fixed test_topology_generator test and made it so that topology_manag…

…er_tests now navigate to the test directory before running tests, so that files generated from tests are not left in whatever directory you `run pytest` from

terphenyl_simulations/force_fields.py

@@ -53,7 +53,7 @@ def _get_partial_charges(self, method="am1bcc"):
             self.molecule.assign_partial_charges(partial_charge_method=method)
             self.molecule.to_file(self.sdf_file, file_format="sdf")
         else:
-            self.molecule = Molecule.from_file(sdf_file)
+            self.molecule = Molecule.from_file(self.sdf_file)
 
     def _generate_ff_topologies(self):
         interchange = Interchange.from_smirnoff(

terphenyl_simulations/tests/test_build_workflow/test_build_objects.py

@@ -5,7 +5,9 @@
 using just the input foldamer.build file
 """
 
-from terphenyl_simulations.build import FoldamerBuilder, SystemBuilder
+from terphenyl_simulations.build import FoldamerBuilder
+import terphenyl_simulations
+from unittest.mock import patch, mock_open, MagicMock
 from terphenyl_simulations.utils import ROOT_DIR
 import pytest
 import shutil
@@ -26,22 +28,8 @@ def setup_foldamer_builder_tests():
     yield FoldamerBuilder("mop_tetramer.build", path="output")
     os.chdir(top_dir)
 
-
-@pytest.fixture
-def setup_system_builder_tests():
-    # Navigate to specific test directory
-    top_dir = os.path.abspath("")
-    os.chdir(os.path.join(ROOT_DIR, "tests/test_build_workflow"))
-    if os.path.isdir("output"):
-        shutil.rmtree("output")
-    fb = FoldamerBuilder("mop_tetramer.build", path="output")
-    fb.build_foldamer()
-    fb.write_pdb()
-    yield SystemBuilder("TCM", "mop_tetramer.build", path="output")
-    os.chdir(top_dir)
-
-
-def test_foldamer_builder_chain(setup_foldamer_builder_tests):
+@patch("terphenyl_simulations.build.TopologyManager.add_structure")
+def test_foldamer_builder_chain(mock_add_structure, setup_foldamer_builder_tests):
     builder = setup_foldamer_builder_tests
     builder.build_foldamer()
     assert builder.chain.n_particles == 197
@@ -50,33 +38,11 @@ def test_foldamer_builder_chain(setup_foldamer_builder_tests):
     for label in builder.chain.labels["Compound"]:
         assert label.name == "CAP"
 
-
-def test_foldamer_builder_file_writing(setup_foldamer_builder_tests):
+@patch("terphenyl_simulations.build.TopologyManager.add_structure")
+def test_foldamer_builder_file_writing(mock_add_stricture, setup_foldamer_builder_tests):
     builder = setup_foldamer_builder_tests
     builder.build_foldamer()
     builder.write_pdb()
     builder.write_mol()
     assert os.path.exists("output/mop_tetramer.pdb")
     assert os.path.exists("output/mop_tetramer.mol")
-
-
-def test_system_builder_inp(setup_system_builder_tests):
-    builder = setup_system_builder_tests
-    builder.build_packmol_inp()
-    assert os.path.exists("output/solvate.inp")
-    with open("output/solvate.inp", "r") as f:
-        for line in f.readlines():
-            assert "OUTPUT_FILENAME" not in line
-            assert "SOLUTE_PDB" not in line
-            assert "SOLUTE_POSITION" not in line
-            assert "SOLVENT_PDB" not in line
-            assert "N_SOLVENT" not in line
-            assert "SOLVENT_BOX" not in line
-
-
-def test_system_builder_packmol(setup_system_builder_tests):
-    system_builder = setup_system_builder_tests
-    system_builder.build_packmol_inp()
-    system_builder.solvate_system()
-    assert os.path.exists("output/solvated_mop_tetramer.pdb")
-    assert os.path.exists("output/TCM.pdb")

