7.1.1. cobrame.core package¶
7.1.1.1. Submodules¶
7.1.1.2. cobrame.core.reaction module¶
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class
cobrame.core.reaction.
ComplexFormation
(id)[source]¶ Bases:
cobrame.core.reaction.MEReaction
Formation of a functioning enzyme complex that can act as a catalyst for a ME-model reaction.
This reaction class produces a reaction that combines the protein subunits and adds any coenyzmes, prosthetic groups or enzyme modifications to form complete enzyme complex.
Parameters: id (str) – Identifier of the complex formation reaction. As a best practice, this ID should be prefixed with ‘formation + _ + <complex_id>’. If there are multiple ways of producing complex, this can be suffixed with ‘_ + alt’ -
_complex_id
¶ str – Name of the complex being produced by the complex formation reaction
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complex_data_id
¶ str – Name of ComplexData that defines the subunit stoichiometry or subreactions (modfications). This will not always be the same as the _complex_id. Sometimes complexes can be modified using different processes/enzymes
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complex
¶ Get the metabolite product of the complex formation reaction
Returns: Instance of complex metabolite from self._complex_id Return type: cobrame.core.component.Complex
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update
(verbose=True)[source]¶ Creates reaction using the associated complex data and adds chemical formula to complex metabolite product.
This function adds the following components to the reaction stoichiometry (using ‘data’ as shorthand for
cobrame.core.processdata.ComplexData
):- Complex product defined in self._complex_id
- Protein subunits with stoichiometery defined in data.stoichiometry
- Metabolites and enzymes w/ coupling coefficients defined in data.subreactions. This often includes enzyme complex modifications by coenzymes or prosthetic groups.
- Biomass
cobrame.core.component.Constraint
corresponding to modifications detailed in data.subreactions, if any
Parameters: verbose (bool) – Prints when new metabolites are added to the model when executing update()
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class
cobrame.core.reaction.
GenericFormationReaction
(id)[source]¶ Bases:
cobrame.core.reaction.MEReaction
Some components in an ME-model can perform exactly the same function. To handle this, GenericFormationReactions are used to create generic forms of these components.
Parameters: id (str) – Identifier of the generic formation reaction. As a best practice, this ID should be prefixed with ‘metabolite_id + _to_ + generic_metabolite_id’
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class
cobrame.core.reaction.
MEReaction
(id=None, name='')[source]¶ Bases:
cobra.core.Reaction.Reaction
MEReaction is a general reaction class from which all ME-Model reactions will inherit
This class contains functionality that can be used by all ME-model reactions
Parameters: id (str) – Identifier of the MEReaction. Should follow best practices of child class -
add_biomass_from_subreactions
(process_data, biomass=0.0)[source]¶ Account for the biomass of metabolites added to macromolecule (protein, complex, etc.) due to a modification such as prosthetic group addition.
Parameters: - process_data (
cobrame.core.processdata.ProcessData
) – ProcessData that is used to construct MEReaction - biomass (float) – Initial biomass value in kDa
Returns: Initial biomass value + biomass added from subreactions in kDa
Return type: - process_data (
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add_subreactions
(process_data_id, stoichiometry, scale=1.0)[source]¶ Function to add subreaction process data to reaction stoichiometry
Parameters: - process_data_id (str) –
ID of the process data associated with the metabolic reaction.
For example, if the modifications are being added to a complex formation reaction, the process data id would be the name of the complex.
- stoichiometry (dict) – Dictionary of {metabolite_id: float} or {metabolite_id: float * (sympy.Symbol)}
- scale (float) – Some processes (ie. tRNA charging) are reformulated such that other involved metabolites need scaling
Returns: Stoichiometry dictionary with updated entries
Return type: - process_data_id (str) –
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check_me_mass_balance
()[source]¶ Checks the mass balance of ME reaction, ignoring charge balances
Returns: {element: number_of_elemental_imbalances} Return type: dict
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get_components_from_ids
(id_stoichiometry, default_type=<class 'cobrame.core.component.Metabolite'>, verbose=True)[source]¶ Function to convert stoichiometry dictionary entries from strings to cobra objects.
