@yeyuan98/opencode-bioresearcher-plugin 1.6.6 → 1.6.8-alpha.0

package/dist/skills/gromacs-guides/guides/inspect_tpr.md

@@ -1,160 +1,160 @@
-# Inspecting TPR Files for Molecule Information
-
-## Quick Summary
-
-```bash
-gmx dump -s <tpr_file> 2>&1 | grep -A 5 "moltype"
-```
-
-## Detailed Breakdown
-
-```bash
-# Full dump (verbose)
-gmx dump -s <tpr_file>
-
-# Extract molecule block info
-gmx dump -s <tpr_file> 2>&1 | grep -E "(molblock|#molecules|moltype.*=)"
-```
-
-**Output interpretation:**
-```
-molblock (N):
-   moltype              = M "MoleculeName"    # Molecule type name
-   #molecules           = X                    # Number of copies in system
-
-moltype (M):
-   name="MoleculeName"
-   atoms:
-      atom (N):                              # N atoms in this molecule type
-```
-
-**Note:** Atoms are 0-indexed. `atom (275):` means 276 atoms with indices 0-275.
-
-## Key Information to Extract
-
-| Information | How to Find |
-|-------------|-------------|
-| Molecule type names | `grep 'moltype.*='` after `gmx dump` |
-| Molecule counts | `grep '#molecules'` after `gmx dump` |
-| Atoms per molecule type | Check `atom (N):` line under each `moltype` section |
-| Solvent molecule count | Find SOL/Water moltype, read `#molecules` |
-| Ion counts by type | Find NA, CL, etc. moltypes, read `#molecules` each |
-| Protein molecule chains | Count moltypes with "Protein" or similar in name |
-
-## Detecting Cyclic Molecule Configuration
-
-For protein chains, check if the molecule is cyclic (e.g., cyclic peptides) by examining bonds within the moltype.
-
-**Detection strategy:**
-1. Get atom count for the moltype from `atom (N):` line (N atoms, indexed 0 to N-1)
-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)
-3. If such a bond exists, the molecule is cyclic
-
-If no bond is found between atom 0 and the C-terminal atom, the molecule is linear (non-cyclic).
-
-**Bond format in gmx dump:**
-```
-      Bond:
-         nr: <count>
-         iatoms:
-            0 type=441 (BONDS)   0   2
-            1 type=442 (BONDS)   0 273    <-- bond from atom 0 to atom 273
-```
-
-**Example:** For a 275-atom cyclic peptide (atoms 0-274):
-- Atom 0: N-terminal N
-- Atom 273: C-terminal C (the backbone carbon)
-- Atom 274: C-terminal O
-- A bond `0 273` indicates the N-C cyclization
-
-**Quick check for cyclic bond:**
-```bash
-# Get atom count for a protein moltype
-gmx dump -s <tpr_file> 2>&1 | grep -A 1 "atom (" | head -4
-
-# Search for bonds involving atom 0 and the C-terminal atom (N-2)
-# Replace <N-2> with actual value (e.g., 273 for 275-atom molecule)
-
-# Standard pattern
-gmx dump -s <tpr_file> 2>&1 | grep -E "BONDS.*0.*<N-2>"
-
-# More robust pattern (explicit whitespace, works better on Windows)
-gmx dump -s <tpr_file> 2>&1 | grep -E "BONDS\ +0 +<N-2>"
-```
-
-**Example command for 275-atom molecule:**
-```bash
-gmx dump -s <tpr_file> 2>&1 | grep -E "BONDS.*0.*273"
-```
-
-#### Verifying the C-Terminal Atom
-
-The C-terminal C atom is typically at index N-2, but this can vary by force field. Verify with:
-```bash
-# Check atom type at index N-2 (e.g., 273 for 275-atom molecule)
-gmx dump -s <tpr_file> 2>&1 | grep -A2 "atom (273):"
-```
-Look for `type="C"` to confirm it's the backbone carbon.
-
-#### Isolating Bonds for a Specific Moltype
-
-When multiple moltypes exist, grep captures all bonds. To isolate one moltype's bonds:
-
-**Method 1: sed range (Recommended)**
-```bash
-# Extract bonds for moltype M (e.g., moltype 1)
-gmx dump -s <tpr_file> 2>&1 | sed -n '/moltype (1)/,/moltype (2)/p' | grep -E "BONDS.*0.*273"