terphenyl_simulations/tests/test_topology_generator/test_topology_generator.py

@@ -77,74 +77,4 @@ def test_default_tg_output(setup_default_ff_tests_post_charges):
     default_ff_object._get_partial_charges()
     default_ff_object._generate_ff_topologies()
     assert os.path.exists("output/mop_dimer_openff-2.0.0.top")
-    assert os.path.exists("output/mop_dimer_openff-2.0.0.gro")
-
-
-def test_topology_manager_save_load(navigate_to_test_dir):
-    assert navigate_to_test_dir is None
-    tp_manager = TopologyManager(topology_dir="", topology_object="top_manager.pkl")
-    tp_manager.topology_dictionary["test_key"] = "test_value"
-    tp_manager.save()
-
-    tp_manager_load = TopologyManager(
-        topology_dir="", topology_object="top_manager.pkl"
-    )
-
-    assert os.path.exists("top_manager.pkl")
-    assert "test_key" in tp_manager_load.topology_dictionary.keys()
-    assert tp_manager_load.topology_dictionary["test_key"] == "test_value"
-    os.remove("top_manager.pkl")
-
-
-def test_topology_manager_save_top_file(setup_default_ff_tests_post_charges):
-    default_ff_object = setup_default_ff_tests_post_charges
-    default_ff_object._get_partial_charges()
-    default_ff_object._generate_ff_topologies()
-
-    tp_manager = TopologyManager(
-        topology_dir="output_2", topology_object="top_manager.pkl"
-    )
-    tp_manager.add_topology(
-        "mop_tetramer.build",
-        [
-            "output/mop_dimer_charges.sdf",
-            "output/mop_dimer_openff-2.0.0.gro",
-            "output/mop_dimer_openff-2.0.0.top",
-            "output/mop_dimer_renum.pdb",
-        ],
-    )
-
-    assert os.path.exists("output_2/top_manager.pkl")
-    assert os.path.exists("output_2/mop_dimer_charges.sdf")
-    assert os.path.exists("output_2/mop_dimer_openff-2.0.0.gro")
-    assert os.path.exists("output_2/mop_dimer_openff-2.0.0.top")
-    assert os.path.exists("output_2/mop_dimer_renum.pdb")
-
-    shutil.rmtree("output_2")
-
-
-def test_topology_manager_save_top_file(setup_default_ff_tests_post_charges):
-    default_ff_object = setup_default_ff_tests_post_charges
-    default_ff_object._get_partial_charges()
-    default_ff_object._generate_ff_topologies()
-
-    tp_manager = TopologyManager(
-        topology_dir="output_2", topology_object="top_manager.pkl"
-    )
-    tp_manager.add_topology(
-        "mop_tetramer.build",
-        [
-            "output/mop_dimer_charges.sdf",
-            "output/mop_dimer_openff-2.0.0.gro",
-            "output/mop_dimer_openff-2.0.0.top",
-            "output/mop_dimer_renum.pdb",
-        ],
-    )
-
-    loaded_tp = TopologyManager(
-        topology_dir="output_2", topology_object="top_manager.pkl"
-    )
-    print(loaded_tp)
-
-    assert loaded_tp.topology_dictionary.keys() == tp_manager.topology_dictionary.keys()
-    shutil.rmtree("output_2")
+    assert os.path.exists("output/mop_dimer_openff-2.0.0.gro")

terphenyl_simulations/tests/test_topology_manager/test_topology_manager.py

@@ -6,14 +6,21 @@
 import uuid
 import yaml
 import json
+import pytest
 from glob import glob
 from terphenyl_simulations.build import (
-    TopologyManager,
+    TopologyManager, ROOT_DIR
 )  # Assuming this class is in a module named 'topology_manager'
 import terphenyl_simulations
 
 
 class TestTopologyManager(unittest.TestCase):
+    @pytest.fixture(autouse = True)
+    def navigate_to_test_dir(self):
+        top_dir = os.path.abspath("")
+        os.chdir(os.path.join(ROOT_DIR, "tests/test_topology_manager"))
+        yield
+        os.chdir(top_dir)
 
     @patch("os.makedirs")
     @patch("os.path.isdir", return_value=False)