AChemKit.randomnet.Linear — AChemKit v0.1 documentation

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# AChemKit.randomnet.Linear

static `randomnet.` `Linear`(natoms, maxlength, pform, pbreak, directed=True, rates=1.0, cls=<class 'AChemKit.reactionnet.ReactionNetwork'>, rng=None)

  Generates a random `reactionnet.ReactionNetwork` from molecules that are strings of atoms and can join together or break apart.

  Based on the paper Autocatalytic sets of proteins. 1986. Journal of Theoretical Biology 119:1-24 by Kauffman, Stuart A. but without the explicit catalytic activity.

  Arguments:

  natoms
    Number of atoms to use. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution).

  Note

  `reactionnet.ReactionNetwork` tracks molecules by their reactions, so if a molecule is not part of any reaction it will not appear at all e.g. in `seen()`.

  maxlength
    Maximum number of atoms in a molecule. If this is None, then they are unbounded; this might cause problems with a computational explosion. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution).
  pform
    Probability that a pair of molecules will join together per orientation. Must be between 0 and 1. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution).
  pbreak
    Probability that any pair of atoms will break. Must be between 0 and 1.
  directed
    If false, molecules have no intrinsic direction so AlphBeta is equivlanet to BetaAlpha. NOT IMPLEMENTED
  rates
    Rate of each reaction in the reaction network. Can be a single value or a tuple/list which will be uniformly sampled from (duplicates can be used to give a non-uniform distribution).
  cls
    Alternative class to use for constructing the return rather than `reactionnet.ReactionNetwork`.
  rng
    Random number generator to use. If not specifed, one will be generated at random.

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