diff --git a/examples/basic_usage.ipynb b/examples/basic_usage.ipynb index eae212f..3db6a3e 100644 --- a/examples/basic_usage.ipynb +++ b/examples/basic_usage.ipynb @@ -15,211 +15,97 @@ "metadata": {}, "outputs": [], "source": [ - "from chemscii.parsers import parse_smiles\n", - "from chemscii.renderers import AsciiMagicRenderer, AsciiRenderer, UnicodeRenderer" + "from chemscii.parsers import name_to_smiles, parse_smiles\n", + "from chemscii.renderers import AsciiMagicRenderer, AsciiRenderer" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "## Rendering Ethanol\n", - "\n", - "Let's start with a simple molecule: ethanol (CCO)." + "## Parse Molecules By Name" ] }, { "cell_type": "code", "execution_count": 2, "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "ASCII Renderer:\n", - "\n", - "\n", - "\n", - "\n", - " C\n", - " .. ..\n", - " O C\n" - ] - } - ], - "source": [ - "# Parse the SMILES string\n", - "ethanol = parse_smiles(\"CCO\")\n", - "\n", - "# Render with ASCII renderer\n", - "ascii_renderer = AsciiRenderer()\n", - "print(\"ASCII Renderer:\")\n", - "art = ascii_renderer.render_molecule(ethanol)" - ] - }, - { - "cell_type": "code", - "execution_count": 3, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Unicode Renderer:\n", - "\n", - "\n", - "\n", - "\n", - " C\n", - " ·· ··\n", - " O C\n" - ] - } - ], - "source": [ - "# Render with Unicode renderer\n", - "unicode_renderer = UnicodeRenderer()\n", - "print(\"Unicode Renderer:\")\n", - "art = unicode_renderer.render_molecule(ethanol)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Rendering Benzene\n", - "\n", - "Now let's render a ring structure: benzene." - ] - }, - { - "cell_type": "code", - "execution_count": 4, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "ASCII Renderer:\n", - "\n", - " C\n", - " .. $$\n", - " .. $$\n", - " .. $$\n", - " .. $$\n", - " C C\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " C C\n", - " .. $$\n", - " .. $$\n", - " .. $$\n", - " .. $$\n", - " C\n", - "\n", - "Unicode Renderer:\n", - "\n", - " C\n", - " ·· $$\n", - " ·· $$\n", - " ·· $$\n", - " ·· $$\n", - " C C\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " $ :\n", - " C C\n", - " ·· $$\n", - " ·· $$\n", - " ·· $$\n", - " ·· $$\n", - " C\n" - ] - } - ], + "outputs": [], "source": [ - "benzene = parse_smiles(\"c1ccccc1\")\n", - "\n", - "print(\"ASCII Renderer:\")\n", - "art = ascii_renderer.render_molecule(benzene)\n", - "print()\n", - "print(\"Unicode Renderer:\")\n", - "art = unicode_renderer.render_molecule(benzene)" + "smiles = name_to_smiles(\"Tamoxifen\")\n", + "mol = parse_smiles(smiles)" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "## Double and Triple Bonds\n", - "\n", - "chemscii supports different bond orders with distinct characters." - ] - }, - { - "cell_type": "code", - "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Ethene (C=C) - Double Bond:\n", - "\n", - "\n", - "\n", - "\n", - " C$$$C\n" - ] - } - ], - "source": [ - "# Ethene (double bond)\n", - "ethene = parse_smiles(\"C=C\")\n", - "print(\"Ethene (C=C) - Double Bond:\")\n", - "art = unicode_renderer.render_molecule(ethene)" + "# Comically Basic Rendering" ] }, { "cell_type": "code", - "execution_count": 6, + "execution_count": 3, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "Ethyne (C#C) - Triple Bond:\n", - "\n", - "\n", - "\n", "\n", - " C###C\n" + " C\n", + " |\n", + " |\n", + " |\n", + " \u001b[94mN\u001b[0m\n", + " // \\\\\n", + " / \\\n", + " C C\n", + " |\n", + " |\n", + " |\n", + " C\\\n", + " \\\n", + " \\\u001b[91mO\u001b[0m\n", + " |\n", + " |\n", + " |\n", + " |\n", + " C\n", + " === \\\\\\\n", + " C C\n", + " | =\n", + " | =\n", + " | =\n", + " C