COBRAme
v0.0.6
1. ME-Model Fundamentals
2. ME-Model Architecture
3. Building a ME-Model
4. Reaction Properties
5. cobrame package
COBRAme
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Index
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A
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B
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C
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E
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F
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G
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K
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L
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M
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N
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O
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P
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R
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S
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T
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U
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_complex_id (cobrame.core.reaction.ComplexFormation attribute)
_element_contribution (cobrame.core.processdata.SubreactionData attribute)
(SubreactionData attribute)
_stoichiometry (cobrame.core.processdata.StoichiometricData attribute)
(StoichiometricData attribute)
A
add_biomass_constraints_to_model() (cobrame.core.model.MEModel method)
add_biomass_from_subreactions() (cobrame.core.reaction.MEReaction method)
(cobrame.MEReaction method)
add_complex_to_model() (in module cobrame.util.building)
add_dummy_reactions() (in module cobrame.util.building)
add_elongation_subreactions() (cobrame.core.processdata.TranslationData method)
add_initiation_subreactions() (cobrame.core.processdata.TranslationData method)
add_m_model_content() (in module cobrame.util.building)
add_metabolic_reaction_to_model() (in module cobrame.util.building)
add_model_complexes() (in module cobrame.util.building)
add_reactions_from_stoichiometric_data() (in module cobrame.util.building)
add_subreaction_data() (in module cobrame.util.building)
add_subreactions() (cobrame.core.reaction.MEReaction method)
(cobrame.MEReaction method)
add_termination_subreactions() (cobrame.core.processdata.TranslationData method)
add_transcription_reaction() (in module cobrame.util.building)
add_translation_reaction() (in module cobrame.util.building)
add_translocation_pathways() (cobrame.core.reaction.PostTranslationReaction method)
aggregation_propensity (cobrame.core.processdata.PostTranslationData attribute)
amino_acid_count (cobrame.core.processdata.TranslationData attribute)
amino_acid_sequence (cobrame.core.component.TranslatedGene attribute)
(cobrame.core.processdata.TranslationData attribute)
B
biomass_type (cobrame.core.processdata.PostTranslationData attribute)
build_reactions_from_genbank() (in module cobrame.util.building)
C
calculate_biomass_contribution() (cobrame.core.processdata.SubreactionData method)
calculate_element_contribution() (cobrame.core.processdata.SubreactionData method)
check_me_mass_balance() (cobrame.core.reaction.MEReaction method)
(cobrame.MEReaction method)
check_me_model_mass_balance() (in module cobrame.util.massbalance)
check_transcription_mass_balance() (in module cobrame.util.massbalance)
clear_metabolites() (cobrame.core.reaction.MEReaction method)
(cobrame.MEReaction method)
cobrame (module)
,
[1]
cobrame.core (module)
cobrame.core.component (module)
cobrame.core.model (module)
cobrame.core.processdata (module)
cobrame.core.reaction (module)
cobrame.util (module)
cobrame.util.building (module)
cobrame.util.dogma (module)
cobrame.util.mass (module)
cobrame.util.massbalance (module)
codes_stable_rna (cobrame.core.processdata.TranscriptionData attribute)
codon_count (cobrame.core.processdata.TranslationData attribute)
Complex (class in cobrame.core.component)
complex (cobrame.core.processdata.ComplexData attribute)
(cobrame.core.reaction.ComplexFormation attribute)
complex_data (cobrame.core.model.MEModel attribute)
(cobrame.core.reaction.MetabolicReaction attribute)
complex_data_id (cobrame.core.reaction.ComplexFormation attribute)
complex_id (cobrame.core.processdata.ComplexData attribute)
ComplexData (class in cobrame.core.processdata)
complexes (cobrame.core.component.TranslatedGene attribute)
ComplexFormation (class in cobrame.core.reaction)
compute_protein_mass() (in module cobrame.util.mass)
