Question regarding AutoDock Vina of DockStream as Score component in staged learning

[yutaeho]

Instead Glide or Gold which requires license key, I want to use AutoDock Vina as score component to reproduce the process in the paper.
I set the toml as below box

run_type = "staged_learning"
use_cuda = true
tb_logdir = "tb_rl_direct"

[parameters]
use_checkpoint = true  
summary_csv_prefix = "rl_direct"
agent_file = "/home/user/REINVENT4/priors/reinvent.prior"
prior_file = "/home/user/REINVENT4/priors/reinvent.prior"

batch_size = 128          
#uniquify_smiles = true   
randomize_smiles = true  

[learning_strategy]

type = "dap"    
sigma = 128      
rate = 0.0005     

[diversity_filter] 

type = "IdenticalMurckoScaffold" 
bucket_size = 50
minscore = 0.4

[[stage]]
chkpt_file = 'rl_direct.chkpt'
termination = "simple"
max_steps = 50

[stage.scoring]
type = "geometric_mean"

[[stage.scoring.component]]
[[stage.scoring.component.DockStream.endpoint]]
name = "Docking into 7E14 grid"
weight = 1
params.configuration_path = "/home/user/REINVENT4/GLPR/dockstream_rl_direct_AutoDockVina.json"
params.docker_script_path = "/home/user/DockStream/docker.py"
params.docker_python_path =  "/home/user/anaconda3/envs/DockStream/bin/python"
transform.type = "reverse_sigmoid"
transform.high = -7
transform.low = -13.5
transform.k = 0.2

[[stage.scoring.component]]
[stage.scoring.component.QED]
[[stage.scoring.component.QED.endpoint]]
name = "QED"
weight = 1

and set the configuration of docking as below (dockstream_rl_direct_AutoDockVina.json file)

{
  "docking": {
    "header": {
      "logging": {
        "logfile": "/home/user/REINVENT4/dockstream_rl_direct_AutodockVina.log"
      }
    },
    "ligand_preparation": {
      "embedding_pools": [
        {
          "pool_id": "RDkit",
          "type": "RDkit",
          "parameters": {
            "protonate": true,
            "coordinate_generation": {
              "method": "UFF",
              "maximum_iterations": 600
            }
          },
          "input": {
            "standardize_smiles": false,
            "type": "console",
            "use_taut_enum": {
              "prefix_execution": "module load taut_enum", 
              "enumerate_protonation": true
            },
            "stereo_enumeration":{
              "stereo_backend":"RDKit"
          }
        }
      ]
    },
    "docking_runs": [
      {
        "backend": "AutoDockVina",
        "run_id": "AutoDockVina",
        "input_pools": ["RDkit"],
        "parameters": {
          "binary_location": "/home/user/autodock_vina_1_1_2_linux_x86/bin", 
          "parallelization": {
            "number_cores": 4
          },
          "seed": 42,
          "receptor_pdbqt_path": ["/home/user/REINVENT4/test.pdbqt"], 
          "number_poses": 2,
          "search_space": {
            "--center_x": 101.321938,
            "--center_y": 123.555185,
            "--center_z": 79.452985,
            "--size_x": 10,
            "--size_y": 10,
            "--size_z": 10
          }
        },
        "output": {
          "poses": { "poses_path": "/home/user/REINVENT4/GLPR/AutodockVina_rl_direct_poses_test.sdf" },
          "scores": { "scores_path": "/home/user/REINVENT4/GLPR/AutodockVina_rl_direct_poses_test.csv" }
        }
      }
   ]
  }
}

As a result, I got the error code about docking simulation.
The partial of error codes are below (I removed some SMILES which were randomly generated at the first stage)

Traceback (most recent call last):
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent_plugins/components/run_program.py", line 26, in run_command
    result = sp.run(command, **args)
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/subprocess.py", line 526, in run
    raise CalledProcessError(retcode, process.args,
....
During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/user/anaconda3/envs/reinvent4/bin/reinvent", line 8, in <module>
    sys.exit(main())
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/Reinvent.py", line 334, in main
    runner(
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/runmodes/RL/run_staged_learning.py", line 367, in run_staged_learning
    terminate = optimize(package.terminator)
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/runmodes/RL/learning.py", line 118, in optimize
    results = self.score()
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/runmodes/RL/learning.py", line 192, in score
    results = self.scoring_function(
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/scoring/scorer.py", line 138, in compute_results
    transform_result = compute_transform(
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/scoring/compute_scores.py", line 101, in compute_transform
    component_results = compute_component_scores(
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent/scoring/compute_scores.py", line 62, in compute_component_scores
    component_results = scoring_function(smilies_non_cached)
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent_plugins/normalize.py", line 22, in wrapper
    return func(self, cleaned_smilies)
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent_plugins/components/comp_dockstream.py", line 77, in __call__
    result = run_command(command)
  File "/home/user/anaconda3/envs/reinvent4/lib/python3.10/site-packages/reinvent_plugins/components/run_program.py", line 32, in run_command
    raise RuntimeError(
RuntimeError: reinvent_plugins.components.run_program: /home/user/anaconda3/envs/DockStream/bin/python /home/user/DockStream/docker.py -conf /home/user/REINVENT4/dockstream_rl_direct_AutoDockVina.json -output_prefix 0 -smiles "CC(=O)c1...
....
raceback (most recent call last):
  File "/home/user/DockStream/docker.py", line 67, in <module>
    config = DockingContainer(conf=args.conf, validation=args.validation)
  File "/home/user/DockStream/dockstream/containers/docking_container.py", line 9, in __init__
    super().__init__(conf=conf)
  File "/home/user/DockStream/dockstream/containers/container.py", line 18, in __init__
    conf = json.loads(conf)
  File "/home/user/anaconda3/envs/DockStream/lib/python3.7/json/__init__.py", line 348, in loads
    return _default_decoder.decode(s)
  File "/home/user/anaconda3/envs/DockStream/lib/python3.7/json/decoder.py", line 337, in decode
    obj, end = self.raw_decode(s, idx=_w(s, 0).end())
  File "/home/user/anaconda3/envs/DockStream/lib/python3.7/json/decoder.py", line 353, in raw_decode
    obj, end = self.scan_once(s, idx)
json.decoder.JSONDecodeError: Expecting ',' delimiter: line 1 column 784 (char 783)

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
  File "/home/user/DockStream/docker.py", line 69, in <module>
    raise DockingRunFailed() from e
dockstream.utils.dockstream_exceptions.DockingRunFailed

I hope to find the cause of error which I missed

[halx]

Hi,

Welcome to the REINVENT community and many thanks for your interest in the software!

We do not support DockStream anymore and recommend transitioning to maize. See #32, in particular this message.

Many thanks,
Hannes.

[yutaeho]

Oh I don't recognize that news, sorry.

I really appreciate your help, thank you!

Sincerely,
Taeho yu