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Y
A
add() (psamm.moma.ConstraintGroup method)
add_all_database_reactions() (in module psamm.gapfilling)
add_all_exchange_reactions() (in module psamm.gapfilling)
add_all_transport_reactions() (in module psamm.gapfilling)
add_ignore() (psamm.manual_curation.Curator method)
add_linear_constraints() (psamm.lpsolver.cplex.Problem method)
(psamm.lpsolver.glpk.Problem method)
(psamm.lpsolver.gurobi.Problem method)
(psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.qsoptex.Problem method)
add_mapping() (psamm.manual_curation.Curator method)
add_node() (psamm.graph.Graph method)
add_reaction() (psamm.metabolicmodel.MetabolicModel method)
add_thermodynamic() (psamm.fluxanalysis.FluxBalanceProblem method)
And (class in psamm.expression.boolean)
argument_error() (psamm.command.Command method)
arguments (psamm.reaction.Compound attribute)
Atom (class in psamm.formula)
B
balance() (psamm.formula.Formula class method)
bayes_posterior() (in module psamm.bayesian)
BayesianCompoundPredictor (class in psamm.bayesian)
BayesianReactionPredictor (class in psamm.bayesian)
Binary (psamm.lpsolver.lp.VariableType attribute)
biomass_reaction (psamm.datasource.native.ModelReader attribute)
(psamm.datasource.native.NativeModel attribute)
boundary (psamm.datasource.sbml.SBMLSpeciesEntry attribute)
bounds (psamm.metabolicmodel.FluxBounds attribute)
C
cas (psamm.bayesian.CompoundEntry attribute)
ChainedDatabase (class in psamm.database)
charge (psamm.bayesian.CompoundEntry attribute)
(psamm.datasource.entry.CompoundEntry attribute)
(psamm.datasource.entry.DictCompoundEntry attribute)
(psamm.datasource.sbml.SBMLSpeciesEntry attribute)
charge_balance() (in module psamm.balancecheck)
check_compound_consistency() (in module psamm.massconsistency)
check_constraints() (psamm.fluxanalysis.FluxBalanceProblem method)
check_reaction_compounds() (psamm.bayesian.MappingModel method)
check_reaction_consistency() (in module psamm.massconsistency)
classify_coupling() (in module psamm.fluxcoupling)
Command (class in psamm.command)
CommandError
compartment (psamm.datasource.sbml.SBMLSpeciesEntry attribute)
(psamm.reaction.Compound attribute)
compartment_boundaries (psamm.datasource.native.NativeModel attribute)
CompartmentEntry (class in psamm.datasource.entry)
compartments (psamm.database.ChainedDatabase attribute)
(psamm.database.DictDatabase attribute)
(psamm.database.MetabolicDatabase attribute)
(psamm.datasource.native.NativeModel attribute)
(psamm.datasource.sbml.SBMLReader attribute)
(psamm.metabolicmodel.MetabolicModel attribute)
Compound (class in psamm.reaction)
compound_checked() (psamm.manual_curation.Curator method)
compound_ignored() (psamm.manual_curation.Curator method)
CompoundEntry (class in psamm.bayesian)
(class in psamm.datasource.entry)
(class in psamm.datasource.kegg)
(class in psamm.datasource.modelseed)
CompoundMapper (class in psamm.datasource.kegg)
compounds (psamm.database.ChainedDatabase attribute)
(psamm.database.DictDatabase attribute)
(psamm.database.MetabolicDatabase attribute)
(psamm.datasource.native.NativeModel attribute)
(psamm.metabolicmodel.MetabolicModel attribute)
(psamm.reaction.Reaction attribute)
consistency_check() (in module psamm.fluxanalysis)
Constraint (class in psamm.lpsolver.cplex)
(class in psamm.lpsolver.glpk)
(class in psamm.lpsolver.gurobi)
(class in psamm.lpsolver.lp)
(class in psamm.lpsolver.qsoptex)
ConstraintGroup (class in psamm.moma)
constraints() (psamm.moma.MOMAProblem method)
ContextError
Continuous (psamm.lpsolver.lp.VariableType attribute)
convert_compartment_entry() (psamm.datasource.native.ModelWriter method)
convert_compound_entry() (psamm.datasource.native.ModelWriter method)
convert_exchange_to_compounds() (in module psamm.datasource.sbml)
convert_model_entries() (in module psamm.datasource.sbml)