-```
-
-**Method 2: grep with context**
-```bash
-# Get bonds within 200 lines after moltype declaration
-gmx dump -s <tpr_file> 2>&1 | grep -A200 "moltype (1)" | grep -E "BONDS.*0.*273"
-```
-Replace moltype numbers and context lines as appropriate for your system.
-
-## Checking Molecule Independence
-
-```bash
-gmx dump -s <tpr_file> 2>&1 | grep "bIntermolecularInteractions"
-```
-- `false` = Molecules are independent (correct for most simulations)
-- `true` = Bonded interactions exist between molecule types (unusual)
-
-## Quick System Overview
-
-```bash
-echo "q" | gmx make_ndx -f <tpr_file> 2>&1 | grep -E "(System|Protein|Water|Ion|atoms)"
-```
-
-## Standardized TPR Summary Template
-
-When users ask generic questions like "summarize this TPR" or "list all components", use this template for consistent output:
-
-### <tpr_file> Analysis Summary
-
-| Component | Count | Atoms | Structure |
-|-----------|-------|-------|-----------|
-| <moltype_name> | <N_copies> | <atoms_per_copy> | <Linear/Cyclic/-> |
-| ... | ... | ... | ... |
-| **Total** | - | **<sum_atoms>** | - |
-
-**Key Information:**
-- **Total protein residues**: <X> (<Y> atoms total)
-- **Molecules are <independent/linked>** (bIntermolecularInteractions=<true/false>)
-- <Notable features>
-
-### Populating the Template
-
-Use commands from:
-- **Key Information to Extract** table → Component, Count, Atoms columns
-- **Detecting Cyclic Molecule Configuration** → Structure column (Linear/Cyclic)
-- **Checking Molecule Independence** → bIntermolecularInteractions value
-
-### Structure Column Values
-
-| Value | When to Use |
-|-------|-------------|
-| `Linear` | Standard protein/peptide without cyclization |
-| `**Cyclic** (bond 0→<N-2>)` | N-to-C cyclization detected |
-| `-` | Non-protein (solvent, ions, ligands) |
+# Inspecting TPR Files for Molecule Information
+
+## Quick Summary
+
+```bash
+gmx dump -s <tpr_file> 2>&1 | grep -A 5 "moltype"
+```
+
+## Detailed Breakdown
+
+```bash
+# Full dump (verbose)
+gmx dump -s <tpr_file>
+
+# Extract molecule block info
+gmx dump -s <tpr_file> 2>&1 | grep -E "(molblock|#molecules|moltype.*=)"
+```
+
+**Output interpretation:**
+```
+molblock (N):
+   moltype              = M "MoleculeName"    # Molecule type name
+   #molecules           = X                    # Number of copies in system
+
+moltype (M):
+   name="MoleculeName"
+   atoms:
+      atom (N):                              # N atoms in this molecule type
+```
+
+**Note:** Atoms are 0-indexed. `atom (275):` means 276 atoms with indices 0-275.
+
+## Key Information to Extract
+
+| Information | How to Find |
+|-------------|-------------|
+| Molecule type names | `grep 'moltype.*='` after `gmx dump` |
+| Molecule counts | `grep '#molecules'` after `gmx dump` |
+| Atoms per molecule type | Check `atom (N):` line under each `moltype` section |
+| Solvent molecule count | Find SOL/Water moltype, read `#molecules` |
+| Ion counts by type | Find NA, CL, etc. moltypes, read `#molecules` each |
+| Protein molecule chains | Count moltypes with "Protein" or similar in name |
+
+## Detecting Cyclic Molecule Configuration
+
+For protein chains, check if the molecule is cyclic (e.g., cyclic peptides) by examining bonds within the moltype.
+
+**Detection strategy:**
+1. Get atom count for the moltype from `atom (N):` line (N atoms, indexed 0 to N-1)
+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)
+3. If such a bond exists, the molecule is cyclic
+
