psamm.datasource.entry – Model entry representations

Representation of compound/reaction entries in models.

class psamm.datasource.entry.ModelEntry

Abstract model entry.

Provdides a base class for model entries which are representations of any entity (such as compound, reaction or compartment) in a model. An entity has an ID, and may have a name and filemark. The ID is a unique string identified within a model. The name is a string identifier for human consumption. The filemark indicates where the entry originates from (e.g. file name and line number). Any additional properties for an entity exist in properties which is any dict-like object mapping from string keys to any value type. The name entry in the dictionary corresponds to the name. Entries can be mutable, where the properties can be modified, or immutable, where the properties cannot be modified or where modifications are ignored. The ID is always immutable.

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 but may be mutable for specific subclasses. If the id exists in this dictionary, it must never change the actual entry ID as obtained from the id property, even if other properties are mutable.

filemark

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

class psamm.datasource.entry.CompoundEntry

Abstract compound entry.

Entry subclass for representing compounds. This standardizes the properties formula and charge.

formula

Chemical formula of compound.

charge

Compound charge value.

class psamm.datasource.entry.ReactionEntry

Abstract reaction entry.

Entry subclass for representing compounds. This standardizes the properties equation and genes.

equation

Reaction equation.

genes

Gene association expression.

class psamm.datasource.entry.CompartmentEntry

Abstract compartment entry.

Entry subclass for representing compartments.

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)

formula

Chemical formula of compound.

charge

Compound charge value.

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)

equation

Reaction equation.

genes

Gene association expression.

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)