chemart / srsim

{"species": [{"id": "M(a[.],b[.])", "structure": "M(a[.],b[.])"}, {"id": "M(a[.],b[1]),M(a[1],b[.])", "structure": "M(a[.],b[1]),M(a[1],b[.])"}, {"id": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])", "structure": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])"}, {"id": "M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])", "structure": "M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])"}, {"id": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[4],b[3])", "structure": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[4],b[3])"}, {"id": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[.])", "structure": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[.])"}, {"id": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[.]),M(a[4],b[3]),M(a[5],b[4]),M(a[6],b[5]),M(a[7],b[6]),M(a[.],b[7])", "structure": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[.]),M(a[4],b[3]),M(a[5],b[4]),M(a[6],b[5]),M(a[7],b[6]),M(a[.],b[7])"}, {"id": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[5])", "structure": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[5])"}, {"id": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[5]),M(a[5],b[.])", "structure": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[5]),M(a[5],b[.])"}, {"id": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[6]),M(a[.],b[5]),M(a[6],b[7]),M(a[7],b[8]),M(a[8],b[.])", "structure": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[6]),M(a[.],b[5]),M(a[6],b[7]),M(a[7],b[8]),M(a[8],b[.])"}, {"id": "M13#2078c4", "structure": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[.]),M(a[6],b[5]),M(a[7],b[6]),M(a[8],b[7]),M(a[9],b[8]),M(a[10],b[9]),M(a[11],b[10]),M(a[12],b[11]),M(a[.],b[12])"}, {"id": "M10#df2d2d", "structure": "M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[5]),M(a[5],b[6]),M(a[6],b[7]),M(a[7],b[8]),M(a[8],b[9]),M(a[9],b[.])"}, {"id": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[6]),M(a[.],b[5]),M(a[6],b[.])", "structure": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[6]),M(a[.],b[5]),M(a[6],b[.])"}], "reactions": [{"reactants": {"M(a[.],b[.])": 2}, "products": {"M(a[.],b[1]),M(a[1],b[.])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 20}, {"reactants": {"M(a[.],b[.])": 1, "M(a[.],b[1]),M(a[1],b[.])": 1}, "products": {"M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 8}, {"reactants": {"M(a[.],b[.])": 1, "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])": 1}, "products": {"M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 4}, {"reactants": {"M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])": 1}, "products": {"M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[4],b[3])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 2}, {"reactants": {"M(a[.],b[1]),M(a[1],b[.])": 1, "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])": 1}, "products": {"M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[.])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 3}, {"reactants": {"M(a[.],b[1]),M(a[1],b[.])": 1}, "products": {"M(a[.],b[.])": 2}, "rate": {"law": "mass-action", "k": 0.01, "rules": "grow_rev"}, "count": 3}, {"reactants": {"M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[.])": 1, "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])": 1}, "products": {"M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[.]),M(a[4],b[3]),M(a[5],b[4]),M(a[6],b[5]),M(a[7],b[6]),M(a[.],b[7])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 1}, {"reactants": {"M(a[.],b[1]),M(a[1],b[.])": 2}, "products": {"M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 2}, {"reactants": {"M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])": 1, "M(a[.],b[.])": 1}, "products": {"M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[.])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 1}, {"reactants": {"M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[.])": 1}, "products": {"M(a[.],b[1]),M(a[1],b[.])": 1, "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])": 1}, "rate": {"law": "mass-action", "k": 0.01, "rules": "grow_rev"}, "count": 2}, {"reactants": {"M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[.])": 1}, "products": {"M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[5])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 1}, {"reactants": {"M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])": 1, "M(a[.],b[1]),M(a[1],b[.])": 1}, "products": {"M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[5]),M(a[5],b[.])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 1}, {"reactants": {"M(a[.],b[.])": 1, "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[.]),M(a[4],b[3]),M(a[5],b[4]),M(a[6],b[5]),M(a[7],b[6]),M(a[.],b[7])": 1}, "products": {"M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[6]),M(a[.],b[5]),M(a[6],b[7]),M(a[7],b[8]),M(a[8],b[.])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 1}, {"reactants": {"M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])": 1, "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[6]),M(a[.],b[5]),M(a[6],b[7]),M(a[7],b[8]),M(a[8],b[.])": 1}, "products": {"M13#2078c4": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 1}, {"reactants": {"M(a[.],b[1]),M(a[1],b[.])": 1, "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[5]),M(a[5],b[.])": 1}, "products": {"M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[.]),M(a[4],b[3]),M(a[5],b[4]),M(a[6],b[5]),M(a[7],b[6]),M(a[.],b[7])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 1}, {"reactants": {"M(a[.],b[1]),M(a[1],b[.])": 1, "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[.]),M(a[4],b[3]),M(a[5],b[4]),M(a[6],b[5]),M(a[7],b[6]),M(a[.],b[7])": 1}, "products": {"M10#df2d2d": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 1}, {"reactants": {"M13#2078c4": 