files to ckpt

mdagent/tools/base_tools/analysis_tools/rgy.py

@@ -49,7 +49,9 @@ def rad_gyration_per_frame(self, pdb_id: str) -> str:
         self._load_traj(pdb_id)
         rg_per_frame = md.compute_rg(self.traj)
 
-        self.rgy_file = f"files/radii_of_gyration_{self.pdb_id}.csv"
+        self.rgy_file = (
+            f"{self.path_registry}/files/radii_of_gyration_{self.pdb_id}.csv"
+        )
 
         np.savetxt(
             self.rgy_file, rg_per_frame, delimiter=",", header="Radius of Gyration (nm)"

mdagent/tools/base_tools/preprocess_tools/clean_tools.py

@@ -349,7 +349,7 @@ def _run(self, **input_args) -> str:
             #                    version += 1
             #
             #                file_name = f"tidy_{name}v{version}.{end}"
-            directory = "files/pdb"
+            directory = f"{self.path_registry}/files/pdb"
             if not os.path.exists(directory):
                 os.makedirs(directory)
             if end == "pdb":

mdagent/tools/base_tools/preprocess_tools/packing.py

@@ -96,7 +96,9 @@ def generate_input_header(self) -> None:
                 ]
             )
         )
-        while os.path.exists(f"files/pdb/{_final_name}_v{self.file_number}.pdb"):
+        while os.path.exists(
+            f"{self.path_registry}/pdb/{_final_name}_v{self.file_number}.pdb"
+        ):
             self.file_number += 1
 
         self.final_name = f"{_final_name}_v{self.file_number}.pdb"
@@ -155,7 +157,7 @@ def run_packmol(self):
             os.rename(self.final_name, f"files/pdb/{self.final_name}")
             self.path_registry.map_path(
                 f"PACKED_{time_stamp}",
-                f"files/pdb/{self.final_name}",
+                f"{self.path_registry}/files/pdb/{self.final_name}",
                 self.file_description,
             )
             # move file to files/pdb

mdagent/tools/base_tools/preprocess_tools/pdb_get.py

@@ -45,7 +45,7 @@ def get_pdb(query_string: str, path_registry: PathRegistry):
             file_format=filetype,
         )
         file_id = path_registry.get_fileid(filename, FileType.PROTEIN)
-        directory = "files/pdb"
+        directory = "{self.path_registry}/files/pdb"
         # Create the directory if it does not exist
         if not os.path.exists(directory):
             os.makedirs(directory)
@@ -184,7 +184,7 @@ def small_molecule_pdb(self, mol_str: str) -> str:
             except Exception:
                 pass
             Chem.AllChem.EmbedMolecule(m)
-            file_name = f"files/pdb/{mol_name}.pdb"
+            file_name = f"{self.path_registry}/files/pdb/{mol_name}.pdb"
             Chem.MolToPDBFile(m, file_name)
             self.path_registry.map_path(
                 mol_name, file_name, f"pdb file for the small molecule {mol_name}"

mdagent/tools/base_tools/simulation_tools/create_simulation.py

@@ -129,7 +129,7 @@ def _run(self, *args, **input):
             type=FileType.SIMULATION, Sim_id=base_script_id, modified=True
         )
         file_id = self.path_registry.get_fileid(filename, type=FileType.SIMULATION)
-        directory = "files/simulations"
+        directory = "{self.path_registry}/files/simulations"
         if not os.path.exists(directory):
             os.makedirs(directory)
         with open(f"{directory}/{filename}", "w") as file:

mdagent/tools/base_tools/simulation_tools/setup_and_run.py

@@ -793,9 +793,17 @@ def create_simulation(self):
                 )
             )
             self.registry_records = [
-                ("holder", f"files/records/{trajectory_name}", traj_desc),
-                ("holder", f"files/records/{log_name}", log_desc),
-                ("holder", f"files/records/{topology_name}", top_desc),
+                (
+                    "holder",
+                    f"{self.path_registry}/files/records/{trajectory_name}",
+                    traj_desc,
+                ),
+                ("holder", f"{self.path_registry}/files/records/{log_name}", log_desc),
+                (
+                    "holder",
+                    f"{self.path_registry}/files/records/{topology_name}",
+                    top_desc,
+                ),
             ]
 
             # TODO add checkpoint too?
@@ -1128,7 +1136,7 @@ def remove_leading_spaces(text):
         script_content = textwrap.dedent(script_content).strip()
 