C\n", + " === ///\n", + " C C\n", + " | |\n", + " | |\n", + " | |\n", + " | |\n", + " C\\ /C= /C\n", + " == \\ / = /\n", + " C \\C/ =C/\n", + " | = |\n", + " | = |\n", + " | = |\n", + " C /C /C=\n", + " == / / =\n", + " C/ C/ =C\n", + " = |\n", + " = |\n", + " = |\n", + " = |\n", + " C C\n", + " \\\\\\ ===\n", + " C\n" ] } ], "source": [ - "# Ethyne (triple bond)\n", - "ethyne = parse_smiles(\"C#C\")\n", - "print(\"Ethyne (C#C) - Triple Bond:\")\n", - "art = unicode_renderer.render_molecule(ethyne)" + "ascii_renderer = AsciiRenderer(width=50, height=50)\n", + "txt = ascii_renderer.render_molecule(mol)" ] }, { @@ -233,279 +119,74 @@ }, { "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Ethanol:\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m '>v; \u001b[39m\n", - "\u001b[90m _\\}ooI*e7!): \u001b[39m\n", - "\u001b[90m `|{e7!): _\\}ooI\\_ \u001b[39m\n", - "\u001b[90m '\u001b[31m/>l\u001b[90m]v; '>?7e*|- \u001b[39m\n", - "\u001b[90m _+\u001b[31m/\u001b[90m' ^x1ztc=. \u001b[39m\n", - "\u001b[90m \u001b[31m/{\u001b[90m==\u001b[31m*\u001b[90m;\u001b[31m%|\u001b[90m \u001b[31m>i\u001b[90m`. .+ltz+ \u001b[39m\n", - "\u001b[90m +\u001b[31mv\u001b[90m..\u001b[31m%\u001b[90m;+\u001b[31m)\u001b[90m^^\u001b[31mi\u001b[90m^ `. \u001b[39m\n", - "\u001b[90m . . .__. \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\u001b[90m \u001b[39m\n", - "\n" - ] - } - ], - "source": [ - "# Create the magic renderer with a smaller column width for the notebook\n", - "magic_renderer = AsciiMagicRenderer(columns=60)\n", - "\n", - "print(\"Ethanol:\")\n", - "art = magic_renderer.render_molecule(ethanol)" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, - "outputs": [ - { - "name": "stdout", - "output_type": "stream", - "text": [ - "Benzene:\n", - "\u001b[90m _\\?ju}*LL!<_ \u001b[39m\n", - "\u001b[90m `/sa7!), _>?7es\"` \u001b[39m\n", - "\u001b[90m .+ltz[%; _tal^ 'i[zal+. \u001b[39m\n", - "\u001b[90m ^x1ztc=. .^x1z1%, ;x1z1x^ \u001b[39m\n", - "\u001b[90m ,v[zar/. ./raz[i' ^laz]v, \u001b[39m\n", - "\u001b[90m :)!7e{|` `|{e7?>- /{e7!): \u001b[39m\n", - "\u001b[90m iJ7}\\` _\\}oo}). `\\}7Jv \u001b[39m\n", - "\u001b[90m n\u001b[37my\u001b[90m ;. '>?7o\\ w# \u001b[39m\n", - "\u001b[90m jT :\u001b[37mE\u001b[90m^ ;, nL \u001b[39m\n", - "\u001b[90m jT :\u001b[37mP\u001b[90m^ nL \u001b[39m\n", - "\u001b[90m jT :\u001b[37mX\u001b[90m^ TL \u001b[39m\n", - "\u001b[90m jT ,\u001b[37mP\u001b[90m^ TL \u001b[39m\n", - "\u001b[90m jT ,\u001b[37mP\u001b[90m^ TL \u001b[39m\n", - "\u001b[90m LT ,\u001b[37mP\u001b[90m^ TL \u001b[39m\n", - "\u001b[90m LT ,\u001b[37mP\u001b[90m; Tj \u001b[39m\n", - "\u001b[90m LT ,\u001b[37mP\u001b[90m; Tj \u001b[39m\n", - "\u001b[90m Ln ,\u001b[37mP\u001b[90m; Tj \u001b[39m\n", - "\u001b[90m Ln ,\u001b[37mP\u001b[90m; Tj \u001b[39m\n", - "\u001b[90m Ln ,\u001b[37mE\u001b[90m; ,: Tj \u001b[39m\n", - "\u001b[90m #w ;. '>?7o\\ \u001b[37my\u001b[90mn \u001b[39m\n", - "\u001b[90m vJ7}\\- _\\}oo})` `\\}7Ji \u001b[39m\n", - "\u001b[90m '>?7e{|- `|{e7!>- /{e7!): \u001b[39m\n", - "\u001b[90m ,v]zar/. ./raz]i' ^laz[v; \u001b[39m\n", - "\u001b[90m ^x1ztc= .=ctz1%, ;x1z1x^ \u001b[39m\n", - "\u001b[90m .+ltz[%; 'atc^ :v[ztl+. \u001b[39m\n", - "\u001b[90m `\"se7!): _>!7as\"` \u001b[39m\n", - "\u001b[90m _\\?ju}}uj?