pytfa
dev
Contents:
1. Quick start
2. pyTFA models
3. Thermodynamic Databases
4. Solver setup
5. Integrating metabolomics
6. API Reference
pytfa
Docs
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Index
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Index
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A
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B
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C
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D
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E
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F
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G
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I
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J
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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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V
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W
_
__add__() (pytfa.GenericVariable method)
(pytfa.optim.GenericVariable method)
,
[1]
__attrname__() (pytfa.GenericConstraint property)
(pytfa.GenericVariable property)
(pytfa.optim.GenericConstraint property)
,
[1]
(pytfa.optim.GenericVariable property)
,
[1]
__cmp__() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
__contains__() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
__deepcopy__() (pytfa.thermo.ThermoModel method)
(pytfa.ThermoModel method)
,
[1]
__getitem__() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
__iter__() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
__mul__() (pytfa.GenericVariable method)
(pytfa.optim.GenericVariable method)
,
[1]
__radd__() (pytfa.GenericVariable method)
(pytfa.optim.GenericVariable method)
,
[1]
__repr__() (pytfa.GenericConstraint method)
(pytfa.GenericVariable method)
(pytfa.MetaboliteThermo method)
(pytfa.optim.GenericConstraint method)
,
[1]
(pytfa.optim.GenericVariable method)
,
[1]
(pytfa.thermo.MetaboliteThermo method)
,
[1]
__rmul__() (pytfa.GenericVariable method)
(pytfa.optim.GenericVariable method)
,
[1]
__rsub__() (pytfa.GenericVariable method)
(pytfa.optim.GenericVariable method)
,
[1]
__rtruediv__() (pytfa.GenericVariable method)
(pytfa.optim.GenericVariable method)
,
[1]
__sub__() (pytfa.GenericVariable method)
(pytfa.optim.GenericVariable method)
,
[1]
__truediv__() (pytfa.GenericVariable method)
(pytfa.optim.GenericVariable method)
,
[1]
__unicode__() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
_bool2str() (in module pytfa)
(in module pytfa.analysis)
_build_lump() (pytfa.redgem.lumpgem.LumpGEM method)
_calc_pka() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
_convert_metabolite() (pytfa.thermo.ThermoModel method)
(pytfa.ThermoModel method)
,
[1]
_convert_reaction() (pytfa.thermo.ThermoModel method)
(pytfa.ThermoModel method)
,
[1]
_extract_inorganics() (redgem.RedGEM method)
_generate_objective() (pytfa.redgem.lumpgem.LumpGEM method)
_generate_usage_constraints() (pytfa.redgem.lumpgem.LumpGEM method)
_init_thermo() (pytfa.thermo.ThermoModel method)
(pytfa.ThermoModel method)
,
[1]
_lump_min_plus_p() (pytfa.redgem.lumpgem.LumpGEM method)
_lump_one_per_bbb() (pytfa.redgem.lumpgem.LumpGEM method)
_prepare_metabolite() (pytfa.thermo.ThermoModel method)
(pytfa.ThermoModel method)
,
[1]
_prepare_reaction() (pytfa.thermo.ThermoModel method)
(pytfa.ThermoModel method)
,
[1]
_prepare_sinks() (pytfa.redgem.lumpgem.LumpGEM method)
_push_queue() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
_remove_associated_consvar() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
_variability_analysis_element() (in module pytfa)
