pandadock-report - Docking Analysis and Reporting ================================================== The ``pandadock-report`` command generates comprehensive analysis reports, visualizations, and summaries from PandaDock docking results. Essential for interpreting large docking studies and communicating results. Synopsis -------- .. code-block:: bash pandadock-report [OPTIONS] Description ----------- Analyzes docking results and generates: * **Summary statistics** - Success rates, RMSD distributions, runtime * **Interactive visualizations** - Binding modes, energy plots, interaction maps * **Comparison reports** - Compare multiple algorithms or targets * **Export formats** - PDF, HTML, CSV, JSON Supports analysis of standard docking, flexible docking, metal docking, and virtual screening results. Required Options ---------------- ``-i, --input-dir PATH`` Input directory containing docking results Can be output from ``pandadock``, ``pandadock-flex``, ``pandadock-metal``, etc. ``-o, --output-dir PATH`` Output directory for report. Default: ``report_output`` Report Type Options ------------------- ``-t, --report-type TYPE`` Type of report to generate. Default: ``standard`` Options: * ``standard`` - Standard docking analysis report * ``comparison`` - Compare multiple docking runs * ``screening`` - Virtual screening enrichment analysis * ``validation`` - Validation study (requires reference structures) * ``interactive`` - Interactive HTML dashboard * ``publication`` - Publication-quality figures ``--format FORMAT`` Output format. Default: ``html`` Options: * ``html`` - Interactive HTML report * ``pdf`` - Static PDF report * ``pptx`` - PowerPoint presentation * ``jupyter`` - Jupyter notebook * ``markdown`` - Markdown document Analysis Options ---------------- ``--include-structures / --no-include-structures`` Include structure visualizations. Default: enabled ``--include-interactions / --no-include-interactions`` Include interaction analysis. Default: enabled ``--include-energy-decomposition / --no-energy-decomposition`` Include energy decomposition. Default: enabled (if available) ``--include-statistics / --no-statistics`` Include statistical analysis. Default: enabled ``--top-n-poses N`` Analyze top N poses per ligand. Default: 10 ``--reference-structures PATH`` Reference structures for validation (optional) Directory containing PDB files for RMSD calculation. Visualization Options --------------------- ``--viz-style STYLE`` Visualization style. Default: ``modern`` Options: ``modern``, ``classic``, ``publication``, ``dark`` ``--color-scheme SCHEME`` Color scheme for plots. Default: ``viridis`` Options: ``viridis``, ``plasma``, ``cool_warm``, ``greyscale`` ``--dpi DPI`` Figure resolution (DPI). Default: 300 ``--figure-format FORMAT`` Figure file format. Default: ``png`` Options: ``png``, ``svg``, ``pdf`` ``--interactive-plots / --no-interactive-plots`` Generate interactive plots (plotly). Default: enabled for HTML Comparison Options ------------------ For ``--report-type comparison``: ``--compare-algorithms`` Compare different algorithms ``--compare-scoring`` Compare different scoring functions ``--compare-targets`` Compare docking to different targets ``--baseline PATH`` Baseline result for comparison Screening Options ----------------- For ``--report-type screening``: ``--active-compounds PATH`` File with known active compound IDs ``--decoy-compounds PATH`` File with decoy compound IDs ``--calculate-enrichment / --no-enrichment`` Calculate enrichment factors. Default: enabled ``--roc-curve / --no-roc-curve`` Generate ROC curve. Default: enabled Export Options -------------- ``--export-csv / --no-export-csv`` Export results to CSV. Default: enabled ``--export-json / --no-export-json`` Export results to JSON. Default: enabled ``--export-sdf / --no-export-sdf`` Export top poses to SDF. Default: disabled ``--export-pdb / --no-export-pdb`` Export complexes to PDB. Default: disabled Examples -------- Basic Report Generation ^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -i docking_output/ \\ -o report/ \\ -t standard Generate standard HTML report with visualizations. PDF Report ^^^^^^^^^^ .. code-block:: bash pandadock-report -i docking_output/ \\ -o report_pdf/ \\ --format pdf \\ --viz-style publication \\ --dpi 600 Publication-Quality Report ^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -i docking_output/ \\ -t publication \\ --format pdf \\ --viz-style publication \\ --color-scheme greyscale \\ --dpi 600 \\ --figure-format svg \\ -o publication_report/ Algorithm Comparison ^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -t comparison \\ -i results1/ results2/ results3/ \\ --compare-algorithms \\ --format html \\ -o algorithm_comparison/ Where ``results1/``, ``results2/``, ``results3/`` contain docking results from different algorithms. Virtual Screening Report ^^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -i screening_results/ \\ -t screening \\ --active-compounds actives.txt \\ --decoy-compounds decoys.txt \\ --calculate-enrichment \\ --roc-curve \\ -o screening_report/ Validation Study Report ^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -i validation_results/ \\ -t validation \\ --reference-structures crystal_structures/ \\ --format html \\ -o validation_report/ Interactive Dashboard ^^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -i large_screening/ \\ -t interactive \\ --interactive-plots \\ --format html \\ -o interactive_dashboard/ Generates browsable HTML dashboard with interactive plots. Flexible Docking Report ^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -i flex_docking_output/ \\ --include-energy-decomposition \\ --include-interactions \\ --top-n-poses 20 \\ -o flex_report/ Export Results to CSV ^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -i docking_output/ \\ --export-csv \\ --export-json \\ --export-sdf \\ -o exported_results/ Multi-Target Comparison ^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -t comparison \\ -i target1_results/ target2_results/ target3_results/ \\ --compare-targets \\ -o multi_target_report/ Output Files ------------ Standard Report ^^^^^^^^^^^^^^^ * ``report.html`` or ``report.pdf`` - Main report * ``summary_statistics.csv`` - Summary table * ``all_results.csv`` - Detailed results * ``figures/`` - Directory with all figures * ``binding_affinity_distribution.png`` * ``rmsd_distribution.png`` * ``top_poses_overlay.png`` * ``interaction_heatmap.png`` * ``energy_decomposition.png`` Comparison Report ^^^^^^^^^^^^^^^^^ * ``comparison_report.html`` * ``algorithm_performance.csv`` * ``head_to_head_comparison.png`` * ``success_rate_comparison.png`` * ``runtime_comparison.png`` Screening Report ^^^^^^^^^^^^^^^^ * ``screening_report.html`` * ``enrichment_factors.csv`` * ``roc_curve.png`` * ``enrichment_plot.png`` * ``active_recovery.png`` * ``top_hits.csv`` Validation Report ^^^^^^^^^^^^^^^^^ * ``validation_report.html`` * ``rmsd_to_crystal.csv`` * ``success_rate_by_target.png`` * ``pose_reproduction_quality.png`` Interactive Dashboard ^^^^^^^^^^^^^^^^^^^^^ * ``index.html`` - Dashboard home page * ``js/`` - Interactive JavaScript components * ``data/`` - JSON data for plots * ``poses/`` - 3D structure viewers Report Contents --------------- Standard Report Sections ^^^^^^^^^^^^^^^^^^^^^^^^ 1. **Executive Summary** * Number of ligands docked * Success rate * Mean binding affinity * Runtime statistics 2. **Binding Affinity Analysis** * Distribution of binding scores * Top scoring compounds * Score histogram 3. **Pose Quality Analysis** * RMSD distribution (if reference provided) * Pose clustering analysis * Conformational diversity 4. **Interaction Analysis** * Protein-ligand interaction frequency * Hydrogen bonding patterns * Hydrophobic contacts * Key binding residues 5. **Energy Decomposition** * Van der Waals contribution * Electrostatic energy * Desolvation energy * Component breakdown 6. **Top Compounds** * Ranked list with structures * Binding mode visualizations * 2D interaction diagrams Comparison Report Sections ^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1. **Performance Comparison** * Accuracy comparison * Speed comparison * Success rate comparison 2. **Head-to-Head Analysis** * Pose RMSD comparison * Binding score correlation * Ranking agreement 3. **Consensus