convert_reaction_entry() (psamm.datasource.native.ModelWriter method)
convert_sbml_model() (in module psamm.datasource.sbml)
convex_cardinality_relaxed() (in module psamm.util)
copy() (psamm.metabolicmodel.MetabolicModel method)
count_genes() (in module psamm.importer)
CouplingClass (class in psamm.fluxcoupling)
cplex (psamm.lpsolver.cplex.Problem attribute)
CplexRangedProperty (class in psamm.lpsolver.cplex)
create_convert_sbml_id_function() (in module psamm.datasource.sbml)
create_exchange_id() (in module psamm.metabolicmodel)
create_extended_model() (in module psamm.gapfilling)
create_metabolic_model() (psamm.datasource.native.NativeModel method)
create_model() (psamm.datasource.native.ModelReader method)
(psamm.datasource.sbml.SBMLReader method)
create_problem() (psamm.lpsolver.cplex.Solver method)
(psamm.lpsolver.generic.Solver method)
(psamm.lpsolver.glpk.Solver method)
(psamm.lpsolver.gurobi.Solver method)
(psamm.lpsolver.lp.Solver method)
(psamm.lpsolver.qsoptex.Solver method)
create_transport_id() (in module psamm.metabolicmodel)
create_unique_id() (in module psamm.util)
Curator (class in psamm.manual_curation)
D
decode_name() (in module psamm.datasource.modelseed)
default_compartment (psamm.datasource.native.ModelReader attribute)
(psamm.datasource.native.NativeModel attribute)
default_flux_limit (psamm.datasource.native.ModelReader attribute)
(psamm.datasource.native.NativeModel attribute)
default_weight() (in module psamm.mapmaker)
define() (psamm.lpsolver.cplex.Problem method)
(psamm.lpsolver.glpk.Problem method)
(psamm.lpsolver.gurobi.Problem method)
(psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.lp.VariableNamespace method)
(psamm.lpsolver.qsoptex.Problem method)
delete() (psamm.lpsolver.cplex.Constraint method)
(psamm.lpsolver.glpk.Constraint method)
(psamm.lpsolver.gurobi.Constraint method)
(psamm.lpsolver.lp.Constraint method)
(psamm.lpsolver.qsoptex.Constraint method)
(psamm.moma.ConstraintGroup method)
detect_best_flux_limit() (in module psamm.importer)
detect_extracellular_compartment() (in module psamm.datasource.sbml)
DictCompartmentEntry (class in psamm.datasource.entry)
DictCompoundEntry (class in psamm.datasource.entry)
DictDatabase (class in psamm.database)
DictReactionEntry (class in psamm.datasource.entry)
DictView (class in psamm.util)
dir_value() (in module psamm.graph)
Direction (class in psamm.reaction)
direction (psamm.reaction.Reaction attribute)
DirectionalForward (psamm.fluxcoupling.CouplingClass attribute)
DirectionalReverse (psamm.fluxcoupling.CouplingClass attribute)
E
ec (psamm.bayesian.ReactionEntry attribute)
Edge (class in psamm.graph)
Entity (class in psamm.graph)
entry_id_from_cobra_encoding() (in module psamm.datasource.sbml)
equation (psamm.bayesian.ReactionEntry attribute)
(psamm.datasource.entry.DictReactionEntry attribute)
(psamm.datasource.entry.ReactionEntry attribute)
(psamm.datasource.sbml.SBMLReactionEntry attribute)
exchange (psamm.datasource.native.NativeModel attribute)
ExecutorError
expr() (psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.lp.VariableNamespace method)
Expression (class in psamm.expression.affine)
(class in psamm.expression.boolean)
(class in psamm.lpsolver.lp)
expression (psamm.lpsolver.lp.Relation attribute)
extracellular_compartment (psamm.datasource.native.ModelReader attribute)
(psamm.datasource.native.NativeModel attribute)
F
fail() (psamm.command.Command method)
fake_likelihood() (in module psamm.bayesian)
fastcc() (in module psamm.fastcore)
fastcc_consistent_subset() (in module psamm.fastcore)
fastcc_is_consistent() (in module psamm.fastcore)
fastcore() (in module psamm.fastcore)
FastcoreError
FastcoreProblem (class in psamm.fastcore)
fastgapfill() (in module psamm.fastgapfill)
feasibility_tolerance (psamm.lpsolver.cplex.Problem attribute)
(psamm.lpsolver.glpk.Problem attribute)