{metabolite_id: value} to {
cobrame.core.component.Metabolite
: value}Parameters: - id_stoichiometry (Dict {string: float}) – Input Dict of {metabolite_id: value}
- default_type (String) – The type of cobra.Metabolite to default to if the metabolite is not yet present in the model
- verbose (Boolean) – If True, print metabolites added to model if not yet present in model
Returns: {
cobrame.core.component.Metabolite
: float}Return type:
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class
cobrame.core.reaction.
MetabolicReaction
(id)[source]¶ Bases:
cobrame.core.reaction.MEReaction
Irreversible metabolic reaction including required enzymatic complex
This reaction class’s update function processes the information contained in the complex data for the enzyme that catalyzes this reaction as well as the stoichiometric data which contains the stoichiometry of the metabolic conversion being performed (i.e. the stoichiometry of the M-model reaction analog)
Parameters: id (str) – Identifier of the metabolic reaction. As a best practice, this ID should use the following template (FWD=forward, REV=reverse): “<StoichiometricData.id> + _ + <FWD or REV> + _ + <Complex.id>” -
keff
¶ float – The turnover rete (keff) couples enzymatic dilution to metabolic flux
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reverse
¶ boolean – If True, the reaction corresponds to the reverse direction of the reaction. This is necessary since all reversible enzymatic reactions in an ME-model are broken into two irreversible reactions
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complex_data
¶ Get or set the ComplexData instance that details the enzyme that catalyzes the metabolic reaction. Can be set with instance of ComplexData or with its id.
Returns: Complex data detailing enzyme that catalyzes this reaction Return type: cobrame.core.processdata.ComplexData
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stoichiometric_data
¶ Get or set the StoichiometricData instance that details the metabolic conversion of the metabolic reaction. Can be set with instance of StoichiometricData or with its id.
Returns: Stoichiometric data detailing enzyme that catalyzes this reaction Return type: :class:`cobrame.core.processdata.StoichiometricData `
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update
(verbose=True)[source]¶ Creates reaction using the associated stoichiometric data and complex data.
This function adds the following components to the reaction stoichiometry (using ‘data’ as shorthand for
cobrame.core.processdata.StoichiometricData
):- Complex w/ coupling coefficients defined in self.complex_data.id and self.keff
- Metabolite stoichiometry defined in data.stoichiometry. Sign is flipped if self.reverse == True
Also sets the lower and upper bounds based on self.reverse and data.upper_bound and data.lower_bound.
Parameters: verbose (bool) – Prints when new metabolites are added to the model when executing update()
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class
cobrame.core.reaction.
PostTranslationReaction
(id)[source]¶ Bases:
cobrame.core.reaction.MEReaction
Reaction class that includes all posttranslational modification reactions (translocation, protein folding, modification (for lipoproteins) etc)
There are often multiple different reactions/enzymes that can accomplish the same modification/function. In order to account for these and maintain one translation reaction per protein, these processes need to be modeled as separate reactions.
Parameters: id (str) – Identifier of the post translation reaction -
add_translocation_pathways
(process_data_id, protein_id, stoichiometry=None)[source]¶ Add complexes and metabolites required to translocate the protein into cell membranes.
Parameters: Returns: Stoichiometry dictionary with updated entries from translocation
Return type:
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posttranslation_data
¶ Get or set PostTranslationData that defines the type of post translation modification/process (folding/translocation) that the reaction accounts for. Can be set with instance of PostTranslationData or with its id.
Returns: The PostTranslationData that defines the PostTranslationReaction Return type: cobrame.core.processdata.PostTranslationData
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update
(verbose=True)[source]¶ Creates reaction using the associated posttranslation data and adds chemical formula to processed protein product
This function adds the following components to the reaction stoichiometry (using ‘data’ as shorthand for
cobrame.core.processdata.PostTranslationData
):- Processed protein product defined in data.processed_protein_id
- Unprocessed protein reactant defined in data.unprocessed_protein_id
- Metabolites and enzymes defined in data.subreactions
- Translocation pathways defined in data.translocation
- Folding mechanism defined in data.folding_mechanims w/ coupling coefficients defined in data.keq_folding, data.k_folding, model.global_info[‘temperature’], data.aggregation_propensity, and data.propensity_scaling
- Surface area constraints defined in data.surface_are
- Biomass if a significant chemical modification takes place (i.e. lipid modifications for lipoproteins)
Parameters: verbose (bool) – Prints when new metabolites are added to the model when executing update()
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class
cobrame.core.reaction.
