COBRAme
v0.0.7
1. ME-model Fundamentals
2. COBRAme Software Architecture
3. Building a ME-model
4. Reaction Properties
5. ME-model Saving and Loading
6. 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)
,
[1]
_stoichiometry (cobrame.core.processdata.StoichiometricData attribute)
,
[1]
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)
,
[1]
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)
,
[1]
(cobrame.MetabolicReaction attribute)
(cobrame.core.processdata.TranslocationData attribute)
(cobrame.core.reaction.MetabolicReaction attribute)
,
[1]
keq_folding (cobrame.core.processdata.PostTranslationData attribute)
L
last_codon (cobrame.core.processdata.TranslationData attribute)
left_pos (cobrame.core.component.TranscribedGene attribute)
,
[1]
length_dependent_energy (cobrame.core.processdata.TranslocationData attribute)
lower_bound (cobrame.core.processdata.StoichiometricData attribute)
,
[1]
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)
,
[1]
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)
,
[1]
(cobrame.core.processdata.TranslationData attribute)
,
[1]
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)
,
[1]
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)
,
[1]
(cobrame.MetabolicReaction attribute)
reverse_transcribe() (in module cobrame.util.dogma)
Ribosome (class in cobrame.core.component)
right_pos (cobrame.core.component.TranscribedGene attribute)
,
[1]
RNA_polymerase (cobrame.core.processdata.TranscriptionData attribute)
,
[1]
RNA_products (cobrame.core.processdata.TranscriptionData attribute)
,
[1]
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)
,
[1]
(cobrame.core.processdata.StoichiometricData attribute)
(cobrame.core.processdata.TranslocationData attribute)
strand (cobrame.core.component.TranscribedGene attribute)
,
[1]
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)
,
[1]
(cobrame.core.processdata.PostTranslationData attribute)
(cobrame.core.processdata.StoichiometricData attribute)
,
[1]
(cobrame.core.processdata.TranscriptionData attribute)
,
[1]
(cobrame.core.processdata.TranslationData attribute)
,
[1]
(cobrame.core.processdata.tRNAData attribute)
,
[1]
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)
,
[1]
synthetase_keff (cobrame.core.processdata.tRNAData attribute)
,
[1]
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)
,
[1]
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