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MCP server · Developer Tools

Surfacia

by · github.com/sym823808458/Surfacia

SURF Atomic Chemical Interaction Analyzer，Surfacia，表面原子化学相互作用分析程序

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Scored 6 months ago · breakdown

About Surfacia

Surfacia is an MCP server published by sym823808458 in the Developer Tools category: sURF Atomic Chemical Interaction Analyzer，Surfacia，表面原子化学相互作用分析程序.

The repository has 5 stars and 1 forks, with the last commit 9 days ago. Recent commit activity is the strongest signal that reported issues will get attention.

Install

From source
git clone https://github.com/sym823808458/Surfacia

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  • ✓README presentThe repository ships documentation.

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README

Surfacia

Surface Atomic Chemical Interaction Analyzer for descriptor extraction and interpretable machine learning in computational chemistry.

At a Glance

  • End-to-end workflow: SMILES -> 3D -> xTB/Gaussian -> Multiwfn -> descriptors -> ML/SHAP
  • CLI-first design for local and remote Linux/HPC usage
  • Supports full workflow mode and modular step-by-step execution

Current Release

  • Latest stable version: 3.0.2
  • Python requirement: >= 3.9
  • License: MIT

PyPI: https://pypi.org/project/surfacia/

Quick Install (Recommended for Most Users)

# optional but recommended
python -m venv .venv
source .venv/bin/activate  # Windows: .venv\Scripts\activate

pip install --upgrade pip
pip install surfacia

Check installation:

surfacia --help
python -c "import surfacia; print(surfacia.__version__)"

Important Compatibility Note (ML Stage)

To avoid ML parsing failures such as:

could not convert string to float: '[-3.xxxE0]'

use the validated dependency range:

  • xgboost>=2.1.4,<3.0.0
  • shap>=0.48.0,<0.49.0

Quick fix:

pip install --force-reinstall "xgboost==2.1.4" "shap==0.48.0"

External Software Requirements

Surfacia orchestrates external quantum-chemistry tools. Ensure these commands are available in your PATH:

  • xtb
  • g16 (and formchk)
  • Multiwfn or Multiwfn_noGUI

Minimal Usage

Run full workflow:

surfacia workflow -i molecules.csv --test-samples "1,3"

Run ML only (for existing descriptor table):

surfacia ml-analysis -i FinalFull_Mode3_20_168.csv \
  --max-features 1 --stepreg-runs 1 \
  --train-test-split 0.85 --epoch 32 --cores 8 \
  --test-samples "1,2,3"

MCP Server (New)

Surfacia now ships an MCP stdio server so agent clients can call workflow stages as structured tools.

Start MCP server:

surfacia-mcp --log-level INFO
# or
python -m surfacia.mcp.server --log-level INFO

Typical first tool calls:

  1. surfacia_check_environment
  2. surfacia_detect_workflow_state

Source Install (Developers)

git clone https://github.com/sym823808458/Surfacia.git
cd Surfacia
pip install -e .

Documentation

Citation

If Surfacia helps your research, please cite the project and related publication when available.

Contact

README copy captured when this server was indexed; it may lag the repository. The original is authoritative.

Questions

About Surfacia

How do I install Surfacia?

No package has been published for this server, so install it from source: clone the repository and follow its README.

Is Surfacia safe to use with an AI agent?

Its trust score is 34 out of 100 (low). It passes 1 of the 1 static security checks run so far. It has no ConduID identity yet, so agent calls to it are not receipted.

Is Surfacia still maintained?

Yes — the last commit was 9 days ago. The repository has 5 stars and 1 forks.