PSAMM
v0.29
Overview
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Command line interface
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PSAMM API
References
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Index
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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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H
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I
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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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Q
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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
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Y
A
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_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_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)
biomass_reaction (psamm.datasource.native.ModelReader attribute)
(psamm.datasource.native.NativeModel attribute)
boundary (psamm.datasource.sbml.SpeciesEntry attribute)
bounds (psamm.metabolicmodel.FluxBounds attribute)
C
ChainedDatabase (class in psamm.database)
charge (psamm.datasource.entry.CompoundEntry attribute)
(psamm.datasource.sbml.SpeciesEntry attribute)
charge_balance() (in module psamm.balancecheck)
check_compound_consistency() (in module psamm.massconsistency)
check_constraints() (psamm.fluxanalysis.FluxBalanceProblem method)
check_reaction_consistency() (in module psamm.massconsistency)
classify_coupling() (in module psamm.fluxcoupling)
Command (class in psamm.command)
CommandError
compartment (psamm.datasource.sbml.SpeciesEntry attribute)
(psamm.reaction.Compound attribute)
compartment_boundaries (psamm.datasource.native.NativeModel attribute)
CompartmentEntry (class in psamm.datasource.entry)
(class in psamm.datasource.sbml)
compartments (psamm.database.MetabolicDatabase attribute)
(psamm.datasource.native.NativeModel attribute)
(psamm.datasource.sbml.SBMLReader attribute)
Compound (class in psamm.reaction)
CompoundEntry (class in psamm.datasource.entry)
(class in psamm.datasource.kegg)
(class in psamm.datasource.modelseed)
CompoundMapper (class in psamm.datasource.kegg)
compounds (psamm.database.MetabolicDatabase attribute)
(psamm.datasource.native.NativeModel 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)
ContextError
convert_compartment_entry() (psamm.datasource.native.ModelWriter method)
convert_compound_entry() (psamm.datasource.native.ModelWriter method)
convert_reaction_entry() (psamm.datasource.native.ModelWriter method)
convex_cardinality_relaxed() (in module psamm.util)
copy() (psamm.metabolicmodel.MetabolicModel method)
CouplingClass (class in psamm.fluxcoupling)
cplex (psamm.lpsolver.cplex.Problem attribute)
CplexRangedProperty (class in psamm.lpsolver.cplex)
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)
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)
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.lp.Constraint method)
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)
Direction (class in psamm.reaction)
direction (psamm.reaction.Reaction attribute)
E
equation (psamm.datasource.entry.ReactionEntry attribute)
(psamm.datasource.sbml.ReactionEntry 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)
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
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)
FilePathContext (class in psamm.datasource.context)
FilePrefixAppendAction (class in psamm.command)
filter_solvers() (in module psamm.lpsolver.generic)
flattened() (psamm.formula.Formula 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)
FluxBoundEntry (class in psamm.datasource.sbml)
FluxBounds (class in psamm.metabolicmodel)
FluxCouplingProblem (class in psamm.fluxcoupling)
Formula (class in psamm.formula)
formula (psamm.datasource.entry.CompoundEntry attribute)
(psamm.datasource.sbml.SpeciesEntry attribute)
formula_balance() (in module psamm.balancecheck)
FormulaElement (class in psamm.formula)
forward (psamm.reaction.Direction attribute)
FrozenOrderedSet (class in psamm.util)
G
gapfill() (in module psamm.gapfill)
GapFillError
gapfind() (in module psamm.gapfill)
GeneDeletionStrategy (class in psamm.randomsparse)
genes (psamm.datasource.entry.ReactionEntry attribute)
get_compartment() (psamm.datasource.sbml.SBMLReader method)
get_compound_reactions() (psamm.database.MetabolicDatabase method)
(psamm.metabolicmodel.MetabolicModel method)
get_exchange_reactions() (in module psamm.randomsparse)
get_flux() (psamm.fluxanalysis.FluxBalanceProblem method)
get_flux_var() (psamm.fluxanalysis.FluxBalanceProblem method)
get_gene_associations() (in module psamm.randomsparse)
get_objective() (psamm.datasource.sbml.SBMLReader method)
get_reaction() (psamm.database.MetabolicDatabase method)
(psamm.datasource.sbml.SBMLReader method)
get_reaction_values() (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
gurobi (psamm.lpsolver.gurobi.Problem attribute)
H
has_model_definition() (psamm.datasource.native.ModelReader method)
has_reaction() (psamm.database.MetabolicDatabase 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.datasource.entry.ModelEntry attribute)
(psamm.datasource.sbml.FluxBoundEntry attribute)
(psamm.datasource.sbml.ReactionEntry attribute)
