The mnova-mcp server provides a local MCP interface for MestReNova 15, automating 1D NMR data processing, structural assignment, and workflow orchestration. Key capabilities:
System status (mnova_status): Check MestReNova and bridge readiness, list supported formats, and review workflows.
Process 1D NMR (mnova_process_1d): Load Bruker, Varian/Agilent, or Mnova-readable datasets, apply processing templates, and export auditable spectrum artifacts (peak lists, integrals, etc.).
Prepare for assignment (mnova_prepare_structure_1d): Open a 1D NMR file with a chemical structure (CDX/CDXML), process the spectrum, extract atom metadata and stable peak/multiplet UUIDs, optionally run Mnova Verify, and save a prepared.mnova evidence package.
Apply assignments (mnova_apply_assignments_1d): Validate an assignment plan against the prepared document, link atoms/protons to multiplet UUIDs, add letter labels to structures and peaks, optionally rerun Verify, reject low-confidence assignments by default, and preserve an audit trail of unresolved signals.
Generate synthetic FIDs: Create reproducible 1D NMR FID data with source records and clear attribution.
Manage configuration: Control MestReNova execution paths, workspace, output directories, and bridge script locations.
Click on "Deploy Server".
Wait a few minutes for the server to deploy. Once ready, it will show a "Started" state.
In the chat, type @ followed by the MCP server name and your instructions, e.g., "@mnova-mcp Process this 1D NMR and prepare the structure for assignment"
That's it! The server will respond to your query, and you can continue using it as needed.
Here is a step-by-step guide with screenshots.
一个面向 MestReNova 15 的本地 STDIO MCP 服务，附带可直接安装的 Codex NMR Skill。它可以处理一维 NMR、导入 ChemDraw 结构、运行 Mnova Verify、将审核过的原子—多重峰指认写回 Mnova，并生成带来源记录的仿真一维 NMR FID。
本项目不包含 MestReNova 本体或许可证。Mnova Verify 功能取决于本地安装与授权。
检查本地 MestReNova 及 MCP 桥接状态。
处理 Bruker、Varian/Agilent 或 Mnova 可读的一维 NMR 数据。
导入 .cdx / .cdxml 等机器可读结构，建立可审计的两阶段指认流程。
在结构上使用小写字母编号，并把对应字母水平放在目标峰正上方。
重叠指认使用 k,l 格式；同一原子的非等价氢可使用 a,d 格式。
默认拒绝低置信度写回，并保留未解决信号的审计记录。
生成可复现、明确标记为 synthetic 的复数 FID 和 Varian/Agilent .fid 数据集。
Related MCP server: scifinder-route-mcp
mnova-mcp/
├─ mnova/bridge.qs # Mnova 15 桥接脚本
├─ src/mnova_mcp/ # Python MCP 服务
├─ tests/ # 单元测试和 STDIO 探针
├─ examples/cases/ # 实测数据、结构和可审计产出
└─ skill/nmr-analyze-simulate/ # 可安装的 Codex SkillWindows 10/11
MestReNova 15.x
Python 3.11 或 3.12
如需 Verify：本地可用的 Mnova Verify/ASV 许可
git clone https://github.com/cyx1874cyx/mnova-mcp.git
cd mnova-mcp
uv sync --extra dev
uv run pytest
uv run mnova-mcpMCP 默认通过 STDIO 运行。可用下面的探针检查握手和工具调用：
uv run python tests/stdio_probe.py变量 | 用途 |
|
|
| 允许 MCP 读写的项目根目录 |
| 任务输出根目录 |
| 传递给 Mnova 的 ASCII 临时桥接目录 |
| 自定义 |
| Mnova 任务超时秒数，默认 300 |
mnova_status
mnova_process_1d
mnova_prepare_structure_1d
mnova_apply_assignments_1d
结构指认采用两阶段流程：
mnova_prepare_structure_1d 读取实测 NMR 和 ChemDraw 结构，输出原子索引、氢位点、multiplet UUID、Verify 信息和 prepared.mnova。
调用方审核 analysis.json，构建 assignment-plan JSON，再调用 mnova_apply_assignments_1d 生成新的 assigned.mnova。
每个要写回的指认都需要独立的小写字母 label：
{
"schema_version": "1.1",
"assignments": [
{
"label": "a",
"atom_index": 4,
"h_index": 1,
"multiplet_uuid": "{uuid-from-analysis}",
"ppm": 3.651,
"range_min_ppm": 3.620,
"range_max_ppm": 3.681,
"confidence": "high",
"evidence": "2H integral, expected OCH2 shift, and consistent splitting"
}
],
"unresolved": []
}将 skill/nmr-analyze-simulate 复制到你的 $CODEX_HOME/skills/ 目录，然后重新加载 Codex。Skill 中的解读、Mnova 指认和仿真规则位于：
skill/nmr-analyze-simulate/SKILL.md
skill/nmr-analyze-simulate/references/
skill/nmr-analyze-simulate/scripts/
DEGMA / CDCl3 / 400 MHz 1H NMR：包含未修改的 Varian/Agilent FID 压缩包、目标结构、独立处理结果、Mnova 两阶段指认文档、最终标峰 PDF、归属表和 Verify 记录。
原始数据、ChemDraw 结构和已准备 Mnova 文档不会被覆盖。
每次运行写入新输出目录。
自动拾峰、自动积分和 Verify 分数只是决策支持，不是结构身份的独立证明。
仿真输出始终保留 synthetic: true、模型哈希、参数和随机种子。
当一维证据不唯一时，应保留 unresolved，并优先建议 COSY、HSQC 或 HMBC。
uv sync --extra dev
uv run pytest
uv run python tests/stdio_probe.pyMIT © 2026 cyx1874cyx
Validate and write an assignment plan into a prepared Mnova document.
Links molecule atoms/protons to real Mnova multiplet UUIDs, writes matching
lowercase letter labels onto the structure and directly above the assigned
peaks, optionally reruns Mnova Verify, and saves a new assigned .mnova file.
Each plan entry requires a lowercase ``label``. Low-confidence assignments
are rejected unless explicitly allowed.
Inputs: prepared_mnova_path (required), assignment_plan_path (required), output_dir, run_verification, +1 more. Returns: object
Open 1D NMR plus CDX/CDXML (or another supported structure) in Mnova.
Processes the spectrum, extracts atom metadata and stable peak/multiplet IDs, optionally runs Mnova Verify, and saves a prepared .mnova document. The result is the evidence package used to create a separate assignment-plan JSON.
Inputs: input_path (required), structure_path (required), output_dir, run_verification, +1 more. Returns: object
Process 1D NMR data with Mnova and export auditable spectrum artifacts.
Inputs: input_path (required), output_dir, processing_template_path. Returns: object
Check MestReNova, bridge readiness, supported formats, and workflow.
Inputs: no named parameters. Returns: object
Recent tool additions, removals, and schema changes observed during successful MCP inspections.
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Scored across 4 tools
Each tool targets a distinct stage of the workflow, but mnova_process_1d and mnova_prepare_structure_1d overlap in that both process 1D NMR data; the descriptions help clarify that one is for standalone processing and the other for preparing a structure-linked document.
All tools follow a consistent mnova_<verb>_<object> pattern with clear action-oriented verbs (status, process, prepare, apply), making the naming predictable and easy to scan.
Four tools is well-scoped for the dedicated NMR processing and assignment workflow. Each tool covers a necessary step without redundancy or bloat.
The tool set covers the core lifecycle from status check through processing, preparation, and assignment application. Minor gaps like explicit retrieval of assignment results or undo functionality could exist, but the pipeline appears functionally complete for its purpose.
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