1}, "products": {"M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[6]),M(a[.],b[5]),M(a[6],b[7]),M(a[7],b[8]),M(a[8],b[.])": 1, "M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])": 1}, "rate": {"law": "mass-action", "k": 0.01, "rules": "grow_rev"}, "count": 1}, {"reactants": {"M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[6]),M(a[.],b[5]),M(a[6],b[7]),M(a[7],b[8]),M(a[8],b[.])": 1}, "products": {"M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])": 1, "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[5]),M(a[5],b[.])": 1}, "rate": {"law": "mass-action", "k": 0.01, "rules": "grow_rev"}, "count": 1}, {"reactants": {"M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])": 1, "M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])": 1}, "products": {"M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[6]),M(a[.],b[5]),M(a[6],b[.])": 1}, "rate": {"law": "mass-action", "k": 25.656340004316643, "rules": "grow"}, "count": 1}], "status": "observed", "initial_state": {"M(a[.],b[.])": 50.0}, "inflow": null, "outflow": null, "extras": {"model": "polymer", "molecule_types": [{"name": "M", "radius": 0.5, "mass": 1.0, "diffusion": 1.0, "sites": [{"name": "a", "dist": 1.0, "theta": 90.0, "phi": 0.0}, {"name": "b", "dist": 1.0, "theta": 90.0, "phi": 90.0}]}], "rules": ["'grow' M(a) + M(b) <-> M(a!1).M(b!1) @ 0.5, 0.01"], "init": {"M": 50}, "bngl": "begin species\n  M()  50\nend species\n\nbegin reaction rules\n  'grow' M(a) + M(b) <-> M(a!1).M(b!1) @ 0.5, 0.01\nend reaction rules\n", "reaction_rules": [["grow"], ["grow"], ["grow"], ["grow"], ["grow"], ["grow_rev"], ["grow"], ["grow"], ["grow"], ["grow_rev"], ["grow"], ["grow"], ["grow"], ["grow"], ["grow"], ["grow"], ["grow_rev"], ["grow_rev"], ["grow"]], "space": {"kind": "continuous", "dimensions": 3, "units": "arbitrary (as in the paper's examples)", "box": [[0.0, 12.0], [0.0, 12.0], [0.0, 12.0]], "boundary": "periodic (minimum image)", "timestep": 0.02, "steps": 1500, "temperature": 1.0, "integrator": "langevin", "diffusion": {"M": 1.0}, "radius": {"M": 0.5}, "mass": {"M": 1.0}, "sites": {"M": [{"name": "a", "dist": 1.0, "theta": 90.0, "phi": 0.0, "states": []}, {"name": "b", "dist": 1.0, "theta": 90.0, "phi": 90.0, "states": []}]}, "ideal_angles": {"M": [[0.0, 90.0], [90.0, 0.0]]}, "tolerances": {"distance": 0.5, "angle_degrees": 30.0, "orientation": "bound-only"}, "refractory_time": 1.0, "reaction_criterion": "a bimolecular rule fires between two elementary molecules only if their distance is within distance_tolerance of the ideal bond length d_ij + d_kl and, for every bond either of them already carries, the angle between the direction to the partner and that bond is within angle_tolerance of the ideal angle; an unbound molecule has no orientation and passes (orientation='sampled': with probability (1 - cos t_ang)/2). A compatible pair then reacts with probability 1 - exp(-k dt).", "particles": [{"species": "M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])", "type": "M", "position": [7.8962, 3.0905, 3.1927]}, {"species": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])", "type": "M", "position": [1.8895, 9.9175, 6.2548]}, {"species": "M10#df2d2d", "type": "M", "position": [5.5314, 0.5743, 3.3279]}, {"species": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[5]),M(a[5],b[.])", "type": "M", "position": [2.7997, 4.2866, 0.0585]}, {"species": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[6]),M(a[.],b[5]),M(a[6],b[.])", "type": "M", "position": [5.708, 5.8675, 10.0254]}, {"species": "M10#df2d2d", "type": "M", "position": [6.0589, 3.0656, 2.8]}, {"species": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[4],b[3])", "type": "M", "position": [5.4298, 4.3011, 9.7863]}, {"species": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[4],b[3])", "type": "M", "position": [3.5156, 2.2608, 9.474]}, {"species": "M(a[.],b[.])", "type": "M", "position": [7.0711, 1.3343, 9.5085]}, {"species": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])", "type": "M", "position": [9.2101, 9.7503, 7.7987]}, {"species": "M10#df2d2d", "type": "M", "position": [8.0372, 2.0213, 2.7182]}, {"species": "M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])", "type": "M", "position": [7.1254, 11.9533, 1.1097]}, {"species": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[.])", "type": "M", "position": [2.7855, 7.8986, 6.0069]}, {"species": "M10#df2d2d", "type": "M", "position": [4.7725, 5.81, 2.2499]}, {"species": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[5])", "type": "M", "position": [2.053, 9.7174, 11.7114]}, {"species": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[5])", "type": "M", "position": [0.2234, 11.3352, 11.516]}, {"species": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[5]),M(a[5],b[.])", "type": "M", "position": [4.0284, 6.1343, 0.2818]}, {"species": "M(a[1],b[2]),M(a[.],b[1]),M(a[2],b[3]),M(a[3],b[.])", "type": "M", "position": [9.2587, 11.2426, 2.4101]}, {"species": "M10#df2d2d", "type": "M", "position": [5.2342, 5.1713, 4.4772]}, {"species": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[5]),M(a[5],b[.])", "type": "M", "position": [2.8915, 8.2777, 2.4634]}, {"species": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[4],b[3])", "type": "M", "position": [8.2631, 1.9686, 8.9448]}, {"species": "M(a[.],b[1]),M(a[1],b[.])", "type": "M", "position": [11.6649, 0.9767, 8.1484]}, {"species": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[5],b[3]),M(a[4],b[6]),M(a[.],b[5]),M(a[6],b[.])", "type": "M", "position": [5.6895, 6.7591, 8.621]}, {"species": "M(a[1],b[2]),M(a[3],b[1]),M(a[2],b[4]),M(a[4],b[3])", "type": "M", "position": [7.5289, 2.3887, 10.9489]}, {"species": "M(a[.],b[1]),M(a[1],b[2]),M(a[2],b[3]),M(a[3],b[4]),M(a[4],b[5]),M(a[5],b[.])", "type": "M", "position": [0.7517, 7.5695, 3.5947]}, {"species": "M(a[.],b[.])", 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