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asap-docking Update POSITDockingResults object to write multi-pose results to docking_results.json #988

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apayne97 opened this issue Apr 17, 2024 · 0 comments · May be fixed by #1009
Open

asap-docking Update POSITDockingResults object to write multi-pose results to docking_results.json #988

apayne97 opened this issue Apr 17, 2024 · 0 comments · May be fixed by #1009
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bug Something isn't working docking Related to docking parts of the package

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@apayne97
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apayne97 commented Apr 17, 2024 •
edited

In docking.openeye.POSITDocker._dock() we have logic that looks like:

for result in pose_res.GetSinglePoseResults():
          posed_mol = result.GetPose()

          posed_ligand = Ligand.from_oemol(posed_mol, **set.ligand.dict())

          docking_result = POSITDockingResults(
              input_pair=input_pair,
              posed_ligand=posed_ligand,
              probability=prob,
              provenance=self.provenance(),
          )

          docking_results.append(docking_result)
          if output_dir is not None:
              docking_result.write_docking_files(output_dir)

The result of this is that the different poses overwrite each other in output_dir when they are written in this line. This is clearly a bug that needs to be fixed.

Confusingly (from a user perspective), since all the docking_results are returned as a list to this line of code, they get successfully written to a multi-pose sdf file in workflows.docking_workflows.cross_docking:

    if inputs.write_final_sdf:
        logger.info("Writing final docked poses to SDF file")
        write_ligands_to_multi_sdf(
            output_dir / "docking_results.sdf", [r.posed_ligand for r in results]
        )

this is ok unless this part fails, as in #989
@apayne97 apayne97 added bug Something isn't working docking Related to docking parts of the package labels Apr 17, 2024
@apayne97 apayne97 linked a pull request Apr 24, 2024 that will close this issue
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asap-docking | Correctly save multipose docking results asapdiscovery/asapdiscovery
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@apayne97