@yeyuan98/opencode-bioresearcher-plugin 1.5.3 → 1.5.4-alpha.0
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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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