\\_ \u001b[39m\n", - "\n" - ] - } - ], - "source": [ - "print(\"Benzene:\")\n", - "art = magic_renderer.render_molecule(benzene)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "## Complex Natural Product: Caffeine\n", - "\n", - "Let's compare all three renderers on a more complex molecule: caffeine." - ] - }, - { - "cell_type": "code", - "execution_count": 9, + "execution_count": 4, "metadata": {}, "outputs": [ { "name": "stdout", "output_type": "stream", "text": [ - "ASCII Renderer:\n", - "\n", - "\n", - "\n", - " C\n", - " :\n", - " :\n", - " :\n", - " :\n", - " :\n", - " :\n", - " :\n", - " :\n", - " :\n", - " : O\n", - " : $$\n", - " N. $\n", - " . .. $$\n", - " .. .. $\n", - " . .. $\n", - " . .. $$\n", - " N... .. .C\n", - " $ ..... . :\n", - " $ ...C :\n", - " $ $ :\n", - " $ $ :\n", - " $ $ :\n", - " $ $ :\n", - " $ $ :\n", - " $ $ :\n", - " $ $ :\n", - " C $ :\n", - " . $ :\n", - " . $ N.\n", - " . $ . ..\n", - " . .C. .. ..\n", - " . .. .. . ..\n", - " . .. .. . ..\n", - " . .. .. .. .C\n", - " . .. .. .\n", - " N. .C\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " C $\n", - " O\n", - "\n", - "Unicode Renderer:\n", - "\n", - "\n", - "\n", - " C\n", - " :\n", - " :\n", - " :\n", - " :\n", - " :\n", - " :\n", - " :\n", - " :\n", - " :\n", - " : O\n", - " : $$\n", - " N· $\n", - " · ·· $$\n", - " ·· ·· $\n", - " · ·· $\n", - " · ·· $$\n", - " N··· ·· ·C\n", - " $ ····· · :\n", - " $ ···C :\n", - " $ $ :\n", - " $ $ :\n", - " $ $ :\n", - " $ $ :\n", - " $ $ :\n", - " $ $ :\n", - " $ $ :\n", - " C $ :\n", - " · $ :\n", - " · $ N·\n", - " · $ · ··\n", - " · ·C· ·· ··\n", - " · ·· ·· · ··\n", - " · ·· ·· · ··\n", - " · ·· ·· ·· ·C\n", - " · ·· ·· ·\n", - " N· ·C\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " : $\n", - " C $\n", - " O\n", - "\n", - "ASCII Magic Renderer:\n", - "\u001b[90m i\u001b[37mq\u001b[90m \u001b[39m\n", - "\u001b[90m ;\u001b[37mG\u001b[90m; \u001b[39m\n", - "\u001b[90m \u001b[34mC\u001b[90m\\ \u001b[39m\n", - "\u001b[90m \u001b[34mxi\u001b[90m `- \u001b[39m\n", - "\u001b[90m \u001b[34m|l\u001b[90m :\u001b[31m)\u001b[90m+=\u001b[31m>/\u001b[39m\n", - "\u001b[90m \u001b[34m>>\u001b[90m, \u001b[34m\\%\u001b[90m=\u001b[34m<)>|\u001b[90m|=` |Ia\u001b[31mcvvi)\u001b[90m: \u001b[39m\n", - "\u001b[90m _\u001b[34m}i\u001b[90m/\u001b[34m)<\u001b[90m'_` _vs\u001b[34mv\\\u001b[90m, -,v1ota\u001b[37m5\u001b[90mLzjz): \u001b[39m\n", - "\u001b[90m -\u001b[34mr\u001b[90m \u001b[34m|I<|\\>><\u001b[90ms!{x>\")eL?/ ,<\u001b[37mP\u001b[90mC{+ \u001b[39m\n", - "\u001b[90m .\u001b[34m%\u001b[90m\",`'. ._=|%{T\u001b[37mV\u001b[90m/ \u001b[37m3\u001b[90ma \u001b[39m\n", - "\u001b[90m '\u001b[34ms)>r\u001b[90m_ %\u001b[37my\u001b[90m|\u001b[37m4\u001b[90m. s\u001b[34m7\u001b[90m \u001b[39m\n", - "\u001b[90m r\u001b[34mn\u001b[90m)\u001b[34m7x\u001b[90m. /\u001b[37mX\u001b[90m^\u001b[37mg\u001b[90m\" ,\u001b[34m!\u001b[90m. \u001b[39m\n", - "\u001b[90mzCc\u001b[37mp\u001b[90m* .\u001b[37m4\u001b[90m\\\u001b[37mp\u001b[90m* `\u001b[34m}\u001b[90m' \u001b[39m\n", - "\u001b[37mX\u001b[90mx\\/ \u001b[37m2\u001b[90m!eJ '\u001b[34m{|\u001b[90m \u001b[34m>\u001b[90m, \u001b[39m\n", - "\u001b[90m^e#> ?L)\u001b[37mV\u001b[90m ^\u001b[34ml\u001b[90m\"\u001b[34m>s\u001b[90m\",` \u001b[39m\n", - "\u001b[90m =\u001b[34mlx\u001b[90m+ ')*e\u001b[37mV\u001b[90m[c\"_ '\u001b[34m)v)\\\u001b[90m ,\u001b[34ml\u001b[90m+\u001b[34m)))\\\u001b[90m|\"' \u001b[39m\n", - "\u001b[90m '\u001b[34mii\u001b[90m:- ._ `,/\u001b[34m\\\u001b[90m?e?v+`+%?ee!x\"_ \"{\u001b[34m%)\u001b[90m+` .'|?ee!c\u001b[39m\n", - "\u001b[90m .\u001b[34mll\u001b[90m=,\u001b[34ml)))\u001b[90m='. _/x!ee!%<]Lai` -/v\u001b[39m\n", - "\u001b[90m \u001b[34mr\u001b[90m:\u001b[34m)lr\u001b[90m _i\u001b[37mk\u001b[90me\u001b[37mb\u001b[90m> \u001b[39m\n", - "\u001b[90m +\u001b[34m)\u001b[90m`=+ \u001b[37m4\u001b[90m\\\u001b[37m5\u001b[90m! 