pharmaclaw-cheminformatics
Advanced cheminformatics agent for 3D molecular analysis, pharmacophore mapping, format conversion, RECAP fragmentation, and stereoisomer enumeration. The "senior cheminformatician" upgrade to Chemistry Query. Use for 3D conformer generation/ensembles (ETKDG + MMFF/UFF), pharmacophore feature extraction and fingerprints, molecular format conversion (SMILES/SDF/MOL/InChI/PDB/XYZ), RECAP retrosynthetic fragmentation for library design, stereoisomer enumeration (R/S, E/Z), and cheminformatics profiling. Chains from chemistry-query (receives SMILES) and feeds into pharmacology, catalyst-design, ip-expansion. Triggers on conformer, 3D structure, pharmacophore, SDF, MOL file, format conversion, RECAP, fragmentation, stereoisomer, chirality, enantiomer, cheminformatics, library design, building blocks, docking prep.
Install via CLI (Recommended)
clawhub install openclaw/skills/skills/cheminem/pharmaclaw-cheminformaticsWhat This Skill Does
The pharmaclaw-cheminformatics skill serves as the senior-level cheminformatician agent for OpenClaw. While basic tools focus on 2D property retrieval, this skill enables complex 3D molecular modeling, spatial analysis, and structural transformation. It provides robust capabilities for conformer ensemble generation using ETKDG (Experimental-Torsion Knowledge Distance Geometry) with force-field optimization (MMFF/UFF). Users can perform sophisticated pharmacophore mapping, extract 3D feature sets, generate fingerprints for virtual screening, perform RECAP-based retrosynthetic fragmentation, and handle stereoisomer enumeration. Whether you need to convert between diverse file formats like PDB, XYZ, SDF, and InChI or calculate conformational energy landscapes, this skill automates the heavy lifting required for modern drug discovery and medicinal chemistry workflows.
Installation
To integrate this agent into your OpenClaw environment, execute the following command in your terminal: clawhub install openclaw/skills/skills/cheminem/pharmaclaw-cheminformatics
Use Cases
This skill is engineered for medicinal chemists, computational biologists, and drug discovery engineers. Key use cases include:
- Preparing ligands for high-throughput docking by generating optimized 3D ensembles.
- Performing pharmacophore-based virtual screening to identify structural analogues.
- Analyzing chemical libraries via RECAP fragmentation to identify essential building blocks.
- Converting experimental structural data (PDB/XYZ) into computational-ready SMILES or SDF formats.
- Determining chiral centers and enumerating stereoisomers for library expansion projects.
Example Prompts
- "Generate a 3D conformer ensemble for the following SMILES string, using the MMFF optimization method, and save the top 20 results to a file named docking_ligand.sdf."
- "Perform a pharmacophore feature extraction on my molecule. Can you also generate a mapping image to visualize the hydrogen bond acceptors and hydrophobic regions?"
- "Convert this batch of SDF molecules into SMILES format and identify all possible stereoisomers for each structure to expand our library."
Tips & Limitations
- Energy Optimization: Always specify the force field (MMFF or UFF) to ensure the conformers are chemically relevant for docking.
- Resource Usage: Generating large ensembles (num_confs > 100) is computationally expensive; use the 'best' action for rapid structural lookups.
- Format Handling: While the tool supports many formats, ensure your input 3D coordinates are reasonable, as highly strained geometries may fail during MMFF optimization.
- Chaining: This skill acts as a powerful middleware. Pair it with 'chemistry-query' for initial lookup, and feed the output into 'pharmacology' or 'catalyst-design' for downstream predictive analysis.
Metadata
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Find the right skillPaste this into your clawhub.json to enable this plugin.
{
"plugins": {
"official-cheminem-pharmaclaw-cheminformatics": {
"enabled": true,
"auto_update": true
}
}
}Tags(AI)
Flags: file-write, file-read, code-execution
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