(psamm.lpsolver.gurobi.Problem attribute)
(psamm.lpsolver.qsoptex.Problem attribute)
FileMark (class in psamm.datasource.context)
filemark (psamm.datasource.entry.ModelEntry attribute)
(psamm.datasource.modelseed.CompoundEntry attribute)
(psamm.datasource.sbml.SBMLCompartmentEntry attribute)
(psamm.datasource.sbml.SBMLReactionEntry attribute)
(psamm.datasource.sbml.SBMLSpeciesEntry attribute)
FilePathContext (class in psamm.datasource.context)
FilePrefixAppendAction (class in psamm.command)
filter_solvers() (in module psamm.lpsolver.generic)
find_sparse_mode() (psamm.fastcore.FastcoreProblem method)
flattened() (psamm.formula.Formula method)
flip() (psamm.fastcore.FastcoreProblem method)
FlipableFluxBounds (class in psamm.metabolicmodel)
FlipableLimitsView (class in psamm.metabolicmodel)
FlipableModelView (class in psamm.metabolicmodel)
FlipableStoichiometricMatrixView (class in psamm.metabolicmodel)
flipped() (psamm.reaction.Direction method)
float_constructor() (in module psamm.datasource.native)
flush() (psamm.util.LoggerFile method)
flux_balance() (in module psamm.fluxanalysis)
flux_bound() (psamm.fluxanalysis.FluxBalanceProblem method)
flux_bounds (psamm.datasource.sbml.SBMLReader attribute)
flux_expr() (psamm.fluxanalysis.FluxBalanceProblem method)
flux_minimization() (in module psamm.fluxanalysis)
flux_randomization() (in module psamm.fluxanalysis)
flux_variability() (in module psamm.fluxanalysis)
FluxBalanceError
FluxBalanceProblem (class in psamm.fluxanalysis)
FluxBounds (class in psamm.metabolicmodel)
FluxCouplingProblem (class in psamm.fluxcoupling)
Formula (class in psamm.formula)
formula (psamm.bayesian.CompoundEntry attribute)
(psamm.datasource.entry.CompoundEntry attribute)
(psamm.datasource.entry.DictCompoundEntry attribute)
(psamm.datasource.modelseed.CompoundEntry attribute)
(psamm.datasource.sbml.SBMLSpeciesEntry attribute)
formula_balance() (in module psamm.balancecheck)
formula_equals() (in module psamm.bayesian_util)
formula_exact() (in module psamm.bayesian_util)
FormulaElement (class in psamm.formula)
forward (psamm.reaction.Direction attribute)
FrozenOrderedSet (class in psamm.util)
Full (psamm.fluxcoupling.CouplingClass attribute)
G
gapfill() (in module psamm.gapfill)
GapFillError
gapfind() (in module psamm.gapfill)
GeneDeletionStrategy (class in psamm.randomsparse)
genes (psamm.bayesian.ReactionEntry attribute)
(psamm.datasource.entry.DictReactionEntry attribute)
(psamm.datasource.entry.ReactionEntry attribute)
genes_equals() (in module psamm.bayesian_util)
get() (psamm.formula.Formula method)
get_best_map() (psamm.bayesian.BayesianCompoundPredictor method)
(psamm.bayesian.BayesianReactionPredictor method)
get_best_p_value_set() (in module psamm.bayesian)
get_compartment() (psamm.datasource.sbml.SBMLReader method)
get_compound_dict() (in module psamm.graph)
get_compound_reactions() (psamm.database.ChainedDatabase method)
(psamm.database.DictDatabase method)
(psamm.database.MetabolicDatabase method)
(psamm.metabolicmodel.MetabolicModel method)
get_cpd_pred() (psamm.bayesian.BayesianCompoundPredictor method)
get_default_compartment() (in module psamm.importer)
get_exchange_reactions() (in module psamm.randomsparse)
get_fba_flux() (psamm.moma.MOMAProblem method)
get_fba_obj_flux() (psamm.moma.MOMAProblem method)
get_flux() (psamm.fluxanalysis.FluxBalanceProblem method)
(psamm.moma.MOMAProblem method)
get_flux_var() (psamm.fluxanalysis.FluxBalanceProblem method)
(psamm.moma.MOMAProblem method)
get_gene_associations() (in module psamm.randomsparse)
get_minimal_fba_flux() (psamm.moma.MOMAProblem method)
get_node() (psamm.graph.Graph method)
get_objective() (psamm.datasource.sbml.SBMLReader method)
get_raw_map() (psamm.bayesian.BayesianCompoundPredictor method)
(psamm.bayesian.BayesianReactionPredictor method)
get_reaction() (psamm.database.MetabolicDatabase method)