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The chemscii MCP server exposes a `render_molecule` tool that Claude can call to render chemical structures without needing CLI instructions. + +Unlike the CLAUDE.md approach, MCP integration: +- Works globally (not directory-scoped) +- Provides a structured tool interface +- Gives Claude direct access to rendering parameters + +## Setup + +1. Install chemscii: + ```bash + pip install chemscii + ``` + +2. Add the MCP server to your Claude Code settings. Edit `~/.claude.json`: + ```json + "mcpServers": { + "chemscii": { + "command": "chemscii", + "type": "stdio", + "args": [ + "--mcp" + ] + } + } + ``` + +3. Restart Claude Code to load the MCP server. Check with `claude mcp list` + +## Example Usage + +Once configured, Claude Code has access to the `render_molecule` tool. Try these prompts: + +### Basic Rendering +> "Show me caffeine" + +> "What does aspirin look like?" + +> "Render the molecule that gives bananas their smell" + +### Renderer Options +> "Show me cholesterol using the unicode renderer" + +> "Render dopamine with ascii art" + +### Chemistry Questions +> "What's the structure of the active ingredient in coffee?" + +> "Show me the difference between glucose and fructose" + +### Using SMILES Notation +> "Render this SMILES: c1ccc2c(c1)cc1ccccc1n2" + +## Tool Parameters + +The `render_molecule` tool accepts these parameters: + +| Parameter | Type | Default | Description | +|-----------|------|---------|-------------| +| `molecule` | string | required | SMILES string, molecule name, ChEMBL ID, or SDF content | +| `renderer` | string | "magic" | Renderer type: "ascii", "unicode", or "magic" | +| `width` | int | 60 | Canvas width for ascii/unicode renderers | +| `height` | int | 30 | Canvas height for ascii/unicode renderers | +| `columns` | int | 80 | Output width for magic renderer | +| `escape_codes` | bool | false | Include escape codes for color rendering | + +## How This Differs from Other Integrations + +| Approach | Setup Required | Works With | Scope | +|----------|---------------|------------|-------| +| CLAUDE.md | None | Claude Code | Directory-scoped | +| **MCP Server (this)** | JSON config editing | Claude Code, Claude Desktop | Global | +| API Script | API key + environment | Any Python environment | Programmatic | + +## Advantages of MCP + +- **Global availability**: Works in any directory once configured +- **Structured interface**: Claude receives typed parameters and documentation +- **Works with Claude Desktop**: Can also be used with Claude Desktop app +- **Explicit tool calls**: You can see when Claude uses the tool in the conversation + +## Limitations + +- **Requires configuration**: Must edit settings.json to enable +- **Server process**: Runs as a subprocess managed by Claude Code +- **Single instance**: One server configuration per settings file diff --git a/examples/claude_code_via_mcp/settings.example.json b/examples/claude_code_via_mcp/settings.example.json new file mode 100644 index 0000000..0ef447e --- /dev/null +++ b/examples/claude_code_via_mcp/settings.example.json @@ -0,0 +1,8 @@ +{ + "mcpServers": { + "chemscii": { + "command": "chemscii", + "args": ["--mcp"] + } + } +} diff --git a/examples/claude_code/CLAUDE.md b/examples/claude_code_via_md/CLAUDE.md similarity index 80% rename from examples/claude_code/CLAUDE.md rename to examples/claude_code_via_md/CLAUDE.md index 7e7358a..03d87ca 100644 --- a/examples/claude_code/CLAUDE.md +++ b/examples/claude_code_via_md/CLAUDE.md @@ -1,4 +1,4 @@ -# chemscii Claude Code Integration +# chemscii Claude Code Integration Via CLAUDE.md When users ask about chemical structures, molecules, drugs, or compounds, render them using the `chemscii` CLI. If your response to a question includes SMILES, molecules, or ChEMBL IDs render them using the `chemscii` CLI. @@ -8,14 +8,14 @@ If your