+If no bond is found between atom 0 and the C-terminal atom, the molecule is linear (non-cyclic).
+
+**Bond format in gmx dump:**
+```
+      Bond:
+         nr: <count>
+         iatoms:
+            0 type=441 (BONDS)   0   2
+            1 type=442 (BONDS)   0 273    <-- bond from atom 0 to atom 273
+```
+
+**Example:** For a 275-atom cyclic peptide (atoms 0-274):
+- Atom 0: N-terminal N
+- Atom 273: C-terminal C (the backbone carbon)
+- Atom 274: C-terminal O
+- A bond `0 273` indicates the N-C cyclization
+
+**Quick check for cyclic bond:**
+```bash
+# Get atom count for a protein moltype
+gmx dump -s <tpr_file> 2>&1 | grep -A 1 "atom (" | head -4
+
+# Search for bonds involving atom 0 and the C-terminal atom (N-2)
+# Replace <N-2> with actual value (e.g., 273 for 275-atom molecule)
+
+# Standard pattern
+gmx dump -s <tpr_file> 2>&1 | grep -E "BONDS.*0.*<N-2>"
+
+# More robust pattern (explicit whitespace, works better on Windows)
+gmx dump -s <tpr_file> 2>&1 | grep -E "BONDS\ +0 +<N-2>"
+```
+
+**Example command for 275-atom molecule:**
+```bash
+gmx dump -s <tpr_file> 2>&1 | grep -E "BONDS.*0.*273"
+```
+
+#### Verifying the C-Terminal Atom
+
+The C-terminal C atom is typically at index N-2, but this can vary by force field. Verify with:
+```bash
+# Check atom type at index N-2 (e.g., 273 for 275-atom molecule)
+gmx dump -s <tpr_file> 2>&1 | grep -A2 "atom (273):"
+```
+Look for `type="C"` to confirm it's the backbone carbon.
+
+#### Isolating Bonds for a Specific Moltype
+
+When multiple moltypes exist, grep captures all bonds. To isolate one moltype's bonds:
+
+**Method 1: sed range (Recommended)**
+```bash
+# Extract bonds for moltype M (e.g., moltype 1)
+gmx dump -s <tpr_file> 2>&1 | sed -n '/moltype (1)/,/moltype (2)/p' | grep -E "BONDS.*0.*273"
+```
+
+**Method 2: grep with context**
+```bash
+# Get bonds within 200 lines after moltype declaration
+gmx dump -s <tpr_file> 2>&1 | grep -A200 "moltype (1)" | grep -E "BONDS.*0.*273"
+```
+Replace moltype numbers and context lines as appropriate for your system.
+
+## Checking Molecule Independence
+
+```bash
+gmx dump -s <tpr_file> 2>&1 | grep "bIntermolecularInteractions"
+```
+- `false` = Molecules are independent (correct for most simulations)
+- `true` = Bonded interactions exist between molecule types (unusual)
+
+## Quick System Overview
+
+```bash
+echo "q" | gmx make_ndx -f <tpr_file> 2>&1 | grep -E "(System|Protein|Water|Ion|atoms)"
+```
+
+## Standardized TPR Summary Template
+
+When users ask generic questions like "summarize this TPR" or "list all components", use this template for consistent output:
+
+### <tpr_file> Analysis Summary
+
+| Component | Count | Atoms | Structure |
+|-----------|-------|-------|-----------|
+| <moltype_name> | <N_copies> | <atoms_per_copy> | <Linear/Cyclic/-> |
+| ... | ... | ... | ... |
+| **Total** | - | **<sum_atoms>** | - |
+
+**Key Information:**
+- **Total protein residues**: <X> (<Y> atoms total)
+- **Molecules are <independent/linked>** (bIntermolecularInteractions=<true/false>)
+- <Notable features>
+
+### Populating the Template
+
+Use commands from:
+- **Key Information to Extract** table → Component, Count, Atoms columns
+- **Detecting Cyclic Molecule Configuration** → Structure column (Linear/Cyclic)
+- **Checking Molecule Independence** → bIntermolecularInteractions value
+
+### Structure Column Values
+
+| Value | When to Use |
+|-------|-------------|
+| `Linear` | Standard protein/peptide without cyclization |
+| `**Cyclic** (bond 0→<N-2>)` | N-to-C cyclization detected |
+| `-` | Non-protein (solvent, ions, ligands) |

