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Add example JSON launch file for VS Code development and execution
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‎.vscode/launch.json.example‎

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{
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// Use IntelliSense to learn about possible attributes.
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// Hover to view descriptions of existing attributes.
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// For more information, visit: https://go.microsoft.com/fwlink/?linkid=830387
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"version": "0.2.0",
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"configurations": [
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{
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"name": "Python: Current File",
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"type": "debugpy",
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"request": "launch",
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"program": "${file}",
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"console": "integratedTerminal",
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"justMyCode": true,
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"args": []
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},
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{
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"name": "diffdock_inference.py",
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"type": "debugpy",
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"request": "launch",
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"program": "src/models/diffdock_inference.py",
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"console": "integratedTerminal",
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"justMyCode": true,
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"args": [
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"cuda_device_index=0",
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"dataset=posebusters_benchmark",
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// "input_csv_path=forks/DiffDock/inference/diffdock_${dataset}_inputs.csv",
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// "input_data_dir=forks/DiffDock/inference/diffdock_${dataset}_inputs",
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// "output_dir=forks/DiffDock/inference/diffdock_${dataset}_output",
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// "inference_steps=20",
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// "samples_per_complex=40",
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// "batch_size=1",
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// "actual_steps=19",
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// "no_final_step_noise=true",
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"repeat_index=1",
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"skip_existing=true",
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]
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},
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{
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"name": "fabind_inference.py",
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"type": "debugpy",
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"request": "launch",
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"program": "src/models/fabind_inference.py",
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"console": "integratedTerminal",
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"justMyCode": true,
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"args": [
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"cuda_device_index=0",
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"dataset=posebusters_benchmark",
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// "input_csv_path=forks/FABind/inference/fabind_${dataset}_inputs.csv",
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// "input_data_dir=forks/FABind/inference/fabind_${dataset}_inputs",
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// "num_threads=1",
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// "skip_existing=false",
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// "save_pt_dir=forks/FABind/inference/fabind_${dataset}_temp_files",
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// "save_mols_dir=forks/FABind/inference/fabind_${dataset}_temp_files/mol",
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// "output_dir=forks/FABind/inference/fabind_${dataset}_output",
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]
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},
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{
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"name": "dynamicbind_inference.py",
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"type": "debugpy",
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"request": "launch",
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"program": "src/models/dynamicbind_inference.py",
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"console": "integratedTerminal",
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"justMyCode": false,
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"args": [
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"cuda_device_index=0",
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"dataset=posebusters_benchmark",
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// "input_data_dir=forks/DynamicBind/inference/dynamicbind_${dataset}_inputs",
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// "input_ligand_csv_dir=forks/DynamicBind/inference/dynamicbind_${dataset}_inputs",
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// "samples_per_complex=40",
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// "savings_per_complex=1",
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// "inference_steps=20",
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// "batch_size=5",
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// "header=posebusters_benchmark_debugging",
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// "num_workers=1",
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"repeat_index=1",
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"skip_existing=true",
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]
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},
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{
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"name": "rfaa_inference.py",
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"type": "debugpy",
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"request": "launch",
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"program": "src/models/rfaa_inference.py",
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"console": "integratedTerminal",
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"justMyCode": true,
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"args": [
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"dataset=posebusters_benchmark",
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"max_cycles=10",
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"run_inference_directly=true",
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// "inference_config_name=T1152_rfaa_inference.yaml",
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// "inference_dir_name=T1152_for_debugging"
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]
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},
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{
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"name": "vina_inference.py",
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"type": "debugpy",
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"request": "launch",
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"program": "src/models/vina_inference.py",
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"console": "integratedTerminal",
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"justMyCode": false,
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"args": [
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"dataset=posebusters_benchmark",
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"method=diffdock",
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"repeat_index=1",
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"skip_existing=true",
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// "pocket_only_baseline=true",
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]
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},
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{
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"name": "minimize_energy.py",
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"type": "debugpy",
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"request": "launch",
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"program": "src/models/minimize_energy.py",
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"console": "integratedTerminal",
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"justMyCode": true,
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"args": [
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"protein_file=data/test_cases/5S8I_2LY/5S8I_2LY_protein.pdb",
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"ligand_file=data/test_cases/5S8I_2LY/75S8I_2LY_prediction.sdf",
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"output_file=5S8I_2LY_prediction_minimized.sdf",
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// "temp_dir=.",
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// "add_solvent=true",
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// "name=5S8I_2LY",
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// "prep_only=true",
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// "platform=CUDA",
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// "log_level=WARNING",
