chemart / srsim
View on GitHubSRSim (rule-based spatial simulator) — Rule-based chemistry that refuses to forget geometry. Molecules are spheres carrying binding sites at fixed positions, diffusing in three dimensions, and rules are written over patterns as in any rule-based language - bu…
chemistry
official · built in
systems-biology
fidelity: reconstructed
constructive
#banzhaf-yamamoto
SRSim (rule-based spatial simulator)
One of the artificial chemistries of Banzhaf & Yamamoto, Artificial Chemistries (MIT Press, 2015), §18.3.3; first proposed by Gruenert & Dittrich, 2010-2013.
Its generator ships with the chemart library, so loading it runs no code from the hub and needs no trust_remote_code.
import chemart
net = chemart.generate_network("chemart/srsim", seed=0) # same as "srsim"
print(net.summary())