(in module pytfa.analysis)
A
A_COUPLE (in module pytfa.thermo.std)
A_LITTLE (in module pytfa.thermo.std)
A_LOT (in module pytfa.thermo.std)
ABCRequirePrefixMeta (in module pytfa)
(in module pytfa.optim)
,
[1]
add_BBB_sinks() (in module redgem)
add_constraint() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
add_lump() (in module redgem)
add_variable() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
annotate_from_lexicon() (in module pytfa)
(in module pytfa.io)
apply_compartment_data() (in module pytfa)
(in module pytfa.io)
apply_directionality() (in module pytfa.analysis)
(in module pytfa.analysis.manipulation)
apply_generic_variability() (in module pytfa.analysis)
(in module pytfa.analysis.manipulation)
apply_reaction_variability() (in module pytfa.analysis)
(in module pytfa.analysis.manipulation)
B
BackwardDeltaGCoupling (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
BackwardDirectionCoupling (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
BackwardUseVariable (class in pytfa)
(class in pytfa.optim)
,
[1]
(class in pytfa.thermo)
BEST_THREAD_RATIO (in module pytfa)
(in module pytfa.analysis)
BIGM (in module pytfa)
,
[1]
,
[2]
(in module pytfa.optim)
(in module pytfa.thermo)
(in module pytfa.utils.numerics)
BIGM_DG (in module pytfa)
,
[1]
(in module pytfa.io)
(in module pytfa.optim)
(in module pytfa.thermo)
(in module pytfa.utils.numerics)
BIGM_P (in module pytfa)
,
[1]
(in module pytfa.optim)
(in module pytfa.thermo)
(in module pytfa.utils.numerics)
BIGM_THERMO (in module pytfa)
,
[1]
(in module pytfa.optim)
(in module pytfa.thermo)
(in module pytfa.utils.numerics)
BinaryVariable (class in pytfa)
(class in pytfa.optim)
breadth_search_extracellular_system_paths() (redgem.NetworkExpansion method)
breadth_search_subsystems_paths_length_d() (redgem.NetworkExpansion method)
build_thermo_from_equilibrator() (in module pytfa)
C
calc_potential() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
calcDGF_cues() (in module pytfa)
calcDGis() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
calcDGR_cues() (in module pytfa)
(in module pytfa.thermo)
calcDGsp() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
calcDGspA() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
calcDGtpt_rhs() (in module pytfa)
(in module pytfa.thermo)
calculate_dissipation() (in module pytfa)
(in module pytfa.analysis)
camel2underscores() (in module pytfa)
(in module pytfa.optim)
,
[1]
ccache (in module pytfa)
change_expr() (pytfa.GenericConstraint method)
(pytfa.optim.GenericConstraint method)
,
[1]
chebyshev_center() (in module pytfa)
chebyshev_transform() (in module pytfa)
ChebyshevRadius (class in pytfa)
check_BBB_production() (in module redgem)
check_json_extension() (in module pytfa)
check_reaction_balance() (in module pytfa)
(in module pytfa.thermo)
check_transport_reaction() (in module pytfa)
(in module pytfa.thermo)
chunk_sum() (in module pytfa)
(in module pytfa.optim)
,
[1]
compare_solutions() (in module pytfa)
(in module pytfa.optim)
compound_to_entry() (in module pytfa)
compute_dGf() (in module pytfa)
compute_lumps() (pytfa.redgem.lumpgem.LumpGEM method)
constraint() (pytfa.GenericConstraint property)
(pytfa.optim.GenericConstraint property)
,
[1]
ConstraintTuple (in module pytfa)
convert() (pytfa.thermo.ThermoModel method)
(pytfa.ThermoModel method)
,
[1]
copy() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
(pytfa.thermo.ThermoModel method)
(pytfa.ThermoModel method)
,
[1]
copy_solver_configuration() (in module pytfa)
(in module pytfa.optim)
CPD_PROTON (in module pytfa)
CPLEX (in module pytfa.redgem.lumpgem)
