Command Reference

This section is the CLI lookup table for Surfacia. Use it when you already know what stage you want to run and need the exact command, input file, or option name.

Core Commands

Command

Main input

Purpose

surfacia workflow

Molecule table with SMILES

Run the full workflow from structures to ML and SHAP outputs.

surfacia ml-analysis

Descriptor table

Run model selection, prediction, SHAP analysis, and optional test-set outputs.

surfacia shap-viz

Training_Set_Detailed*.csv

Launch the interactive SHAP dashboard.

surfacia-mcp

MCP client launch command

Start the stdio MCP server for agent-based workflows.

Common Examples

surfacia workflow -i molecules.csv --test-samples "1,3"
surfacia ml-analysis -i FinalFull_Mode3_20_168.csv --test-samples "1,2,3"
surfacia shap-viz -i Training_Set_Detailed.csv -x ./xyz_files --test-csv Test_Set_Detailed.csv
surfacia-mcp --log-level INFO

Shared Options

Option

Meaning

-i, --input

Main input file for the command.

-o, --output

Output directory, when supported.

--test-samples

Comma-separated sample indices used as an external test set.

--resume

Continue a partially completed workflow.

--api-key

Optional ZhipuAI key for AI-assisted SHAP interpretation.

--host / --port

Host and port for local web interfaces.

Where To Go Next