@yeyuan98/opencode-bioresearcher-plugin 1.5.3 → 1.5.4-alpha.1
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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@@ -28,6 +28,8 @@ moltype (M):
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atom (N): # N atoms in this molecule type
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```
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**Note:** Atoms are 0-indexed. `atom (275):` means 276 atoms with indices 0-275.
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## Key Information to Extract
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| Information | How to Find |
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@@ -48,6 +50,8 @@ For protein chains, check if the molecule is cyclic (e.g., cyclic peptides) by e
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2. Search the Bond section for a bond between atom 0 and the C-terminal atom (typically atom N-2, which is the C atom before the terminal O)
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3. If such a bond exists, the molecule is cyclic
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If no bond is found between atom 0 and the C-terminal atom, the molecule is linear (non-cyclic).
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**Bond format in gmx dump:**
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```
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Bond:
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@@ -70,7 +74,12 @@ gmx dump -s <tpr_file> 2>&1 | grep -A 1 "atom (" | head -4
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# Search for bonds involving atom 0 and the C-terminal atom (N-2)
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# Replace <N-2> with actual value (e.g., 273 for 275-atom molecule)
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# Standard pattern
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gmx dump -s <tpr_file> 2>&1 | grep -E "BONDS.*0.*<N-2>"
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# More robust pattern (explicit whitespace, works better on Windows)
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gmx dump -s <tpr_file> 2>&1 | grep -E "BONDS\ +0 +<N-2>"
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```
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**Example command for 275-atom molecule:**
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@@ -78,6 +87,32 @@ gmx dump -s <tpr_file> 2>&1 | grep -E "BONDS.*0.*<N-2>"
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gmx dump -s <tpr_file> 2>&1 | grep -E "BONDS.*0.*273"
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```
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#### Verifying the C-Terminal Atom
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The C-terminal C atom is typically at index N-2, but this can vary by force field. Verify with:
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```bash
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# Check atom type at index N-2 (e.g., 273 for 275-atom molecule)
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gmx dump -s <tpr_file> 2>&1 | grep -A2 "atom (273):"
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```
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Look for `type="C"` to confirm it's the backbone carbon.
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#### Isolating Bonds for a Specific Moltype
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When multiple moltypes exist, grep captures all bonds. To isolate one moltype's bonds:
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**Method 1: sed range (Recommended)**
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```bash
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# Extract bonds for moltype M (e.g., moltype 1)
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gmx dump -s <tpr_file> 2>&1 | sed -n '/moltype (1)/,/moltype (2)/p' | grep -E "BONDS.*0.*273"
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```
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**Method 2: grep with context**
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```bash
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# Get bonds within 200 lines after moltype declaration
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gmx dump -s <tpr_file> 2>&1 | grep -A200 "moltype (1)" | grep -E "BONDS.*0.*273"
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```
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Replace moltype numbers and context lines as appropriate for your system.
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## Checking Molecule Independence
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```bash
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@@ -91,3 +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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