chore: rename m7g -> larp1_dm15

tests/conftest.py

@@ -19,27 +19,27 @@ def tmp_dir():
 
 
 @pytest.fixture
-def path_m7g_paths():
+def path_larp1_dm15_paths():
     paths = {
-        "topo": os.path.join(TEST_DIR, "files/m7g/mol.prmtop"),
-        "ref_pdb": os.path.join(TEST_DIR, "files/m7g/mol.pdb"),
-        "traj": os.path.join(TEST_DIR, "files/m7g/mol.nc"),
-        "restart": os.path.join(TEST_DIR, "files/m7g/mol.rst"),
+        "topo": os.path.join(TEST_DIR, "files/larp1_dm15/mol.prmtop"),
+        "ref_pdb": os.path.join(TEST_DIR, "files/larp1_dm15/mol.pdb"),
+        "traj": os.path.join(TEST_DIR, "files/larp1_dm15/mol.nc"),
+        "restart": os.path.join(TEST_DIR, "files/larp1_dm15/mol.rst"),
     }
     return paths
 
 
 @pytest.fixture
-def m7g_config():
+def larp1_dm15_config():
     subpex_config = SubpexConfig()
     subpex_config.pocket.center = [30.037991, 41.463818, 30.3776]
     subpex_config.pocket.radius = 6.5
     subpex_config.pocket.water_dist = 6.7
     subpex_config.pocket.selection_str = "resid 124 or resid 125 or resid 128 or resid 88 or resid 89 or resid 121 or resid 92 or resid 129 and (not name H*)"
     subpex_config.sim.path_traj_relax = os.path.join(
-        TEST_DIR, "files/m7g/equil_frames.nc"
+        TEST_DIR, "files/larp1_dm15/equil_frames.nc"
     )
-    subpex_config.sim.path_topo = os.path.join(TEST_DIR, "files/m7g/mol.prmtop")
+    subpex_config.sim.path_topo = os.path.join(TEST_DIR, "files/larp1_dm15/mol.prmtop")
     for aux_data in subpex_config.data.aux.get_all():
         aux_data.active = True
     return subpex_config

tests/test_pocket_detect.py

@@ -6,8 +6,8 @@
 from subpex.pocket.detect import get_fop_pocket_convenience, get_pocket_selection
 
 
-def test_pocket_selection_m7g(
-    path_m7g_paths: MutableMapping[str, str], m7g_config: SubpexConfig
+def test_pocket_selection_larp1_dm15(
+    path_larp1_dm15_paths: MutableMapping[str, str], larp1_dm15_config: SubpexConfig
 ) -> None:
     """
     Test the selection of atoms for the binding pocket in a molecular dynamics simulation.
@@ -17,28 +17,28 @@ def test_pocket_selection_m7g(
     is compared against a known selection string from the configuration.
 
     Args:
-        path_m7g_paths (dict): Dictionary containing paths to the input files required for the test:
+        path_larp1_dm15_paths (dict): Dictionary containing paths to the input files required for the test:
             - "ref_pdb": Path to the reference PDB file.
-        m7g_config (object): Configuration object for the simulation which includes the parameters
+        larp1_dm15_config (object): Configuration object for the simulation which includes the parameters
             for defining the pocket (center, radius, and selection distance).
 
     Raises:
         AssertionError: If the computed pocket selection string does not match the expected value.
     """
     # Load structure
-    u = mda.Universe(path_m7g_paths["ref_pdb"])
+    u = mda.Universe(path_larp1_dm15_paths["ref_pdb"])
 
     pocket_selection = get_pocket_selection(
         u,
-        center=m7g_config.pocket.center,  # type: ignore
-        radius=m7g_config.pocket.radius,
-        water_dist=m7g_config.pocket.water_dist,  # type: ignore
+        center=larp1_dm15_config.pocket.center,  # type: ignore
+        radius=larp1_dm15_config.pocket.radius,
+        water_dist=larp1_dm15_config.pocket.water_dist,  # type: ignore
     )
-    assert pocket_selection == m7g_config.pocket.selection_str
+    assert pocket_selection == larp1_dm15_config.pocket.selection_str
 
 
-def test_pocket_fop_gen_m7g(
-    path_m7g_paths: MutableMapping[str, str], m7g_config: SubpexConfig
+def test_pocket_fop_gen_larp1_dm15(
+    path_larp1_dm15_paths: MutableMapping[str, str], larp1_dm15_config: SubpexConfig
 ) -> None:
     """
     Test the generation of the Frame of Pocket (FOP) for the binding pocket in a molecular dynamics simulation.
@@ -48,17 +48,17 @@ def test_pocket_fop_gen_m7g(
     and specific coordinates of a known atom are verified against expected values.
 
     Args:
-        path_m7g_paths (dict): Dictionary containing paths to the input files required for the test:
+        path_larp1_dm15_paths (dict): Dictionary containing paths to the input files required for the test:
             - "ref_pdb": Path to the reference PDB file.
-        m7g_config (object): Configuration object for the simulation which includes settings for
+        larp1_dm15_config (object): Configuration object for the simulation which includes settings for
             detecting the pocket.
 
