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81 lines
3.2 KiB
Markdown
81 lines
3.2 KiB
Markdown
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---
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name: molecular-viz
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description: Visualize drug-protein complexes using build_viewer.py, PubChem, and OpenFold3 NIM. Use when asked to show a molecular structure, drug target, or protein visualization.
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metadata:
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openclaw:
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requires:
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bins: ["python3", "curl"]
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---
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# Molecular Visualization
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Generate 3D protein-ligand visualizations using the `build_viewer.py` script. The script handles the full pipeline:
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1. **Drug SMILES** -- looked up automatically from PubChem
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2. **Protein target** -- resolved from a built-in drug-target table (or pass `--sequence` manually)
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3. **Structure prediction** -- protein + drug sent to OpenFold3 NIM for co-structure prediction
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4. **3D viewer** -- self-contained HTML with jQuery + 3Dmol.js inlined, saved to canvas
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## Usage
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Simplest form (target auto-resolved):
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```
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python /sandbox/clinical-intelligence/scripts/build_viewer.py --drug metformin
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```
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With explicit sequence (for drugs not in the built-in table):
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```
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python /sandbox/clinical-intelligence/scripts/build_viewer.py --drug drugname --sequence AMINOACIDSEQ --title "Custom Title"
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```
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### Options
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| Flag | Required | Description |
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|------|----------|-------------|
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| `--drug` | Yes | Drug name for PubChem SMILES lookup (e.g. `metformin`) |
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| `--sequence` | No | Amino acid sequence of protein target. Auto-resolved if omitted. |
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| `--title` | No | Custom viewer title |
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| `--output` | No | Custom output path (defaults to `~/.openclaw/canvas/{drug}_complex.html`) |
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| `--openfold-host` | No | Override OpenFold3 host IP (defaults to `172.17.0.1`) |
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### Built-in drug targets
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The script knows these drugs and auto-resolves their protein targets:
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| Drug | Target protein |
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|------|---------------|
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| metformin | Insulin B-chain |
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| atorvastatin | HMG-CoA reductase |
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| rosuvastatin | HMG-CoA reductase |
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| lisinopril | ACE |
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| enalapril | ACE |
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| losartan | Angiotensin II receptor type 1 |
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| amlodipine | L-type calcium channel Cav1.2 |
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| empagliflozin | SGLT2 |
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| semaglutide | GLP-1 receptor |
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For any drug in this table, just pass `--drug` and the script does the rest.
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### Drugs NOT in the table
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If the drug is not listed, the script exits with an error and prints the list of known drugs. In that case, you need to provide `--sequence` explicitly. Tell the user the drug is not in the built-in table and that you need a protein target sequence to proceed.
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### Drugs that cannot be visualized
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Biologics, enzyme mixtures, or complex formulations that PubChem cannot resolve to a single SMILES (e.g. pancrelipase, insulin glargine) will still get protein-only structure prediction -- the script handles this gracefully by predicting without a ligand.
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## Output
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The script saves an HTML viewer to canvas. Link it in your response as a markdown hyperlink:
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```
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[View 3D structure](http://localhost:18789/__openclaw__/canvas/metformin_complex.html)
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```
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## Confidence Scores
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The viewer header displays OpenFold3 scores:
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- **Confidence** -- overall prediction confidence (higher = better)
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- **pLDDT** -- per-residue local confidence (0-100, >70 is good)
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- **pTM** -- predicted template modeling score (0-1)
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- **ipTM** -- interface predicted TM-score (complexes only, measures protein-ligand interface quality)
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