Added core tests

Author: OliverBScott

tests/core/test_fragment.py

@@ -0,0 +1,52 @@
+"""
+scaffoldgraph tests.core.test_fragment
+"""
+
+import pytest
+from rdkit import Chem
+
+from scaffoldgraph.core.fragment import *
+
+
+@pytest.fixture(name='mol')
+def test_molecule():
+    smiles = 'CCN1CCc2c(C1)sc(NC(=O)Nc3ccc(Cl)cc3)c2C#N'
+    return Chem.MolFromSmiles(smiles)
+
+
+def canon(smiles):
+    """Canonicalize SMILES for safety. If canonicalization ever changes this should remain consistent"""
+    return Chem.MolToSmiles(Chem.MolFromSmiles(smiles))
+
+
+def test_murcko(mol):
+    murcko = get_murcko_scaffold(mol, generic=False)
+    assert Chem.MolToSmiles(murcko) == canon('O=C(Nc1ccccc1)Nc1cc2c(s1)CNCC2')
+    murcko = get_murcko_scaffold(mol, generic=True)
+    assert Chem.MolToSmiles(murcko) == canon('CC(CC1CCCCC1)CC1CC2CCCCC2C1')
+
+
+def test_annotation(mol):
+    annotation = Chem.MolToSmiles(get_annotated_murcko_scaffold(mol))
+    annotation = annotation.replace('1*', '*')
+    annotation = annotation.replace('2*', '*')
+    annotation = annotation.replace('3*', '*')
+    assert annotation == '[*]N1CCc2c(sc(NC(=O)Nc3ccc([*])cc3)c2[*])C1'
+
+
+def test_murcko_all(mol):
+    frags = get_all_murcko_fragments(mol, break_fused_rings=True)
+    assert len(frags) == 6
+    frags = get_all_murcko_fragments(mol, break_fused_rings=False)
+    assert len(frags) == 3
+
+
+def test_murcko_next(mol):
+    scf = get_murcko_scaffold(mol)
+    frags_1 = get_next_murcko_fragments(scf, break_fused_rings=True)
+    frags_1 = {Chem.MolToSmiles(x) for x in frags_1}
+    assert len(frags_1) == 2
+    frags_2 = get_next_murcko_fragments(scf, break_fused_rings=False)
+    frags_2 = {Chem.MolToSmiles(x) for x in frags_2}
+    assert len(frags_2) == 2
+    assert len(frags_1.intersection(frags_2)) == 1

tests/core/test_graph.py

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+"""
+scaffoldgraph tests.core.test_graph
+"""
+
+from rdkit import Chem
+
+from scaffoldgraph.core.graph import *
+
+
+def test_init_molecule_name():
+    x = Chem.MolFromSmiles('CCC')
+    assert bool(x.HasProp('_Name')) is False
+    init_molecule_name(x)
+    assert x.HasProp('_Name')
+    assert x.GetProp('_Name') is not None
+    assert x.GetProp('_Name') != ''
+
+
+def test_graph_subclass():
+    assert issubclass(ScaffoldGraph, DiGraph)
+    assert issubclass(ScaffoldGraph, ABC)

tests/core/test_scaffold.py

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+"""
+scaffoldgraph tests.core.test_scaffold
+"""
+
+import pytest
+from rdkit import Chem
+
+from scaffoldgraph.core.scaffold import *
+
+
+@pytest.fixture(name='scaffold')
+def basic_scaffold():
+    # murcko scaffold smiles
+    mol = Chem.MolFromSmiles('O=C(Nc1ccccc1)Nc1cc2c(s1)CNCC2')
+    scaffold = Scaffold(mol)
+    return scaffold
+
+
+def test_new():
+    scaffold = Scaffold(None)
+    assert scaffold is None
+
+
+def test_smiles(scaffold):
+    assert scaffold.smiles == 'O=C(Nc1ccccc1)Nc1cc2c(s1)CNCC2'
+    assert scaffold.get_canonical_identifier() == scaffold.smiles
+    assert scaffold == Scaffold(Chem.MolFromSmiles(scaffold.smiles))
+    assert scaffold == scaffold.smiles
+    assert str(scaffold) == scaffold.smiles
+    assert hash(scaffold) == hash(scaffold.smiles)
+
+
+def test_name(scaffold):
+    assert scaffold.name is None
+    scaffold.name = 'TEST'
+    assert scaffold.name == 'TEST'
+    assert repr(scaffold) == '<Scaffold at {}>'.format(hex(id(scaffold)))
+    assert bool(scaffold) is True
+
+
+def test_atoms(scaffold):
+    atoms = scaffold.atoms
+    assert len(atoms) == scaffold.mol.GetNumAtoms()
+    assert all([isinstance(x, Chem.Atom) for x in atoms])
+
+
+def test_bonds(scaffold):
+    bonds = scaffold.bonds
+    assert len(bonds) == scaffold.mol.GetNumBonds()
+    assert all([isinstance(x, Chem.Bond) for x in bonds])
+
+
+def test_rings(scaffold):
+    rings = scaffold.rings
+    assert isinstance(rings, RingStack)
+    assert hasattr(rings, 'owner')
+    assert hasattr(rings, 'info')
+    assert hasattr(rings, 'atom_rings')
+    assert hasattr(rings, 'bond_rings')
+    assert rings.count == 3 and len(rings) == 3
+    assert repr(rings) == '<RingStack at {}>'.format(hex(id(rings)))
+    assert isinstance(rings[0], Ring)
+    assert len([x for x in rings]) == 3
+    assert isinstance(rings.info, Chem.RingInfo)
+    assert len(rings.atom_rings) == 3 and len(rings.bond_rings) == 3
+    ring = rings[1]
+    assert hasattr(ring, 'owner')
+    assert hasattr(ring, 'aix')
+    assert hasattr(ring, 'bix')
+    assert all([isinstance(x, Chem.Bond) for x in ring.bonds])
+    assert all([isinstance(x, Chem.Atom) for x in ring.atoms])
+    assert isinstance(ring.size, int)
+    assert len(ring) == len(ring.atoms)
+    assert repr(ring) == '<Ring at {}>'.format(hex(id(ring)))
+
+
+def test_ring_systems(scaffold):
+    rings = scaffold.ring_systems
+    assert isinstance(rings, RingSystemStack)
+    assert hasattr(rings, 'owner')
+    assert hasattr(rings, 'ring_indexes')
+    assert hasattr(rings, 'atom_rings')
+    assert hasattr(rings, 'bond_rings')
+    assert rings.count == 2 and len(rings) == 2
+    assert repr(rings) == '<RingSystemStack at {}>'.format(hex(id(rings)))
+    assert isinstance(rings[0], RingSystem)
+    assert len([x for x in rings]) == 2
+    assert len(rings.atom_rings) == 2 and len(rings.bond_rings) == 2
+    ring = rings[1]
+    assert hasattr(ring, 'owner')
+    assert hasattr(ring, 'aix')
+    assert hasattr(ring, 'bix')
+    assert hasattr(ring, 'rix')
+    assert all([isinstance(x, Chem.Bond) for x in ring.bonds])
+    assert all([isinstance(x, Chem.Atom) for x in ring.atoms])
+    assert isinstance(ring.size, int)
+    assert len(ring) == len(ring.atoms)
+    assert repr(ring) == '<RingSystem at {}>'.format(hex(id(ring)))
+    assert isinstance(ring[0], Ring)
+    assert len(list(ring.get_rings())) == 2