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

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

pandadock-report -i docking_output/ \\
                 -o report/ \\
                 -t standard

Generate standard HTML report with visualizations.

PDF Report

pandadock-report -i docking_output/ \\
                 -o report_pdf/ \\
                 --format pdf \\
                 --viz-style publication \\
                 --dpi 600

Publication-Quality Report

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

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

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

pandadock-report -i validation_results/ \\
                 -t validation \\
                 --reference-structures crystal_structures/ \\
                 --format html \\
                 -o validation_report/

Interactive Dashboard

pandadock-report -i large_screening/ \\
                 -t interactive \\
                 --interactive-plots \\
                 --format html \\
                 -o interactive_dashboard/

Generates browsable HTML dashboard with interactive plots.

Flexible Docking Report

pandadock-report -i flex_docking_output/ \\
                 --include-energy-decomposition \\
                 --include-interactions \\
                 --top-n-poses 20 \\
                 -o flex_report/

Export Results to CSV

pandadock-report -i docking_output/ \\
                 --export-csv \\
                 --export-json \\
                 --export-sdf \\
                 -o exported_results/

Multi-Target Comparison

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 < 2?)

    • 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:

pandadock-report -i results/ \\
                 -t standard \\
                 --include-interactions \\
                 --include-energy-decomposition

For large screening:

pandadock-report -i screening/ \\
                 -t screening \\
                 --top-n-poses 3 \\
                 --export-csv

For publication:

pandadock-report -i results/ \\
                 -t publication \\
                 --format pdf \\
                 --dpi 600 \\
                 --viz-style publication \\
                 --figure-format svg

Customization

Create custom report template:

pandadock-report -i results/ \\
                 --template custom_template.html \\
                 --custom-css style.css \\
                 -o custom_report/

Performance Optimization

For large datasets:

# 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

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

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

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