Index

_ | A | B | C | D | E | F | G | H | I | K | L | M | N | O | P | Q | R | S | T | U | V | W | Y

_

__add__() (psamm.expression.affine.Expression method)
(psamm.formula.FormulaElement method)
(psamm.lpsolver.lp.Expression method)
__array__() (psamm.database.StoichiometricMatrixView method)
__bool__() (psamm.lpsolver.lp.Result method)
__div__() (psamm.expression.affine.Expression method)
__eq__() (psamm.expression.affine.Expression method)
(psamm.expression.affine.Variable method)
(psamm.lpsolver.lp.Expression method)
(psamm.metabolicmodel.FluxBounds method)
(psamm.reaction.Reaction method)
__ge__() (psamm.expression.affine.Variable method)
(psamm.formula.Atom method)
(psamm.lpsolver.lp.Expression method)
(psamm.reaction.Compound method)
__gt__() (psamm.expression.affine.Variable method)
(psamm.formula.Atom method)
(psamm.lpsolver.lp.Expression method)
(psamm.reaction.Compound method)
__iter__() (psamm.metabolicmodel.FluxBounds method)
__le__() (psamm.expression.affine.Variable method)
(psamm.formula.Atom method)
(psamm.lpsolver.lp.Expression method)
(psamm.reaction.Compound method)
__lt__() (psamm.lpsolver.lp.Expression method)
__mul__() (psamm.expression.affine.Expression method)
(psamm.formula.Formula method)
(psamm.formula.FormulaElement method)
__ne__() (psamm.metabolicmodel.FluxBounds method)
__nonzero__() (psamm.lpsolver.lp.Result method)
__or__() (psamm.formula.Formula method)
(psamm.formula.FormulaElement method)
__radd__() (psamm.lpsolver.lp.Expression method)
__sub__() (psamm.expression.affine.Expression method)
__truediv__() (psamm.expression.affine.Expression method)
__unicode__() (psamm.formula.Formula method)
(psamm.lpsolver.lp.Expression method)
(psamm.lpsolver.lp.Relation method)
(psamm.reaction.Compound method)

A

add_all_database_reactions() (psamm.metabolicmodel.MetabolicModel method)
add_all_exchange_reactions() (psamm.metabolicmodel.MetabolicModel method)
add_all_transport_reactions() (psamm.metabolicmodel.MetabolicModel method)
add_linear_constraints() (psamm.lpsolver.cplex.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)
boundary (psamm.datasource.sbml.SpeciesEntry attribute)
bounds (psamm.metabolicmodel.FluxBounds attribute)

C

ChainedDatabase (class in psamm.database)
charge (psamm.datasource.sbml.SpeciesEntry attribute)
charge_balance() (in module psamm.balancecheck)
check_compound_consistency() (in module psamm.massconsistency)
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)
compartments (psamm.database.MetabolicDatabase attribute)
Compound (class in psamm.reaction)
CompoundEntry (class in psamm.datasource.kegg)
(class in psamm.datasource.modelseed)
(class in psamm.datasource.native)
compounds (psamm.database.MetabolicDatabase attribute)
(psamm.reaction.Reaction attribute)
consistency_check() (in module psamm.fluxanalysis)
Constraint (class in psamm.lpsolver.cplex)
(class in psamm.lpsolver.gurobi)
(class in psamm.lpsolver.lp)
(class in psamm.lpsolver.qsoptex)
copy() (psamm.metabolicmodel.MetabolicModel method)
CouplingClass (class in psamm.fluxcoupling)
cplex (psamm.lpsolver.cplex.Problem attribute)
create_extended_model() (in module psamm.fastgapfill)
create_metabolic_model() (psamm.datasource.native.NativeModel method)
create_problem() (psamm.lpsolver.cplex.Solver method)
(psamm.lpsolver.generic.Solver method)
(psamm.lpsolver.gurobi.Solver method)
(psamm.lpsolver.lp.Solver method)
(psamm.lpsolver.qsoptex.Solver method)

D

decode_name() (in module psamm.datasource.modelseed)
define() (psamm.lpsolver.cplex.Problem method)
(psamm.lpsolver.gurobi.Problem method)
(psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.qsoptex.Problem method)
delete() (psamm.lpsolver.lp.Constraint method)
DictDatabase (class in psamm.database)
Direction (class in psamm.reaction)
direction (psamm.reaction.Reaction attribute)

E

equation (psamm.datasource.sbml.ReactionEntry attribute)
ExecutorError
expr() (psamm.lpsolver.lp.Problem method)
Expression (class in psamm.expression.affine)
(class in psamm.expression.boolean)
(class in psamm.lpsolver.lp)
expression (psamm.lpsolver.lp.Relation 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)
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)
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.sbml.SpeciesEntry attribute)
formula_balance() (in module psamm.balancecheck)
FormulaElement (class in psamm.formula)
forward (psamm.reaction.Direction attribute)