SummaryVariable
(id=None)[source]¶ Bases:
cobrame.core.reaction.MEReaction
SummaryVariables are reactions that impose global constraints on the model.
The primary example of this is the biomass_dilution SummaryVariable which forces the rate of biomass production of macromolecules, etc. to be equal to the rate of their dilution to daughter cells during growth.
Parameters: id (str) – Identifier of the SummaryVariable
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class
cobrame.core.reaction.
TranscriptionReaction
(id)[source]¶ Bases:
cobrame.core.reaction.MEReaction
Transcription of a TU to produced TranscribedGene.
RNA is transcribed on a transcription unit (TU) level. This type of reaction produces all of the RNAs contained within a TU, as well as accounts for the splicing/excision of RNA between tRNAs and rRNAs. The appropriate RNA_biomass constrain is produced based on the molecular weight of the RNAs being transcribed
Parameters: id (str) – Identifier of the transcription reaction. As a best practice, this ID should be prefixed with ‘transcription + _’ -
transcription_data
¶ Get or set the
cobrame.core.processdata.TranscriptionData
that defines the transcription unit architecture and the features of the RNAs being transcribed.
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update
(verbose=True)[source]¶ Creates reaction using the associated transcription data and adds chemical formula to RNA products
This function adds the following components to the reaction stoichiometry (using ‘data’ as shorthand for
cobrame.core.processdata.TranscriptionData
):- RNA_polymerase from data.RNA_polymerase w/ coupling coefficient (if present)
- RNA products defined in data.RNA_products
- Nucleotide reactants defined in data.nucleotide_counts
- If tRNA or rRNA contained in data.RNA_types, excised base products
- Metabolites + enzymes w/ coupling coefficients defined in data.subreactions (if present)
- Biomass
cobrame.core.component.Constraint
corresponding to data.RNA_products and their associated masses - Demand reactions for each transcript product of this reaction
Parameters: verbose (bool) – Prints when new metabolites are added to the model when executing update()
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class
cobrame.core.reaction.
TranslationReaction
(id)[source]¶ Bases:
cobrame.core.reaction.MEReaction
Reaction class for the translation of a TranscribedGene to a TranslatedGene
Parameters: id (str) – Identifier of the translation reaction. As a best practice, this ID should be prefixed with ‘translation + _’ -
translation_data
¶ Get and set the
cobra.core.processdata.TranslationData
that defines the translation of the gene. Can be set with instance of TranslationData or with its id.Returns: Return type: cobra.core.processdata.TranslationData
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update
(verbose=True)[source]¶ Creates reaction using the associated translation data and adds chemical formula to protein product
This function adds the following components to the reaction stoichiometry (using ‘data’ as shorthand for
cobrame.core.processdata.TranslationData
):- Amino acids defined in data.amino_acid_sequence. Subtracting water to account for condensation reactions during polymerization
- Ribosome w/ translation coupling coefficient (if present)
- mRNA defined in data.mRNA w/ translation coupling coefficient
- mRNA + nucleotides + hydrolysis ATP cost w/ degradation coupling coefficient (if kdeg (defined in model.global_info) > 0)
- RNA_degradosome w/ degradation coupling coefficient (if present and kdeg > 0)
- Protein product defined in data.protein
- Subreactions defined in data.subreactions
- protein_biomass
cobrame.core.component.Constraint
corresponding to the protein product’s mass - Subtract mRNA_biomass
cobrame.core.component.Constraint
defined by mRNA degradation coupling coefficinet (if kdeg > 0)
Parameters: verbose (bool) – Prints when new metabolites are added to the model when executing update()
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class
cobrame.core.reaction.
