psamm.datasource.entry – Model entry representations

Representation of compound/reaction entries in models.

class psamm.datasource.entry.CompartmentEntry

Abstract compartment entry.

class psamm.datasource.entry.CompoundEntry

Abstract compound entry.

charge

Compound charge value.

formula

Chemical formula of compound.

class psamm.datasource.entry.DictCompartmentEntry(*args, **kwargs)

Compartment entry backed by dictionary.

The given properties dictionary must contain a key ‘id’ with the identifier.

Parameters:

• properties – dict or CompartmentEntry to construct from.
• filemark – Where the entry was parsed from (optional)

class psamm.datasource.entry.DictCompoundEntry(*args, **kwargs)

Compound entry backed by dictionary.

The given properties dictionary must contain a key ‘id’ with the identifier.

Parameters:

• properties – dict or CompoundEntry to construct from.
• filemark – Where the entry was parsed from (optional)

class psamm.datasource.entry.DictReactionEntry(*args, **kwargs)

Reaction entry backed by dictionary.

The given properties dictionary must contain a key ‘id’ with the identifier.

Parameters:

• properties – dict or ReactionEntry to construct from.
• filemark – Where the entry was parsed from (optional)

class psamm.datasource.entry.ModelEntry

Abstract model entry.

filemark

Position of entry in the source file (or None).

id

Identifier of entry.

name

Name of entry (or None).

properties

Properties of entry as a Mapping subclass (e.g. dict).

Note that the properties are not generally mutable.

class psamm.datasource.entry.ReactionEntry

Abstract reaction entry.

equation

Reaction equation.

genes

Gene association expression.