Report whether VMD is available, its version, and the molecules currently loaded in the persistent session.

Load a structure/trajectory into the persistent VMD session for visualization. Supports PDB, GROMACS (.gro/.xtc/.trr), LAMMPS (.data/dump), DCD. Coordinate-only formats (.xtc/.trr/.dcd) require a topology. Returns the molid used to reference this molecule in later calls.

List molecules currently loaded in the VMD session (molid, path, atoms, frames).

Set the visual representation of a loaded molecule (e.g. style=NewCartoon, Licorice, VDW, Lines; color=Name, ResType, Beta; selection is a VMD atom-selection string like "water" or "name CA").

Render the current view of a loaded molecule headlessly (CPU Tachyon) and return a PNG image. Resolution is capped for safety.

Report how many atoms an MDAnalysis selection matches — use this to catch the common 0-atom trap on bare .gro files before running measurements.

Measure a distance (2 atom indices), angle (3), or dihedral (4) at a frame. Distances are in Angstrom, angles in degrees.

Radius of gyration (Angstrom) of an atom selection at a frame.

Compute clathrate-hydrate water order parameters F3 (tetrahedrality) and F4 (<cos 3phi>) for a frame. F4 ~ 0.7-0.95 indicates hydrate/crystalline order, ~0 liquid, negative ice-Ih. Units are nm; for .gro the native nm parser is used. This is the differentiating capability no other MCP offers.

Build the water-water hydrogen-bond network for a frame and report bond count and average coordination (the substrate for cage identification). rcut is the O-O cutoff (nm), theta the H-O...O angle cutoff (degrees).

Identify clathrate-hydrate cages (5^12, 5^12 6^2, 5^12 6^4, ...) from the water H-bond network and classify the crystal structure (sI/sII/sH). Returns per-type cage counts, the structure label, and a confidence. method="TRACE" (all rings) or "HTR" (primitive rings). GROMACS .gro input.

Render clathrate cages photorealistically (ambient occlusion + shadows, orthographic by default). Each cage type is drawn in ONE unified color for both its water-oxygen vertices and its O-O framework, using a curated palette (512=cyan, 51262=violet, 51264=red, 435663=lime, 51268=blue).

Natural-language styling maps directly to the arguments:

• "show only the sII large cages" -> cage_types=["51264"]

• "... in magenta" -> highlight_color="magenta" (name or #rrggbb)

• "emphasize / thicker width" -> emphasis=True (thicker edges + bigger spheres)

• per-type colors -> colors={"512": "cyan", "51264": "magenta"} cage_types are internal codes: 512, 51262, 51263, 51264, 51268, 435663, ... (sI = 512+51262, sII = 512+51264, sH = 512+435663+51268). Returns a PNG.

Add a representation WITHOUT clearing existing ones — layer several reps (e.g. water as Points + solute as VDW). color is a coloring METHOD (Name, ResName, ResType, Chain, Beta, ...); style is VDW/Lines/Points/ NewCartoon/Licorice/etc.

Remove all representations from a molecule (start a fresh view).

Rotate the camera by degrees about an axis ('x'/'y'/'z'). In GUI/attended mode (VMD_HYDRATE_MCP_DISPLAY=gui) the visible window updates live.

Zoom the view by a multiplicative factor (>1 zoom in, <1 zoom out).

Reset/fit the camera to the loaded molecule.