Python Ligand.smiles_pdbs Examples

Example #1

File: test_ligands.py Project: simondharding/pygtop

 def test_can_get_smiles_pdbs_when_no_results(self, mock_xml_retriever,
                                              mock_json_retriever):
     mock_json_retriever.return_value = {"smiles": "CCC"}
     mock_xml_retriever.return_value = None
     ligand = Ligand(self.ligand_json)
     pdbs = ligand.smiles_pdbs()
     self.assertEqual(pdbs, [])

Example #2

File: test_ligands.py Project: simondharding/pygtop

    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"])

Example #3

File: test_ligands.py Project: samirelanduk/pygtop

    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"])

Example #4

File: test_ligands.py Project: samirelanduk/pygtop

 def test_can_get_smiles_pdbs_when_no_results(self, mock_xml_retriever, mock_json_retriever):
     mock_json_retriever.return_value = {"smiles": "CCC"}
     mock_xml_retriever.return_value = None
     ligand = Ligand(self.ligand_json)
     pdbs = ligand.smiles_pdbs()
     self.assertEqual(pdbs, [])