memote.support.syntax module

Supporting functions for syntax checks performed on the model object.

memote.support.syntax.find_abc_tag_transporter(model)[source]

Find Atp-binding cassette transport rxns without ‘abc’ tag.

An ABC transport reaction is defined as follows: 1. It contains metabolites from at least 2 compartments, 2. at least 1 metabolite undergoes no chemical reaction, i.e., the formula stays the same on both sides of the equation, and 3. ATP is converted to ADP (+ Pi + H, yet this isn’t checked for explicitly).

Reactions that only transport protons (‘H’) across the membrane are excluded, as well as reactions with redox cofactors whose formula is either ‘X’ or ‘XH2’

Parameters:

model : cobra.Model

A cobrapy metabolic model

memote.support.syntax.find_false_demand_rxns(model)[source]

Find reactions which are tagged with DM_ but which are not demand rxns.

Parameters:

model : cobra.Model

A cobrapy metabolic model

memote.support.syntax.find_false_exchange_rxns(model)[source]

Find reactions that are tagged with EX_ but are not exchange reactions.

Parameters:

model : cobra.Model

A cobrapy metabolic model

memote.support.syntax.find_false_sink_rxns(model)[source]

Find reactions which are tagged with SK_ but which are not sink rxns.

Parameters:

model : cobra.Model

A cobrapy metabolic model

memote.support.syntax.find_reaction_tag_transporter(model)[source]

Return incorrectly tagged transport reactions.

A transport reaction is defined as follows: 1. It contains metabolites from at least 2 compartments and 2. at least 1 metabolite undergoes no chemical reaction, i.e., the formula stays the same on both sides of the equation.

Reactions that only transport protons (‘H’) across the membrane are excluded, as well as reactions with redox cofactors whose formula is either ‘X’ or ‘XH2’

Parameters:

model : cobra.Model

A cobrapy metabolic model

memote.support.syntax.find_rxn_id_compartment_suffix(model, suffix)[source]

Find un-tagged non-transport reactions.

Find non-transport reactions with metabolites in the given compartment whose ID is not tagged accordingly.

Parameters:

model : cobra.Model

A cobrapy metabolic model.

suffix : str

The suffix of the compartment to be checked.

Returns:

list

Non-transport reactions that have at least one metabolite in the compartment given by suffix but whose IDs do not have the suffix appended.

memote.support.syntax.find_rxn_id_suffix_compartment(model, suffix)[source]

Find mis-tagged non-transport reactions.

Find non-transport reactions whose ID bear a compartment tag but which do not contain any metabolites in the given compartment.

Parameters:

model : cobra.Model

A cobrapy metabolic model.

suffix : str

The suffix of the compartment to be checked.

Returns:

list

Non-transport reactions that have at least one metabolite in the compartment given by suffix but whose IDs do not have the suffix appended.

memote.support.syntax.find_untagged_demand_rxns(model)[source]

Find demand reactions whose IDs do not begin with DM_.

Parameters:

model : cobra.Model

A cobrapy metabolic model

memote.support.syntax.find_untagged_exchange_rxns(model)[source]

Find exchange reactions whose identifiers do not begin with EX_.

Parameters:

model : cobra.Model

A cobrapy metabolic model

memote.support.syntax.find_untagged_sink_rxns(model)[source]

Find demand reactions whose IDs do not begin with SK_.

Parameters:

model : cobra.Model

A cobrapy metabolic model

memote.support.syntax.find_upper_case_mets(model)[source]

Find metabolites whose ID roots contain uppercase characters.

In metabolite names, individual uppercase exceptions are allowed: – Dextorotary prefix: ‘D’ – Levorotary prefix: ‘L’ – Prefixes for the absolute configuration of a stereocenter: ‘R’ and ‘S’ – Prefixes for the absolute stereochemistry of double bonds ‘E’ and ‘Z’ – Acyl carrier proteins can be labeled as ‘ACP’

Parameters:

model : cobra.Model

A cobrapy metabolic model