CPU_COUNT (in module pytfa)
(in module pytfa.analysis)
create_generalized_matrix() (in module pytfa)
(in module pytfa.io)
create_new_stoichiometric_matrix() (redgem.NetworkExpansion method)
create_problem_dict() (in module pytfa)
(in module pytfa.io)
create_thermo_dict() (in module pytfa)
(in module pytfa.io)
D
debug_iis() (in module pytfa)
DEBYE_HUCKEL_A (in module pytfa.thermo.std)
DEBYE_HUCKEL_B_0 (in module pytfa.thermo.std)
default() (pytfa.io.MyEncoder method)
(pytfa.MyEncoder method)
DEFAULT_EPS (in module pytfa.redgem.lumpgem)
DEFAULT_VAL (in module pytfa)
DeltaG (class in pytfa)
(class in pytfa.analysis)
(class in pytfa.optim)
(class in pytfa.thermo)
DeltaGErr (class in pytfa)
(class in pytfa.optim)
DeltaGFormstd (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
DeltaGstd (class in pytfa)
(class in pytfa.optim)
,
[1]
(class in pytfa.thermo)
dg_relax_config() (in module pytfa)
(in module pytfa.optim)
disambiguate (in module pytfa.redgem.lumpgem)
DisplacementCoupling (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
E
EPSILON (in module pytfa)
,
[1]
(in module pytfa.optim)
(in module pytfa.thermo)
(in module pytfa.utils.numerics)
evaluate_constraint_at_solution() (in module pytfa)
(in module pytfa.optim)
export_reactions_for_escher() (in module pytfa)
export_variable_for_escher() (in module pytfa)
expr() (pytfa.GenericConstraint property)
(pytfa.optim.GenericConstraint property)
,
[1]
extract_sub_network() (redgem.NetworkExpansion method)
extract_subsystem_metabolites() (redgem.NetworkExpansion method)
extract_subsystem_reactions() (redgem.NetworkExpansion method)
F
fill_default_params() (redgem.RedGEM method)
find_bidirectional_reactions() (in module pytfa)
(in module pytfa.analysis)
find_directionality_profiles() (in module pytfa)
(in module pytfa.analysis)
find_extreme_coeffs() (in module pytfa)
find_maxed_vars() (in module pytfa)
find_min_distance_between_subsystems() (redgem.NetworkExpansion method)
find_transported_mets() (in module pytfa)
(in module pytfa.thermo)
FluxKO (class in pytfa.redgem.lumpgem)
ForbiddenProfile (class in pytfa)
(class in pytfa.analysis)
(class in pytfa.optim)
Formula_regex (in module pytfa)
ForwardBackwardUseVariable (class in pytfa)
(class in pytfa.optim)
ForwardDeltaGCoupling (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
ForwardDirectionCoupling (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
ForwardUseVariable (class in pytfa)
(class in pytfa.analysis)
(class in pytfa.optim)
,
[1]
(class in pytfa.thermo)
from_constraints() (pytfa.LinearizationConstraint static method)
(pytfa.optim.LinearizationConstraint static method)
G
gene() (pytfa.GeneConstraint property)
(pytfa.GeneVariable property)
(pytfa.optim.GeneConstraint property)
(pytfa.optim.GeneVariable property)
GeneConstraint (class in pytfa)
(class in pytfa.optim)
GeneralizedACHRSampler (class in pytfa)
(class in pytfa.analysis)
GeneralizedHRSampler (class in pytfa)
(class in pytfa.analysis)
GeneralizedOptGPSampler (class in pytfa)
(class in pytfa.analysis)
generate_fva_warmup() (pytfa.analysis.GeneralizedHRSampler method)
(pytfa.GeneralizedHRSampler method)
GenericConstraint (class in pytfa)
(class in pytfa.optim)
,
[1]
GenericVariable (class in pytfa)
(class in pytfa.optim)
,
[1]
GeneVariable (class in pytfa)
(class in pytfa.optim)
get_active_use_variables() (in module pytfa)
(in module pytfa.analysis)
(in module pytfa.optim)
get_all_subclasses() (in module pytfa)
(in module pytfa.optim)
get_binary_type() (in module pytfa)
(in module pytfa.optim)
get_bistream_logger() (in module pytfa)
(in module pytfa.analysis)
(in module pytfa.thermo)
