Chemistry

This page lists the safe and destructive patterns in the Molecular Dynamics shell guard pack. See Shell Tool for how these patterns are evaluated.

Molecular Dynamics

Pack ID: chemistry.molecular_dynamics

Guards against destructive molecular dynamics and chemistry tool operations

Safe patterns

Rule ID	Pattern
`chemistry.molecular_dynamics.obabel_list`	`^obabel\s+-L\b[^\|><]*$`
`chemistry.molecular_dynamics.gmx_check`	`^gmx\s+check\b[^\|><]*$`
`chemistry.molecular_dynamics.gmx_dump`	`^gmx\s+dump\b[^\|><]*$`

Destructive patterns

Rule ID	Reason	Suggestion	Confidence
`chemistry.molecular_dynamics.gmx_trjconv_overwrite`	Trajectory conversion can overwrite existing trajectory files	Use `-o` with a new filename; backup the original trajectory first	Medium
`chemistry.molecular_dynamics.gmx_eneconv_overwrite`	Energy file conversion can overwrite existing energy files	Use `-o` with a new filename; backup the original file first	Medium
`chemistry.molecular_dynamics.obabel_overwrite`	Open Babel format conversion overwrites output files	Verify the output path; backup existing files first	Medium

This documentation was generated from rust/agents/src/tool_guard/shell/packs/chemistry.rs.