     Raises:
         AssertionError: If the number of detected pocket atoms or the coordinates of a specific
             atom do not match the expected values.
     """
-    u = mda.Universe(path_m7g_paths["ref_pdb"])
-    fop_frame = get_fop_pocket_convenience(u.atoms, m7g_config)
+    u = mda.Universe(path_larp1_dm15_paths["ref_pdb"])
+    fop_frame = get_fop_pocket_convenience(u.atoms, larp1_dm15_config)
 
     assert len(fop_frame) == 1057
     assert fop_frame[57] == [31.5, 38.5, 31.0]

tests/test_traj_compute.py

@@ -8,7 +8,7 @@
 from subpex.pocket.detect import get_fop_pocket_convenience
 
 
-def test_traj_data_m7g(path_m7g_paths, m7g_config, tmp_dir):
+def test_traj_data_larp1_dm15(path_larp1_dm15_paths, larp1_dm15_config, tmp_dir):
     """
     Test the computation of auxiliary data during a simulation for the binding pocket descriptors.
 
@@ -17,11 +17,11 @@ def test_traj_data_m7g(path_m7g_paths, m7g_config, tmp_dir):
     topology, and trajectory files, and verifies the computed auxiliary data against known values.
 
     Args:
-        path_m7g_paths (dict): Dictionary containing paths to the input files required for the test:
+        path_larp1_dm15_paths (dict): Dictionary containing paths to the input files required for the test:
             - "ref_pdb": Path to the reference PDB file.
             - "topo": Path to the topology file.
             - "traj": Path to the trajectory file.
-        m7g_config (object): Configuration object for the simulation which includes settings and
+        larp1_dm15_config (object): Configuration object for the simulation which includes settings and
             parameters for computing the auxiliary data.
         tmp_dir (str): Path to a temporary directory for writing output data during the test.
 
@@ -52,20 +52,20 @@ def test_traj_data_m7g(path_m7g_paths, m7g_config, tmp_dir):
         is the last frame of the same simulation, properties compared to the reference should
         be close to zero.
     """
-    u = mda.Universe(path_m7g_paths["ref_pdb"])
-    fop_ref = get_fop_pocket_convenience(u.atoms, m7g_config)
+    u = mda.Universe(path_larp1_dm15_paths["ref_pdb"])
+    fop_ref = get_fop_pocket_convenience(u.atoms, larp1_dm15_config)
 
-    write_dir = os.path.join(tmp_dir, "m7g/calc-data/")
+    write_dir = os.path.join(tmp_dir, "larp1_dm15/calc-data/")
     if os.path.exists(write_dir):
         shutil.rmtree(write_dir)
     os.makedirs(write_dir, exist_ok=False)
 
     run_compute_data(
-        topo_path=path_m7g_paths["topo"],
-        traj_path=path_m7g_paths["traj"],
-        ref_path=path_m7g_paths["ref_pdb"],
+        topo_path=path_larp1_dm15_paths["topo"],
+        traj_path=path_larp1_dm15_paths["traj"],
+        ref_path=path_larp1_dm15_paths["ref_pdb"],
         fop_ref=fop_ref,
-        subpex_config=m7g_config,
+        subpex_config=larp1_dm15_config,
         selection_align_suffix=" and backbone",
         write=False,
         write_dir=write_dir,
@@ -81,7 +81,7 @@ def test_traj_data_m7g(path_m7g_paths, m7g_config, tmp_dir):
                 0.0002885486464947462,
             ]
         ),
-        np.array(m7g_config.data.aux.backbone_rmsd.values),
+        np.array(larp1_dm15_config.data.aux.backbone_rmsd.values),
     )
     assert np.allclose(
         np.array(
@@ -93,7 +93,7 @@ def test_traj_data_m7g(path_m7g_paths, m7g_config, tmp_dir):
                 0.0,
             ]
         ),
-        np.array(m7g_config.data.aux.pocket_jd.values),
+        np.array(larp1_dm15_config.data.aux.pocket_jd.values),
     )
     assert np.allclose(
         np.array(
@@ -105,7 +105,7 @@ def test_traj_data_m7g(path_m7g_paths, m7g_config, tmp_dir):
                 0.0003747374867089093,
             ]
         ),
-        np.array(m7g_config.data.aux.pocket_rmsd.values),
+        np.array(larp1_dm15_config.data.aux.pocket_rmsd.values),
     )
     assert np.allclose(
         np.array(
@@ -117,9 +117,9 @@ def test_traj_data_m7g(path_m7g_paths, m7g_config, tmp_dir):
                 3.2499845795814117,
             ]
         ),
-        np.array(m7g_config.data.aux.pocket_rog.values),
+        np.array(larp1_dm15_config.data.aux.pocket_rog.values),
     )
     assert np.allclose(
         np.array([129.625, 123.25, 126.25, 124.625, 129.0]),
-        np.array(m7g_config.data.aux.pocket_volume.values),
+        np.array(larp1_dm15_config.data.aux.pocket_volume.values),
     )

tests/test_westpa_init.py

@@ -5,17 +5,17 @@
 from subpex.setup.westpa.main import run_westpa_setup
 
 
-def test_westpa_init_m7g(path_m7g_paths, m7g_config, tmp_dir):
+def test_westpa_init_larp1_dm15(path_larp1_dm15_paths, larp1_dm15_config, tmp_dir):
     westpa_config = WestpaConfig()
-    write_dir = os.path.join(tmp_dir, "westpa_init_m7g")
+    write_dir = os.path.join(tmp_dir, "westpa_init_larp1_dm15")
     if os.path.exists(write_dir):
         shutil.rmtree(write_dir)
 
     # Setup WESTPA
     westpa_config.env.load_modules = ["gcc/10.2.0", "openmpi/4.1.1", "amber/22"]
 
     run_westpa_setup(
-        subpex_config=m7g_config,
+        subpex_config=larp1_dm15_config,
         westpa_config=westpa_config,
         write_dir=write_dir,
         overwrite=True,