Removed "-log" parameter to support ADV 1.2.0 and updated to use the new version…

Removed "-log" parameter to support ADV 1.2.0 and updated to use the new version of "OpenMM" in the PDB preparation stage.

dockstream/core/AutodockVina/AutodockVina_docker.py

@@ -253,8 +253,6 @@ class AutodockVina(Docker, BaseModel):
         return parts[_ROE.RESULT_LINE_POS_SCORE]
 
     def _dock_subjob(self, input_path_pdbqt, output_path_sdf):
-        # at the moment, the log file is not parsed
-        path_log_file = gen_temp_file(suffix=".log", dir=os.path.dirname(input_path_pdbqt))
 
         # set up arguments list and execute
         # TODO: support "ensemble docking" - currently, only the first entry is used
@@ -271,8 +269,7 @@ class AutodockVina(Docker, BaseModel):
                      _EE.VINA_SIZE_X, str(search_space.size_x),
                      _EE.VINA_SIZE_Y, str(search_space.size_y),
                      _EE.VINA_SIZE_Z, str(search_space.size_z),
-                     _EE.VINA_NUM_MODES, self.parameters.number_poses,
-                     _EE.VINA_LOG, path_log_file]
+                     _EE.VINA_NUM_MODES, self.parameters.number_poses]
 
         execution_result = self._ADV_executor.execute(command=_EE.VINA,
                                                       arguments=arguments,

dockstream/core/AutodockVina/AutodockVina_target_preparator.py

-import os
-import tempfile
 from rdkit import Chem
 
 from dockstream.utils.dockstream_exceptions import TargetPreparationFailed

dockstream/core/pdb_preparator.py

 import warnings
 from pdbfixer import PDBFixer
-from simtk.openmm.vec3 import Vec3
-from simtk.openmm.app import PDBFile
+from openmm.vec3 import Vec3
+from openmm.app import PDBFile
 
 from dockstream.loggers.target_preparation_logger import TargetPreparationLogger
 from dockstream.utils.dockstream_exceptions import TargetPreparationFailed

environment.yml

@@ -15,6 +15,7 @@ dependencies:
   - numpy
   - openeye-toolkits >= 2019
   - openbabel
+  - openmm
   - scipy
   - pydantic
   - pdbfixer

environment_full.yml

@@ -17,6 +17,7 @@ dependencies:
   - numpy
   - openeye-toolkits >= 2019
   - openbabel
+  - openmm
   - scipy
   - pydantic
   - pdbfixer