Merge pull request #4 from andrewtarzia/mae_test

Make MAEExtractor public, add test.

docs/source/optimizers.rst

@@ -29,4 +29,5 @@ Optimizers
 
 
   GulpUFFMDOptimizer <_autosummary/stko.GulpUFFMDOptimizer>
-  MacroModelMD <_autosummary/stko.MacroModelMD>
+  MacroModelMD <_autosummary/stko.MacroModelMD>
+  MAEExtractor <_autosummary/stko.MAEExtractor>

src/stko/__init__.py

@@ -79,6 +79,7 @@
     TryCatchOptimizer,
 )
 from stko._internal.optimizers.rdkit import ETKDG, MMFF, UFF, MetalOptimizer
+from stko._internal.optimizers.utilities import MAEExtractor
 from stko._internal.optimizers.xtb import XTB, XTBCREST, XTBFF, XTBFFCREST
 from stko._internal.utilities.exceptions import (
     CalculatorError,
@@ -141,6 +142,7 @@
     "XTBCREST",
     "XTBFF",
     "XTBFFCREST",
+    "MAEExtractor",
     "PositionedAtom",
     "Du",
     "MDAnalysis",

src/stko/_internal/optimizers/utilities.py

@@ -33,37 +33,37 @@ class MAEExtractor:
     converts it to a ``.mae`` file. It then creates and additional
     ``.mae`` file holding only the lowest energy conformer found.
 
-    Attributes
-    ----------
-    maegz_path : :class:`str`
-        The path to the ``-out.maegz`` file generated by the macromodel
-        conformer search.
+    Attributes:
 
-    mae_path : :class:`str`
-        The path to the ``.mae`` file holding the conformers generated
-        by the macromodel conformer search.
+        maegz_path : :class:`str`
+            The path to the ``-out.maegz`` file generated by the macromodel
+            conformer search.
 
-    content : :class:`str`
-        The content of the ``.mae`` file hodling all the conformers
-        from the macromodel conformer search. This holds other data
-        such as their energies too.
+        mae_path : :class:`str`
+            The path to the ``.mae`` file holding the conformers generated
+            by the macromodel conformer search.
 
-    energies : :class:`list`
-        The :class:`list` has the form
+        content : :class:`str`
+            The content of the ``.mae`` file hodling all the conformers
+            from the macromodel conformer search. This holds other data
+            such as their energies too.
 
-        .. code-block:: python
+        energies : :class:`list`
+            The :class:`list` has the form
 
-            energies = [(0, 231.0), (1, 144.4), ...]
+            .. code-block:: python
+
+                energies = [(231.0, 0), (144.4, 1), ...]
 
-        Each :class:`tuple` holds the id and energy of every conformer
-        in the ``.mae`` file, respectively.
+            Where each :class:`tuple` holds the energy of the
+            `n` lowest energy conformers and the id, respectively.
 
-    min_energy : :class:`float`
-        The minimum energy found in the ``.mae`` file.
+        min_energy : :class:`float`
+            The minimum energy found in the ``.mae`` file.
 
-    path : :class:`str`
-        The full path of the ``.mae`` file holding the extracted lowest
-        energy conformer.
+        path : :class:`str`
+            The full path of the ``.mae`` file holding the extracted lowest
+            energy conformer.
 
     """
 

tests/optimizers/maeextractor/case_data.py

@@ -0,0 +1,23 @@
+class CaseData:
+    """
+    A test case.
+
+    """
+
+    def __init__(
+        self,
+        run_name: str,
+        mae_path: str,
+        n: int,
+        energies: list,
+        min_energy: float,
+        path: str,
+        name: str,
+    ) -> None:
+        self.run_name = run_name
+        self.n = n
+        self.mae_path = mae_path
+        self.energies = energies
+        self.min_energy = min_energy
+        self.path = path
+        self.name = name