get_cofactor_adjusted_stoich() (pytfa.redgem.lumpgem.LumpGEM method)
get_cons_var_classes() (in module pytfa)
get_constraints_of_type() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
get_debye_huckel_b() (in module pytfa)
(in module pytfa.thermo)
get_direction_use_variables() (in module pytfa)
(in module pytfa.analysis)
(in module pytfa.optim)
get_interface() (pytfa.GenericConstraint method)
(pytfa.GenericVariable method)
(pytfa.optim.GenericConstraint method)
,
[1]
(pytfa.optim.GenericVariable method)
,
[1]
get_operand() (pytfa.GenericVariable method)
(pytfa.optim.GenericVariable method)
,
[1]
get_pka() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
get_primal() (in module pytfa)
(in module pytfa.optim)
(pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
get_reaction_compartment() (in module pytfa)
get_reaction_data() (in module pytfa)
get_solution() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
get_solution_value_for_variables() (in module pytfa)
(in module pytfa.optim)
,
[1]
get_timestr() (in module pytfa)
get_variables() (in module pytfa)
get_variables_of_type() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
glovers_linearization() (in module pytfa)
GLPK (in module pytfa.redgem.lumpgem)
GUROBI (in module pytfa.redgem.lumpgem)
I
id() (pytfa.GeneConstraint property)
(pytfa.GenericConstraint property)
(pytfa.GenericVariable property)
(pytfa.GeneVariable property)
(pytfa.MetaboliteConstraint property)
(pytfa.MetaboliteVariable property)
(pytfa.optim.GeneConstraint property)
(pytfa.optim.GenericConstraint property)
,
[1]
(pytfa.optim.GenericVariable property)
,
[1]
(pytfa.optim.GeneVariable property)
(pytfa.optim.MetaboliteConstraint property)
(pytfa.optim.MetaboliteVariable property)
(pytfa.optim.ReactionConstraint property)
(pytfa.optim.ReactionVariable property)
(pytfa.ReactionConstraint property)
(pytfa.ReactionVariable property)
(pytfa.thermo.MetaboliteConstraint property)
(pytfa.thermo.MetaboliteVariable property)
(pytfa.thermo.ReactionConstraint property)
(pytfa.thermo.ReactionVariable property)
import_matlab_model() (in module pytfa)
(in module pytfa.io)
InfeasibleExcept
init_params() (pytfa.redgem.lumpgem.LumpGEM method)
INTEGER_VARIABLE_TYPES (in module pytfa)
(in module pytfa.optim)
IntegerVariable (class in pytfa)
(class in pytfa.optim)
is_exchange() (in module pytfa)
is_inequality() (in module pytfa)
is_node_allowed() (redgem.NetworkExpansion method)
is_node_allowed_extracellular() (redgem.NetworkExpansion method)
is_same_stoichiometry() (in module pytfa)
items() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
J
json_dumps_model() (in module pytfa)
json_loads_model() (in module pytfa)
K
keys() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
L
LCSBModel (class in pytfa)
(class in pytfa.core)
(class in pytfa.thermo)
LinearizationConstraint (class in pytfa)
(class in pytfa.optim)
LinearizationVariable (class in pytfa)
(class in pytfa.optim)
linearize_product() (in module pytfa)
load_json_model() (in module pytfa)
load_thermoDB() (in module pytfa)
(in module pytfa.io)
LogConcentration (class in pytfa)
(class in pytfa.optim)
,
[1]
(class in pytfa.thermo)
LOGFOLDERNAME (in module pytfa)
logger (in module pytfa)
LowerBoundLogConcentration (class in pytfa)
(class in pytfa.optim)
Lump (in module pytfa.redgem.lumpgem)
LumpGEM (class in pytfa.redgem.lumpgem)
M
make_name() (pytfa.GenericConstraint method)
(pytfa.GenericVariable method)
(pytfa.optim.GenericConstraint method)
,
[1]
(pytfa.optim.GenericVariable method)
,
[1]
make_result() (pytfa.GenericVariable method)
(pytfa.optim.GenericVariable method)
,
[1]
