chemart / smn

{"species": [{"id": "eg", "structure": null}, {"id": "abg", "structure": null}, {"id": "bcg", "structure": null}, {"id": "cg", "structure": null}, {"id": "d", "structure": null}, {"id": "ea", "structure": null}, {"id": "cgbcg", "structure": null}, {"id": "eaeg", "structure": null}, {"id": "cgcg", "structure": null}, {"id": "cgd", "structure": null}, {"id": "bg", "structure": null}, {"id": "ecg", "structure": null}, {"id": "abgecg", "structure": null}, {"id": "ad", "structure": null}, {"id": "cgbg", "structure": null}, {"id": "bgbcg", "structure": null}, {"id": "egcg", "structure": null}, {"id": "caeg", "structure": null}, {"id": "cgdcgbcg", "structure": null}, {"id": "abgbg", "structure": null}, {"id": "ecgcgbcg", "structure": null}], "reactions": [{"reactants": {"cg": 1, "bcg": 1}, "products": {"cgbcg": 1}, "rate": null, "count": null}, {"reactants": {"cgbcg": 1}, "products": {"cg": 1, "bcg": 1}, "rate": null, "count": null}, {"reactants": {"ea": 1, "eg": 1}, "products": {"eaeg": 1}, "rate": null, "count": null}, {"reactants": {"eaeg": 1}, "products": {"ea": 1, "eg": 1}, "rate": null, "count": null}, {"reactants": {"cg": 2}, "products": {"cgcg": 1}, "rate": null, "count": null}, {"reactants": {"cgcg": 1}, "products": {"cg": 2}, "rate": null, "count": null}, {"reactants": {"cg": 1, "d": 1}, "products": {"cgd": 1}, "rate": null, "count": null}, {"reactants": {"cgd": 1}, "products": {"cg": 1, "d": 1}, "rate": null, "count": null}, {"reactants": {"bcg": 1, "eg": 1}, "products": {"bg": 1, "ecg": 1}, "rate": null, "count": null}, {"reactants": {"bg": 1, "ecg": 1}, "products": {"bcg": 1, "eg": 1}, "rate": null, "count": null}, {"reactants": {"abg": 1, "ecg": 1}, "products": {"abgecg": 1}, "rate": null, "count": null}, {"reactants": {"abgecg": 1}, "products": {"abg": 1, "ecg": 1}, "rate": null, "count": null}, {"reactants": {"abg": 1, "cgd": 1}, "products": {"ad": 1, "cgbg": 1}, "rate": null, "count": null}, {"reactants": {"ad": 1, "cgbg": 1}, "products": {"abg": 1, "cgd": 1}, "rate": null, "count": null}, {"reactants": {"bg": 1, "bcg": 1}, "products": {"bgbcg": 1}, "rate": null, "count": null}, {"reactants": {"bgbcg": 1}, "products": {"bg": 1, "bcg": 1}, "rate": null, "count": null}, {"reactants": {"eaeg": 1, "cgcg": 1}, "products": {"egcg": 1, "caeg": 1}, "rate": null, "count": null}, {"reactants": {"egcg": 1, "caeg": 1}, "products": {"eaeg": 1, "cgcg": 1}, "rate": null, "count": null}, {"reactants": {"cgd": 1, "cgbcg": 1}, "products": {"cgdcgbcg": 1}, "rate": null, "count": null}, {"reactants": {"cgdcgbcg": 1}, "products": {"cgd": 1, "cgbcg": 1}, "rate": null, "count": null}, {"reactants": {"abg": 1, "cgbg": 1}, "products": {"abgbg": 1, "cg": 1}, "rate": null, "count": null}, {"reactants": {"abgbg": 1, "cg": 1}, "products": {"abg": 1, "cgbg": 1}, "rate": null, "count": null}, {"reactants": {"ecg": 1, "cgbcg": 1}, "products": {"ecgcgbcg": 1}, "rate": null, "count": null}, {"reactants": {"ecgcgbcg": 1}, "products": {"ecg": 1, "cgbcg": 1}, "rate": null, "count": null}], "status": "complete", "initial_state": {"eg": 1.0, "abg": 1.0, "bcg": 1.0, "cg": 1.0, "d": 1.0, "ea": 1.0}, "inflow": null, "outflow": "constant-total", "extras": {"genome": [{"enzyme": "E0", "kind": "ligation", "educts": "cg + bcg", "reaction": "cg + bcg <-> cgbcg", "reactions": [0, 