tRNAChargingReaction
(id)[source]¶ Bases:
cobrame.core.reaction.MEReaction
Reaction class for the charging of a tRNA with an amino acid
Parameters: id (str) – Identifier for the charging reaction. As a best practice, ID should follow the template “charging_tRNA + _ + <tRNA_locus> + _ + <codon>”. If tRNA initiates translation, <codon> should be replaced with START. -
tRNA_data
¶ Get and set the
cobra.core.processdata.tRNAData
that defines the translation of the gene. Can be set with instance of tRNAData or with its id.Returns: Return type: cobra.core.processdata.tRNAData
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update
(verbose=True)[source]¶ Creates reaction using the associated tRNA data
This function adds the following components to the reaction stoichiometry (using ‘data’ as shorthand for
cobrame.core.processdata.tRNAData
):- Charged tRNA product following template: “generic_tRNA + _ + <data.codon> + _ + <data.amino_acid>”
- tRNA metabolite (defined in data.RNA) w/ charging coupling coefficient
- Charged amino acid (defined in data.amino_acid) w/ charging coupling coefficient
- Synthetase (defined in data.synthetase) w/ synthetase coupling coefficient found, in part, using data.synthetase_keff
- Post transcriptional modifications defined in data.subreactions
Parameters: verbose (bool) – Prints when new metabolites are added to the model when executing update()
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7.1.1.3. cobrame.core.processdata module¶
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class
cobrame.core.processdata.
ComplexData
(id, model)[source]¶ Bases:
cobrame.core.processdata.ProcessData
Contains all information associated with the formation of an functional enzyme complex.
This can include any enzyme complex modifications required for the enzyme to become active.
Parameters: - id (str) – Identifier of the complex data. As a best practice, this should typically use the same ID as the complex being formed. In cases with multiple ways to form complex ‘_ + alt’ or similar suffixes can be used.
- model (
cobrame.core.model.MEModel
) – ME-model that the ComplexData is associated with
-
stoichiometry
¶ collections.DefaultDict(int)
– Dictionary containing {protein_id: count} for all protein subunits comprising enzyme complex
-
subreactions
¶ dict – Dictionary of {subreaction_data_id: count} for all complex formation subreactions/modifications. This can include cofactor/prosthetic group binding or enzyme side group addition.
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complex
¶ Get complex metabolite object
Returns: Instance of complex metabolite that ComplexData is used to synthesize Return type: cobrame.core.component.Complex
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complex_id
¶ Get and set complex ID for product of complex formation reaction
There are cases where multiple equivalent processes can result in the same final complex. This allows the equivalent final complex complex_id to be queried. This only needs set in the above case
Returns: ID of complex that ComplexData is used to synthesize Return type: str
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create_complex_formation
(verbose=True)[source]¶ creates a complex formation reaction
This assumes none exists already. Will create a reaction (prefixed by “formation”) which forms the complex
Parameters: verbose (bool) – If True, print if a metabolite is added to model during update
-
formation
¶ Get the formation reaction object
Returns: Complex formation reaction detailed in ComplexData Return type: cobrame.core.reaction.ComplexFormation
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class
cobrame.core.processdata.
GenericData
(id, model, component_list)[source]¶ Bases:
cobrame.core.processdata.ProcessData
Class for storing information about generic metabolites
Parameters: - id (str) – Identifier of the generic metabolite. As a best practice, this ID should be prefixed with ‘generic + _’
- model (
cobrame.core.model.MEModel
) – ME-model that the GenericData is associated with - component_list (list) – List of metabolite ids for all metabolites that can provide identical functionality
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class
cobrame.core.processdata.
PostTranslationData
(id, model, processed_protein, preprocessed_protein)[source]¶ Bases:
cobrame.core.processdata.ProcessData
Parameters: - id (str) – Identifier for post translation process.
- model (
cobrame.core.model.MEModel
) – ME-model that the PostTranslationData is associated with - processed_protein (str) – ID of protein following post translational process
- preprocessed_protein (str) – ID of protein before post translational process
-
translocation
¶ set – Translocation pathways involved in post translation reaction.
Set of {
cobrame.core.processdata.TranslocationData.id
}
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translocation_multipliers
¶ dict – Some proteins require different coupling of translocation enzymes.
Dictionary of {
cobrame.core.processdata.TranslocationData.id
: float}
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surface_area
¶ dict – If protein is translated into the inner or outer membrane, the surface area the protein occupies can be accounted for as well.
Dictionary of {SA_+<inner_membrane or outer_membrane>: float}
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subreactions
¶ collections.DefaultDict(float)
– If a protein is modified following translation, this is accounted for hereDictionary of {subreaction_id: float}
-
biomass_type
¶ str – If the subreactions add biomass to the translated gene, the biomass type (
cobrame.core.compontent.Constraint.id
) of the modification must be defined.
