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rdkit-conf

Generate RDKit conformers from SMILES and output SDF or XYZ files.

124|25|Updated Feb 20, 2026
Search Tags:#docking#rdkit#chemoinformatics#conformer-generation#3d-embedding#2d-fallback
One-click install
npx skills add https://github.com/jinzhezenggroup/computational-chemistry-agent-skills --skill rdkit-conf
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: rdkit-conf
Source: https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/main/molecular-conformer/rdkit-conf
Command: npx skills add https://github.com/jinzhezenggroup/computational-chemistry-agent-skills --skill rdkit-conf

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires rdkit, pandas, and includes scripts (resource) components.

What problem does it solve?

This tool automates RDKit 3D/2D conformer generation from SMILES or CSV/SMI inputs, producing reliable 3D structures for downstream docking, visualization, and descriptor calculations, while handling failures gracefully.

Core Features & Use Cases

  • Multi-conformer sampling (ETKDGv3 by default) per molecule with optional force-field minimization (MMFF94s/UFF) and selection of the lowest-energy conformer.
  • Automatic 2D fallback with logging when 3D embedding fails, enabling continued workflows and traceability.
  • Supports inputs in .csv and .smi formats and outputs in SDF or XYZ formats for seamless integration into cheminformatics pipelines.

Quick Start

Run the CLI wrapper to generate multiple RDKit conformers from SMILES data and output the results as an SDF or XYZ file.

Frequently Asked Questions about rdkit-conf

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

FAQPage Schema
How do I generate 3D conformers from SMILES for docking preparation?▼

RDKit conformer generation automates 3D embedding from SMILES or CSV inputs using ETKDGv3 sampling with optional MMFF94s/UFF minimization, outputting SDF or XYZ files for docking, visualization, and descriptor calculations.

What happens when RDKit 3D embedding fails for a molecule?▼

When RDKit 3D embedding fails, the tool automatically applies a 2D fallback and logs the affected molecules, ensuring your cheminformatics workflow continues without interruption while maintaining full traceability of skipped structures.

Do I need to manually install RDKit and pandas to use this conformer generator?▼

No, you do not need to manually install RDKit and pandas. The conformer generator requires only the uv runtime, as RDKit and pandas dependencies are installed automatically via inline metadata during execution.

Can I generate multiple conformers per molecule and select the lowest energy structure?▼

Yes, you can sample multiple RDKit conformers per molecule using ETKDGv3 with a default of 10 conformers, apply optional force-field minimization via MMFF94s or UFF, and select the lowest-energy conformer for output.

What input and output formats are supported for cheminformatics conformer generation?▼

Cheminformatics conformer generation supports CSV and SMI input formats containing SMILES data, and outputs 3D or 2D molecular structures as SDF or XYZ files, ensuring seamless integration into existing cheminformatics pipelines.

Why does RDKit 3D conformer generation skip certain molecules and how is it tracked?▼

RDKit 3D conformer generation skips molecules that fail embedding due to complex structures or valence issues, automatically logging these skipped molecules alongside 2D fallback entries to maintain workflow traceability and data integrity.

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