psamm.database
– Reaction database¶
Representation of metabolic network databases.
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class
psamm.database.
StoichiometricMatrixView
(database)¶ Provides a sparse matrix view on the stoichiometry of a database.
This object is used internally in the database to expose a sparse matrix view of the model stoichiometry. This class should not be instantied, instead use the
MetabolicDatabase.matrix
property. Any compound, reaction-pair can be looked up to obtain the corresponding stoichiometric value. If the value is not defined (implicitly zero) aKeyError
will be raised.In addition, instances also support the NumPy __array__ protocol which means that a
numpy.array
can by created directly from the matrix.>>> model = MetabolicModel() >>> matrix = numpy.array(model.matrix)
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class
psamm.database.
MetabolicDatabase
¶ Database of metabolic reactions.
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reactions
¶ Iterator of reactions IDs in the database.
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compartments
¶ Iterator of compartment IDs in the database.
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has_reaction
(reaction_id)¶ Whether the given reaction exists in the database.
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is_reversible
(reaction_id)¶ Whether the given reaction is reversible.
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get_reaction_values
(reaction_id)¶ Return an iterator of reaction compounds and stoichiometric values.
The returned iterator contains (
Compound
, value)-tuples. The value is negative for left-hand side compounds and positive for right-hand side.
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get_compound_reactions
(compound_id)¶ Return an iterator of reactions containing the compound.
Reactions are returned as IDs.
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reversible
¶ The set of reversible reactions.
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matrix
¶ Mapping from compound, reaction to stoichiometric value.
This is an instance of
StoichiometricMatrixView
.
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class
psamm.database.
DictDatabase
¶ Metabolic database backed by in-memory dictionaries
This is a subclass of
MetabolicDatabase
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reactions
¶ Iterator of reactions IDs in the database.
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compartments
¶ Iterator of compartment IDs in the database.
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has_reaction
(reaction_id)¶ Whether the given reaction exists in the database.
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is_reversible
(reaction_id)¶ Whether the given reaction is reversible.
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get_reaction_values
(reaction_id)¶ Return an iterator of reaction compounds and stoichiometric values.
The returned iterator contains (
Compound
, value)-tuples. The value is negative for left-hand side compounds and positive for right-hand side.
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get_compound_reactions
(compound_id)¶ Return an iterator of reactions containing the compound.
Reactions are returned as IDs.
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class
psamm.database.
ChainedDatabase
(*databases)¶ Links a number of databases so they can be treated a single database
This is a subclass of
MetabolicDatabase
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reactions
¶ Iterator of reactions IDs in the database.
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compartments
¶ Iterator of compartment IDs in the database.
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has_reaction
(reaction_id)¶ Whether the given reaction exists in the database.
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is_reversible
(reaction_id)¶ Whether the given reaction is reversible.
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get_reaction_values
(reaction_id)¶ Return an iterator of reaction compounds and stoichiometric values.
The returned iterator contains (
Compound
, value)-tuples. The value is negative for left-hand side compounds and positive for right-hand side.
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get_compound_reactions
(compound)¶ Return an iterator of reactions containing the compound.
Reactions are returned as IDs.
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