-
folding_mechanism
¶ str – ID of folding mechanism for post translation reaction
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aggregation_propensity
¶ float – Aggregation propensity for the protein
-
keq_folding
¶ dict – Temperature dependant keq for folding protein
Dictionary of {str(temperature): value}
-
k_folding
¶ dict – Temperature dependant rate constant (k) for folding protein
Dictionary of {str(temperature): value}
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propensity_scaling
¶ float – Some small peptides are more likely to be folded by certain chaperones. This is accounted for using propensity_scaling.
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class
cobrame.core.processdata.
ProcessData
(id, model)[source]¶ Bases:
object
Generic class for storing information about a process
This class essentially acts as a database that contains all of the relevant information needed to construct a particular reaction. For example, to construct a transcription reaction, following information must be accessed in some way:
- nucleotide sequence of the transcription unit
- RNA_polymerase (w/ sigma factor)
- RNAs transcribed from transcription unit
- other processes involved in transcription of RNAs (splicing, etc.)
ME-model reactions are built from information in these objects.
Parameters: - id (str) – Identifier of the ProcessData instance.
- model (
cobrame.core.model.MEModel
) – ME-model that the ProcessData is associated with
-
model
¶ Get the ME-model the process data is associated with
Returns: ME-model that uses this process data Return type: class:`cobrame.core.model.MEModel
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class
cobrame.core.processdata.
StoichiometricData
(id, model)[source]¶ Bases:
cobrame.core.processdata.ProcessData
Encodes the stoichiometry for a metabolic reaction.
StoichiometricData defines the metabolite stoichiometry and upper/lower bounds of metabolic reaction
Parameters: - id (str) – Identifier of the metabolic reaction. Should be identical to the M-model reactions in most cases.
- model (
cobrame.core.model.MEModel
) – ME-model that the StoichiometricData is associated with
-
_stoichiometry
¶ dict – Dictionary of {metabolite_id: stoichiometry} for reaction
-
subreactions
¶ collections.DefaultDict(int)
– Cases where multiple enzymes (often carriers ie. Acyl Carrier Protein) are involved in a metabolic reactions.
-
upper_bound
¶ int – Upper reaction bound of metabolic reaction. Should be identical to the M-model reactions in most cases.
-
lower_bound
¶ int – Lower reaction bound of metabolic reaction. Should be identical to the M-model reactions in most cases.
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class
cobrame.core.processdata.
SubreactionData
(id, model)[source]¶ Bases:
cobrame.core.processdata.ProcessData
Parameters: - id (str) – Identifier of the subreaction data. As a best practice, if the subreaction data details a modification, the ID should be prefixed with “mod + _”
- model (
cobrame.core.model.MEModel
) – ME-model that the SubreactionData is associated with
-
enzyme
¶ list or str or None – List of
cobrame.core.component.Complex.id
s for enzymes that catalyze this processor
String of single
cobrame.core.component.Complex.id
for enzyme that catalyzes this process
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keff
¶ float – Effective turnover rate of enzyme(s) in subreaction process
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_element_contribution
¶ dict – If subreaction adds a chemical moiety to a macromolecules via a modification or other means, net element contribution of the modification process should be accounted for. This can be used to mass balance check each of the individual processes.
Dictionary of {element: net_number_of_contributions}
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calculate_biomass_contribution
()[source]¶ Calculate net biomass increase/decrease as a result of the subreaction process.
If subreaction adds a chemical moiety to a macromolecules via a modification or other means, the biomass contribution of the modification process should be accounted for and ultimately included in the reaction it is involved in.
Returns: Mass of moiety transferred to macromolecule by subreaction Return type: float
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calculate_element_contribution
()[source]¶ Calculate net contribution of chemical elements based on the stoichiometry of the subreaction data
Returns: Dictionary of {element: net_number_of_contributions} Return type: dict
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element_contribution
¶ Get net contribution of elements from subreaction process to macromolecule
If subreaction adds a chemical moiety to a macromolecules via a modification or other means, net element contribution of the modification process should be accounted for. This can be used to mass balance check each of the individual processes.
