[DNM] make pure docking workflows minimally dependent on other packages

asapdiscovery-cli/asapdiscovery/cli/cli.py

@@ -4,7 +4,6 @@
 @click.group()
 def cli(help="Command-line interface for asapdiscovery"): ...
 
-
 from asapdiscovery.workflows.docking_workflows.cli import (  # noqa: F401, E402, F811
     docking,
 )

asapdiscovery-docking/asapdiscovery/docking/docking.py

@@ -361,11 +361,13 @@ def write_results_to_multi_sdf(
         raise ValueError("Must provide reconstruct_cls if using disk backend")
 
     for res in results:
-        if backend == BackendType.IN_MEMORY:
+        if backend == BackendType.DISK:
+            res = reconstruct_cls.from_json_file(res)
+        if backend in [BackendType.DISK, BackendType.IN_MEMORY]:
             lig = res.posed_ligand
-        elif backend == BackendType.DISK:
-            lig = reconstruct_cls.from_json_file(res).posed_ligand
         else:
             raise ValueError(f"Unknown backend type {backend}")
 
+        lig.set_SD_data({"ReferenceStructureName": res.input_pair.complex.target.target_name,
+                         "ReferenceLigandName": res.input_pair.complex.ligand.compound_name})
         lig.to_sdf(sdf_file, allow_append=True)

asapdiscovery-docking/asapdiscovery/docking/openeye.py

@@ -225,6 +225,7 @@ def _dock(
 
         docking_results = []
 
+        logger.info(f"Running docking on {len(inputs)} sets")
         for set in inputs:
             try:
                 # make sure its a path
@@ -253,9 +254,11 @@ def _dock(
                             )
                 # run docking if output does not exist
                 else:
+                    logger.info("Making design units")
                     dus = set.to_design_units()
                     lig_oemol = oechem.OEMol(set.ligand.to_oemol())
                     if self.use_omega:
+                        logger.info("Running omega on ligand")
                         if self.omega_dense:
                             omegaOpts = oeomega.OEOmegaOptions(
                                 oeomega.OEOmegaSampling_Dense
@@ -276,12 +279,13 @@ def _dock(
                                 raise ValueError(
                                     f"Unknown error handling option {failure_mode}"
                                 )
-
+                    logger.info("Prepping docking options")
                     opts = oedocking.OEPositOptions()
                     opts.SetIgnoreNitrogenStereo(True)
                     opts.SetPositMethods(self.posit_method.value)
                     opts.SetPoseRelaxMode(self.relax_mode.value)
 
+                    logger.info("Run docking")
                     pose_res = oedocking.OEPositResults()
                     pose_res, retcode = self.run_oe_posit_docking(
                         opts, pose_res, dus, lig_oemol, self.num_poses
@@ -336,9 +340,11 @@ def _dock(
                         )
 
                     if retcode == oedocking.OEDockingReturnCode_Success:
+                        logger.info("Docking Success!")
                         input_pairs = []
                         posed_ligands = []
                         num_poses = pose_res.GetNumPoses()
+                        logger.info(f"Prepping results for {num_poses} poses")
                         for i, result in enumerate(pose_res.GetSinglePoseResults()):
                             posed_mol = result.GetPose()
                             prob = result.GetProbability()
@@ -370,6 +376,7 @@ def _dock(
                                 input_pairs.append(set)
 
                         # Create Docking Results Objects
+                        logger.info("Creating POSITDockingResults objects")
                         docking_results_objects = []
                         for input_pair, posed_ligand in zip(input_pairs, posed_ligands):
                             docking_results_objects.append(