G

gapfill() (in module psamm.gapfill)
GapFillError
gapfind() (in module psamm.gapfill)
GeneDeletionStrategy (class in psamm.randomsparse)
get_biomass_reaction() (psamm.datasource.native.NativeModel method)
get_compound_reactions() (psamm.database.MetabolicDatabase method)
(psamm.metabolicmodel.MetabolicModel method)
get_default_flux_limit() (psamm.datasource.native.NativeModel method)
get_exchange_reactions() (in module psamm.randomsparse)
get_extracellular_compartment() (psamm.datasource.native.NativeModel method)
get_flux() (psamm.fluxanalysis.FluxBalanceProblem method)
get_flux_var() (psamm.fluxanalysis.FluxBalanceProblem method)
get_gene_associations() (in module psamm.randomsparse)
get_name() (psamm.datasource.native.NativeModel method)
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.gurobi.Result method)
(psamm.lpsolver.lp.Result method)
(psamm.lpsolver.qsoptex.Result method)
gurobi (psamm.lpsolver.gurobi.Problem attribute)

H

has_model_definition() (psamm.datasource.native.NativeModel method)
has_reaction() (psamm.database.MetabolicDatabase method)
has_value() (psamm.expression.boolean.Expression method)
has_variable() (psamm.lpsolver.cplex.Problem method)
(psamm.lpsolver.gurobi.Problem method)
(psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.qsoptex.Problem method)

I

id (psamm.datasource.sbml.ReactionEntry attribute)
(psamm.datasource.sbml.SBMLReader attribute)
in_compartment() (psamm.reaction.Compound method)
init_parser() (psamm.command.Command class method)
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

kinetic_law_reaction_parameters (psamm.datasource.sbml.ReactionEntry attribute)

L

left (psamm.reaction.Reaction attribute)
LimitsView (class in psamm.metabolicmodel)
list_solvers() (in module psamm.lpsolver.generic)
load_model() (psamm.metabolicmodel.MetabolicModel class method)
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)
MetabolicDatabase (class in psamm.database)
MetabolicMixin (class in psamm.command)
MetabolicModel (class in psamm.metabolicmodel)
minimize_l1() (psamm.fluxanalysis.FluxBalanceProblem method)

N

name (psamm.datasource.sbml.ReactionEntry attribute)
(psamm.datasource.sbml.SBMLReader attribute)
(psamm.datasource.sbml.SpeciesEntry attribute)
(psamm.reaction.Compound attribute)
NativeModel (class in psamm.datasource.native)
normalized() (psamm.reaction.Reaction method)

O

ObjectiveEntry (class in psamm.datasource.sbml)
objectives (psamm.datasource.sbml.SBMLReader attribute)
ObjectiveSense (class in psamm.lpsolver.lp)
offset (psamm.lpsolver.lp.Expression 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_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.NativeModel method)
parse_limit() (in module psamm.datasource.native)
parse_limits() (psamm.datasource.native.NativeModel 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.NativeModel 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.NativeModel 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_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.NativeModel 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.gurobi)
(class in psamm.lpsolver.lp)
(class in psamm.lpsolver.qsoptex)
Product (class in psamm.lpsolver.lp)
properties (psamm.datasource.sbml.ReactionEntry attribute)
(psamm.datasource.sbml.SpeciesEntry attribute)
psamm.balancecheck (module)
psamm.command (module)
psamm.database (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.lpsolver.cplex (module)
psamm.lpsolver.generic (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)

Q

qsoptex (psamm.lpsolver.qsoptex.Problem attribute)

R

Radical (class in psamm.formula)
random_sparse() (in module psamm.randomsparse)
Reaction (class in psamm.reaction)
reaction_charge() (in module psamm.balancecheck)
reaction_formula() (in module psamm.balancecheck)
ReactionDeletionStrategy (class in psamm.randomsparse)
ReactionEntry (class in psamm.datasource.kegg)
(class in psamm.datasource.native)
(class in psamm.datasource.sbml)
ReactionParser (class in psamm.datasource.reaction)
reactions (psamm.database.MetabolicDatabase attribute)
(psamm.datasource.sbml.SBMLReader attribute)
Relation (class in psamm.lpsolver.lp)
remove_reaction() (psamm.metabolicmodel.MetabolicModel method)
repeat() (psamm.formula.FormulaElement method)
RequirementsError
Result (class in psamm.lpsolver.cplex)
(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)
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)
set_linear_objective() (psamm.lpsolver.cplex.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.gurobi.Problem method)
(psamm.lpsolver.lp.Problem method)
(psamm.lpsolver.qsoptex.Problem method)
set_objective_sense() (psamm.lpsolver.cplex.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.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.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.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.gurobi.Result attribute)
(psamm.lpsolver.lp.Result attribute)
(psamm.lpsolver.qsoptex.Result attribute)
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.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.expression.boolean.Expression attribute)
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)
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)

W

whendefined() (in module psamm.datasource.native)
write_model() (psamm.datasource.sbml.SBMLWriter method)

Y

yaml_load() (in module psamm.datasource.native)