def test_show_rdkit():
rdkit_mol = Chem.AddHs(
Chem.MolFromSmiles(
'COc1ccc2[C@H](O)[C@@H](COc2c1)N3CCC(O)(CC3)c4ccc(F)cc4'))
AllChem.EmbedMultipleConfs(
rdkit_mol, useExpTorsionAnglePrefs=True, useBasicKnowledge=True)
view = nv.show_rdkit(rdkit_mol, parmed=False)
assert not view._trajlist
view = nv.show_rdkit(rdkit_mol, parmed=True)
assert view._trajlist
view = nv.RdkitStructure(rdkit_mol)
def test_show_rdkit():
import rdkit.Chem as Chem
rdkit_mol = Chem.AddHs(
Chem.MolFromSmiles(
'COc1ccc2[C@H](O)[C@@H](COc2c1)N3CCC(O)(CC3)c4ccc(F)cc4'))
AllChem.EmbedMultipleConfs(rdkit_mol,
useExpTorsionAnglePrefs=True,
useBasicKnowledge=True)
# FIXME: create test_adaptor.py?
# Test RdkitStructure
structure = nglview.RdkitStructure(rdkit_mol)
assert "HETATM" in structure.get_structure_string()
structure = nglview.RdkitStructure(rdkit_mol, ext="sdf")
assert "RDKit 3D" in structure.get_structure_string()
structure2 = nglview.RdkitStructure(rdkit_mol, ext="sdf", conf_id=0)
assert "RDKit 3D" in structure2.get_structure_string()
assert structure.get_structure_string() == structure2.get_structure_string(
)
structure3 = nglview.RdkitStructure(rdkit_mol, ext="sdf", conf_id=1)
assert "RDKit 3D" in structure3.get_structure_string()
assert structure.get_structure_string() != structure3.get_structure_string(
)
# Test show_rdkit
with patch.object(Chem, 'MolToPDBBlock') as mock_MolToPDBBlock,\
patch.object(Chem, 'MolToMolBlock') as mock_MolToMolBlock:
nglview.show_rdkit(rdkit_mol, fmt='sdf', conf_id=1)
assert mock_MolToMolBlock.called
assert not mock_MolToPDBBlock.called
assert mock_MolToMolBlock.call_args_list[-1][-1] == {'confId': 1}
with patch.object(Chem, 'MolToPDBBlock') as mock_MolToPDBBlock,\
patch.object(Chem, 'MolToMolBlock') as mock_MolToMolBlock:
nglview.show_rdkit(rdkit_mol)
assert not mock_MolToMolBlock.called
assert mock_MolToPDBBlock.called
assert mock_MolToPDBBlock.call_args_list[-1][-1] == {'confId': -1}