1], "parent": null}, {"enzyme": "E1", "kind": "ligation", "educts": "ea + eg", "reaction": "ea + eg <-> eaeg", "reactions": [2, 3], "parent": null}, {"enzyme": "E2", "kind": "ligation", "educts": "cg + cg", "reaction": "cg + cg <-> cgcg", "reactions": [4, 5], "parent": null}, {"enzyme": "E3", "kind": "ligation", "educts": "cg + d", "reaction": "cg + d <-> cgd", "reactions": [6, 7], "parent": null}, {"enzyme": "E4", "kind": "recombination", "educts": "b|cg + e|g", "reaction": "bcg + eg <-> bg + ecg", "reactions": [8, 9], "parent": null}, {"enzyme": "E5", "kind": "ligation", "educts": "abg + ecg", "reaction": "abg + ecg <-> abgecg", "reactions": [10, 11], "parent": null}, {"enzyme": "E6", "kind": "recombination", "educts": "a|bg + cg|d", "reaction": "abg + cgd <-> ad + cgbg", "reactions": [12, 13], "parent": null}, {"enzyme": "E7", "kind": "ligation", "educts": "bg + bcg", "reaction": "bg + bcg <-> bgbcg", "reactions": [14, 15], "parent": null}, {"enzyme": "E8", "kind": "recombination", "educts": "e|aeg + c|gcg", "reaction": "eaeg + cgcg <-> egcg + caeg", "reactions": [16, 17], "parent": null}, {"enzyme": "E9", "kind": "ligation", "educts": "cgd + cgbcg", "reaction": "cgd + cgbcg <-> cgdcgbcg", "reactions": [18, 19], "parent": null}, {"enzyme": "E10", "kind": "recombination", "educts": "ab|g + c|gbg", "reaction": "abg + cgbg <-> abgbg + cg", "reactions": [20, 21], "parent": null}, {"enzyme": "E11", "kind": "ligation", "educts": "ecg + cgbcg", "reaction": "ecg + cgbcg <-> ecgcgbcg", "reactions": [22, 23], "parent": null}], "initial_metabolites": ["eg", "abg", "bcg", "cg", "d", "ea"], "conservation": [{"name": "letter a", "vector": {"abg": 1, "ea": 1, "eaeg": 1, "abgecg": 1, "ad": 1, "caeg": 1, "abgbg": 1}}, {"name": "letter b", "vector": {"abg": 1, "bcg": 1, "cgbcg": 1, "bg": 1, "abgecg": 1, "cgbg": 1, "bgbcg": 2, "cgdcgbcg": 1, "abgbg": 2, "ecgcgbcg": 1}}, {"name": "letter c", "vector": {"bcg": 1, "cg": 1, "cgbcg": 2, "cgcg": 2, "cgd": 1, "ecg": 1, "abgecg": 1, "cgbg": 1, "bgbcg": 1, "egcg": 1, "caeg": 1, "cgdcgbcg": 3, "ecgcgbcg": 3}}, {"name": "letter d", "vector": {"d": 1, "cgd": 1, "ad": 1, "cgdcgbcg": 1}}, {"name": "letter e", "vector": {"eg": 1, "ea": 1, "eaeg": 2, "ecg": 1, "abgecg": 1, "egcg": 1, "caeg": 1, "ecgcgbcg": 1}}, {"name": "letter f", "vector": {}}, {"name": "letter g", "vector": {"eg": 1, "abg": 1, "bcg": 1, "cg": 1, "cgbcg": 2, "eaeg": 1, "cgcg": 2, "cgd": 1, "bg": 1, "ecg": 1, "abgecg": 2, "cgbg": 2, "bgbcg": 2, "egcg": 2, "caeg": 1, "cgdcgbcg": 3, "abgbg": 2, "ecgcgbcg": 3}}, {"name": "letter h", "vector": {}}], "flow_law": "regulated inflow/outflow keeps the total amount of substance in the cell constant (book 18.3.1): outflow = constant-total", "kinetics": "not published in the book: each enzyme catalyses its reaction in both directions, and synthesising longer molecules is harder; rates are None", "fitness": "mass of the organism in letters, sum_s len(s) [s], after a fixed number of timesteps (book 18.3.1); used for selection across generations, not computed here"}, "chemistry": "smn", "params": {"alphabet_size": 8, "n_metabolites": 6, "max_metabolite_length": 3, "initial_metabolites": [], "n_enzymes": 12, "ligation_fraction": 0.5, "genome": [], "mutations": 0, "max_length": 12, "initial_amount": 1.0}, "seed": 1}