(psamm.datasource.sbml.SBMLReader method)
(psamm.metabolicmodel.MetabolicModel method)
get_reaction_values() (psamm.database.ChainedDatabase method)
(psamm.database.DictDatabase method)
(psamm.database.MetabolicDatabase method)
(psamm.metabolicmodel.MetabolicModel method)
get_species() (psamm.datasource.sbml.SBMLReader method)
get_value() (psamm.lpsolver.cplex.Result method)
(psamm.lpsolver.glpk.Result method)
(psamm.lpsolver.gurobi.Result method)
(psamm.lpsolver.lp.Result method)
(psamm.lpsolver.qsoptex.Result method)
git_try_describe() (in module psamm.util)
glpk (psamm.lpsolver.glpk.Problem attribute)
GLPKError
Graph (class in psamm.graph)
gurobi (psamm.lpsolver.gurobi.Problem attribute)
H
has_model_definition() (psamm.datasource.native.ModelReader method)
has_reaction() (psamm.database.ChainedDatabase method)
(psamm.database.DictDatabase method)
(psamm.database.MetabolicDatabase method)
(psamm.metabolicmodel.MetabolicModel method)
has_value() (psamm.expression.boolean.Expression method)
has_variable() (psamm.lpsolver.cplex.Problem method)
(psamm.lpsolver.glpk.Problem method)
(psamm.lpsolver.gurobi.Problem method)
(psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.qsoptex.Problem method)
I
id (psamm.bayesian.CompoundEntry attribute)
(psamm.bayesian.ReactionEntry attribute)
(psamm.datasource.entry.ModelEntry attribute)
(psamm.datasource.modelseed.CompoundEntry attribute)
(psamm.datasource.sbml.SBMLFluxBoundEntry attribute)
(psamm.datasource.sbml.SBMLReactionEntry attribute)
(psamm.datasource.sbml.SBMLReader attribute)
id_equals() (in module psamm.bayesian_util)
Importer (class in psamm.importer)
ImportError
in_compartment() (psamm.reaction.Compound method)
Inconsistent (psamm.fluxcoupling.CouplingClass attribute)
infer_compartment_adjacency() (in module psamm.importer)
infer_compartment_entries() (in module psamm.importer)
init_parser() (psamm.command.Command class method)
Integer (psamm.lpsolver.lp.VariableType attribute)
integrality_tolerance (psamm.lpsolver.cplex.Problem attribute)
(psamm.lpsolver.glpk.Problem attribute)
(psamm.lpsolver.gurobi.Problem attribute)
InvalidResultError
is_consistent() (in module psamm.massconsistency)
is_exchange() (psamm.metabolicmodel.MetabolicModel method)
is_flipped() (psamm.fastcore.FastcoreProblem method)
is_reversible() (psamm.database.ChainedDatabase method)
(psamm.database.DictDatabase method)
(psamm.database.MetabolicDatabase method)
(psamm.metabolicmodel.MetabolicModel method)
items() (psamm.formula.Formula method)
J
jaccard() (in module psamm.bayesian_util)
K
kegg (psamm.bayesian.CompoundEntry attribute)
KEGGEntry (class in psamm.datasource.kegg)
kinetic_law_reaction_parameters (psamm.datasource.sbml.SBMLReactionEntry attribute)
L
left (psamm.reaction.Reaction attribute)
levenshtein() (in module psamm.bayesian_util)
likelihood_products() (in module psamm.bayesian)
limits (psamm.datasource.native.NativeModel attribute)
LimitsView (class in psamm.metabolicmodel)
lin_moma() (psamm.moma.MOMAProblem method)
lin_moma2() (psamm.moma.MOMAProblem method)
list_solvers() (in module psamm.lpsolver.generic)
load_model() (psamm.metabolicmodel.MetabolicModel class method)
LoggerFile (class in psamm.util)
LoopRemovalMixin (class in psamm.command)
lower (psamm.metabolicmodel.FlipableFluxBounds attribute)
(psamm.metabolicmodel.FluxBounds attribute)
lp10() (psamm.fastcore.FastcoreProblem method)
lp7() (psamm.fastcore.FastcoreProblem method)
M
main() (in module psamm.command)
(in module psamm.importer)
main_bigg() (in module psamm.importer)
main_sbml() (in module psamm.command)
make_bipartite_graph_object() (in module psamm.graph)
make_cpair_dict() (in module psamm.graph)
make_irreversible() (psamm.metabolicmodel.MetabolicModel method)
make_network_dict() (in module psamm.graph)
map_model_compounds() (in module psamm.bayesian)