make_sink() (in module redgem)
MANY (in module pytfa.thermo.std)
MAX_PH (in module pytfa.thermo.std)
MAX_STOICH (in module pytfa)
(in module pytfa.thermo)
metabolite() (pytfa.MetaboliteConstraint property)
(pytfa.MetaboliteVariable property)
(pytfa.optim.MetaboliteConstraint property)
(pytfa.optim.MetaboliteVariable property)
(pytfa.thermo.MetaboliteConstraint property)
(pytfa.thermo.MetaboliteVariable property)
MetaboliteConstraint (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
MetaboliteThermo (class in pytfa)
(class in pytfa.thermo)
,
[1]
MetaboliteVariable (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
min_BBB_uptake() (in module redgem)
MIN_PH (in module pytfa.thermo.std)
model() (pytfa.GeneConstraint property)
(pytfa.GenericConstraint property)
(pytfa.GenericVariable property)
(pytfa.GeneVariable property)
(pytfa.MetaboliteConstraint property)
(pytfa.MetaboliteVariable property)
(pytfa.optim.GeneConstraint property)
(pytfa.optim.GenericConstraint property)
,
[1]
(pytfa.optim.GenericVariable property)
,
[1]
(pytfa.optim.GeneVariable property)
(pytfa.optim.MetaboliteConstraint property)
(pytfa.optim.MetaboliteVariable property)
(pytfa.optim.ReactionConstraint property)
(pytfa.optim.ReactionVariable property)
(pytfa.ReactionConstraint property)
(pytfa.ReactionVariable property)
(pytfa.thermo.MetaboliteConstraint property)
(pytfa.thermo.MetaboliteVariable property)
(pytfa.thermo.ReactionConstraint property)
(pytfa.thermo.ReactionVariable property)
ModelConstraint (class in pytfa)
(class in pytfa.optim)
ModelVariable (class in pytfa)
(class in pytfa.optim)
module
pytfa
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
,
[6]
,
[7]
,
[8]
,
[9]
,
[10]
,
[11]
,
[12]
,
[13]
,
[14]
,
[15]
,
[16]
,
[17]
,
[18]
,
[19]
,
[20]
,
[21]
,
[22]
,
[23]
,
[24]
pytfa.analysis
pytfa.analysis.chebyshev
pytfa.analysis.manipulation
pytfa.analysis.sampling
pytfa.analysis.variability
pytfa.core
pytfa.core.model
pytfa.io
pytfa.io.base
pytfa.io.enrichment
pytfa.io.json
pytfa.io.plotting
pytfa.io.viz
pytfa.optim
pytfa.optim.config
pytfa.optim.constraints
pytfa.optim.debugging
pytfa.optim.meta
pytfa.optim.reformulation
pytfa.optim.relaxation
pytfa.optim.utils
pytfa.optim.variables
pytfa.redgem
pytfa.redgem.debugging
pytfa.redgem.lumpgem
pytfa.redgem.network_expansion
pytfa.redgem.redgem
pytfa.redgem.utils
pytfa.thermo
pytfa.thermo.equilibrator
pytfa.thermo.metabolite
pytfa.thermo.reaction
pytfa.thermo.std
pytfa.thermo.tmodel
pytfa.thermo.utils
pytfa.utils
pytfa.utils.logger
pytfa.utils.numerics
pytfa.utils.str
redgem
,
[1]
,
[2]
MyEncoder (class in pytfa)
(class in pytfa.io)
N
name() (pytfa.GenericConstraint property)
(pytfa.GenericVariable property)
(pytfa.optim.GenericConstraint property)
,
[1]
(pytfa.optim.GenericVariable property)
,
[1]
NegativeDeltaG (class in pytfa)
(class in pytfa.optim)
,
[1]
(class in pytfa.thermo)
NegativeDeltaGIneq (class in pytfa)
(class in pytfa.optim)
NegSlackLC (class in pytfa)
(class in pytfa.optim)
,
[1]
NegSlackVariable (class in pytfa)
(class in pytfa.optim)
,
[1]
NegSlackVariableInt (class in pytfa)
(class in pytfa.optim)
,
[1]
NetworkExpansion (class in redgem)
normalize_reactions() (pytfa.thermo.ThermoModel method)
(pytfa.ThermoModel method)
,
[1]
NullspaceConstraint (class in pytfa)
(class in pytfa.optim)
O
op_replace_dict (in module pytfa)
(in module pytfa.optim)
optimize() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
OPTLANG_BINARY (in module pytfa)
P
parallel_variability_analysis() (in module pytfa)
(in module pytfa.analysis)
petersen_linearization() (in module pytfa)
plot_fva_tva_comparison() (in module pytfa)
