DECIMER MCP Server

MCP server for DECIMER image-to-SMILES chemical structure recognition

Quick Install

Automated & IDE Setup

Copy the AI prompt to install this server into Claude Code, Cursor, or another agent — or use 1-click editor setup below.

Add to Cursor Add to VS Code

Not yet automatically verified

We haven't yet run this listing's install command through our automated sandbox check. This isn't a red flag — we're steadily working through the catalog.

Manual Client & Custom JSON ConfigExpand JSON ▾

Client Config & Setup

Choose your client or environment

Target File:~/Library/Application Support/Claude/claude_desktop_config.json

claude_desktop_config.json

{
  "mcpServers": {
    "decimer-mcp-server": {
      "command": "uvx",
      "args": [
        "jsonschema"
      ]
    }
  }
}

💡 Paste the JSON block into your client's configuration file under mcpServers, then restart the application.

Capabilities & Tool Schemas (2)Self-reported

Inspect callable tools, capabilities, and parameters exposed to AI agents by DECIMER MCP Server.

server_health

Checks whether the DECIMER FastAPI server is reachable.

analyze_chemical_image

Sends a base64-encoded image to `/image2smiles/` and returns structured output.

Documentation Overview

DecimerMCPServer

mcp-name: io.github.DocMinus/decimer-mcp-server

MCP server that exposes DECIMER image-to-SMILES functionality as tool calls.

This project is a thin adapter over the existing FastAPI service in DecimerServerAPI. It does not run DECIMER models directly. The adapter sends JSON requests by default, with automatic fallback to form payloads for compatibility.

Tools

server_health: Checks whether the DECIMER FastAPI server is reachable.
analyze_chemical_image: Sends a base64-encoded image to /image2smiles/ and returns structured output.

Requirements

Python 3.10+
Running DECIMER API server (default: http://localhost:8099)

find it at either of these two versions:

GitHub: https://github.com/DocMinus/DecimerServerAPI
Dockerhub: https://hub.docker.com/r/docminus/decimer_api

Install

bash

cd /Users/a/dev/DecimerMCPServer
uv venv
uv sync

Configuration

Copy .env.example values into your environment:

DECIMER_API_BASE_URL (default http://localhost:8099)
DECIMER_API_TIMEOUT_SECONDS (default 60)
DECIMER_MAX_IMAGE_BYTES (default 10000000)
DECIMER_MCP_LOG_LEVEL (default INFO)

Run (stdio transport)

bash

uv run decimer-mcp-server

bash

uv run python -m decimer_mcp_server

Example MCP client config

config.json

{
  "mcpServers": {
    "decimer": {
      "command": "uv",
      "args": ["run", "python", "-m", "decimer_mcp_server"],
      "env": {
        "DECIMER_API_BASE_URL": "http://localhost:8099"
      }
    }
  }
}

Output shape

analyze_chemical_image returns:

config.json

{
  "ok": true,
  "smiles": "CCO",
  "reason": null,
  "api_status_code": 200,
  "api_message": null,
  "classifier_score": 0.0000012,
  "classifier_threshold": 0.3,
  "classifier_decision": "structure_like"
}

When no SMILES is returned by API classifier behavior:

config.json

{
  "ok": true,
  "smiles": null,
  "reason": "not_chemical_structure",
  "api_status_code": 200,
  "api_message": "No SMILES returned by API",
  "classifier_score": 0.99999,
  "classifier_threshold": 0.3,
  "classifier_decision": "not_structure_like"
}

Development tests

bash

uv sync --extra dev
uv run pytest

Make targets:

bash

make sync
make test

Smoke test helper

Run one health check + one inference call against your DECIMER API:

bash

cd /Users/a/dev/DecimerMCPServer
DECIMER_API_BASE_URL=http://chitchat:8099 uv run decimer-mcp-smoke-test --image /Users/a/dev/DecimerServerAPI/example_usage/structure.png

If you keep settings in .env, load it with:

bash

uv run --env-file .env decimer-mcp-smoke-test --image /Users/a/dev/DecimerServerAPI/example_usage/structure.png

or use make:

bash

make smoke

Override the image path if needed:

bash

make smoke SMOKE_IMAGE=/absolute/path/to/image.png

## MCP Registry publishing

Tags matching `v*` trigger `.github/workflows/publish-mcp.yml`.