map_model_reactions() (in module psamm.bayesian)
MappingModel (class in psamm.bayesian)
MassConsistencyError
matrix (psamm.database.MetabolicDatabase attribute)
max_min_l1() (psamm.fluxanalysis.FluxBalanceProblem method)
Maximize (psamm.lpsolver.lp.ObjectiveSense attribute)
maximize() (psamm.fluxanalysis.FluxBalanceProblem method)
MaybeRelative (class in psamm.util)
merge_equivalent_compounds() (in module psamm.datasource.sbml)
merge_partial_p_set() (in module psamm.bayesian)
MetabolicDatabase (class in psamm.database)
MetabolicMixin (class in psamm.command)
MetabolicModel (class in psamm.metabolicmodel)
Minimize (psamm.lpsolver.lp.ObjectiveSense attribute)
minimize_l1() (psamm.fluxanalysis.FluxBalanceProblem method)
MIPResult (class in psamm.lpsolver.glpk)
mkdir_p() (in module psamm.util)
model (psamm.datasource.native.NativeModel attribute)
model_exchange() (in module psamm.importer)
model_reaction_limits() (in module psamm.importer)
ModelEntry (class in psamm.datasource.entry)
ModelLoadError
ModelReader (class in psamm.datasource.native)
ModelWriter (class in psamm.datasource.native)
moma() (psamm.moma.MOMAProblem method)
moma2() (psamm.moma.MOMAProblem method)
MOMAError
MOMAProblem (class in psamm.moma)
N
name (psamm.bayesian.CompoundEntry attribute)
(psamm.bayesian.ReactionEntry attribute)
(psamm.datasource.entry.ModelEntry attribute)
(psamm.datasource.modelseed.CompoundEntry attribute)
(psamm.datasource.native.ModelReader attribute)
(psamm.datasource.native.NativeModel attribute)
(psamm.datasource.sbml.SBMLFluxBoundEntry attribute)
(psamm.datasource.sbml.SBMLReactionEntry attribute)
(psamm.datasource.sbml.SBMLReader attribute)
(psamm.datasource.sbml.SBMLSpeciesEntry attribute)
(psamm.reaction.Compound attribute)
name_equals() (in module psamm.bayesian_util)
name_similar() (in module psamm.bayesian_util)
namespace() (psamm.lpsolver.lp.Problem method)
NativeModel (class in psamm.datasource.native)
Node (class in psamm.graph)
normalized() (psamm.reaction.Reaction method)
O
ObjectiveMixin (class in psamm.command)
objectives (psamm.datasource.sbml.SBMLReader attribute)
ObjectiveSense (class in psamm.lpsolver.lp)
offset (psamm.lpsolver.lp.Expression attribute)
operation (psamm.datasource.sbml.SBMLFluxBoundEntry attribute)
optimality_tolerance (psamm.lpsolver.cplex.Problem attribute)
(psamm.lpsolver.glpk.Problem attribute)
(psamm.lpsolver.gurobi.Problem attribute)
(psamm.lpsolver.qsoptex.Problem attribute)
Or (class in psamm.expression.boolean)
P
pairwise_distance() (in module psamm.bayesian_util)
pairwise_likelihood() (in module psamm.bayesian)
ParallelTaskMixin (class in psamm.command)
parse() (psamm.datasource.reaction.ReactionParser method)
(psamm.formula.Formula class method)
parse_compartments() (psamm.datasource.native.ModelReader method)
parse_compound() (in module psamm.datasource.native)
(in module psamm.datasource.reaction)
parse_compound_count() (in module psamm.datasource.reaction)
parse_compound_file() (in module psamm.datasource.kegg)
(in module psamm.datasource.modelseed)
(in module psamm.datasource.native)
parse_compound_list() (in module psamm.datasource.native)
parse_compound_table_file() (in module psamm.datasource.native)
parse_compound_yaml_file() (in module psamm.datasource.native)
parse_compounds() (psamm.datasource.native.ModelReader method)
parse_exchange() (in module psamm.datasource.native)
(psamm.datasource.native.ModelReader method)
parse_exchange_file() (in module psamm.datasource.native)
parse_exchange_list() (in module psamm.datasource.native)
parse_exchange_table_file() (in module psamm.datasource.native)
parse_exchange_yaml_file() (in module psamm.datasource.native)
parse_flux_bounds() (in module psamm.datasource.sbml)
parse_kegg_entries() (in module psamm.datasource.kegg)
parse_limit() (in module psamm.datasource.native)
parse_limits() (psamm.datasource.native.ModelReader method)
