Interactive diagrams¶
Two self-contained, interactive diagrams of how TOPO fits together. Each is a full-screen SVG with clickable nodes, flow chips that light up and animate a sequence, and a light/dark theme toggle. They open in a new tab.
Architecture — the stack
The four runners (topo-mdrun, topo-optimize, topo-csp,
topo-cylinder), the one shared MD engine they all delegate to, the
coarse-grained force field, and the outputs. Flow chips trace Equilibrium,
Optimize, Synthesis, Cylinder, and Analysis paths through the stack.
Open the architecture diagram →
Call flow — end to end
The end-to-end function-call sequence for the two workflows side by side:
isolated-protein MD (topo-mdrun) and protein synthesis
(topo-csp), both funneling into the shared per-segment core
(setup_simulation → attach_reporters → step → finalize_simulation).
Numbered badges show call order; chips replay Isolated MD, CSP synthesis, the
per-residue 3-stage loop, Model build, and Engine step.