HEDGEHOG Pipeline Report

Generated: {{ generated_at }}

Run path: {{ data.metadata.run_path }}

Version: {{ data.metadata.hedgehog_version }}

{% if data.summary.stage_statuses %}

Stage Execution Summary

{% for stage in data.summary.stage_statuses %} {% endfor %}

Stage	Status
{{ stage.name }}	{% if stage.completed %} ✓ COMPLETED {% elif stage.enabled %} ✗ FAILED {% else %} − DISABLED {% endif %}

{% endif %}

Pipeline Flow

{% if data.available_models %}

All Models Compare {% for model in data.available_models %} {{ model }} {% endfor %}

{% endif %} {% if plots.sankey %}

{{ plots.sankey | safe }}

{% else %}

No data available

{% endif %}

{% if data.models %}

Model Comparison

{% if plots.model_comparison %}

{{ plots.model_comparison | safe }}

{% endif %} {% for model in data.models %} {% endfor %}

Model	Initial	Final	Retention
{{ model.model_name }}	{{ model.initial }}	{{ model.final }}	{% set retention = (model.final / model.initial * 100) if model.initial > 0 else 0 %} {{ "%.1f"|format(retention) }}%

{% if plots.model_losses %}

Molecule Losses by Stage

{{ plots.model_losses | safe }}

{% endif %}

{% endif %} {% if data.descriptors.distributions or data.descriptors_detailed.raw_data %}

Descriptor Analysis

{% if data.available_models and plots.descriptors_data %}

All Models Compare {% for model in data.available_models %} {{ model }} {% endfor %}

{% endif %} {% if plots.descriptors_data %}

Mean Median Filter Threshold Out of Range

{% else %} {% if plots.descriptors_violin %}

Descriptor Distributions by Model

{{ plots.descriptors_violin | safe }}

{% endif %} {% endif %} {% if plots.descriptors_table %}

Mean Values by Model

{{ plots.descriptors_table | safe }} {% endif %}

{% endif %} {% if data.filters.by_filter or data.filters.totals or data.filters_detailed.by_filter or plots.filters_data %}

Structural Filters Analysis

{% if data.filters.totals %}

{{ data.filters.totals|length }}

Filters Applied

{{ data.filters.totals.values()|sum }}

Total Rejected

{% if data.filters_detailed.filter_metrics %} {% for filter_name, metrics in data.filters_detailed.filter_metrics.items() %} {% if metrics.avg_demerit_score %}

{{ "%.1f"|format(metrics.avg_demerit_score) }}

Avg Demerit (Lilly)

{% endif %} {% if metrics.avg_sas %}

{{ "%.2f"|format(metrics.avg_sas) }}

Avg SAS

{% endif %} {% endfor %} {% endif %}

{% endif %} {% if plots.filters_data %}

Overview Sub-filters

Filter Descriptions:

NIBR — Novartis structural alerts: flags reactive warheads, toxic motifs, and metabolically labile groups that cause safety failures in preclinical studies

bredt — Bredt's rule: rejects molecules with impossible bridgehead double bonds — these cannot exist or be synthesized

common_alerts — PAINS, toxicophores, skin sensitizers, frequent hitters — removes promiscuous binders and false positives from biochemical assays

lilly — Eli Lilly MedChem rules: demerit scoring of 275+ structural features linked to poor ADMET, toxicity, or synthetic infeasibility

molcomplexity — Synthetic accessibility (SAS), QED drug-likeness, Bertz complexity — ensures practical synthesizability and drug-like properties

molgraph_stats — Topological constraints on ring count, heavy atoms, connectivity — excludes chemically unreasonable structures

protecting_groups — Detects residual protecting groups (Boc, Fmoc, Cbz, etc.) that should be removed before biological testing

ring_infraction — Flags strained ring systems and small heterocycles below minimum size — chemically unstable or synthetically challenging

stereo_center — Limits number of stereo centers and undefined stereocenters — excessive chirality makes synthesis difficult and costly

halogenicity — Limits halogen atom counts (F, Cl, Br) — over-halogenated molecules often have poor metabolic stability and toxicity

symmetry — Rejects highly symmetric molecules (off by default) — many real drugs are symmetric, use cautiously

{% endif %}

{% endif %} {% if data.synthesis.distributions or data.synthesis_detailed.sa_scores %}

Synthesis Analysis

{% if data.available_models and data.synthesis_detailed.by_model %}

All Models {% for model in data.available_models %} {{ model }} {% endfor %}

{% endif %}

Synthesis Scores

Mean Threshold Out of Range

SA Score Distribution

{% if plots.synthesis_sa_hist %}{{ plots.synthesis_sa_hist | safe }}{% endif %}

SYBA Score Distribution

{% if plots.synthesis_syba_hist %}{{ plots.synthesis_syba_hist | safe }}{% endif %}

RA Score Distribution

{% if plots.synthesis_ra_hist %}{{ plots.synthesis_ra_hist | safe }}{% endif %}

SA Score (lower = easier)

SYBA Score (higher = easier)

RA Score (higher = easier)

{% if data.retrosynthesis and data.retrosynthesis.summary %}

AiZynthFinder Retrosynthesis

{% if data.synthesis_detailed.summary.pct_solved is defined %}

{{ "%.1f"|format(data.synthesis_detailed.summary.pct_solved) }}%

Routes Found

{% endif %} {% if data.synthesis_detailed.summary.avg_search_time %}

{{ "%.1f"|format(data.synthesis_detailed.summary.avg_search_time) }}s

Avg Search Time

{% endif %} {% if data.retrosynthesis.summary.avg_route_score is defined %}

{{ "%.2f"|format(data.retrosynthesis.summary.avg_route_score) }}

Avg Route Score

{% endif %} {% if data.retrosynthesis.summary.avg_steps is defined %}

{{ "%.1f"|format(data.retrosynthesis.summary.avg_steps) }}

Avg Steps

{% endif %} {% if data.retrosynthesis.summary.avg_precursors is defined %}

{{ "%.1f"|format(data.retrosynthesis.summary.avg_precursors) }}

Avg Precursors

{% endif %}

Route Status

{% if plots.synthesis_solved_pie %}{{ plots.synthesis_solved_pie | safe }}{% endif %}

