Scripts & Automation

The scripts/ directory provides end-to-end automation for experiment execution, multi-model analysis, and target calibration.

Multi-Model Experiment Analysis

scripts/analysis/analyze_experiments.py aggregates results across multiple models, benchmarks, and random seeds:

python scripts/analysis/analyze_experiments.py \
  --exps-dir exps/ \
  --output-dir analysis_results/

Generated outputs:

• metrics_summary.csv: Per-model, per-benchmark detailed evaluation table.

• metrics_summary_macro.csv: Macro-averaged metrics across all target benchmarks.

• Publication Figures: * Figure 1: Generative quality & diversity metrics. * Figure 2: Optimization & docking performance (top-10, AUC). * Figure 3: Medicinal chemistry & property filters. * Figure 4: Cumulative trajectory curves over oracle calls.

Variance & Baseline Calibration

scripts/variance/run_variance.py runs multi-seed docking calibration on ChEMBL compounds to determine target baseline energy bounds and validate scoring reliability:

python scripts/variance/run_variance.py \
  --config src/mockdock/configs/CHK1.toml \
  --run-dir variance_runs/CHK1 \
  --output-dir variance_analysis/CHK1 \
  --n-iters 5

Docking Workflow Runner

scripts/docking/run_workflow.py executes docking directly for given SMILES files or datasets without launching a full generative training loop:

python scripts/docking/run_workflow.py \
  --benchmark CHK1 \
  --smiles-file input_molecules.smi \
  --output-dir docking_results/