(psamm.datasource.sbml.SBMLReader attribute)
in_compartment() (psamm.reaction.Compound method)
init_parser() (psamm.command.Command class method)
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_reversible() (psamm.database.MetabolicDatabase method)
(psamm.metabolicmodel.MetabolicModel method)
items() (psamm.formula.Formula method)
K
KEGGEntry (class in psamm.datasource.kegg)
kinetic_law_reaction_parameters (psamm.datasource.sbml.ReactionEntry attribute)
L
left (psamm.reaction.Reaction attribute)
limits (psamm.datasource.native.NativeModel attribute)
LimitsView (class in psamm.metabolicmodel)
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)
M
main() (in module psamm.command)
MassConsistencyError
matrix (psamm.database.MetabolicDatabase attribute)
max_min_l1() (psamm.fluxanalysis.FluxBalanceProblem method)
maximize() (psamm.fluxanalysis.FluxBalanceProblem method)
MaybeRelative (class in psamm.util)
MetabolicDatabase (class in psamm.database)
MetabolicMixin (class in psamm.command)
MetabolicModel (class in psamm.metabolicmodel)
minimize_l1() (psamm.fluxanalysis.FluxBalanceProblem method)
MIPResult (class in psamm.lpsolver.glpk)
model (psamm.datasource.native.NativeModel attribute)
ModelEntry (class in psamm.datasource.entry)
ModelReader (class in psamm.datasource.native)
ModelWriter (class in psamm.datasource.native)
N
name (psamm.datasource.entry.ModelEntry attribute)
(psamm.datasource.native.ModelReader attribute)
(psamm.datasource.native.NativeModel attribute)
(psamm.datasource.sbml.FluxBoundEntry attribute)
(psamm.datasource.sbml.ReactionEntry attribute)
(psamm.datasource.sbml.SBMLReader attribute)
(psamm.datasource.sbml.SpeciesEntry attribute)
(psamm.reaction.Compound attribute)
namespace() (psamm.lpsolver.lp.Problem method)
NativeModel (class in psamm.datasource.native)
normalized() (psamm.reaction.Reaction method)
O
ObjectiveEntry (class in psamm.datasource.sbml)
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.FluxBoundEntry 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
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_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_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)
ParseError
,
[1]
,
[2]
,
[3]
,
[4]
,
[5]
prob (psamm.fluxanalysis.FluxBalanceProblem 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.sbml.CompartmentEntry attribute)
(psamm.datasource.sbml.ReactionEntry attribute)
(psamm.datasource.sbml.SpeciesEntry attribute)
psamm.balancecheck (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.lpsolver.cplex (module)
psamm.lpsolver.generic (module)
psamm.lpsolver.glpk (module)
psamm.lpsolver.gurobi (module)
psamm.lpsolver.lp (module)
psamm.lpsolver.qsoptex (module)
psamm.massconsistency (module)
psamm.metabolicmodel (module)
psamm.randomsparse (module)
psamm.reaction (module)
psamm.util (module)
Q
qsoptex (psamm.lpsolver.qsoptex.Problem attribute)
R
Radical (class in psamm.formula)
random_sparse() (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.FluxBoundEntry attribute)
reaction_charge() (in module psamm.balancecheck)
reaction_formula() (in module psamm.balancecheck)
ReactionDeletionStrategy (class in psamm.randomsparse)
ReactionEntry (class in psamm.datasource.entry)
(class in psamm.datasource.kegg)
(class in psamm.datasource.sbml)
ReactionMapper (class in psamm.datasource.kegg)
ReactionParser (class in psamm.datasource.reaction)
reactions (psamm.database.MetabolicDatabase attribute)
(psamm.datasource.native.NativeModel attribute)
(psamm.datasource.sbml.SBMLReader attribute)
reader_from_path() (psamm.datasource.native.ModelReader class method)
reference (psamm.util.MaybeRelative attribute)
Relation (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.lp.Problem attribute)
reverse (psamm.reaction.Direction attribute)
reversible (psamm.database.MetabolicDatabase attribute)
(psamm.datasource.sbml.ReactionEntry attribute)
right (psamm.reaction.Reaction attribute)
root (psamm.expression.boolean.Expression attribute)
run() (psamm.command.Command method)
S
SBMLReader (class in psamm.datasource.sbml)
SBMLWriter (class in psamm.datasource.sbml)
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.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)
species (psamm.datasource.sbml.SBMLReader attribute)
SpeciesEntry (class in psamm.datasource.sbml)
status (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)
StoichiometricMatrixView (class in psamm.database)
substitute() (psamm.expression.affine.Expression method)
(psamm.expression.affine.Variable method)
(psamm.expression.boolean.Expression method)
(psamm.formula.FormulaElement method)
SubstitutionError
success (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)
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)
translated_compounds() (psamm.reaction.Reaction method)
U
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)
upper (psamm.metabolicmodel.FlipableFluxBounds attribute)
(psamm.metabolicmodel.FluxBounds attribute)
V
value (psamm.datasource.sbml.FluxBoundEntry 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.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_model() (psamm.datasource.sbml.SBMLWriter method)
write_reactions() (psamm.datasource.native.ModelWriter method)
Y
yaml_load() (in module psamm.datasource.native)
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