parse_limits_file() (in module psamm.datasource.native)
parse_limits_list() (in module psamm.datasource.native)
parse_limits_table_file() (in module psamm.datasource.native)
parse_limits_yaml_file() (in module psamm.datasource.native)
parse_medium() (in module psamm.datasource.native)
(psamm.datasource.native.ModelReader method)
parse_medium_file() (in module psamm.datasource.native)
parse_medium_list() (in module psamm.datasource.native)
parse_medium_table_file() (in module psamm.datasource.native)
parse_medium_yaml_file() (in module psamm.datasource.native)
parse_model() (psamm.datasource.native.ModelReader method)
parse_model_file() (in module psamm.datasource.native)
parse_model_group() (in module psamm.datasource.native)
parse_model_group_list() (in module psamm.datasource.native)
parse_model_table_file() (in module psamm.datasource.native)
parse_model_yaml_file() (in module psamm.datasource.native)
parse_objective_coefficient() (in module psamm.datasource.sbml)
parse_reaction() (in module psamm.datasource.kegg)
(in module psamm.datasource.native)
(in module psamm.datasource.reaction)
parse_reaction_equation() (in module psamm.datasource.native)
parse_reaction_equation_string() (in module psamm.datasource.native)
parse_reaction_file() (in module psamm.datasource.kegg)
(in module psamm.datasource.native)
parse_reaction_list() (in module psamm.datasource.native)
parse_reaction_table_file() (in module psamm.datasource.native)
parse_reaction_yaml_file() (in module psamm.datasource.native)
parse_reactions() (psamm.datasource.native.ModelReader method)
parse_solver_setting() (in module psamm.lpsolver.generic)
parse_xhtml_notes() (in module psamm.datasource.sbml)
parse_xhtml_reaction_notes() (in module psamm.datasource.sbml)
parse_xhtml_species_notes() (in module psamm.datasource.sbml)
ParseError
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
,
[6]
,
[7]
Partial (psamm.fluxcoupling.CouplingClass attribute)
predict_compound_pairs() (in module psamm.mapmaker)
print_summary() (psamm.bayesian.MappingModel method)
prob (psamm.fluxanalysis.FluxBalanceProblem attribute)
(psamm.moma.MOMAProblem attribute)
Problem (class in psamm.lpsolver.cplex)
(class in psamm.lpsolver.glpk)
(class in psamm.lpsolver.gurobi)
(class in psamm.lpsolver.lp)
(class in psamm.lpsolver.qsoptex)
Product (class in psamm.lpsolver.lp)
properties (psamm.datasource.entry.ModelEntry attribute)
(psamm.datasource.modelseed.CompoundEntry attribute)
(psamm.datasource.sbml.SBMLCompartmentEntry attribute)
(psamm.datasource.sbml.SBMLReactionEntry attribute)
(psamm.datasource.sbml.SBMLSpeciesEntry attribute)
psamm.balancecheck (module)
psamm.bayesian (module)
psamm.bayesian_util (module)
psamm.command (module)
psamm.database (module)
psamm.datasource.context (module)
psamm.datasource.entry (module)
psamm.datasource.kegg (module)
psamm.datasource.modelseed (module)
psamm.datasource.native (module)
psamm.datasource.reaction (module)
psamm.datasource.sbml (module)
psamm.expression.affine (module)
psamm.expression.boolean (module)
psamm.fastcore (module)
psamm.fastgapfill (module)
psamm.fluxanalysis (module)
psamm.fluxcoupling (module)
psamm.formula (module)
psamm.gapfill (module)
psamm.gapfilling (module)
psamm.graph (module)
psamm.importer (module)
psamm.lpsolver.cplex (module)
psamm.lpsolver.generic (module)
psamm.lpsolver.glpk (module)
psamm.lpsolver.gurobi (module)
psamm.lpsolver.lp (module)
psamm.lpsolver.qsoptex (module)
psamm.manual_curation (module)
psamm.mapmaker (module)
psamm.massconsistency (module)
psamm.metabolicmodel (module)
psamm.moma (module)
psamm.randomsparse (module)
psamm.reaction (module)
psamm.translate_id (module)
psamm.util (module)
Q
qsoptex (psamm.lpsolver.qsoptex.Problem attribute)
R
Radical (class in psamm.formula)
random_sparse() (in module psamm.randomsparse)
