Geometry Helpers

These tools provide visualization and bonding analysis.

Geometry Tools

• Robust Structural Alignment
• Fragment Detection

Library Modules

The rgpycrumbs.geom package also includes importable library modules:

rgpycrumbs.geom.analysis

Structure analysis: distance matrices, bond matrices, fragment detection, centroid distances, and RMSD-corrected distances. Uses ASE’s NeighborList and depth-first search for fragment identification.

rgpycrumbs.geom.ira

IRA (Iterative Rotations and Assignments) matching for RMSD-based structure comparison. Provides do_ira(), calculate_rmsd(), and is_ira_pair() functions along with the IRAComp dataclass.

API Reference

For developer details, see the Geometry Helper Reference [1] .

[1]

Also linked in each section.