response to a question includes SMILES, molecules, or ChEMBL IDs render Use the magic renderer (default) with 100 columns: ```bash -chemscii "" --columns 80 +chemscii "" ``` Examples: -- `chemscii "caffeine" --columns 80` - render by common name -- `chemscii "aspirin" --columns 80` - render by drug name -- `chemscii "CCO" --columns 80` - render by SMILES notation -- `chemscii "CHEMBL25" --columns 80` - render by ChEMBL ID +- `chemscii "caffeine"` - render by common name +- `chemscii "aspirin"` - render by drug name +- `chemscii "CCO"` - render by SMILES notation +- `chemscii "CHEMBL25"` - render by ChEMBL ID ## Larger Renderings diff --git a/examples/claude_code/README.md b/examples/claude_code_via_md/README.md similarity index 100% rename from examples/claude_code/README.md rename to examples/claude_code_via_md/README.md diff --git a/poetry.lock b/poetry.lock index 1433a19..8d6ebde 100644 --- a/poetry.lock +++ b/poetry.lock @@ -1,5 +1,37 @@ # This file is automatically @generated by Poetry 2.2.1 and should not be changed by hand. +[[package]] +name = "annotated-types" +version = "0.7.0" +description = "Reusable constraint types to use with typing.Annotated" +optional = false +python-versions = ">=3.8" +groups = ["main"] +files = [ + {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"}, + {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"}, +] + +[[package]] +name = "anyio" +version = "4.12.1" +description = "High-level concurrency and networking framework on top of asyncio or Trio" +optional = false +python-versions = ">=3.9" +groups = ["main"] +files = [ + {file = "anyio-4.12.1-py3-none-any.whl", hash = "sha256:d405828884fc140aa80a3c667b8beed277f1dfedec42ba031bd6ac3db606ab6c"}, + 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ASCII/Unicode art" authors = ["Benjamin J. Shields"] readme = "README.md" @@ -13,6 +13,7 @@ pillow = "^10.0" rich = "^13.0" ascii-magic = "^2.7.2" typer = "^0.15" +mcp = "^1.25" [tool.poetry.group.dev.dependencies] pytest = "^8.0" diff --git a/src/chemscii/cli.py b/src/chemscii/cli.py index 2f2b0bd..b572007 100644 --- a/src/chemscii/cli.py +++ b/src/chemscii/cli.py @@ -102,10 +102,15 @@ def parse_input(input_type: InputType, value: str) -> str | None: @app.command() def main( - molecule: str = typer.Argument( - ..., + molecule: str | None = typer.Argument( + None, help="SMILES string, molecule name, ChEMBL ID, or file path.", ), + mcp_mode: bool = typer.Option( + False, + "--mcp", + help="Start MCP server instead of rendering a molecule.", + ), ascii_mode: bool = typer.Option( False, "--ascii", @@ -125,17 +130,11 @@ def main( help="Use image-to-ASCII magic renderer (default).", ), columns: int = typer.Option( - 50, + 80, "--columns", "-c", help="Output width for magic renderer.", ), - escape_codes: bool = typer.Option( - False, - "--codes", - "-e", - help="Include escape codes for color rendering after copying text.", - ), width: int = typer.Option( 60, "--width", @@ -153,7 +152,43 @@ def main( Automatically detects input type: SMILES strings, molecule names, ChEMBL IDs, or structure files (.sdf, .mol, .smi). + + Use --mcp to start an MCP server for AI assistant integration. """ + # Handle MCP mode + if mcp_mode: + from chemscii.mcp import run_server + + # Determine default renderer from CLI flags + renderer: Literal["ascii", "unicode", "magic"] + if ascii_mode: + renderer = "ascii" + elif unicode_mode: + renderer = "unicode" + else: + renderer = "magic" + + run_server( + renderer=renderer, + width=width, + height=height, + columns=columns, + ) + return + + # Require molecule argument when not in MCP mode + if molecule is None: + error_console.print( + Panel( + "[red]Missing