random_sparse_return_all() (in module psamm.randomsparse)
ranged_property() (in module psamm.lpsolver.lp)
RangedProperty (class in psamm.lpsolver.lp)
Reaction (class in psamm.reaction)
reaction (psamm.datasource.sbml.SBMLFluxBoundEntry attribute)
reaction_charge() (in module psamm.balancecheck)
reaction_checked() (psamm.manual_curation.Curator method)
reaction_equation_compound_mapping_likelihood() (in module psamm.bayesian)
reaction_equation_mapping_approx_max_likelihood() (in module psamm.bayesian)
reaction_formula() (in module psamm.balancecheck)
reaction_ignored() (psamm.manual_curation.Curator method)
reaction_signature() (in module psamm.datasource.native)
ReactionDeletionStrategy (class in psamm.randomsparse)
ReactionEntry (class in psamm.bayesian)
(class in psamm.datasource.entry)
(class in psamm.datasource.kegg)
ReactionMapper (class in psamm.datasource.kegg)
ReactionParser (class in psamm.datasource.reaction)
reactions (psamm.database.ChainedDatabase attribute)
(psamm.database.DictDatabase attribute)
(psamm.database.MetabolicDatabase attribute)
(psamm.datasource.native.NativeModel attribute)
(psamm.datasource.sbml.SBMLReader attribute)
(psamm.metabolicmodel.MetabolicModel attribute)
reactions_to_files() (in module psamm.importer)
reader_from_path() (psamm.datasource.native.ModelReader class method)
reference (psamm.util.MaybeRelative attribute)
Relation (class in psamm.lpsolver.lp)
RelationSense (class in psamm.lpsolver.lp)
relative (psamm.util.MaybeRelative attribute)
remove_reaction() (psamm.metabolicmodel.MetabolicModel method)
repeat() (psamm.formula.FormulaElement method)
RequirementsError
resolve_format() (in module psamm.datasource.native)
Result (class in psamm.lpsolver.cplex)
(class in psamm.lpsolver.glpk)
(class in psamm.lpsolver.gurobi)
(class in psamm.lpsolver.lp)
(class in psamm.lpsolver.qsoptex)
result (psamm.lpsolver.cplex.Problem attribute)
(psamm.lpsolver.glpk.Problem attribute)
(psamm.lpsolver.gurobi.Problem attribute)
(psamm.lpsolver.lp.Problem attribute)
(psamm.lpsolver.qsoptex.Problem attribute)
reverse (psamm.reaction.Direction attribute)
reversible (psamm.database.MetabolicDatabase attribute)
(psamm.datasource.sbml.SBMLReactionEntry attribute)
right (psamm.reaction.Reaction attribute)
root (psamm.expression.boolean.Expression attribute)
run() (psamm.command.Command method)
S
save() (psamm.manual_curation.Curator method)
SBMLCompartmentEntry (class in psamm.datasource.sbml)
SBMLFluxBoundEntry (class in psamm.datasource.sbml)
SBMLObjectiveEntry (class in psamm.datasource.sbml)
SBMLReactionEntry (class in psamm.datasource.sbml)
SBMLReader (class in psamm.datasource.sbml)
SBMLSpeciesEntry (class in psamm.datasource.sbml)
SBMLWriter (class in psamm.datasource.sbml)
search_compound() (in module psamm.manual_curation)
search_reaction() (in module psamm.manual_curation)
sense (psamm.lpsolver.lp.Relation attribute)
set() (psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.lp.VariableNamespace method)
set_linear_objective() (psamm.lpsolver.cplex.Problem method)
(psamm.lpsolver.glpk.Problem method)
(psamm.lpsolver.gurobi.Problem method)
(psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.qsoptex.Problem method)
set_objective() (psamm.lpsolver.cplex.Problem method)
(psamm.lpsolver.glpk.Problem method)
(psamm.lpsolver.gurobi.Problem method)
(psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.qsoptex.Problem method)
set_objective_sense() (psamm.lpsolver.cplex.Problem method)
(psamm.lpsolver.glpk.Problem method)
(psamm.lpsolver.gurobi.Problem method)
(psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.qsoptex.Problem method)
set_reaction() (psamm.database.DictDatabase method)
simplify() (psamm.expression.affine.Expression method)
(psamm.expression.affine.Variable method)
solve() (psamm.fluxcoupling.FluxCouplingProblem method)
(psamm.lpsolver.lp.Problem method)