Returns: Dictionary of {element: net_number_of_contributions} Return type: dict
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get_all_usages
()[source]¶ Get all process data that the subreaction is involved in
Yields: cobrame.core.processdata.ProcessData
– ProcessData that subreaction is involved in
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get_complex_data
()[source]¶ Get the complex data that the subreaction is involved in
Yields: cobrame.core.processdata.ComplexData
– ComplexData that subreaction is involved in
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class
cobrame.core.processdata.
TranscriptionData
(id, model, rna_products=set([]))[source]¶ Bases:
cobrame.core.processdata.ProcessData
Class for storing information needed to define a transcription reaction
Parameters: - id (str) – Identifier of the transcription unit, typically beginning with ‘TU’
- model (
cobrame.core.model.MEModel
) – ME-model that the TranscriptionData is associated with
-
nucleotide_sequence
¶ str – String of base pair abbreviations for nucleotides contained in the transcription unit
-
RNA_products
¶ set – IDs of
cobrame.core.component.TranscribedGene
that the transcription unit encodes. Each member should be prefixed with “RNA + _”
-
RNA_polymerase
¶ str – ID of the
cobrame.core.component.RNAP
that transcribes the transcription unit. Different IDs are used for different sigma factors
-
subreactions
¶ collections.DefaultDict(int)
– Dictionary of {cobrame.core.processdata.SubreactionData
ID: num_usages} required for the transcription unit to be transcribed
-
RNA_types
¶ Get generator consisting of the RNA type for each RNA product
Yields: str – (mRNA, tRNA, rRNA, ncRNA)
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codes_stable_rna
¶ Get whether transcription unit codes for a stable RNA
Returns: True if tRNA or rRNA in RNA products False if not Return type: bool
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excised_bases
¶ Get count of bases that are excised during transcription
If a stable RNA (e.g. tRNA or rRNA) is coded for in the transcription unit, the transcript must be spliced in order for these to function.
This determines whether the transcription unit requires splicing and, if so, returns the count of nucleotides within the transcription unit that are not accounted for in the RNA products, thus identifying the appropriate introns nucleotides.
Returns: {nucleotide_monophosphate_id: number_excised} i.e. {“amp_c”: 10, “gmp_c”: 11, “ump_c”: 9, “cmp_c”: 11}
Return type: dict
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class
cobrame.core.processdata.
TranslationData
(id, model, mrna, protein)[source]¶ Bases:
cobrame.core.processdata.ProcessData
Class for storing information about a translation reaction.
Parameters: - id (str) – Identifier of the gene being translated, typically the locus tag
- model (
cobrame.core.model.MEModel
) – ME-model that the TranslationData is associated with - mrna (str) – ID of the mRNA that is being translated
- protein (str) – ID of the protein product.
-
mRNA
¶ str – ID of the mRNA that is being translated
-
protein
¶ str – ID of the protein product.
-
subreactions
¶ collections.DefaultDict(int)
– Dictionary of {cobrame.core.processdata.SubreactionData.id
: num_usages} required for the mRNA to be translated
-
nucleotide_sequence
¶ str – String of base pair abbreviations for nucleotides contained in the gene being translated
-
add_elongation_subreactions
(elongation_subreactions=set([]))[source]¶ Add all subreactions involved in translation elongation.
This includes:
- tRNA activity subreactions returned with
subreactions_from_sequence()
which is called within this function. - Elongation subreactions passed into this function. These will be added with a value of len(amino_acid_sequence) - 1 as these are involved in each amino acid addition
Some additional enzymatic processes are required for each amino acid addition during translation elongation
Parameters: elongation_subreactions (set) – Subreactions that are required for each amino acid addition - tRNA activity subreactions returned with
-
add_initiation_subreactions
(start_codons=set([]), start_subreactions=set([]))[source]¶ Add all subreactions involved in translation initiation.
Parameters:
-
add_termination_subreactions
(translation_terminator_dict=None)[source]¶ Add all subreactions involved in translation termination.
Parameters: translation_terminator_dict (dict or None) – {stop_codon : enzyme_id_of_terminator_enzyme}
-
amino_acid_count
¶ Get number of each amino acid in the translated protein
Returns: {amino_acid_id: number_of_occurrences} Return type: dict
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amino_acid_sequence
¶ Get amino acid sequence from mRNA’s nucleotide sequence
Returns: Amino acid sequence Return type: str
-
codon_count
¶ Get the number of each codon contained within the gene sequence
Returns: {codon_sequence: number_of_occurrences} Return type: dict
-
first_codon
¶ Get the first codon contained in the mRNA sequence. This should correspond to the start codon for the gene.