         # Write to file
-        directory = "files/simulations"
+        directory = "{self.path_registry}/files/simulations"
         if not os.path.exists(directory):
             os.makedirs(directory)
 
@@ -1272,15 +1280,15 @@ def _run(self, **input_args):
             openmmsim.write_standalone_script(filename=file_name)
             self.path_registry.map_path(
                 sim_id,
-                f"files/simulations/{file_name}",
+                f"{self.path_registry}/files/simulations/{file_name}",
                 f"Basic Simulation of Protein {pdb_id}",
             )
             if save:
                 records = openmmsim.registry_records
                 # move record files to files/records/
                 print(os.listdir("."))
-                if not os.path.exists("files/records"):
-                    os.makedirs("files/records")
+                if not os.path.exists(f"{self.path_registry}/files/records"):
+                    os.makedirs(f"{self.path_registry}/files/records")
                 for record in records:
                     os.rename(record[1].split("/")[-1], f"{record[1]}")
                 for record in records:

tests/test_pdb_tools.py

@@ -34,16 +34,16 @@ def test_getpdb(fibronectin, get_registry):
     assert name.endswith(".pdb")
 
 
-def test_small_molecule_pdb(molpdb):
+def test_small_molecule_pdb(molpdb, get_registry):
     # Test with a valid SMILES string
     valid_smiles = "C1=CC=CC=C1"  # Benzene
     expected_output = (
         "PDB file for C1=CC=CC=C1 successfully created and saved to "
         "files/pdb/benzene.pdb."
     )
     assert molpdb.small_molecule_pdb(valid_smiles) == expected_output
-    assert os.path.exists("files/pdb/benzene.pdb")
-    os.remove("files/pdb/benzene.pdb")  # Clean up
+    assert os.path.exists(f"{get_registry}/files/pdb/benzene.pdb")
+    os.remove(f"{get_registry}/files/pdb/benzene.pdb")  # Clean up
 
     # test with invalid SMILES string and invalid molecule name
     invalid_smiles = "C1=CC=CC=C1X"
@@ -60,33 +60,33 @@ def test_small_molecule_pdb(molpdb):
         "PDB file for water successfully created and " "saved to files/pdb/water.pdb."
     )
     assert molpdb.small_molecule_pdb(valid_name) == expected_output
-    assert os.path.exists("files/pdb/water.pdb")
-    os.remove("files/pdb/water.pdb")  # Clean up
+    assert os.path.exists(f"{get_registry}/pdb/water.pdb")
+    os.remove(f"{get_registry}/files/pdb/water.pdb")  # Clean up
 
 
-def test_packmol_pdb_download_only(packmol):
+def test_packmol_pdb_download_only(packmol, get_registry):
     packmol.path_registry._remove_path_from_json("water")
     packmol.path_registry._remove_path_from_json("benzene")
     small_molecules = ["water", "benzene"]
     packmol._get_sm_pdbs(small_molecules)
-    assert os.path.exists("files/pdb/water.pdb")
-    assert os.path.exists("files/pdb/benzene.pdb")
-    os.remove("files/pdb/water.pdb")
-    os.remove("files/pdb/benzene.pdb")
+    assert os.path.exists(f"{get_registry}/files/pdb/water.pdb")
+    assert os.path.exists(f"{get_registry}/files/pdb/benzene.pdb")
+    os.remove(f"{get_registry}/files/pdb/water.pdb")
+    os.remove(f"{get_registry}/files/pdb/benzene.pdb")
 
 
-def test_packmol_download_only_once(packmol):
+def test_packmol_download_only_once(packmol, get_registry):
     packmol.path_registry._remove_path_from_json("water")
     small_molecules = ["water"]
     packmol._get_sm_pdbs(small_molecules)
-    assert os.path.exists("files/pdb/water.pdb")
-    water_time = os.path.getmtime("files/pdb/water.pdb")
+    assert os.path.exists(f"{get_registry}/files/pdb/water.pdb")
+    water_time = os.path.getmtime(f"{get_registry}/files/pdb/water.pdb")
     time.sleep(5)
 
     # Call the function again with the same molecule
     packmol._get_sm_pdbs(small_molecules)
-    water_time_after = os.path.getmtime("files/pdb/water.pdb")
+    water_time_after = os.path.getmtime(f"{get_registry}/files/pdb/water.pdb")
 
     assert water_time == water_time_after
     # Clean up
-    os.remove("files/pdb/water.pdb")
+    os.remove(f"{get_registry}/files/pdb/water.pdb")