rdkit-conf
OfficialRDKit conformer generator: 3D/2D
Authorjinzhezenggroup
Version1.0.0
Installs0
System Documentation
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.
Dependency Matrix
Required Modules
rdkitpandas
Components
scripts
💻 Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: rdkit-conf Download link: https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/archive/main.zip#rdkit-conf Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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