Returns: First 3 nucleotides comprising the first codon in the mRNA gene sequence Return type: str
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last_codon
¶ Get the last codon contained in the mRNA sequence. This should correspond to the stop codon for the gene.
Returns: Last 3 nucleotides comprising the last codon in the mRNA gene sequence Return type: str
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subreactions_from_sequence
¶ Get subreactions associated with each tRNA/AA addition.
tRNA activity is accounted for as subreactions. This returns the subreaction counts associated with each amino acid addition, based on the sequence of the mRNA.
Returns: { cobrame.core.processdata.SubreactionData.id
: num_usages}Return type: dict
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class
cobrame.core.processdata.
TranslocationData
(id, model)[source]¶ Bases:
cobrame.core.processdata.ProcessData
Class for storing information about a protein translocation pathway
Parameters: - id (str) – Identifier for translocation pathway.
- model (
cobrame.core.model.MEModel
) – ME-model that the TranslocationData is associated with
-
keff
¶ float – Effective turnover rate of the enzymes in the translocation pathway
-
enzyme_dict
¶ dict – Dictionary containing enzyme specific information about the way it is coupled to protein translocation
- {enzyme_id: {length_dependent: <True or False>,
- fixed_keff: <True or False>}}
-
length_dependent_energy
¶ bool – True if the ATP cost of translocation is dependent on the length of the protein
-
stoichiometry
¶ dict – Stoichiometry of translocation pathway, typically ATP/GTP hydrolysis
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class
cobrame.core.processdata.
tRNAData
(id, model, amino_acid, rna, codon)[source]¶ Bases:
cobrame.core.processdata.ProcessData
Class for storing information about a tRNA charging reaction.
Parameters: - id (str) – Identifier for tRNA charging process. As best practice, this should be follow “tRNA + _ + <tRNA_locus> + _ + <codon>” template. If tRNA initiates translation, <codon> should be replaced with START.
- model (
cobrame.core.model.MEModel
) – ME-model that the tRNAData is associated with - amino_acid (str) – Amino acid that the tRNA transfers to an peptide
- rna (str) – ID of the uncharged tRNA metabolite. As a best practice, this ID should be prefixed with ‘RNA + _’
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subreactions
¶ collections.DefaultDict(int)
– Dictionary of {cobrame.core.processdata.SubreactionData.id
: num_usages} required for the tRNA to be charged
-
synthetase
¶ str – ID of the tRNA synthetase required to charge the tRNA with an amino acid
-
synthetase_keff
¶ float – Effective turnover rate of the tRNA synthetase
7.1.1.4. cobrame.core.component module¶
-
class
cobrame.core.component.
Complex
(id)[source]¶ Bases:
cobrame.core.component.MEComponent
Metabolite class for protein complexes
Parameters: id (str) – Identifier of the protein complex. -
metabolic_reactions
¶ Get metabolic reactions catalyzed by complex
Returns: List of cobrame.core.reaction.MetabolicReaction
s catalyzed by complex.Return type: list
-
-
class
cobrame.core.component.
Constraint
(id)[source]¶ Bases:
cobrame.core.component.MEComponent
Metabolite class for global constraints such as biomass
Parameters: id (str) – Identifier of the constraint
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class
cobrame.core.component.
GenericComponent
(id)[source]¶ Bases:
cobrame.core.component.MEComponent
Metabolite class for generic components created from
cobrame.core.reaction.GenericFormationReaction
Parameters: id (str) – Identifier of the generic tRNA. As a best practice should follow template: ‘generic + _ + <generic metabolite id>’
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class
cobrame.core.component.
GenerictRNA
(id)[source]¶ Bases:
cobrame.core.component.MEComponent
Metabolite class for generic tRNAs created from
cobrame.core.reaction.tRNAChargingReaction
Parameters: id (str) – Identifier of the generic tRNA. As a best practice should follow template: ‘generic_tRNA + _ + <codon> + _ + <amino acid metabolite id>’
-
class
cobrame.core.component.
