@yeyuan98/opencode-bioresearcher-plugin 1.5.4-alpha.0 → 1.5.4-alpha.1
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@@ -126,3 +126,35 @@ gmx dump -s <tpr_file> 2>&1 | grep "bIntermolecularInteractions"
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```bash
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echo "q" | gmx make_ndx -f <tpr_file> 2>&1 | grep -E "(System|Protein|Water|Ion|atoms)"
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```
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## Standardized TPR Summary Template
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When users ask generic questions like "summarize this TPR" or "list all components", use this template for consistent output:
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### <tpr_file> Analysis Summary
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| Component | Count | Atoms | Structure |
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|-----------|-------|-------|-----------|
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| <moltype_name> | <N_copies> | <atoms_per_copy> | <Linear/Cyclic/-> |
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| ... | ... | ... | ... |
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| **Total** | - | **<sum_atoms>** | - |
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**Key Information:**
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- **Total protein residues**: <X> (<Y> atoms total)
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- **Molecules are <independent/linked>** (bIntermolecularInteractions=<true/false>)
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- <Notable features>
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### Populating the Template
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Use commands from:
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- **Key Information to Extract** table → Component, Count, Atoms columns
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- **Detecting Cyclic Molecule Configuration** → Structure column (Linear/Cyclic)
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- **Checking Molecule Independence** → bIntermolecularInteractions value
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### Structure Column Values
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| Value | When to Use |
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|-------|-------------|
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| `Linear` | Standard protein/peptide without cyclization |
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| `**Cyclic** (bond 0→<N-2>)` | N-to-C cyclization detected |
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| `-` | Non-protein (solvent, ions, ligands) |
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package/package.json
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