{% if plots.synthesis_time_box %}

Search Time by Model

{{ plots.synthesis_time_box | safe }}

{% endif %}

Route Score Distribution

{% if plots.retrosynthesis_route_score_hist %} {{ plots.retrosynthesis_route_score_hist | safe }} {% else %}

No route score data available

{% endif %}

Synthesis Steps

{% if plots.retrosynthesis_steps_hist %} {{ plots.retrosynthesis_steps_hist | safe }} {% else %}

No steps data available

{% endif %}

{% endif %}

{% endif %} {% if data.docking.gnina or data.docking.smina or data.docking_detailed.gnina.raw_data or data.docking_detailed.smina.raw_data %}

Docking Results

{% if data.available_models and (data.docking_detailed.gnina.by_model or data.docking_detailed.smina.by_model) %}

All Models Compare {% for model in data.available_models %} {{ model }} {% endfor %}

{% endif %}

{% if data.docking_detailed.gnina.summary %}

{{ "%.2f"|format(data.docking_detailed.gnina.summary.avg_affinity) }}

Avg Affinity (GNINA)

{{ "%.2f"|format(data.docking_detailed.gnina.summary.best_affinity) }}

Best Affinity (GNINA)

{{ data.docking_detailed.gnina.summary.count }}

Molecules Docked

{% elif data.docking_detailed.smina.summary %}

{{ "%.2f"|format(data.docking_detailed.smina.summary.avg_affinity) }}

Avg Affinity (SMINA)

{{ "%.2f"|format(data.docking_detailed.smina.summary.best_affinity) }}

Best Affinity (SMINA)

{{ data.docking_detailed.smina.summary.count }}

Molecules Docked

{% endif %}

{% if data.docking_detailed.gnina.raw_data or plots.docking_gnina %}

GNINA Results

{% if plots.docking_gnina_affinity_hist %}{{ plots.docking_gnina_affinity_hist | safe }} {% elif plots.docking_gnina %}{{ plots.docking_gnina | safe }}{% endif %}

{% if plots.docking_gnina_top_molecules %}{{ plots.docking_gnina_top_molecules | safe }}{% endif %}

{% if plots.docking_gnina_affinity_box %}

Binding Affinity by Model

{{ plots.docking_gnina_affinity_box | safe }}

{% endif %}

{% endif %} {% if data.docking_detailed.smina.raw_data or plots.docking_smina %}

SMINA Results

{% if plots.docking_smina_affinity_hist %}{{ plots.docking_smina_affinity_hist | safe }} {% elif plots.docking_smina %}{{ plots.docking_smina | safe }}{% endif %}

{% if plots.docking_smina_top_molecules %}{{ plots.docking_smina_top_molecules | safe }}{% endif %}

{% if plots.docking_smina_affinity_box %}

Binding Affinity by Model

{{ plots.docking_smina_affinity_box | safe }}

{% endif %}

{% endif %}

{% endif %} {% if data.docking_filters_detailed and data.docking_filters_detailed.per_filter %}

Docking Filters

{% if data.available_models and data.docking_filters_detailed.by_model %}

All Models {% for model in data.available_models %} {{ model }} {% endfor %}

{% endif %}

{{ data.docking_filters_detailed.total_poses }}

Total Poses

{{ data.docking_filters_detailed.passed_poses }}

Passed Poses

{{ data.docking_filters_detailed.pass_rate }}%

Pass Rate

{{ data.docking_filters_detailed.unique_molecules_passed }}

Unique Molecules

{{ data.docking_filters_detailed.aggregation_mode }}

Aggregation Mode

{% if plots.docking_filters_pass_fail %}

Per-Filter Results

{{ plots.docking_filters_pass_fail | safe }}

{% endif %} {% if plots.docking_filters_metric_hists %}

Metric Distributions

Filter Threshold

{{ plots.docking_filters_metric_hists | safe }}

{% endif %} {% if plots.docking_filters_by_model %}

Pass Rate by Model

{{ plots.docking_filters_by_model | safe }}

{% endif %}

{% endif %} {% if data.descriptors_final_detailed and data.descriptors_final_detailed.raw_data %}

Final Descriptors

{% if data.descriptors_final.summary %}

{% for desc_name, desc_stats in data.descriptors_final.summary.items() %}

{{ "%.2f"|format(desc_stats.mean) }}

{{ desc_name }} (mean)

{% endfor %}

{% endif %} {% if plots.descriptors_comparison_data %}

Initial vs Final Descriptor Comparison

Initial Final Initial Mean Final Mean

{% endif %}

{% endif %} {% if data.moleval and data.moleval.by_stage %}

Generative Metrics (MolEval)

Distribution quality metrics computed at key pipeline stages. Shows how molecular diversity, uniqueness, and filter passage rates evolve through the filtering funnel.

Detailed Values

{% for stage in data.moleval.stages %} {% endfor %} {% for metric in data.moleval.metrics %} {% for stage in data.moleval.stages %} {% set val = data.moleval.by_stage[stage][metric] if metric in data.moleval.by_stage.get(stage, {}) else None %} {% endfor %} {% endfor %}

Metric	{{ stage }}
{{ metric }}	{% if val is not none %}{{ "%.4f"|format(val) }}{% else %}—{% endif %}

{% endif %}