plot_histogram() (in module pytfa)
plot_thermo_displacement_histogram() (in module pytfa)
PosSlackLC (class in pytfa)
(class in pytfa.optim)
,
[1]
PosSlackVariable (class in pytfa)
(class in pytfa.optim)
,
[1]
PosSlackVariableInt (class in pytfa)
(class in pytfa.optim)
,
[1]
PotentialConstraint (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
PotentialCoupling (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
prefix (pytfa.analysis.DeltaG attribute)
(pytfa.analysis.ForbiddenProfile attribute)
(pytfa.analysis.ForwardUseVariable attribute)
(pytfa.BackwardDeltaGCoupling attribute)
(pytfa.BackwardDirectionCoupling attribute)
(pytfa.BackwardUseVariable attribute)
(pytfa.BinaryVariable attribute)
(pytfa.ChebyshevRadius attribute)
(pytfa.DeltaG attribute)
(pytfa.DeltaGErr attribute)
(pytfa.DeltaGFormstd attribute)
(pytfa.DeltaGstd attribute)
(pytfa.DisplacementCoupling attribute)
(pytfa.ForbiddenProfile attribute)
(pytfa.ForwardBackwardUseVariable attribute)
(pytfa.ForwardDeltaGCoupling attribute)
(pytfa.ForwardDirectionCoupling attribute)
(pytfa.ForwardUseVariable attribute)
(pytfa.GeneConstraint attribute)
(pytfa.GenericConstraint attribute)
(pytfa.GenericVariable attribute)
(pytfa.GeneVariable attribute)
(pytfa.IntegerVariable attribute)
(pytfa.LinearizationConstraint attribute)
(pytfa.LinearizationVariable attribute)
(pytfa.LogConcentration attribute)
(pytfa.LowerBoundLogConcentration attribute)
(pytfa.MetaboliteConstraint attribute)
(pytfa.MetaboliteVariable attribute)
(pytfa.ModelConstraint attribute)
(pytfa.ModelVariable attribute)
(pytfa.NegativeDeltaG attribute)
(pytfa.NegativeDeltaGIneq attribute)
(pytfa.NegSlackLC attribute)
(pytfa.NegSlackVariable attribute)
(pytfa.NegSlackVariableInt attribute)
(pytfa.NullspaceConstraint attribute)
(pytfa.optim.BackwardDeltaGCoupling attribute)
(pytfa.optim.BackwardDirectionCoupling attribute)
(pytfa.optim.BackwardUseVariable attribute)
,
[1]
(pytfa.optim.BinaryVariable attribute)
(pytfa.optim.DeltaG attribute)
(pytfa.optim.DeltaGErr attribute)
(pytfa.optim.DeltaGFormstd attribute)
(pytfa.optim.DeltaGstd attribute)
,
[1]
(pytfa.optim.DisplacementCoupling attribute)
(pytfa.optim.ForbiddenProfile attribute)
(pytfa.optim.ForwardBackwardUseVariable attribute)
(pytfa.optim.ForwardDeltaGCoupling attribute)
(pytfa.optim.ForwardDirectionCoupling attribute)
(pytfa.optim.ForwardUseVariable attribute)
,
[1]
(pytfa.optim.GeneConstraint attribute)
(pytfa.optim.GenericConstraint attribute)
,
[1]
(pytfa.optim.GenericVariable attribute)
,
[1]
(pytfa.optim.GeneVariable attribute)
(pytfa.optim.IntegerVariable attribute)
(pytfa.optim.LinearizationConstraint attribute)
(pytfa.optim.LinearizationVariable attribute)
(pytfa.optim.LogConcentration attribute)
,
[1]
(pytfa.optim.LowerBoundLogConcentration attribute)
(pytfa.optim.MetaboliteConstraint attribute)
(pytfa.optim.MetaboliteVariable attribute)
(pytfa.optim.ModelConstraint attribute)
(pytfa.optim.ModelVariable attribute)
(pytfa.optim.NegativeDeltaG attribute)
,
[1]
(pytfa.optim.NegativeDeltaGIneq attribute)
(pytfa.optim.NegSlackLC attribute)
,
[1]
(pytfa.optim.NegSlackVariable attribute)
,
[1]
(pytfa.optim.NegSlackVariableInt attribute)
,
[1]
(pytfa.optim.NullspaceConstraint attribute)
(pytfa.optim.PosSlackLC attribute)
,
[1]
(pytfa.optim.PosSlackVariable attribute)
,
[1]
(pytfa.optim.PosSlackVariableInt attribute)
,
[1]
(pytfa.optim.PotentialConstraint attribute)
(pytfa.optim.PotentialCoupling attribute)
(pytfa.optim.ReactionConstraint attribute)
(pytfa.optim.ReactionVariable attribute)
(pytfa.optim.SimultaneousUse attribute)
(pytfa.optim.ThermoDisplacement attribute)
