assertEqual(pdbs, ["2XG3", "3A1I"])
def test_can_find_ligand_in_pdb_by_smiles(self, mock_json_retriever):
mock_json_retriever.return_value = {"smiles": "CCCOOOCOCOCO"}
ligand = Ligand(self.ligand_json)
molecule = ligand.find_in_pdb_by_smiles(self.pdb)
self.assertIs(molecule, self.molecule1)
def test_can_get_name_pdbs(self, mock_xml_retriever):
mock_xml_retriever.return_value = ["2XG3", "3A1I"]
ligand = Ligand(self.ligand_json)
pdbs = ligand.name_pdbs()
self.assertEqual(pdbs, ["2XG3", "3A1I"])
def test_can_find_ligand_in_pdb_by_mass(self, mock_json_retriever):
mock_json_retriever.return_value = {"molecularWeight": 100}
ligand = Ligand(self.ligand_json)
molecule = ligand.find_in_pdb_by_mass(self.pdb)
self.assertIs(molecule, self.molecule3)
def test_can_get_sequence_pdbs(self, mock_xml_retriever, mock_json_retriever):
mock_json_retriever.return_value = {"oneLetterSeq": "CCC"}
mock_xml_retriever.return_value = ["2XG3", "3A1I"]
ligand = Ligand(self.ligand_json)
pdbs = ligand.sequence_pdbs()
self.assertEqual(pdbs, ["2XG3", "3A1I"])
def test_can_find_ligand_in_pdb_by_smiles(self, mock_json_retriever):
mock_json_retriever.return_value = {"smiles": "CCCOOOCOCOCO"}
ligand = Ligand(self.ligand_json)
molecule = ligand.find_in_pdb_by_smiles(self.pdb)
self.assertIs(molecule, self.molecule1)
def test_can_get_interaction_by_id(self, mock_json_retriever):
mock_json_retriever.return_value = [self.interaction_json, self.interaction_json]
ligand = Ligand(self.ligand_json)
interaction = ligand.get_interaction_by_id(self.interaction_json["interactionId"])
self.assertIsInstance(interaction, Interaction)
def test_interaction_id_id_must_be_int(self, mock_json_retriever):
mock_json_retriever.return_value =[self.interaction_json, self.interaction_json]
ligand = Ligand(self.ligand_json)
with self.assertRaises(TypeError):
ligand.get_interaction_by_id("1")
def test_can_find_ligand_in_pdb_by_name(self):
ligand = Ligand(self.ligand_json)
molecule = ligand.find_in_pdb_by_name(self.pdb)
self.assertIs(molecule, self.molecule2)
def test_cannot_get_interaction_by_invalid_id(self, mock_json_retriever):
mock_json_retriever.return_value = None
ligand = Ligand(self.ligand_json)
with self.assertRaises(exceptions.NoSuchInteractionError):
interaction = ligand.get_interaction_by_id(0)
def test_can_find_ligand_in_pdb_by_peptide_string(self, mock_json_retriever):
mock_json_retriever.return_value = {"oneLetterSeq": "ABCDEFG"}
ligand = Ligand(self.ligand_json)
molecule = ligand.find_in_pdb_by_peptide_string(self.pdb)
self.assertIs(molecule, self.chain1)
def test_can_get_name_pdbs_when_no_results(self, mock_xml_retriever):
mock_xml_retriever.return_value = None
ligand = Ligand(self.ligand_json)
pdbs = ligand.name_pdbs()
self.assertEqual(pdbs, [])