package/dist/tools/misc/index.d.ts

@@ -3,3 +3,4 @@ export { calculator } from './calculator';
 export { jsonExtract } from './json-extract';
 export { jsonValidate } from './json-validate';
 export { jsonInfer } from './json-infer';
+export { markdownToHtml } from './markdown-to-html';

package/dist/tools/misc/index.js

@@ -3,3 +3,4 @@ export { calculator } from './calculator';
 export { jsonExtract } from './json-extract';
 export { jsonValidate } from './json-validate';
 export { jsonInfer } from './json-infer';
+export { markdownToHtml } from './markdown-to-html';

package/dist/tools/misc/markdown-to-html.d.ts

@@ -0,0 +1,19 @@
+import { ToolContext } from '@opencode-ai/plugin/tool';
+import { z } from 'zod';
+export declare const markdownToHtml: {
+    description: string;
+    args: {
+        markdown: z.ZodOptional<z.ZodString>;
+        markdownPath: z.ZodOptional<z.ZodString>;
+        outputPath: z.ZodString;
+        title: z.ZodOptional<z.ZodString>;
+        css: z.ZodOptional<z.ZodString>;
+    };
+    execute(args: {
+        outputPath: string;
+        markdown?: string | undefined;
+        markdownPath?: string | undefined;
+        title?: string | undefined;
+        css?: string | undefined;
+    }, context: ToolContext): Promise<import("@opencode-ai/plugin").ToolResult>;
+};