required argument: molecule[/red]\n\n" + "Usage: chemscii [MOLECULE]\n\n" + "Use --mcp to start the MCP server instead.", + title="Error", + border_style="red", + ) + ) + raise typer.Exit(1) + from rdkit.rdBase import BlockLogs # Detect input type @@ -212,7 +247,7 @@ def main( unicode_renderer.render_molecule(mol) else: # Default to magic - magic_renderer = AsciiMagicRenderer(columns=columns, codes=escape_codes) + magic_renderer = AsciiMagicRenderer(columns=columns) magic_renderer.render_molecule(mol) diff --git a/src/chemscii/mcp.py b/src/chemscii/mcp.py new file mode 100644 index 0000000..b100655 --- /dev/null +++ b/src/chemscii/mcp.py @@ -0,0 +1,144 @@ +"""MCP server for chemscii molecule rendering.""" + +from __future__ import annotations + +import io +import sys +from typing import Literal + +from mcp.server.fastmcp import FastMCP + +from chemscii.cli import detect_input_type, parse_input +from chemscii.parsers.molecule import parse_smiles +from chemscii.renderers.ascii import AsciiRenderer +from chemscii.renderers.magic import AsciiMagicRenderer +from chemscii.renderers.unicode import UnicodeRenderer + +RendererType = Literal["ascii", "unicode", "magic"] + +mcp = FastMCP("chemscii") + + +def _resolve_smiles(molecule: str) -> str | None: + """Resolve molecule input to SMILES string. + + Args: + molecule: SMILES string, molecule name, ChEMBL ID, or SDF content. + + Returns: + SMILES string if resolution succeeds, None otherwise. + """ + from rdkit.rdBase import BlockLogs + + # Check if it looks like SDF content (multi-line with atom block markers) + if "\n" in molecule and ("V2000" in molecule or "V3000" in molecule): + from rdkit import Chem + + from chemscii.parsers.molecule import parse_sdf + + mol = parse_sdf(molecule) + if mol is not None: + return str(Chem.MolToSmiles(mol)) + return None + + # Use existing detection logic for SMILES/name/ChEMBL + with BlockLogs(): + input_type, normalized = detect_input_type(molecule) + + return parse_input(input_type, normalized) + + +def _render( + smiles: str, + renderer: RendererType, + width: int, + height: int, + columns: int, +) -> str: + """Render a molecule using the specified renderer. + + Args: + smiles: SMILES string to render. + renderer: Renderer type to use. + width: Canvas width for ascii/unicode renderers. + height: Canvas height for ascii/unicode renderers. + columns: Output width for magic renderer. + + Returns: + ASCII/Unicode art representation of the molecule. + """ + mol = parse_smiles(smiles) + if mol is None: + raise ValueError(f"Failed to parse SMILES: {smiles}") + + # Capture stdout since renderers print to stdout + old_stdout = sys.stdout + sys.stdout = io.StringIO() + + try: + r: AsciiRenderer | UnicodeRenderer | AsciiMagicRenderer + if renderer == "ascii": + r = AsciiRenderer(width=width, height=height) + elif renderer == "unicode": + r = UnicodeRenderer(width=width, height=height) + else: + r = AsciiMagicRenderer(columns=columns, codes=True) + result: str = r.render_molecule(mol) + # result: str = repr(sys.stdout.getvalue()) + + return result + finally: + sys.stdout.close() + sys.stdout = old_stdout + + +@mcp.tool() # type: ignore[misc] +def render_molecule( + molecule: str, + renderer: RendererType = "magic", + width: int = 60, + height: int = 30, + columns: int = 80, +) -> str: + """Render a chemical structure as ASCII/Unicode art. + + Args: + molecule: SMILES string, molecule name, ChEMBL ID, or SDF content. + renderer: Renderer type: "ascii", "unicode", or "magic" (default). + width: Canvas width for ascii/unicode renderers. + height: Canvas height for ascii/unicode renderers. + columns: Output width for magic renderer. + + Returns: + ASCII/Unicode art representation of the molecule. + """ + smiles = _resolve_smiles(molecule) + if smiles is None: + return f"Error: Could not parse molecule input: {molecule}" + + try: + return _render(smiles, renderer, width, height, columns) + except Exception as e: + return f"Error rendering molecule: {e}" + + +def run_server( + renderer: RendererType = "magic", + width: int = 60, + height: int = 30, + columns: int = 80, +) -> None: + """Run the MCP server with optional default settings. + + Args: + renderer: Default renderer type. + width: Default canvas width for ascii/unicode renderers. + height: Default canvas height for ascii/unicode renderers. + columns: Default output width for magic renderer. + escape_codes: Default for including escape codes. + """ + # Store defaults that could be used by the tool + # For now, the tool uses its own defaults but this allows future extension + _ = (renderer, width, height, columns) + + mcp.run() diff --git a/src/chemscii/renderers/magic.py b/src/chemscii/renderers/magic.py index 86e90c1..ec60bf9 100644 --- a/src/chemscii/renderers/magic.py +++ b/src/chemscii/renderers/magic.py @@ -39,10 +39,10 @@ def render_molecule(self, mol: Mol) -> str: img = self._mol_to_image(mol) art = AsciiArt.from_pillow_image(img) if self.codes: - txt: str = art.to_ascii(self.columns) - print(repr(txt)) + txt: str = art.to_terminal(self.columns) else: - txt = art.to_terminal(self.columns) + txt = art.to_ascii(self.columns) + print(repr(txt)) return txt def _mol_to_image( diff --git a/tests/test_mcp.py b/tests/test_mcp.py new file mode 100644 index 0000000..9ed9793 --- /dev/null +++ b/tests/test_mcp.py @@ -0,0 +1,180 @@ +"""Tests for chemscii.mcp module.""" + +from __future__ import annotations + +import pytest + +from chemscii.mcp import _render, _resolve_smiles, render_molecule + + +class TestResolveSmiles: + """Tests for SMILES resolution.""" + + def test_resolve_smiles_direct(self) -> None: + """Test resolving direct SMILES string.""" + result = _resolve_smiles("CCO") + assert result == "CCO" + + def test_resolve_smiles_aromatic(self) -> None: + """Test resolving aromatic SMILES.""" + result = _resolve_smiles("c1ccccc1") + assert result == "c1ccccc1" + + def test_resolve_smiles_complex(self) -> None: + """Test resolving complex SMILES.""" + result = _resolve_smiles("CC(=O)O") + assert result == "CC(=O)O" + + def test_resolve_name_aspirin(self) -> None: + """Test resolving molecule name.""" + result = _resolve_smiles("aspirin") + assert result is not None + assert len(result) > 0 + + def test_resolve_name_benzene(self) -> None: + """Test resolving benzene by name.""" + result = _resolve_smiles("benzene") + assert result is not None + assert "c" in result.lower() or "C" in result + + def test_resolve_chembl_id(self) -> None: + """Test resolving ChEMBL ID.""" + result = _resolve_smiles("CHEMBL25") + assert result is not None + assert len(result) > 0 + + def test_resolve_sdf_content(self) -> None: + """Test resolving SDF content.""" + sdf_content = """ + RDKit 2D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5981 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 +M END +""" + result = _resolve_smiles(sdf_content) + assert result is not None + # Should return SMILES for ethanol-like structure + assert "C" in result or "c" in result + + def test_resolve_invalid_returns_none(self) -> None: + """Test that invalid input returns None.""" + result = _resolve_smiles("notarealmolecule12345xyz") + assert result is None + + +class TestRender: + """Tests for rendering function.""" + + def test_render_ascii(self) -> None: + """Test ASCII renderer.""" + result = _render("CCO", "ascii", width=40, height=20, columns=50) + assert isinstance(result, str) + assert len(result) > 0 + + def test_render_unicode(self) -> None: + """Test Unicode renderer.""" + result = _render("CCO", "unicode", width=40, height=20, columns=50) + assert isinstance(result, str) + assert len(result) > 0 + + def test_render_magic(self) -> None: + """Test Magic renderer.""" + result = _render("CCO", "magic", width=40, height=20, columns=50) + assert isinstance(result, str) + assert len(result) > 0 + + def test_render_invalid_smiles_raises(self) -> None: + """Test that invalid SMILES raises ValueError.""" + with pytest.raises(ValueError, match="Failed to parse SMILES"): + _render("invalid_smiles_xyz", "ascii", width=40, height=20, columns=50) + + def test_render_benzene_ascii(self) -> None: + """Test rendering benzene with ASCII.""" + result = _render("c1ccccc1", "ascii", width=40, height=20, columns=50) + assert isinstance(result, str) + assert len(result) > 0 + + def test_render_custom_dimensions(self) -> None: + """Test rendering with custom dimensions.""" + result = _render("CCO", "unicode", width=80, height=40, columns=100) + assert isinstance(result, str) + + +class TestRenderMoleculeTool: + """Tests for the MCP tool function.""" + + def test_render_molecule_smiles(self) -> None: + """Test rendering molecule from SMILES.""" + result = render_molecule("CCO") + assert isinstance(result, str) + assert "Error" not in result + + def test_render_molecule_name(self) -> None: + """Test rendering molecule from name.""" + result = render_molecule("ethanol") + assert isinstance(result, str) + assert "Error" not in result + + def test_render_molecule_ascii_renderer(self) -> None: + """Test rendering with ASCII renderer.""" + result = render_molecule("CCO", renderer="ascii") + assert isinstance(result, str) + assert "Error" not in result + + def test_render_molecule_unicode_renderer(self) -> None: + """Test rendering with Unicode renderer.""" + result = render_molecule("CCO", renderer="unicode") + assert isinstance(result, str) + assert "Error" not in result + + def test_render_molecule_magic_renderer(self) -> None: + """Test rendering with Magic renderer.""" + result = render_molecule("CCO", renderer="magic") + assert isinstance(result, str) + assert "Error" not in result + + def test_render_molecule_custom_width_height(self) -> None: + """Test rendering with custom width and height.""" + result = render_molecule("CCO", renderer="ascii", width=80, height=40) + assert isinstance(result, str) + assert "Error" not in result + + def test_render_molecule_custom_columns(self) -> None: + """Test rendering with custom columns.""" + result = render_molecule("CCO", renderer="magic", columns=80) + assert isinstance(result, str) + assert "Error" not in result + + def test_render_molecule_invalid_input(self) -> None: + """Test rendering with invalid input returns error message.""" + result = render_molecule("notarealmolecule12345xyz") + assert isinstance(result, str) + assert "Error" in result + + def test_render_molecule_chembl(self) -> None: + """Test rendering ChEMBL ID.""" + result = render_molecule("CHEMBL25") + assert isinstance(result, str) + assert "Error" not in result + + def test_render_molecule_sdf_content(self) -> None: + """Test rendering SDF content.""" + sdf_content = """ + RDKit 2D + + 3 2 0 0 0 0 0 0 0 0999 V2000 + 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 1.2990 0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 + 2.5981 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 + 1 2 1 0 + 2 3 1 0 +M END +""" + result = render_molecule(sdf_content) + assert isinstance(result, str) + assert "Error" not in result