Workflow steps:
- installs `mcp-publisher`
- validates `server.json`
- calls registry publish using secret `MCP_REGISTRY_TOKEN`
- publishes slug `io.github.DocMinus/decimer-mcp-server` (case sensitive; must match registry grant)

Before tagging:
1. Update `pyproject.toml` + `server.json` versions
2. Ensure `server.json` stays valid (`uv pip install jsonschema && python validate snippet from AGENTS.md`)
3. Add GitHub repo secret `MCP_REGISTRY_TOKEN` (GitHub PAT with `repo`, `workflow` scopes)

Release flow:
```bash
git tag v0.1.1
git push origin v0.1.1

Monitor Actions tab. If publish fails, rerun using workflow dispatch after fixing issues.

Code


## Contribution
This project was built by DocMinus with AI-assisted coding support (OpenCode/Copilot-style tooling), then reviewed and tested by the author.

## AI usage policy

- AI assistance was used for scaffolding, implementation drafts, and documentation edits.
- Final technical decisions, validation runs, and acceptance were performed by the maintainer.
- Runtime behavior should be validated with local tests (`make test`) and smoke tests (`make smoke`) before release.

Read the full README →View source on GitHub →

Related MCP Servers

View all in Developer Tools View all alternatives

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

npm downloads

21M

Package downloads in the last 30 days.

Last commit

5mo ago

Most recent push to the default branch.

Tools exposed

Callable tools this server registers over MCP.

Directory activity

1 views

Config copies, upvotes, and views on AllMCPs.

Reviews

No reviews yet — be the first to share how this listing worked for you.

Frequently Asked Questions about DECIMER MCP Server

Add the following block to your claude_desktop_config.json under mcpServers: "mcpServers": { "decimer-mcp-server": { "command": "uvx", "args": ["jsonschema"] } }

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Technical Specs & Signals

CategoryDeveloper Tools

16/16 checks healthy over the last 45d

51Quality signal: Good · 51/100How this signal is calculated ▾

Server availabilityNot measured

Not scored for repo-hosted servers — we can't reach the running server, only its GitHub page. Hosted MCP endpoints are health-checked live.

Verified ownership10/20

Documentation & tools23/30

Adoption & activity5/15

Community engagement0/10

A guidance signal from public completeness & health data — not a user rating. New listings start lower and rise as they add docs, get verified, and grow adoption. Signals we can't observe for a listing are skipped, not counted against it.

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 5d ago via OSV.dev · jsonschema (PyPI)

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More in 💻 Developer Tools →Best MCP servers for Developers →Alternatives to DECIMER MCP Server →Install in Claude Desktop Install in Cursor Install in VS Code Setup guides for all 13 MCP clients

DECIMER MCP Server

MCP server for DECIMER image-to-SMILES chemical structure recognition

Quick Install

Automated & IDE Setup

Copy the AI prompt to install this server into Claude Code, Cursor, or another agent — or use 1-click editor setup below.

Add to Cursor Add to VS Code

Not yet automatically verified

We haven't yet run this listing's install command through our automated sandbox check. This isn't a red flag — we're steadily working through the catalog.

Manual Client & Custom JSON ConfigExpand JSON ▾

Client Config & Setup

Choose your client or environment

Target File:~/Library/Application Support/Claude/claude_desktop_config.json

claude_desktop_config.json

{
  "mcpServers": {
    "decimer-mcp-server": {
      "command": "uvx",
      "args": [
        "jsonschema"
      ]
    }
  }
}

💡 Paste the JSON block into your client's configuration file under mcpServers, then restart the application.

Capabilities & Tool Schemas (2)Self-reported

Inspect callable tools, capabilities, and parameters exposed to AI agents by DECIMER MCP Server.

server_health

Checks whether the DECIMER FastAPI server is reachable.

analyze_chemical_image

Sends a base64-encoded image to `/image2smiles/` and returns structured output.

Documentation Overview

DecimerMCPServer

mcp-name: io.github.DocMinus/decimer-mcp-server

MCP server that exposes DECIMER image-to-SMILES functionality as tool calls.

Tools

server_health: Checks whether the DECIMER FastAPI server is reachable.
analyze_chemical_image: Sends a base64-encoded image to /image2smiles/ and returns structured output.

Requirements

Python 3.10+
Running DECIMER API server (default: http://localhost:8099)

find it at either of these two versions:

GitHub: https://github.com/DocMinus/DecimerServerAPI
Dockerhub: https://hub.docker.com/r/docminus/decimer_api

Install

bash

cd /Users/a/dev/DecimerMCPServer
uv venv
uv sync

Configuration

Copy .env.example values into your environment:

DECIMER_API_BASE_URL (default http://localhost:8099)
DECIMER_API_TIMEOUT_SECONDS (default 60)
DECIMER_MAX_IMAGE_BYTES (default 10000000)
DECIMER_MCP_LOG_LEVEL (default INFO)

Run (stdio transport)

bash

uv run decimer-mcp-server

bash

uv run python -m decimer_mcp_server

Example MCP client config

config.json

{
  "mcpServers": {
    "decimer": {
      "command": "uv",
      "args": ["run", "python", "-m", "decimer_mcp_server"],
      "env": {
        "DECIMER_API_BASE_URL": "http://localhost:8099"
      }
    }
  }
}

Output shape

analyze_chemical_image returns:

config.json

{
  "ok": true,
  "smiles": "CCO",
  "reason": null,
  "api_status_code": 200,
  "api_message": null,
  "classifier_score": 0.0000012,
  "classifier_threshold": 0.3,
  "classifier_decision": "structure_like"
}

When no SMILES is returned by API classifier behavior:

config.json

{
  "ok": true,
  "smiles": null,
  "reason": "not_chemical_structure",
  "api_status_code": 200,
  "api_message": "No SMILES returned by API",
  "classifier_score": 0.99999,
  "classifier_threshold": 0.3,
  "classifier_decision": "not_structure_like"
}

Development tests

bash

uv sync --extra dev
uv run pytest

Make targets:

bash

make sync
make test

Smoke test helper

Run one health check + one inference call against your DECIMER API:

bash

cd /Users/a/dev/DecimerMCPServer
DECIMER_API_BASE_URL=http://chitchat:8099 uv run decimer-mcp-smoke-test --image /Users/a/dev/DecimerServerAPI/example_usage/structure.png

If you keep settings in .env, load it with:

bash

uv run --env-file .env decimer-mcp-smoke-test --image /Users/a/dev/DecimerServerAPI/example_usage/structure.png

or use make:

bash

make smoke

Override the image path if needed:

bash

make smoke SMOKE_IMAGE=/absolute/path/to/image.png

## MCP Registry publishing

Tags matching `v*` trigger `.github/workflows/publish-mcp.yml`.

Workflow steps:
- installs `mcp-publisher`
- validates `server.json`
- calls registry publish using secret `MCP_REGISTRY_TOKEN`
- publishes slug `io.github.DocMinus/decimer-mcp-server` (case sensitive; must match registry grant)

Before tagging:
1. Update `pyproject.toml` + `server.json` versions
2. Ensure `server.json` stays valid (`uv pip install jsonschema && python validate snippet from AGENTS.md`)
3. Add GitHub repo secret `MCP_REGISTRY_TOKEN` (GitHub PAT with `repo`, `workflow` scopes)

Release flow:
```bash
git tag v0.1.1
git push origin v0.1.1