package/dist/tools/misc/markdown-to-html.js

@@ -0,0 +1,109 @@
+import { tool } from '@opencode-ai/plugin/tool';
+import { z } from 'zod';
+import { readFileSync, mkdirSync, existsSync, writeFileSync } from 'node:fs';
+import { dirname, resolve, isAbsolute } from 'node:path';
+import { MARKED_BUNDLE } from './marked-bundle';
+const DEFAULT_CSS = `
+body { max-width: 900px; margin: 2rem auto; padding: 0 1rem; font-family: -apple-system, BlinkMacSystemFont, "Segoe UI", Helvetica, Arial, sans-serif; line-height: 1.6; color: #24292f; background: #ffffff; }
+h1, h2, h3, h4, h5, h6 { margin-top: 1.5em; margin-bottom: 0.5em; font-weight: 600; line-height: 1.25; }
+h1 { font-size: 2em; border-bottom: 1px solid #d0d7de; padding-bottom: 0.3em; }
+h2 { font-size: 1.5em; border-bottom: 1px solid #d0d7de; padding-bottom: 0.3em; }
+h3 { font-size: 1.25em; }
+p { margin: 1em 0; }
+a { color: #0969da; text-decoration: none; }
+a:hover { text-decoration: underline; }
+ul, ol { padding-left: 2em; margin: 1em 0; }
+ul ul, ol ol, ul ol, ol ul { margin: 0; }
+li { margin: 0.25em 0; }
+blockquote { border-left: 4px solid #d0d7de; margin: 1em 0; padding: 0.5em 1em; color: #656d76; background: #f6f8fa; border-radius: 0 6px 6px 0; }
+pre { background: #f6f8fa; padding: 1rem; border-radius: 6px; overflow-x: auto; border: 1px solid #d0d7de; }
+code { background: #f6f8fa; padding: 0.2rem 0.4rem; border-radius: 3px; font-size: 85%; font-family: "SFMono-Regular", Consolas, "Liberation Mono", Menlo, monospace; }
+pre code { background: none; padding: 0; font-size: 100%; }
+table { border-collapse: collapse; width: 100%; margin: 1em 0; }
+th, td { border: 1px solid #d0d7de; padding: 0.5rem 0.75rem; text-align: left; }
+th { background: #f6f8fa; font-weight: 600; }
+tr:nth-child(even) { background: #f6f8fa; }
+hr { border: none; border-top: 1px solid #d0d7de; margin: 2em 0; }
+img { max-width: 100%; border-radius: 6px; }
+`.trim();
+function buildHtml(markdown, title, extraCss) {
+    const escapedMarkdown = JSON.stringify(markdown).replace(/<\//g, String.raw `<\/`);
+    const css = extraCss ? `${DEFAULT_CSS}\n${extraCss}` : DEFAULT_CSS;
+    const safeCss = css.replace(/<\/style/gi, String.raw `<\/style`);
+    return `<!DOCTYPE html>
+<html lang="en">
+<head>
+<meta charset="utf-8"/>
+<meta name="viewport" content="width=device-width, initial-scale=1.0"/>
+<title>${escapeHtml(title)}</title>
+<style>${safeCss}</style>
+</head>
+<body>
+<div id="content"></div>
+<script>${MARKED_BUNDLE}</script>
+<script>document.getElementById('content').innerHTML = marked.parse(${escapedMarkdown});</script>
+</body>
+</html>`;
+}
+function escapeHtml(str) {
+    return str.replace(/&/g, '&amp;').replace(/</g, '&lt;').replace(/>/g, '&gt;').replace(/"/g, '&quot;');
+}
+export const markdownToHtml = tool({
+    description: `Convert markdown to a standalone HTML file that can be opened in any browser. The generated HTML embeds marked.js fully — no internet access required. Accepts markdown as a string or from a file path. Raw HTML in markdown is rendered as-is; do not use with untrusted content.`,
+    args: {
+        markdown: z.string().optional()
+            .describe("Inline markdown content to render"),
+        markdownPath: z.string().optional()
+            .describe("Path to a markdown (.md) file to render"),
+        outputPath: z.string()
+            .describe("Output path for the generated HTML file"),
+        title: z.string().optional()
+            .describe("HTML page title (default: 'Markdown Document')"),
+        css: z.string().optional()
+            .describe("Additional CSS to embed in the HTML (appended after default styles)"),
+    },
+    execute: async (args, context) => {
+        await context.ask({ permission: "markdownToHtml", patterns: ["*"], always: ["*"], metadata: {} });
+        if (!args.markdown && !args.markdownPath) {
+            return "Error: exactly one of 'markdown' or 'markdownPath' must be provided";
+        }
+        if (args.markdown && args.markdownPath) {
+            return "Error: provide either 'markdown' or 'markdownPath', not both";
+        }
+        let markdown;
+        if (args.markdownPath) {
+            const mdPath = isAbsolute(args.markdownPath)
+                ? args.markdownPath
+                : resolve(context.directory, args.markdownPath);
+            if (!existsSync(mdPath)) {
+                return `Error: markdown file not found: ${mdPath}`;
+            }
+            try {
+                markdown = readFileSync(mdPath, 'utf-8');
+            }
+            catch (e) {
+                return `Error: failed to read markdown file: ${e instanceof Error ? e.message : String(e)}`;
+            }
+        }
+        else {
+            markdown = args.markdown;
+        }
+        const html = buildHtml(markdown, args.title ?? "Markdown Document", args.css);
+        const outPath = isAbsolute(args.outputPath)
+            ? args.outputPath
+            : resolve(context.directory, args.outputPath);
+        try {
+            mkdirSync(dirname(outPath), { recursive: true });
+        }
+        catch (e) {
+            return `Error: failed to create output directory: ${e instanceof Error ? e.message : String(e)}`;
+        }
+        try {
+            writeFileSync(outPath, html, 'utf-8');
+        }
+        catch (e) {
+            return `Error: failed to write HTML file: ${e instanceof Error ? e.message : String(e)}`;
+        }
+        return `HTML file written to: ${outPath}`;
+    }
+});