tests/optimizers/maeextractor/conftest.py

@@ -0,0 +1,136 @@
+import pytest
+
+from .case_data import CaseData
+
+_energies = [
+    (1649.50158691406, 1),
+    (1722.63293457031, 2),
+    (1607.67626953125, 3),
+    (1604.86291503906, 4),
+    (1588.51037597656, 5),
+    (1577.38671875, 6),
+    (1628.57958984375, 7),
+    (1579.61926269531, 8),
+    (1621.49975585938, 9),
+    (1627.87585449219, 10),
+    (1615.9462890625, 11),
+    (1600.01208496094, 12),
+    (1601.82263183594, 13),
+    (1669.08312988281, 14),
+    (1677.03796386719, 15),
+    (1598.83813476562, 16),
+    (1623.77331542969, 17),
+    (1601.51000976562, 18),
+    (1595.39501953125, 19),
+    (1601.62170410156, 20),
+    (1585.79992675781, 21),
+    (1692.82690429688, 22),
+    (1641.13891601562, 23),
+    (1648.33898925781, 24),
+    (1701.05114746094, 25),
+    (1609.71362304688, 26),
+    (1668.08581542969, 27),
+    (1642.79821777344, 28),
+    (1626.81860351562, 29),
+    (1598.40185546875, 30),
+    (1596.69543457031, 31),
+    (1670.2080078125, 32),
+    (1608.22106933594, 33),
+    (1657.68298339844, 34),
+    (1616.05322265625, 35),
+    (1574.47778320312, 36),
+    (1578.36291503906, 37),
+    (1610.46337890625, 38),
+    (1648.68884277344, 39),
+    (1607.71716308594, 40),
+    (1649.50402832031, 41),
+    (1672.12194824219, 42),
+    (1610.67810058594, 43),
+    (1630.57885742188, 44),
+    (1602.98059082031, 45),
+    (1638.20202636719, 46),
+    (1667.32836914062, 47),
+    (1581.57482910156, 48),
+    (1606.1328125, 49),
+    (1649.66223144531, 50),
+    (1610.92443847656, 51),
+    (1609.87719726562, 52),
+    (1650.9794921875, 53),
+    (1668.99499511719, 54),
+    (1700.49877929688, 55),
+    (1674.94970703125, 56),
+    (1642.20751953125, 57),
+    (1702.6923828125, 58),
+    (1672.70031738281, 59),
+    (1672.16320800781, 60),
+    (1670.28076171875, 61),
+    (1686.03771972656, 62),
+    (1664.91577148438, 63),
+    (1647.33508300781, 64),
+    (1714.8671875, 65),
+    (1696.59802246094, 66),
+    (1645.01538085938, 67),
+    (1597.09240722656, 68),
+    (1613.04235839844, 69),
+    (1622.42114257812, 70),
+    (1605.45751953125, 71),
+    (1602.25036621094, 72),
+    (1594.09802246094, 73),
+    (1654.03540039062, 74),
+    (1609.90295410156, 75),
+    (1563.08666992188, 76),
+    (1652.13793945312, 77),
+    (1565.83251953125, 78),
+    (1640.81762695312, 79),
+    (1607.97631835938, 80),
+    (1649.76391601562, 81),
+    (1665.44958496094, 82),
+    (1651.71862792969, 83),
+    (1687.31689453125, 84),
+    (1679.642578125, 85),
+    (1676.05688476562, 86),
+    (1660.06896972656, 87),
+    (1610.8662109375, 88),
+    (1718.63208007812, 89),
+    (1694.84851074219, 90),
+    (1719.84423828125, 91),
+    (1698.97583007812, 92),
+    (1683.58813476562, 93),
+    (1661.88049316406, 94),
+    (1700.79724121094, 95),
+    (1682.1865234375, 96),
+    (1639.63977050781, 97),
+    (1629.56079101562, 98),
+    (1623.24731445312, 99),
+    (1711.85949707031, 100),
+    (1711.732421875, 101),
+]
+
+
+@pytest.fixture(
+    scope="session",
+    params=(
+        lambda name: CaseData(
+            run_name="test",
+            n=1,
+            mae_path="test-out.mae",
+            energies=_energies,
+            min_energy=1563.08666992188,
+            path="test-outEXTRACTED_76.mae",
+            name=name,
+        ),
+        lambda name: CaseData(
+            run_name="test",
+            n=4,
+            mae_path="test-out.mae",
+            energies=_energies,
+            min_energy=1563.08666992188,
+            path="test-outEXTRACTED_76_conf_0.mae",
+            name=name,
+        ),
+    ),
+)
+def case_data(request) -> CaseData:
+    return request.param(
+        f"{request.fixturename}{request.param_index}",
+    )

tests/optimizers/maeextractor/test_maeextractor.py

@@ -0,0 +1,46 @@
+import os
+
+from stko import MAEExtractor
+
+
+def test_maeextractor(case_data):
+    """
+    Test :class:`.MAEExtractor`.
+
+    """
+    dir_path = os.path.dirname(os.path.realpath(__file__))
+    # Extract the lowest energy conformer into its own .mae file.
+    extractor = MAEExtractor(
+        run_name=os.path.join(dir_path, case_data.run_name),
+        n=case_data.n,
+    )
+
+    print(extractor.mae_path)
+    assert extractor.mae_path.split("/")[-1] == case_data.mae_path
+
+    assert len(extractor.energies) == len(case_data.energies)
+    min_energy = 1e24
+    for test, known in zip(
+        extractor.energies, case_data.energies, strict=True
+    ):
+        assert test == known
+        if test[0] < min_energy:
+            min_energy = test[0]
+
+    print(min_energy)
+    assert min_energy == extractor.min_energy
+
+    print(extractor.min_energy)
+    assert extractor.min_energy == case_data.min_energy
+
+    print(extractor.path)
+    assert extractor.path.split("/")[-1] == case_data.path
+
+    os.remove(os.path.join(dir_path, "test-out.mae"))
+    if case_data.n == 1:
+        os.remove(os.path.join(dir_path, "test-outEXTRACTED_76.mae"))
+    elif case_data.n == 4:
+        os.remove(os.path.join(dir_path, "test-outEXTRACTED_36_conf_2.mae"))
+        os.remove(os.path.join(dir_path, "test-outEXTRACTED_6_conf_3.mae"))
+        os.remove(os.path.join(dir_path, "test-outEXTRACTED_76_conf_0.mae"))
+        os.remove(os.path.join(dir_path, "test-outEXTRACTED_78_conf_1.mae"))