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]
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},
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{
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"name": "inference_relaxation.py",
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"type": "debugpy",
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"request": "launch",
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"program": "src/models/inference_relaxation.py",
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"console": "integratedTerminal",
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"justMyCode": false,
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"args": [
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"method=neuralplexer",
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// "vina_binding_site_method=diffdock",
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"dataset=posebusters_benchmark",
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"remove_initial_protein_hydrogens=true",
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"assign_partial_charges_manually=true",
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"num_processes=1",
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// "temp_dir=.",
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// "add_solvent=true",
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// "name=null",
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// "prep_only=true",
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// "platform=CUDA",
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"cuda_device_index=0",
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// "log_level=INFO",
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// "protein_dir=null",
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// "ligand_dir=null",
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// "output_dir=null",
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// "relax_protein=true",
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"cache_files=false",
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"repeat_index=1",
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"skip_existing=true",
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// "pocket_only_baseline=true",
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]
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},
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{
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"name": "complex_alignment.py",
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"type": "debugpy",
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"request": "launch",
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"program": "src/analysis/complex_alignment.py",
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"console": "integratedTerminal",
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"justMyCode": true,
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"args": [
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"method=neuralplexer",
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"dataset=posebusters_benchmark",
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// "rank_to_align=1",
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// "aligned_filename_postfix='_aligned'",
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// "force_process=false",
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"repeat_index=1",
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// "pocket_only_baseline=true",
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]
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},
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{
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"name": "ensemble_generation.py",
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"type": "debugpy",
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"request": "launch",
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"program": "src/models/ensemble_generation.py",
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"console": "integratedTerminal",
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"justMyCode": true,
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"args": [
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"ensemble_methods=[diffdock, dynamicbind, neuralplexer, rfaa, vina]",
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// "vina_binding_site_methods=[diffdock]",
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// "generate_vina_scripts=false",
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// "rank_single_method_intrinsically=false",
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// "input_dir=forks/NeuralPLexer/inference/neuralplexer_posebusters_benchmark_outputs_1",
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"input_csv_filepath=data/test_cases/posebusters_benchmark/ensemble_inputs.csv",
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"output_dir=data/test_cases/posebusters_benchmark/top_consensus_ensemble_predictions_1",
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"skip_existing=true",
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// "relax_method_ligands_pre_ranking=false",
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"relax_method_ligands_post_ranking=false",
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// "relax_remove_initial_protein_hydrogens=false",
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// "relax_model_ions=true",
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// "relax_assign_partial_charges_manually=false",
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"export_file_format=null",
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"export_top_n=1",
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// "casp_author='001'",
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// "casp_method='Ligand_Predictor'",
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// "combine_casp_output_files=true",
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// "cuda_device_index=0",
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"max_method_predictions=40",
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"method_top_n_to_select=40",
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"resume=true",
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"ensemble_benchmarking=true",
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"ensemble_benchmarking_dataset=posebusters_benchmark",
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"ensemble_ranking_method=consensus",
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"ensemble_benchmarking_repeat_index=1",
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// "pocket_only_baseline=true",
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]
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},
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{
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"name": "inference_analysis.py",
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"type": "debugpy",
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"request": "launch",
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"program": "src/analysis/inference_analysis.py",
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"console": "integratedTerminal",
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"justMyCode": true,
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"args": [
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"method=fabind",
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// "vina_binding_site_method=diffdock",
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"dataset=posebusters_benchmark",
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// "full_report=false",
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// "ensemble_ranking_method=consensus",
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// "input_csv_path=forks/FABind/inference/fabind_${dataset}_inputs.csv",
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// "input_data_dir=forks/FABind/inference/fabind_${dataset}_inputs",
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// "output_dir=forks/FABind/inference/fabind_${dataset}_output",
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"repeat_index=1",
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]
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},
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{
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"name": "inference_analysis_casp.py",
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"type": "debugpy",
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"request": "launch",
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"program": "src/analysis/inference_analysis_casp.py",
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"console": "integratedTerminal",
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"justMyCode": false,
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"args": [
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"method=neuralplexer",
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// "vina_binding_site_method=diffdock",
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"dataset=casp15",
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// "ensemble_ranking_method=consensus",
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// "targets=[T1181]",
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// "fault_tolerant=false",
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// "skip_existing=false",
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// "score_relaxed_structures=true",
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"repeat_index=1",
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]
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},
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]
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}

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