Analysis** * Compounds ranked highly by all methods * Discordant predictions Screening Report Sections ^^^^^^^^^^^^^^^^^^^^^^^^^^ 1. **Enrichment Analysis** * Enrichment factors at 1%, 5%, 10% * ROC AUC * Active recovery rate 2. **Hit List** * Top scoring compounds * Actives in top N * Novel scaffolds 3. **Library Statistics** * Screening size * Chemical diversity * Physicochemical properties Validation Report Sections ^^^^^^^^^^^^^^^^^^^^^^^^^^^ 1. **Pose Reproduction** * RMSD to crystal structure * Success rate (RMSD < 2Å) * Per-target breakdown 2. **Scoring Performance** * Correlation with experimental data * Ranking accuracy * Native pose identification 3. **Recommendations** * Best performing algorithm * Optimal parameters * Confidence assessment Visualizations -------------- Automatically Generated Plots ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ **Distribution Plots:** * Binding affinity histogram * RMSD distribution * Runtime distribution **Comparison Plots:** * Algorithm performance radar chart * Head-to-head scatter plots * Success rate bar charts **Interaction Plots:** * Interaction heatmap (residue × ligand) * 2D interaction diagrams * 3D binding mode visualization **Energy Plots:** * Energy component breakdown (stacked bar) * Per-residue contribution (heatmap) * Energy vs RMSD scatter **Screening Plots:** * ROC curve * Enrichment plot * Active recovery curve Best Practices -------------- Report Organization ^^^^^^^^^^^^^^^^^^^ **For single docking study:** .. code-block:: bash pandadock-report -i results/ \\ -t standard \\ --include-interactions \\ --include-energy-decomposition **For large screening:** .. code-block:: bash pandadock-report -i screening/ \\ -t screening \\ --top-n-poses 3 \\ --export-csv **For publication:** .. code-block:: bash pandadock-report -i results/ \\ -t publication \\ --format pdf \\ --dpi 600 \\ --viz-style publication \\ --figure-format svg Customization ^^^^^^^^^^^^^ Create custom report template: .. code-block:: bash pandadock-report -i results/ \\ --template custom_template.html \\ --custom-css style.css \\ -o custom_report/ Performance Optimization ^^^^^^^^^^^^^^^^^^^^^^^^ **For large datasets:** .. code-block:: bash # Analyze only top poses pandadock-report -i large_screening/ \\ --top-n-poses 1 \\ --no-interactive-plots \\ --format pdf Troubleshooting --------------- Missing Visualizations ^^^^^^^^^^^^^^^^^^^^^^ **Problem:** Figures not generated **Solutions:** 1. Install matplotlib: ``pip install matplotlib`` 2. Install plotly for interactive: ``pip install plotly`` 3. Check ``--no-include-structures`` not set Large Report Size ^^^^^^^^^^^^^^^^^ **Problem:** HTML report very large (>100 MB) **Solutions:** 1. Reduce pose number: ``--top-n-poses 5`` 2. Disable interactive plots: ``--no-interactive-plots`` 3. Use PDF format: ``--format pdf`` 4. Don't embed structures: ``--no-include-structures`` Slow Report Generation ^^^^^^^^^^^^^^^^^^^^^^^ **Problem:** Report generation takes very long **Solutions:** 1. Reduce analyzed poses: ``--top-n-poses 3`` 2. Disable expensive analysis: ``--no-energy-decomposition`` 3. Use simpler format: ``--format markdown`` Integration with Other Tools ----------------------------- Export for PyMOL Visualization ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -i results/ \\ --export-pdb \\ --top-n-poses 5 \\ -o pymol_export/ # Load in PyMOL pymol pymol_export/complex*.pdb Export for Further Analysis ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -i results/ \\ --export-csv \\ --export-json \\ -o data_export/ # Load in pandas import pandas as pd df = pd.read_csv('data_export/all_results.csv') Generate Jupyter Notebook ^^^^^^^^^^^^^^^^^^^^^^^^^^ .. code-block:: bash pandadock-report -i results/ \\ --format jupyter \\ -o analysis_notebook/ # Open and run jupyter notebook analysis_notebook/analysis.ipynb Exit Status ----------- Returns 0 on success, non-zero on error. See Also -------- * :doc:`pandadock` - Main docking command * :doc:`pandadock_flex` - Flexible docking * :doc:`pandadock_metal` - Metal docking * :doc:`../algorithms/overview` - Docking algorithms * :doc:`../scoring/overview` - Scoring functions