Metabolism : The Enzyme class¶

class PyFBA.metabolism.Enzyme(name)¶

The enzyme class has a few components:

• The subunit(s) that make up the enzyme
• The genes that encode those subunit(s)
• The reactions that this enzyme is connected to.

Variables:	name – the name of the enzyme object roles – the set of roles associated with the enzyme object pegs – a dict of pegs associated with the enzyme object and their associated roles roles_w_pegs – a dict of roles associated with the enzyme and their pegs reactions – a set of reaction IDs that this enzyme connects to

add_a_peg(peg, role)¶

Add a single peg and the role that it connects to.

Parameters:	peg (str) – The peg id role (str) – The role it connects to
Raises:	KeyError

add_pegs(pegs)¶

Add a hash of pegs and roles. Keys must be pegs, values must be roles.

Will throw a KeyError if the Role is not present

Parameters:	pegs (dict) – A hash of pegs and roles that encode the enzyme (e.g. from the assigned functions file)
Raises:	KeyError

add_reaction(reaction)¶

Add a reaction that this enzyme is inolved in.

Parameters:	reaction (Reaction) – The reaction object that this is involved with

add_roles(roles)¶

Add roles to this enzyme or complex

Parameters:	roles (set) – A set of functional roles that encode the enzyme

has_peg_for_role(role)¶

Do we have at least one peg for this role?

Parameters:	role (str) – The role we are looking for
Returns:	If a peg is present
Return type:	bool

has_role(role)¶

Does this enzyme have this role?

Parameters:	role (str) – A functional role
Returns:	A boolean
Return type:	bool

number_of_pegs()¶

The number of pegs assocaited with this enzyme.

Return type:	int

number_of_reactions()¶

The number of reactions that this enzyme is involved in

Return type:	int

number_of_roles()¶

How many roles does this enzyme have?

Return type:	int

number_of_roles_with_pegs()¶

How many of our roles have pegs associated with them?

Return type:	int

probability()¶

The probability that this reaction occurs in the cell. Currently the number of pegs/number of roles. Thus if most of the pegs are present then the enzyme is likely to function

Returns:	the probability that this reaction is complete
Return type:	float