(pytfa.optim.ThermoPotential attribute)
(pytfa.optim.UpperBoundLogConcentration attribute)
(pytfa.PosSlackLC attribute)
(pytfa.PosSlackVariable attribute)
(pytfa.PosSlackVariableInt attribute)
(pytfa.PotentialConstraint attribute)
(pytfa.PotentialCoupling attribute)
(pytfa.ReactionConstraint attribute)
(pytfa.ReactionVariable attribute)
(pytfa.redgem.lumpgem.FluxKO attribute)
(pytfa.redgem.lumpgem.UseOrKOFlux attribute)
(pytfa.redgem.lumpgem.UseOrKOInt attribute)
(pytfa.SimultaneousUse attribute)
(pytfa.thermo.BackwardDeltaGCoupling attribute)
(pytfa.thermo.BackwardDirectionCoupling attribute)
(pytfa.thermo.BackwardUseVariable attribute)
(pytfa.thermo.DeltaG attribute)
(pytfa.thermo.DeltaGFormstd attribute)
(pytfa.thermo.DeltaGstd attribute)
(pytfa.thermo.DisplacementCoupling attribute)
(pytfa.thermo.ForwardDeltaGCoupling attribute)
(pytfa.thermo.ForwardDirectionCoupling attribute)
(pytfa.thermo.ForwardUseVariable attribute)
(pytfa.thermo.LogConcentration attribute)
(pytfa.thermo.MetaboliteConstraint attribute)
(pytfa.thermo.MetaboliteVariable attribute)
(pytfa.thermo.NegativeDeltaG attribute)
(pytfa.thermo.PotentialConstraint attribute)
(pytfa.thermo.PotentialCoupling attribute)
(pytfa.thermo.ReactionConstraint attribute)
(pytfa.thermo.ReactionVariable attribute)
(pytfa.thermo.SimultaneousUse attribute)
(pytfa.thermo.ThermoDisplacement attribute)
(pytfa.thermo.ThermoPotential attribute)
(pytfa.ThermoDisplacement attribute)
(pytfa.ThermoPotential attribute)
(pytfa.UpperBoundLogConcentration attribute)
prepare() (pytfa.thermo.ThermoModel method)
(pytfa.ThermoModel method)
,
[1]
print_info() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
(pytfa.thermo.ThermoModel method)
(pytfa.ThermoModel method)
,
[1]
printLP() (in module pytfa)
(in module pytfa.io)
pytfa
module
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
,
[6]
,
[7]
,
[8]
,
[9]
,
[10]
,
[11]
,
[12]
,
[13]
,
[14]
,
[15]
,
[16]
,
[17]
,
[18]
,
[19]
,
[20]
,
[21]
,
[22]
,
[23]
,
[24]
pytfa.analysis
module
pytfa.analysis.chebyshev
module
pytfa.analysis.manipulation
module
pytfa.analysis.sampling
module
pytfa.analysis.variability
module
pytfa.core
module
pytfa.core.model
module
pytfa.io
module
pytfa.io.base
module
pytfa.io.enrichment
module
pytfa.io.json
module
pytfa.io.plotting
module
pytfa.io.viz
module
pytfa.optim
module
pytfa.optim.config
module
pytfa.optim.constraints
module
pytfa.optim.debugging
module
pytfa.optim.meta
module
pytfa.optim.reformulation
module
pytfa.optim.relaxation
module
pytfa.optim.utils
module
pytfa.optim.variables
module
pytfa.redgem
module
pytfa.redgem.debugging
module
pytfa.redgem.lumpgem
module
pytfa.redgem.network_expansion
module
pytfa.redgem.redgem
module
pytfa.redgem.utils
module
pytfa.thermo
module
pytfa.thermo.equilibrator
module
pytfa.thermo.metabolite
module
pytfa.thermo.reaction
module
pytfa.thermo.std
module
pytfa.thermo.tmodel
module
pytfa.thermo.utils
module
pytfa.utils
module
pytfa.utils.logger
module
pytfa.utils.numerics
module
pytfa.utils.str
module
R
reaction() (pytfa.optim.ReactionConstraint property)
(pytfa.optim.ReactionVariable property)
(pytfa.ReactionConstraint property)
(pytfa.ReactionVariable property)
(pytfa.thermo.ReactionConstraint property)
(pytfa.thermo.ReactionVariable property)
ReactionConstraint (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
ReactionVariable (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
read_compartment_data() (in module pytfa)
(in module pytfa.io)
read_lexicon() (in module pytfa)
(in module pytfa.io)
read_parameters() (redgem.RedGEM method)
recover_compartments() (in module pytfa)
(in module pytfa.io)
redgem
