adding tests for chempy models

Author: ye11owSub

testing/tests/chempy/models/test_connected.py

@@ -0,0 +1,68 @@
+from chempy import Atom, Bond
+import pytest
+
+from chempy.models import Indexed, Connected
+
+
+@pytest.fixture
+def connected_model() -> Connected:
+    connected_model = Connected()
+
+    for i in range(3):
+        atom = Atom()
+        atom.symbol = "H" if i == 0 else "He"
+        atom.chain = "AB" if i == 0 else "BA"
+
+        atom.coord = [float(i), 0., 0.]
+        connected_model.add_atom(atom)
+
+    for i in range(len(connected_model.atom)):
+        connected_model.bond.append([])
+
+        bond = Bond()
+        bond.index = [i, i + 1]
+        bond.order = i
+        # note two refs to same object
+        connected_model.bond[bond.index[0]].append(bond)
+        connected_model.bond[bond.index[1]].append(bond)
+    return connected_model
+
+
+def test_base_model_methods(connected_model):
+    assert connected_model.nAtom == 3
+    assert connected_model.nBond == 6
+    assert connected_model.get_residues() == [(0, 1), (1, 3)]
+    assert connected_model.get_coord_list() == [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [2.0, 0.0, 0.0]]
+    assert connected_model.get_mass() == 9.013144
+
+    assert connected_model.index is None
+    connected_model.update_index()
+    assert sorted(list(connected_model.index.values())) == [0, 1, 2]
+
+
+def test_add_atom(connected_model):
+    new_atom = Atom()
+    new_atom.symbol = "Ne"
+
+    assert len(connected_model.atom) == 3
+    connected_model.update_index()
+    previos_last_atom = connected_model.atom[0]
+
+    connected_model.add_atom(new_atom)
+    assert connected_model.atom[-1] is new_atom
+    assert connected_model.atom[-2] is not previos_last_atom
+
+    assert len(connected_model.atom) == 4
+
+
+def test_convert_to_indexed(connected_model):
+    indexed_model = connected_model.convert_to_indexed()
+    assert isinstance(indexed_model, Indexed)
+    assert len(indexed_model.atom) == 3
+    assert len(indexed_model.atom) == 3
+    # maybe a bug ?
+
+    assert connected_model.atom == []
+    assert connected_model.bond == []
+    assert connected_model.index == None
+

testing/tests/chempy/models/test_indexed.py

@@ -0,0 +1,98 @@
+from chempy import Atom, Bond
+import pytest
+
+from chempy.models import Indexed, Connected
+
+
+@pytest.fixture
+def indexed_model() -> Indexed:
+    indexed_model = Indexed()
+
+    for i in range(3):
+        atom = Atom()
+        atom.symbol = "H" if i == 0 else "He"
+        atom.chain = "AB" if i == 0 else "BA"
+
+        atom.coord = [float(i), 0., 0.]
+        indexed_model.add_atom(atom)
+
+        bond = Bond()
+        bond.index = [0, i]
+        bond.order = i
+        indexed_model.add_bond(bond)
+
+    return indexed_model
+
+
+def test_base_model_methods(indexed_model):
+    assert indexed_model.nAtom == 3
+    assert indexed_model.nBond == 3
+    assert indexed_model.get_residues() == [(0, 1), (1, 3)]
+    assert indexed_model.get_coord_list() == [[0.0, 0.0, 0.0], [1.0, 0.0, 0.0], [2.0, 0.0, 0.0]]
+    assert indexed_model.get_mass() == 9.013144
+
+    assert indexed_model.index is None
+    indexed_model.update_index()
+    assert sorted(list(indexed_model.index.values())) == [0, 1, 2]
+
+
+def test_indexed_merge(indexed_model):
+    other_indexed_model = Indexed()
+
+    atom = Atom()
+    atom.symbol = "Ne"
+    atom.chain = "F"
+
+    atom.coord = [0., 0., 7.]
+    other_indexed_model.add_atom(atom)
+
+    bond = Bond()
+    bond.index = [1, 1]
+    bond.order = 1
+    other_indexed_model.add_bond(bond)
+
+    indexed_model.update_index()
+    assert sorted(list(indexed_model.index.values())) == [0, 1, 2]
+
+    indexed_model.merge(other_indexed_model)
+
+    assert sorted(list(indexed_model.index.values())) == [0, 1, 2, 3]
+    assert len(indexed_model.atom) == 4
+    assert len(indexed_model.bond) == 4
+
+    assert other_indexed_model.index is None
+    assert other_indexed_model.bond == []
+    assert other_indexed_model.bond == []
+
+
+def test_add_atom(indexed_model):
+    new_atom = Atom()
+    new_atom.symbol = "Ne"
+
+    assert len(indexed_model.atom) == 3
+    indexed_model.update_index()
+    previos_last_atom = indexed_model.atom[0]
+
+    indexed_model.add_atom(new_atom)
+    assert indexed_model.atom[-1] is new_atom
+    assert indexed_model.atom[-2] is not previos_last_atom
+
+    assert len(indexed_model.atom) == 4
+
+
+def test_convert_to_connected(indexed_model):
+    connected_model = indexed_model.convert_to_connected()
+    assert isinstance(connected_model, Connected)
+    assert len(connected_model.bond) == 3
+    assert connected_model.bond[0] is connected_model.bond[0]
+    # maybe a bug ?
+
+    assert indexed_model.atom == []
+    assert indexed_model.bond == []
+    assert indexed_model.index == None
+
+
+def test_get_internal_tuples(indexed_model):
+    assert indexed_model.get_internal_tuples() == [(0,), (0, 0), (1, 0, 0)]
+
+