compute_rna_mass() (in module cobrame.util.mass)
compute_solution_error() (cobrame.core.model.MEModel method)
Constraint (class in cobrame.core.component)
construct_attribute_vector() (cobrame.core.model.MEModel method)
construct_s_matrix() (cobrame.core.model.MEModel method)
convert_aa_codes_and_add_charging() (in module cobrame.util.building)
create_complex_formation() (cobrame.core.processdata.ComplexData method)
create_component() (in module cobrame.core.component)
create_reactions() (cobrame.core.processdata.GenericData method)
create_transcribed_gene() (in module cobrame.util.building)
E
element_contribution (cobrame.core.processdata.SubreactionData attribute)
elements_to_formula() (in module cobrame.util.massbalance)
enzyme (cobrame.core.processdata.SubreactionData attribute)
(SubreactionData attribute)
enzyme_dict (cobrame.core.processdata.TranslocationData attribute)
eval_reaction_at_growth_rate() (in module cobrame.util.massbalance)
excised_bases (cobrame.core.processdata.TranscriptionData attribute)
extract_sequence() (in module cobrame.util.dogma)
F
first_codon (cobrame.core.processdata.TranslationData attribute)
folding_mechanism (cobrame.core.processdata.PostTranslationData attribute)
formation (cobrame.core.processdata.ComplexData attribute)
G
gam (cobrame.core.model.MEModel attribute)
generic_data (cobrame.core.model.MEModel attribute)
GenericComponent (class in cobrame.core.component)
GenericData (class in cobrame.core.processdata)
GenericFormationReaction (class in cobrame.core.reaction)
GenerictRNA (class in cobrame.core.component)
get_all_usages() (cobrame.core.processdata.SubreactionData method)
get_amino_acid_sequence_from_dna() (in module cobrame.util.dogma)
get_complex_data() (cobrame.core.processdata.SubreactionData method)
get_components_from_ids() (cobrame.core.reaction.MEReaction method)
(cobrame.MEReaction method)
get_elements_from_process_data() (in module cobrame.util.massbalance)
get_metabolic_flux() (cobrame.core.model.MEModel method)
get_transcription_flux() (cobrame.core.model.MEModel method)
get_translation_flux() (cobrame.core.model.MEModel method)
K
k_folding (cobrame.core.processdata.PostTranslationData attribute)
keff (cobrame.core.processdata.SubreactionData attribute)
(MetabolicReaction attribute)
(SubreactionData attribute)
(cobrame.MetabolicReaction attribute)
(cobrame.core.processdata.TranslocationData attribute)
(cobrame.core.reaction.MetabolicReaction attribute)
keq_folding (cobrame.core.processdata.PostTranslationData attribute)
L
last_codon (cobrame.core.processdata.TranslationData attribute)
left_pos (cobrame.core.component.TranscribedGene attribute)
(TranscribedGene attribute)
length_dependent_energy (cobrame.core.processdata.TranslocationData attribute)
lower_bound (cobrame.core.processdata.StoichiometricData attribute)
(StoichiometricData attribute)
M
mass (cobrame.core.component.Complex attribute)
(cobrame.core.component.TranscribedGene attribute)
(cobrame.core.component.TranslatedGene attribute)
(cobrame.core.processdata.TranscriptionData attribute)
(cobrame.core.processdata.TranslationData attribute)
MEComponent (class in cobrame.core.component)
MEModel (class in cobrame.core.model)
MEReaction (class in cobrame)
(class in cobrame.core.reaction)
metabolic_reactions (cobrame.core.component.Complex attribute)
(cobrame.core.component.TranslatedGene attribute)
MetabolicReaction (class in cobrame)
(class in cobrame.core.reaction)
Metabolite (class in cobrame.core.component)
model (cobrame.core.processdata.ProcessData attribute)
mRNA (cobrame.core.processdata.TranslationData attribute)
(TranslationData attribute)
N
ngam (cobrame.core.model.MEModel attribute)
nucleotide_count (cobrame.core.component.TranscribedGene attribute)
(cobrame.core.processdata.TranscriptionData attribute)
nucleotide_sequence (cobrame.core.processdata.TranscriptionData attribute)
(TranscriptionData attribute)
(TranslationData attribute)
(cobrame.core.processdata.TranslationData attribute)
O
objective_coefficient (cobrame.core.reaction.MEReaction attribute)
(cobrame.MEReaction attribute)
P
parent_reactions (cobrame.core.processdata.ProcessData attribute)
posttranslation_data (cobrame.core.model.MEModel attribute)
(cobrame.core.reaction.PostTranslationReaction attribute)
PostTranslationData (class in cobrame.core.processdata)
PostTranslationReaction (class in cobrame.core.reaction)
ProcessData (class in cobrame.core.processdata)
ProcessedProtein (class in cobrame.core.component)