Monitor Actions tab. If publish fails, rerun using workflow dispatch after fixing issues.

Code


## Contribution
This project was built by DocMinus with AI-assisted coding support (OpenCode/Copilot-style tooling), then reviewed and tested by the author.

## AI usage policy

- AI assistance was used for scaffolding, implementation drafts, and documentation edits.
- Final technical decisions, validation runs, and acceptance were performed by the maintainer.
- Runtime behavior should be validated with local tests (`make test`) and smoke tests (`make smoke`) before release.

Read the full README →View source on GitHub →

Related MCP Servers

View all in Developer Tools View all alternatives

Adoption & maintenance

Factual signals from GitHub, npm, and our automated checks — not a rating.

npm downloads

21M

Package downloads in the last 30 days.

Last commit

5mo ago

Most recent push to the default branch.

Tools exposed

Callable tools this server registers over MCP.

Directory activity

1 views

Config copies, upvotes, and views on AllMCPs.

Reviews

No reviews yet — be the first to share how this listing worked for you.

Frequently Asked Questions about DECIMER MCP Server

Add the following block to your claude_desktop_config.json under mcpServers: "mcpServers": { "decimer-mcp-server": { "command": "uvx", "args": ["jsonschema"] } }

AllMCPs Directory Badge

Full Badge Customizer

Showcase your server listing on GitHub or your project documentation. Embed this dynamic SVG badge to highlight official listing status and live engagement.

Badge Style:

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Markdown (GitHub README)

[![AllMCPs](https://allmcps.com/api/badge/decimer-mcp-server?style=directory)](https://allmcps.com/mcp/decimer-mcp-server)

HTML Embed

<a href="https://allmcps.com/mcp/decimer-mcp-server"><img src="https://allmcps.com/api/badge/decimer-mcp-server?style=directory" alt="DECIMER MCP Server on AllMCPs" /></a>

Technical Specs & Signals

CategoryDeveloper Tools

16/16 checks healthy over the last 45d

51Quality signal: Good · 51/100How this signal is calculated ▾

Server availabilityNot measured

Not scored for repo-hosted servers — we can't reach the running server, only its GitHub page. Hosted MCP endpoints are health-checked live.

Verified ownership10/20

Documentation & tools23/30

Adoption & activity5/15

Community engagement0/10

Supply-chain signal

No high-severity advisories surfaced by our automated scan.

Critical 0High 0Medium 0Low 0

Scanned 5d ago via OSV.dev · jsonschema (PyPI)

★ Spotlight Slot

Feature Your MCP Server

Get maximum visibility for your server across our directory, search results, and detail pages.

Spotlight Your Server

Own this project?

Free dofollow backlink: add your website and place the AllMCPs badge on it — no claim needed. We detect it automatically and keep it verified as long as the badge stays live.

Claim & get free dofollow

Share & Embed

Add our SVG badge (dark/light directory styles) or embeddable widget to your site.