Index

_

_units (pykinetic.classes.Energy attribute)

A

ActE2k() (pykinetic.classes.Reaction static method) AE (pykinetic.classes.Reaction attribute)

as_str() (pykinetic.classes.ConvergenceParameters method) as_unit() (pykinetic.classes.Energy method)

B

Batch (class in pykinetic.writers.python)

BiasedChemicalSystem (class in pykinetic.utils)

C

cadd() (pykinetic.classes.ChemicalSystem method) calc_standard_state_correction() (in module pykinetic.utils) cextend() (pykinetic.classes.ChemicalSystem method) check_missing_compounds() (in module pykinetic.userinput) check_missing_TS() (in module pykinetic.userinput) ChemicalSystem (class in pykinetic.classes) clear() (pykinetic.writers._base.Writer method) (pykinetic.writers.cplusplus.CplusplusWriter method) coefficient() (pykinetic.classes.Reaction method) Compound (class in pykinetic.classes)

compounds (pykinetic.classes.ChemicalSystem attribute) (pykinetic.classes.Reaction attribute) constant() (pykinetic.writers._base.Writer method) (pykinetic.writers.cplusplus.CplusplusWriter method) (pykinetic.writers.python.Batch method) ConvergenceParameters (class in pykinetic.classes) copy() (pykinetic.classes.Compound method) CplusplusWriter (class in pykinetic.writers.cplusplus) create_compounds() (in module pykinetic.userinput) create_TS_dict() (in module pykinetic.userinput) cupdate() (pykinetic.classes.ChemicalSystem method)

D

DiffusionTS (class in pykinetic.classes)

E

Energy (class in pykinetic.classes)

F

fill() (pykinetic.writers._base.Writer method) (pykinetic.writers.cplusplus.CplusplusWriter method) (pykinetic.writers.python.SemiBatchExtended method)

I

Indent() (in module pykinetic.writers._base)

is_energy() (in module pykinetic.userinput)

J

jacobian() (pykinetic.classes.ChemicalSystem method) jacobian_element() (pykinetic.writers._base.Writer method) (pykinetic.writers.cplusplus.CplusplusWriter method) (pykinetic.writers.python.Batch method)

JacobianElement (class in pykinetic.classes)

K

k (pykinetic.classes.Reaction attribute)

key (pykinetic.classes.Reaction attribute)

M

MassBalance (class in pykinetic.classes) massbalance() (pykinetic.classes.ChemicalSystem method) (pykinetic.writers._base.Writer method) (pykinetic.writers.cplusplus.CplusplusWriter method) (pykinetic.writers.python.Batch method) (pykinetic.writers.python.SemiBatch method) MissingCompounds MissingTransitionStates

module pykinetic pykinetic.classes pykinetic.userinput pykinetic.utils pykinetic.writers._base pykinetic.writers.cplusplus pykinetic.writers.python

N

Name2Compound (pykinetic.classes.ChemicalSystem attribute)

Name2TS (pykinetic.classes.ChemicalSystem attribute)

P

Parameters (class in pykinetic.classes) partial() (pykinetic.classes.MassBalance method) PFR (class in pykinetic.writers.python) populate_chemicalsystem_fromfiles() (in module pykinetic.userinput) prepare_inline_TS() (in module pykinetic.userinput) products (pykinetic.classes.Reaction attribute) pykinetic module pykinetic.classes module

pykinetic.userinput module pykinetic.utils module pykinetic.writers._base module pykinetic.writers.cplusplus module pykinetic.writers.python module

R

radd() (pykinetic.classes.ChemicalSystem method) ratelaw() (pykinetic.writers._base.Writer method) (pykinetic.writers.cplusplus.CplusplusWriter method) (pykinetic.writers.python.Batch method) ratelaw_partial() (pykinetic.writers._base.Writer method) (pykinetic.writers.cplusplus.CplusplusWriter method) (pykinetic.writers.python.Batch method) reactants (pykinetic.classes.Reaction attribute)

Reaction (class in pykinetic.classes) reactions (pykinetic.classes.ChemicalSystem attribute) read_compounds() (in module pykinetic.userinput) read_from() (pykinetic.classes.Parameters class method) (pykinetic.classes.SimulationParameters class method) read_reactions() (in module pykinetic.userinput) rextend() (pykinetic.classes.ChemicalSystem method) rupdate() (pykinetic.classes.ChemicalSystem method) RxCMatrix() (pykinetic.classes.ChemicalSystem method)

S

ScannableChemicalSystem (class in pykinetic.utils) SemiBatch (class in pykinetic.writers.python) SemiBatchExtended (class in pykinetic.writers.python)

shape (pykinetic.classes.ChemicalSystem attribute) SimulationParameters (class in pykinetic.classes) species (pykinetic.classes.ChemicalSystem attribute) split_reaction_line() (in module pykinetic.userinput)

T

T (pykinetic.classes.ChemicalSystem attribute) (pykinetic.classes.Reaction attribute) to_SI() (pykinetic.classes.Energy method)

to_unit() (pykinetic.classes.Energy method) TransitionState (class in pykinetic.classes) transitionstates (pykinetic.classes.ChemicalSystem attribute) TS (pykinetic.classes.Reaction attribute)

U

unit (pykinetic.classes.Energy attribute)

V

value (pykinetic.classes.Energy attribute)

W

write() (pykinetic.writers._base.Writer method) (pykinetic.writers.cplusplus.CplusplusWriter method) (pykinetic.writers.python.Batch method)

write_indexfile() (in module pykinetic.utils) Writer (class in pykinetic.writers._base)