MEComponent
(id)[source]¶ Bases:
cobra.core.Metabolite.Metabolite
COBRAme component representation. Inherits from
cobra.core.metabolite.Metabolite
Parameters: id (str) – Identifier of the component. Should follow best practices of child classes -
remove_from_me_model
(method='subtractive')[source]¶ Remove metabolite from me model along with any relevant
cobrame.core.processdata.ProcessData
Parameters: method (str) – - destructive: remove metabolite from model and remove reactions it is involved in
- subtractive: remove only metabolite from model
-
-
class
cobrame.core.component.
Metabolite
(id)[source]¶ Bases:
cobrame.core.component.MEComponent
COBRAme metabolite representation
Parameters: id (str) – Identifier of the metabolite
-
class
cobrame.core.component.
ProcessedProtein
(id, unprocessed_protein_id)[source]¶ Bases:
cobrame.core.component.MEComponent
Metabolite class for protein created from
cobrame.core.reaction.PostTranslationReaction
Parameters: -
unprocessed_protein
¶ Get unprocessed protein reactant in PostTranslationReaction
Returns: Unprocessed protein object Return type: cobrame.core.component.TranslatedGene
-
-
class
cobrame.core.component.
RNAP
(id)[source]¶ Bases:
cobrame.core.component.Complex
Metabolite class for RNA polymerase complexes. Inherits from
cobrame.core.component.Complex
Parameters: id (str) – Identifier of the RNA Polymerase.
-
class
cobrame.core.component.
Ribosome
(id)[source]¶ Bases:
cobrame.core.component.Complex
Metabolite class for Ribosome complexes. Inherits from
cobrame.core.component.Complex
Parameters: id (str) – Identifier of the Ribosome.
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class
cobrame.core.component.
TranscribedGene
(id, rna_type, nucleotide_sequence)[source]¶ Bases:
cobrame.core.component.MEComponent
Metabolite class for gene created from
cobrame.core.reaction.TranscriptionReaction
Parameters: -
left_pos
¶ int – Left position of gene on the sequence of the (+) strain
-
right_pos
¶ int – Right position of gene on the sequence of the (+) strain
-
strand
¶ str –
- (+) if the RNA product is on the leading strand
- (-) if the RNA product is on the comple(mentary strand
-
-
class
cobrame.core.component.
TranslatedGene
(id)[source]¶ Bases:
cobrame.core.component.MEComponent
Metabolite class for protein created from
cobrame.core.reaction.TranslationReaction
Parameters: id (str) – Identifier of the translated protein product. Should be prefixed with “protein + _” -
amino_acid_sequence
¶ Get amino acid sequence of protein
Returns: Amino acid sequence of protein Return type: str
-
complexes
¶ Get the complexes that the protein forms
Returns: List of cobrame.core.component.Complex
s that the protein is a subunit ofReturn type: list
-
metabolic_reactions
¶ Get the mtabolic reactions that the protein helps catalyze
Returns: List of cobrame.core.reactions.MetabolicReaction
s that the protein helps catalyzeReturn type: list
-
translation_data
¶ Get translation data that defines protein.
Assumes that TranslatedGene is “protein + _ + <translation data id>”
Returns: Translation data used to form translation reaction of protein Return type: cobrame.core.processdata.TranslationData
-
7.1.1.5. cobra.core.model module¶
-
class
cobrame.core.model.
MEModel
(*args)[source]¶ Bases:
cobra.core.Model.Model
-
complex_data
¶
-
construct_attribute_vector
(attr_name, growth_rate)[source]¶ build a vector of a reaction attribute at a specific growth rate
Mainly used for upper and lower bounds
-
gam
¶
-
generic_data
¶
-
ngam
¶
-
posttranslation_data
¶
-
prune
(skip=None)[source]¶ remove all unused metabolites and reactions
This should be run after the model is fully built. It will be difficult to add new content to the model once this has been run.
- skip: list
- List of complexes/proteins/mRNAs/TUs to remain unpruned from model.
-
stoichiometric_data
¶
-
subreaction_data
¶
-
tRNA_data
¶
-
transcription_data
¶
-
translation_data
¶
-
translocation_data
¶
-
unmodeled_protein
¶
-
unmodeled_protein_biomass
¶
-
unmodeled_protein_fraction
¶
-