Detailed documentation for all the components of AChemKit. It is generated directly from the source code, so should be up-to-date.

AChemKit.reactionnet Core for all ReactionNetwork classes
AChemKit.randomnet Functions that construct random reactionnet.ReactionNetwork instances by various methods.
AChemKit.properties Functions for testing properties of particular reaction networks.
AChemKit.utils Various utility functions and classes.
AChemKit.tools AChemKit comes with a number of complete command-line driven tools for working with various file types.
AChemKit.randomnet.Uniform(nmols, nreactions, nreactants, nproducts, rates=1.0, cls=<class 'AChemKit.reactionnet.ReactionNetwork'>, rng=None)ΒΆ

Generates a random reactionnet.ReactionNetwork by assigning reaction randomly between all molecular species.

Arguments:

nmols
Number of molecules 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).

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(). This could lead to differences from nmols.

nreactions
Number of 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).

Note

The value of nreactions is the number of times a reaction will be added to the reactionnet.ReactionNetwork. If it is already in the reactionnet.ReactionNetwork, it will be replaced. This can lead to reactionnet.ReactionNetwork with less than nreactions reactions.

nreactants

Number of reactants for 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).

Note

If this is a tuple/list it will be sampled for each reaction.

nproducts

Number of products for 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).

If this is None, then nreactants must be a tuple of (nreactants, nproducts) or a list of tuples.

Note

If this is a tuple/list it will be sampled for each reaction.

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).

Note

If this is a tuple/list it will be sampled for each reaction.

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.

These arguments can be a single value or a tuple/list which will be uniformly sampled from.

For example:

Uniform(5,3,2,1) will generate 5 molecules with 3 reactions between them where each reaction has two reactants and one product.

Uniform(5,3,(1,2), (1,2)) will generate 5 molecules with 3 reactions between them where each reaction has one or two reactants and one or two products.

Uniform(5,3,((2,1),(1,2)), None) will generate 5 molecules with 3 reactions between them where each reaction has either two reactants and one product or one reactant and two products.

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