VirtualMicrobes.event package¶
Submodules¶
VirtualMicrobes.event.Molecule module¶
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class
VirtualMicrobes.event.Molecule.
Molecule
(name, toxic_level=None, is_internal=True, pair=True, is_building_block=False, is_gene_product=False, mol_class=None, is_energy=False, environment=None, **kwargs)[source]¶ Bases:
object
Small molecules of the system. Can exist internally or externally. Some are metabolites that can take place in (enzymatic) reactions. Can diffuse over membranes and may be transported into or out of the cell.Version: Author: -
class_version
= '1.0'¶
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energy_level
¶
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environment
¶
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index
= 0¶
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is_building_block
¶
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is_energy
¶
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is_gene_product
¶
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is_influxed
¶
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is_internal
¶
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mol_class
¶
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pair_up
()[source]¶ Create a paired molecule for self on the other side of the Cell membrane. When updating a property of self, the property of the paired molecule is automatically updated (if appropriate; e.g. toxic_level or is_energy)
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toxic_level
¶
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class
VirtualMicrobes.event.Molecule.
MoleculeClass
(name, molecule_species=None, energy_level=1, is_energy=False, has_building_block=False)[source]¶ Bases:
object
VirtualMicrobes.event.Reaction module¶
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exception
VirtualMicrobes.event.Reaction.
BadStoichiometryException
[source]¶ Bases:
exceptions.Exception
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class
VirtualMicrobes.event.Reaction.
Convert
(reactants, products, stoichiometry)[source]¶ Bases:
VirtualMicrobes.event.Reaction.Reaction
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init_sub_reaction_dicts
()[source]¶ Write out dictionaries for the sub_reactions generated by sub_reactions()
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prod_species
¶
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reac_species
¶
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sub_reactions
()[source]¶ Returns a list of all potential reaction schemes in the following form: ([ (reactant, stoichiometry), .. ], [ (product, stoichiometry) ..] ). The general scheme for reactions from and to Molecule Classes maps molecules within a MolClass on lhs to molecules in another class on the rhs as follows:
Reaction scheme as MoleculeClass scheme: A + B -> C , where A :{a0, a1, a2}, B:{b0, b1}, C:{c0, c1, c2*} will be translated into:
a0 + b0 -> c0 a1 + b0 -> c1 a2 + b0 -> c2*
a0 + b1 -> c0 a1 + b1 -> c1 a2 + b1 -> c2*
- If certain molecule species do not exist (e.g. the c2 in the previous example does not
exist, the reaction is omitted from possible sub-reactions, and will therefor not take place. Note that products on the rhs will always be converted in to the species corresponding to the index of the substrate on the lhs. If there is more product than substrates, e.g. A -> C + D where D:{d0, d1}, then there will be subreactions for every possible species of D:
a0 -> c0 + d0 a0 -> c0 + d1
a1 -> c1 + d0 a1 -> c1 + d1
a2 -> c2 + d0 a2 -> c2 + d1
Example 2: F + G -> H + I , where F :{f0, f1, f2}, G:{g0}, H:{h0, h1} , I:{i0, i2} becomes:
f0 + g0 -> h0 + i0 f1 + g0 -> h1 + i0
.
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class
VirtualMicrobes.event.Reaction.
Reaction
(type_, reactants, products, stoichiometry, **kwargs)[source]¶ Bases:
object
A reaction can be associated either with individual molecular species or with a Molecule Classes.
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class
VirtualMicrobes.event.Reaction.
Transport
(substrate_class, energy_source_class, cost, **kwargs)[source]¶
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VirtualMicrobes.event.Reaction.
consumes
(reactions)[source]¶ Set of consumed metabolic species.
Parameters: reactions (iterable of class:Convert or dict) – set of reactions Returns: set of class Return type: `event.Molecule.Molecule`s consumed in the reaction set.
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VirtualMicrobes.event.Reaction.
find_metabolic_closure
(input_set, conversions)[source]¶ Find the autocatalytic closure of metabolites given a set of inputs and reactions.
Iteratively overlap the produced + influxed and consumed metabolites of the set of conversion reactions, yielding a set of ‘potentially autocatalytic metabolites’. Iterate over the set of ‘potentially autocatalytic reactions’ and require that all substrates of the reaction are in the set of ‘potentially autocatalytic’ metabolites. If not, remove the reaction from the ‘potentially autocatalytic’ reaction set.
Parameters: - input_set (iterable of
event.Molecule.Molecule
) – initial set to start expansion of metabolic set - conversions (iterable of :class:`Conversion`s) – enzymatic reactions that convert metabolites into other metabolites
Returns: tuple – molecules and reactions in the core autocatalytic cycle.
Return type: ( set of class:`event.Molecule.Molecule`s , set of :class:`Conversion`s)
- input_set (iterable of
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VirtualMicrobes.event.Reaction.
find_product_set
(input_mols, conversions)[source]¶ Find metabolites that can be produced from a set of input metabolites, given a set of reactions.
Parameters: - input_mols (iterable of
event.Molecule.Molecule
) – initial set to start expansion of metabolic set - conversions (iterable of :class:`Conversion`s) – enzymatic reactions that convert metabolites into other metabolites
Returns: set of produced class
Return type: `event.Molecule.Molecule`s
- input_mols (iterable of