solve_fba() (psamm.moma.MOMAProblem method)
solve_unchecked() (psamm.lpsolver.cplex.Problem method)
(psamm.lpsolver.glpk.Problem method)
(psamm.lpsolver.gurobi.Problem method)
(psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.qsoptex.Problem method)
Solver (class in psamm.lpsolver.cplex)
(class in psamm.lpsolver.generic)
(class in psamm.lpsolver.glpk)
(class in psamm.lpsolver.gurobi)
(class in psamm.lpsolver.lp)
(class in psamm.lpsolver.qsoptex)
SolverCommandMixin (class in psamm.command)
SolverError
species (psamm.datasource.sbml.SBMLReader attribute)
status (psamm.lpsolver.cplex.Result attribute)
(psamm.lpsolver.glpk.MIPResult attribute)
(psamm.lpsolver.glpk.Result attribute)
(psamm.lpsolver.gurobi.Result attribute)
(psamm.lpsolver.lp.Result attribute)
(psamm.lpsolver.qsoptex.Result attribute)
StoichiometricMatrixView (class in psamm.database)
substitute() (psamm.expression.affine.Expression method)
(psamm.expression.affine.Variable method)
(psamm.expression.boolean.Expression method)
(psamm.formula.Formula method)
(psamm.formula.FormulaElement method)
SubstitutionError
subsystem (psamm.bayesian.ReactionEntry attribute)
success (psamm.lpsolver.cplex.Result attribute)
(psamm.lpsolver.glpk.MIPResult attribute)
(psamm.lpsolver.glpk.Result attribute)
(psamm.lpsolver.gurobi.Result attribute)
(psamm.lpsolver.lp.Result attribute)
(psamm.lpsolver.qsoptex.Result attribute)
sum() (psamm.lpsolver.lp.VariableNamespace method)
symbol (psamm.expression.affine.Variable attribute)
(psamm.formula.Atom attribute)
(psamm.formula.Radical attribute)
(psamm.reaction.Direction attribute)
T
translate() (psamm.reaction.Compound method)
translate_sbml_compartment() (in module psamm.datasource.sbml)
translate_sbml_compound() (in module psamm.datasource.sbml)
translate_sbml_reaction() (in module psamm.datasource.sbml)
translated_compounds() (psamm.reaction.Reaction method)
TranslatedModel (class in psamm.translate_id)
U
UnbalancedReactionError
unbounded (psamm.lpsolver.cplex.Result attribute)
(psamm.lpsolver.glpk.Result attribute)
(psamm.lpsolver.gurobi.Result attribute)
(psamm.lpsolver.lp.Result attribute)
(psamm.lpsolver.qsoptex.Result attribute)
Uncoupled (psamm.fluxcoupling.CouplingClass attribute)
upper (psamm.metabolicmodel.FlipableFluxBounds attribute)
(psamm.metabolicmodel.FluxBounds attribute)
V
value (psamm.datasource.sbml.SBMLFluxBoundEntry attribute)
(psamm.expression.boolean.Expression attribute)
value() (psamm.lpsolver.lp.VariableNamespace method)
value_sets() (psamm.lpsolver.lp.Expression method)
values() (psamm.lpsolver.lp.Expression method)
var() (psamm.lpsolver.lp.Problem method)
Variable (class in psamm.expression.affine)
(class in psamm.expression.boolean)
VariableNamespace (class in psamm.lpsolver.lp)
variables (psamm.expression.boolean.Expression attribute)
variables() (psamm.expression.affine.Expression method)
(psamm.formula.Formula method)
(psamm.formula.FormulaElement method)
(psamm.lpsolver.lp.Expression method)
VariableSet (class in psamm.lpsolver.lp)
VariableType (class in psamm.lpsolver.lp)
version_string (psamm.datasource.native.NativeModel attribute)
W
write() (psamm.util.LoggerFile method)
write_compartments() (psamm.datasource.native.ModelWriter method)
write_compounds() (psamm.datasource.native.ModelWriter method)
write_edges_tables() (psamm.graph.Graph method)
write_graphviz() (psamm.graph.Graph method)
write_graphviz_compartmentalized() (psamm.graph.Graph method)
write_model() (psamm.datasource.sbml.SBMLWriter method)
(psamm.translate_id.TranslatedModel method)
write_network_dict() (in module psamm.graph)
write_nodes_tables() (psamm.graph.Graph method)
write_reactions() (psamm.datasource.native.ModelWriter method)
write_yaml_model() (in module psamm.importer)
Y
yaml_load() (in module psamm.datasource.native)
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