module
,
[1]
,
[2]
RedGEM (class in redgem)
regenerate_constraints() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
regenerate_variables() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
relax_dgo() (in module pytfa)
(in module pytfa.optim)
relax_dgo_err() (in module pytfa)
(in module pytfa.optim)
relax_dgo_gurobi() (in module pytfa)
(in module pytfa.optim)
relax_lc() (in module pytfa)
(in module pytfa.optim)
remove_blocked_reactions() (in module pytfa.redgem.utils)
remove_constraint() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
remove_metabolites() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
remove_reactions() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
remove_variable() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
repair() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
RequirePrefixMeta (class in pytfa)
retrieve_all_paths() (redgem.NetworkExpansion method)
retrieve_intermediate_extracellular_metabolites_and_reactions() (redgem.NetworkExpansion method)
retrieve_intermediate_metabolites_and_reactions() (redgem.NetworkExpansion method)
round() (in module pytfa.redgem.utils)
run() (redgem.NetworkExpansion method)
(redgem.RedGEM method)
run_between_all_subsystems() (redgem.NetworkExpansion method)
run_extracellular_system() (redgem.NetworkExpansion method)
S
sample() (in module pytfa)
(in module pytfa.analysis)
save_json_model() (in module pytfa)
scaling_factor() (pytfa.GenericVariable property)
(pytfa.optim.GenericVariable property)
,
[1]
set_medium() (in module pytfa.redgem.utils)
set_solver() (redgem.RedGEM method)
SimultaneousUse (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
slim_optimize() (pytfa.core.LCSBModel method)
(pytfa.LCSBModel method)
(pytfa.thermo.LCSBModel method)
strip_from_integer_variables() (in module pytfa)
(in module pytfa.optim)
subs_bilinear() (in module pytfa)
sum_reactions() (in module pytfa.redgem.lumpgem)
symbol_sum() (in module pytfa)
(in module pytfa.optim)
,
[1]
SYMPY_ADD_CHUNKSIZE (in module pytfa)
(in module pytfa.optim)
T
TEMPERATURE_0 (in module pytfa.thermo.std)
test_consistency() (pytfa.GenericVariable method)
(pytfa.optim.GenericVariable method)
,
[1]
ThermoDisplacement (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
ThermoModel (class in pytfa)
,
[1]
(class in pytfa.thermo)
ThermoPotential (class in pytfa)
(class in pytfa.optim)
(class in pytfa.thermo)
timeit() (in module pytfa)
TimeoutExcept
trim_epsilon_mets() (in module pytfa.redgem.utils)
type() (pytfa.GenericVariable property)
(pytfa.optim.GenericVariable property)
,
[1]
U
unscaled() (pytfa.GenericVariable property)
(pytfa.optim.GenericVariable property)
,
[1]
unscaled_value() (pytfa.GenericVariable property)
(pytfa.optim.GenericVariable property)
,
[1]
UpperBoundLogConcentration (class in pytfa)
(class in pytfa.optim)
UseOrKOFlux (class in pytfa.redgem.lumpgem)
UseOrKOInt (class in pytfa.redgem.lumpgem)
V
value() (pytfa.GenericVariable property)
(pytfa.optim.GenericVariable property)
,
[1]
values() (pytfa.MetaboliteThermo method)
(pytfa.thermo.MetaboliteThermo method)
,
[1]
variability_analysis() (in module pytfa)
(in module pytfa.analysis)
variable() (pytfa.GenericVariable property)
(pytfa.optim.GenericVariable property)
,
[1]
varnames2ids() (in module pytfa)
varnames2matlab() (in module pytfa)
(in module pytfa.io)
W
write_compartment_data() (in module pytfa)
(in module pytfa.io)
write_lexicon() (in module pytfa)
(in module pytfa.io)
write_matlab_model() (in module pytfa)
(in module pytfa.io)
writeLP() (in module pytfa)
(in module pytfa.io)
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