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Analysis Sets

ANALYZE builds an analysis as a stack of blocks. Each block is one published method: cage detection (TRACE, HTR, GRADE), water classification (CHILL+) or an order parameter (F3/F4, averaged q4/q6, MCG). One Run computes only the blocks in the pipeline. Nothing outside it is calculated.

Building the pipeline

The panel has two parts:
  • Pipeline: the blocks that will run, in order, below the input block that names the frames.
  • Blocks: the shelf of methods you can add, grouped by kind.
To add a block, press + on it in the shelf, or drag it into the pipeline at the place you want. To remove one, press × on the block. To reorder, drag a block by its handle. From the keyboard, focus a handle, press Space to lift the block, move it with the arrow keys and press Space again to drop it. Escape cancels the move. Every change is announced to screen readers. On a touch phone each block also has one-step up and down buttons, and + Add block opens a sheet with the shelf. Each block shows:
  • the method’s verification level: checked against the authors’ program, against an open reference implementation, or against the paper’s definitions;
  • a relative cost (● to ●●●) on the shelf;
  • a settings button for the method’s parameters.
MCG needs guest molecules, so it is offered only when guests are found in the structure. The pipeline is remembered in this browser.

Running a set

  1. Upload a structure or trajectory and open ANALYZE. You can also drop a file on the 3D view, or load the example sII crystal from the empty view.
  2. Put the blocks you need in the pipeline.
  3. For streamed GRO, native GROMACS and mapped LAMMPS sessions, set the frame range (start, end, step). In-memory GRO trajectories use the frame step.
  4. Press Run. To analyse only the frame on screen, use Analyze current frame only.
During a run, each block in the pipeline shows its own progress bar. Each frame is read once and shared by every block. If one method fails on a frame, the other methods still finish that frame and the failure count shows on that block. Cancel stops every worker and keeps the frames finished so far.

LIBRARY

The LIBRARY tab lists every method with its citation, DOI and verification level. Pin a method to show it on the Blocks shelf, and drag the list to set the shelf order. Unpinning a method only hides it from the shelf; a block already in the pipeline stays there.

Your own algorithms

+ Enroll your own algorithm adds a block from a JavaScript function you write or import from a .js file:
Test on frame 1 runs it once and shows the value. Enrolled algorithms join the shelf under Your algorithms and run with the rest of the pipeline. The code runs in a separate worker in your browser with no network access, no storage and no way to load other scripts. A frame that takes longer than 2 seconds is stopped and counted as failed, and the run continues. The code is stored only in this browser. Results always carry the USER · UNVERIFIED badge: ClavisCage has not checked them. Your own algorithms run on trajectories held in memory (.gro). For streamed, native GROMACS and LAMMPS sessions they are skipped with a notice, and Analyze current frame only does not run them.

Recipes

Export recipe saves the pipeline, its settings and range as a JSON file, and Import recipe loads one. See Analysis Recipes.

Results

RESULTS shows one figure block for each analysis that ran, in a 5:4 aspect. Each block has its own CSV download and verification badge. Cage methods show cage counts and cage types over time, and TRACE also shows crystallinity. Order parameters and CHILL+ each get their own plot. The blocks follow the pipeline order; drag them to arrange the results differently, and that order is remembered. Methods that were not part of the run are listed under Not run. Add to set and run adds one of them to your pipeline and computes only that method over the same range. The results already shown stay as they are.

Plot conventions

The plots follow common publication practice:
  • a full box frame with inward major and minor ticks, and no grid;
  • axes that end on labelled ticks, with axis titles and units;
  • the colour-blind-safe Okabe–Ito palette, with every second series dashed;
  • a white figure ground in both light and dark themes.