Cosmchlore (Continuous Shape & Symmetry Measurements in Rust) is a fast, pure-Rust toolkit to analyse the geometry and symmetry of a molecular structure (or any set of 3-dimensional points), through various complementary analyses, including: Continuous Shape Measures (CShM), Continuous Symmetry Operation Measures (CSoM) and the calculation of several geometric parameters.
It is a from-scratch command line interface (CLI) tool that reimplements the shape-measure engine found in
cosymlib and SHAPE1 2.1 in Rust, alongside an original implementation of continuous symmetry operation measures inspired by the works of T. J. Sørensen et al.2 and the octahedral distortion parameters popularized by OctaDist3. Cosmochlore accurately reproduces SHAPE’s 2.1 results using a pruned branch-and-bound algorithm for significantly faster performance on larger coordination numbers.
Cosmochlore’s error handling will always tell the user if something went wrong at run-time: the program will never silently crash or give you a number without you knowing something went wrong.
Work in progress
This site is the new home of the Cosmochlore documentation. Pages marked with a To do callout are still being written.
What it measures
| Command | Analysis |
|---|---|
| cshm | Continuous Shape Measures (CShM) against 92 built-in reference polyhedra or your own shapes. A value of CShM = 0 is a perfect match. |
| csom | Continuous Symmetry Operation Measures (CSoM) against any of 47 point groups. A value of CSoM = 0 means the symmetry is fully conserved. |
| odis | Bond-length and angular distortion parameters for six-coordinate centres. |
| gidx | Geometry indices τ4 and τ4′ (four-coordinate), τ5 (five), τ6 and τ6′ (six), and τ8 and τ8′ (eight-coordinate centres). |
Where to start
- New here? Install Cosmochlore, then read the usage overview.
- Looking up a flag? Go to the command reference.
- Choosing a reference shape or point group? See reference polyhedra and supported point groups.
- Want to know how it works? Read the theory section.
Future features
- Include Cosmochlore into Timeo, the Olex2 plugin.
- Automatic point-group detection for
csom(currently--pgselects which of the 47 supported point groups to test, and all of them are tested when it is omitted).
About the name
The name of the tool comes from the mineral Kosmochlor, a rare chromium clinopyroxene found in iron meteorites and as an accessory mineral to various other chromium-containing pyroxenes.