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
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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
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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
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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
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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
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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
suffix : str
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Returns: | list
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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
suffix : str
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Returns: | list
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memote.support.syntax.
find_untagged_demand_rxns
(model)[source]¶Find demand reactions whose IDs do not begin with DM_
.
Parameters: | model : cobra.Model
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memote.support.syntax.
find_untagged_exchange_rxns
(model)[source]¶Find exchange reactions whose identifiers do not begin with EX_
.
Parameters: | model : cobra.Model
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memote.support.syntax.
find_untagged_sink_rxns
(model)[source]¶Find demand reactions whose IDs do not begin with SK_
.
Parameters: | model : cobra.Model
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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
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