Surfacia Documentation¶

Documentation

A practical manual for installing Surfacia, running the molecular surface workflow, and interpreting outputs.

Install from PyPI Quick Start GitHub

Choose Your Path¶

Install and Run

Install the package, check external programs, and run the first workflow.

Getting Started

User Guide

Learn day-to-day workflows, result interpretation, SPES usage, and troubleshooting.

Command Reference

Look up CLI commands, required inputs, common options, and examples.

Command Reference

API and MCP

Use Python APIs directly, or connect Surfacia through the MCP server.

Minimal Commands¶

pip install surfacia==3.0.3
surfacia workflow -i molecules.csv --test-samples "1,3"
surfacia shap-viz -i Training_Set_Detailed.csv -x ./xyz_files --test-csv Test_Set_Detailed.csv

Manual Structure¶

Getting Started: installation, first run, and core concepts
User Guide: practical workflows, SPES guide, best practices, and troubleshooting
Command Reference: command-line reference
API Reference: Python API reference
Integrations: MCP server and automation integration
Molecular Descriptors Reference: descriptor naming and interpretation
Examples: worked examples and reusable templates

Indices and Tables¶