check install

src/haddock/modules/refinement/openmm/__init__.py

@@ -1,12 +1,12 @@
 """OpenMM refinement module for HADDOCK3."""
 import os
 import shutil
+
 from contextlib import suppress
 from pathlib import Path
-
-from haddock.core.exceptions import ThirdPartyIntallationError
+from subprocess import run as subprocrun
+from haddock.core.exceptions import ThirdPartyIntallationError, HaddockModuleError
 from haddock.libs.libontology import PDBFile
-from haddock.libs.libsubprocess import run_subprocess
 from haddock.modules import BaseHaddockModule, get_engine
 
 # allow general testing when OpenMM is not installed
@@ -68,6 +68,16 @@ def confirm_installation(cls) -> None:
         ThirdPartyIntallationError
             When OpenMM pdbfixer is not installed
         """
+        def run_subprocess(command_to_run: str) -> str:
+            """Run subprocess."""
+            subprocess_output = subprocrun(
+                [command_to_run],
+                shell=True,
+                capture_output=True,
+                encoding='utf-8',
+                )
+            return subprocess_output.stdout.strip()
+
         checkOpenMM = run_subprocess("conda list openmm --json")
         checkPdbfixer = run_subprocess("conda list pdbfixer --json")
 
@@ -102,7 +112,6 @@ def _run(self) -> None:
                 Path("."),
                 directory_dict,
                 self.params,
-                self.log,
                 )
             # Hold it
             openmm_jobs.append(openmm_job_i)
@@ -118,21 +127,9 @@ def _run(self) -> None:
 
         # Check if at least one output file was generated
         if len(output_pdbs) == 0:
-            raise Exception("No output models generated. Check Openmm Execution.")  # noqa: E501
-        # ensemble_name = "openmm_ensemble.pdb"
-        # ensemble = make_ensemble(output_pdbs)  # ensemble is a generator
-        # with open(ensemble_name, "w") as wfile:
-        #     for line in ensemble:
-        #         wfile.write(line)
-        # self.log(f'Output ensemble {ensemble_name} created.')
-
-        # Setting the output variable
-        self.output_models = [
-            PDBFile(openmmout)
-            for openmmout in sorted(output_pdbs)
-            ]
-        # Generating standardized haddock3 outputs
-        self.export_output_models()
+            raise HaddockModuleError(
+                "No output models generated. Check Openmm Execution."
+                )
 
         # deleting unnecessary directories
         self.log("Removing unnecessary directories...")
@@ -144,3 +141,11 @@ def _run(self) -> None:
             " the OpenMM module, the next module should be `[topoaa]`, "
             "to rebuild the CNS molecular topologies."
             )
+
+        # Setting the output variable
+        self.output_models = [
+            PDBFile(openmmout)
+            for openmmout in sorted(output_pdbs)
+            ]
+        # Generating standardized haddock3 outputs
+        self.export_io_models()

src/haddock/modules/refinement/openmm/openmm.py

@@ -78,7 +78,6 @@ def __init__(
             path: Path,
             directory_dict: dict[str, str],
             params: ParamDict,
-            logger: Optional,
             ):
         """
         Initialize the class.
@@ -111,14 +110,14 @@ def __init__(
         self.path = path
         self.directory_dict = directory_dict
         self.params = params
-        self.log = logger if logger else log
+        self.log = log
 
         # other parameters
         self.output = Path("output_openmm.log")
         self.constraints = self.import_constraints()
         self.output_filename = self.model.file_name.replace(".pdb", "_omm.pdb")
 
-    def import_constraints(self) -> Optional[Union[AllBonds, HAngles, HBonds]]:
+    def import_constraints(self):  # type: ignore
         """Cast parameter string to proper openmm constraints."""
         if self.params["constraints"] == "HBonds":
             return HBonds
@@ -365,7 +364,7 @@ def equilibrate_solvation_box(
                 simulation,
                 max_temperature,
                 statereporter._dof,
-                tolerence=10.0,
+                tolerance=10.0,
                 steps=50
                 )
             # Print log info
@@ -418,7 +417,7 @@ def _stabilize_temperature(
             simulation: Simulation,
             temperature: float,
             dof: int,
-            tolerence: float = 5.0,
+            tolerance: float = 5.0,
             steps: int = 50,
             ) -> None:
         """
@@ -432,16 +431,16 @@ def _stabilize_temperature(
             The temperature hoped to be reached
         dof : int
             The degree of freedom obtained from the statereporter._dof
-        tolerence : float
-            The tolerence allowed for the temperature
+        tolerance : float
+            The tolerance allowed for the temperature
         steps : int
             The number of steps to do before checking again that
             temperature was reached
         """
         # Makes sure temperature of the system is reached
-        while not ((temperature - tolerence)
+        while not ((temperature - tolerance)
                    <= self._get_simulation_temperature(simulation, dof)
-                   <= (temperature + tolerence)):
+                   <= (temperature + tolerance)):
             # Do several simulation steps
             simulation.step(steps)
 
@@ -721,7 +720,7 @@ def run_openmm(
             simulation,
             qtemp,
             statereporter._dof,
-            tolerence=5.0,
+            tolerance=5.0,
             steps=50
             )
         log.info(