topo — call flow

isolated protein MD · CSP synthesis · end‑to‑end
Isolated protein · topo-mdrun Co-translational · topo-csp for L = L0 .. L_max shared per-segment core · topo.engine + topo.core build model attach + step runs on run_length ×3 → core prev_final seeds L+1 at L_max _final.pdb topo-mdrun CLI entry · python -m topo.mdrun -f md.ini read_simulation_config() md.ini → SimulationConfig mdrun() orchestrates build · setup · run · finalize engine.build_system() CG model (+ n_copies) · dump PSF topo.mdrun.protocol temperature protocol anneal? quench + production : production run_protocol() → simulation.step() topo-csp CLI entry · topo-csp -f csp.ini read_csp_config() csp.ini → CSPConfig · RunParams run_continuous_synthesis() the synthesis driver load_ribosome() rigid mass-0 scenery (once) anchor_coord() ×2 · optimal_ptc_targets() P-/A-anchors → A/P target points PTC-geometry optimization (always on) precompute_contacts() STRIDE once · N×N contacts (L×L reuse) kinetics.build_codon_time_lists() per-codon mFPT schedule from mRNA kinetics.stage_steps(L) sample FPT → s1 / s2 / s3 steps run_length · stage 1 peptidyl-transfer · restrain A-site run_length · stage 2 translocation begins · still A-site run_length · stage 3 tRNA-binding · switch A → P-site ejection / dissociation run_length · restraint OFF · free drift build model buildCoarseGrainModel / build_length_model CSP only append_ribosome · restraint · tunnel rigid beads · A↔P C-term · wall setup_simulation() integrator · platform · restart / chk CSP only minimizeEnergy() · relax the seed attach_reporters() DCD · topoReporter log · checkpoint simulation.step(n) n = md_steps (mdrun) | s1/s2/s3 (CSP) finalize_simulation() save checkpoint · write _final.pdb external OpenMM · LangevinIntegrator · CUDA/CPU outputs .dcd · .log · .psf · _final.pdb · .chk CSP: per-length L_<n>/stage_<1,2,3>/
topo/mdrun · topo/csp/protocol · topo/csp/core · topo/engine

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    call-flow node

    Two entry points — topo-mdrun (an isolated protein) and topo-csp (protein synthesis) — both funnel into one shared per-segment core. Pick a chip to replay a call sequence; the numbered badges show call order.