propensity_scaling (cobrame.core.processdata.PostTranslationData attribute)
protein (cobrame.core.processdata.TranslationData attribute)
(TranslationData attribute)
prune() (cobrame.core.model.MEModel method)
R
remove_from_me_model() (cobrame.core.component.MEComponent method)
remove_genes_from_model() (cobrame.core.model.MEModel method)
return_frameshift_sequence() (in module cobrame.util.dogma)
reverse (cobrame.core.reaction.MetabolicReaction attribute)
(MetabolicReaction attribute)
(cobrame.MetabolicReaction attribute)
reverse_transcribe() (in module cobrame.util.dogma)
Ribosome (class in cobrame.core.component)
right_pos (cobrame.core.component.TranscribedGene attribute)
(TranscribedGene attribute)
RNA_polymerase (cobrame.core.processdata.TranscriptionData attribute)
(TranscriptionData attribute)
RNA_products (cobrame.core.processdata.TranscriptionData attribute)
(TranscriptionData attribute)
RNA_types (cobrame.core.processdata.TranscriptionData attribute)
RNAP (class in cobrame.core.component)
S
set_sasa_keffs() (cobrame.core.model.MEModel method)
stoichiometric_data (cobrame.core.model.MEModel attribute)
(cobrame.core.reaction.MetabolicReaction attribute)
StoichiometricData (class in cobrame.core.processdata)
stoichiometry (cobrame.core.processdata.ComplexData attribute)
(ComplexData attribute)
(cobrame.core.processdata.StoichiometricData attribute)
(cobrame.core.processdata.TranslocationData attribute)
strand (cobrame.core.component.TranscribedGene attribute)
(TranscribedGene attribute)
stringify() (in module cobrame.util.massbalance)
subreaction_data (cobrame.core.model.MEModel attribute)
SubreactionData (class in cobrame.core.processdata)
subreactions (cobrame.core.processdata.ComplexData attribute)
(ComplexData attribute)
(StoichiometricData attribute)
(TranscriptionData attribute)
(TranslationData attribute)
(cobrame.core.processdata.PostTranslationData attribute)
(cobrame.core.processdata.StoichiometricData attribute)
(cobrame.core.processdata.TranscriptionData attribute)
(cobrame.core.processdata.TranslationData attribute)
(cobrame.core.processdata.tRNAData attribute)
(tRNAData attribute)
subreactions_from_sequence (cobrame.core.processdata.TranslationData attribute)
SummaryVariable (class in cobrame.core.reaction)
surface_area (cobrame.core.processdata.PostTranslationData attribute)
synthetase (cobrame.core.processdata.tRNAData attribute)
(tRNAData attribute)
synthetase_keff (cobrame.core.processdata.tRNAData attribute)
(tRNAData attribute)
T
TranscribedGene (class in cobrame.core.component)
transcription_data (cobrame.core.model.MEModel attribute)
(cobrame.core.reaction.TranscriptionReaction attribute)
TranscriptionData (class in cobrame.core.processdata)
TranscriptionReaction (class in cobrame.core.reaction)
TranslatedGene (class in cobrame.core.component)
translation_data (cobrame.core.component.TranslatedGene attribute)
(cobrame.core.model.MEModel attribute)
(cobrame.core.reaction.TranslationReaction attribute)
TranslationData (class in cobrame.core.processdata)
TranslationReaction (class in cobrame.core.reaction)
translocation (cobrame.core.processdata.PostTranslationData attribute)
translocation_data (cobrame.core.model.MEModel attribute)
translocation_multipliers (cobrame.core.processdata.PostTranslationData attribute)
TranslocationData (class in cobrame.core.processdata)
tRNA_data (cobrame.core.model.MEModel attribute)
(cobrame.core.reaction.tRNAChargingReaction attribute)
tRNAChargingReaction (class in cobrame.core.reaction)
tRNAData (class in cobrame.core.processdata)
U
unmodeled_protein (cobrame.core.model.MEModel attribute)
unmodeled_protein_biomass (cobrame.core.model.MEModel attribute)
unmodeled_protein_fraction (cobrame.core.model.MEModel attribute)
unprocessed_protein (cobrame.core.component.ProcessedProtein attribute)
unprocessed_protein_mass (cobrame.core.component.ProcessedProtein attribute)
update() (cobrame.core.model.MEModel method)
(cobrame.core.reaction.ComplexFormation method)
(cobrame.core.reaction.MetabolicReaction method)
(cobrame.core.reaction.PostTranslationReaction method)
(cobrame.core.reaction.TranscriptionReaction method)
(cobrame.core.reaction.TranslationReaction method)
(cobrame.core.reaction.tRNAChargingReaction method)
update_parent_reactions() (cobrame.core.processdata.ProcessData method)
upper_bound (cobrame.core.processdata.StoichiometricData attribute)
(StoichiometricData attribute)
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