pytdc

Load and analyze Therapeutics Data Commons drug discovery datasets and benchmarks.

Updated Jul 1, 2026
One-click install
npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill pytdc-jasrajtulsi
Or copy as Structured Prompt for Agent
Please help me install this Agent Skill.
Skill: pytdc
Source: https://github.com/jasrajtulsi/GRAD-SCOPE/tree/main/.claude/skills/pytdc
Command: npx skills add https://github.com/jasrajtulsi/GRAD-SCOPE --skill pytdc-jasrajtulsi

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires tdc, numpy, pandas, scipy, and includes scripts (resource) and references (resource) components.

What problem does it solve?

It helps researchers and ML practitioners work with curated therapeutics datasets and benchmarks without spending time manually handling dataset discovery, splitting strategies, evaluation setup, or oracle-based molecular scoring.

Core Features & Use Cases

  • Dataset access: Load ADME, toxicity, DTI, DDI, generation, retrosynthesis, and related therapeutic benchmarks from a consistent interface.
  • Evaluation workflows: Apply scaffold, random, cold, and temporal splits, then score results with standardized metrics and multi-seed benchmark-group evaluation.
  • Molecular optimization support: Use oracle functions, label transformations, and utility helpers for drug-likeness, target activity, and generation experiments.
  • Use case: A medicinal chemistry researcher can compare multiple models on Caco2, HIA, and BindingDB tasks, then report reliable mean and standard deviation across five seeds.

Quick Start

Use this skill to load the right TDC dataset, choose the appropriate split and metric, and generate a benchmark-ready evaluation workflow for your therapeutic ML experiment.

Frequently Asked Questions about pytdc

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I load and benchmark ADME and toxicity datasets for drug discovery?

You can load and benchmark ADME and toxicity datasets for drug discovery by using this Skill to access Therapeutics Data Commons workflows, which provide a consistent interface for dataset retrieval, standardized splits, and molecular oracle evaluation.

What's the best way to apply scaffold and cold splits to molecular generation datasets?

The best way to apply scaffold and cold splits to molecular generation datasets is through the built-in splitting strategies provided by the Therapeutics Data Commons workflows, which ensure standardized partitioning for reliable ML model evaluation.

Can I calculate multi-seed benchmark metrics for therapeutic ML models?

Yes, you can calculate multi-seed benchmark metrics for therapeutic ML models because the Skill supports multi-seed benchmark-group evaluation, allowing you to report reliable mean and standard deviation scores across different random seeds.

Does this Skill support oracle functions for molecular optimization and target activity scoring?

Yes, this Skill supports oracle functions for molecular optimization by providing label transformations and utility helpers to evaluate drug-likeness, target activity, and generation experiments within the Therapeutics Data Commons framework.

Do I need specific Python dependencies to run Therapeutics Data Commons workflows?

Yes, you need TDC-compatible Python dependencies including numpy, pandas, and scipy to run Therapeutics Data Commons workflows for numerical analysis, tabular processing, and scientific evaluation of drug discovery datasets.

How does benchmarking drug discovery datasets with TDC compare to manual dataset handling?

Benchmarking drug discovery datasets with TDC eliminates manual dataset discovery, splitting strategy design, and evaluation setup by providing curated datasets, standardized metrics, and consistent interfaces directly within your Python environment.