Class kineticHandler

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Handles the input for alternative kinetics form the commandline or from the annotation of the root model.

Instance Methods

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__init__(self)

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{str:[str]}

getKinetics(self, string, document, macros)
Reads and processes 'string' for alternative kinetics from commandline.

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{str:[str]}

__getKineticsFromString(self, string, macros)
Reads different kinetics from the commandline argument -k/--kinetics

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{str:[str]}

__getKineticsFromModel(self, document)
Reads different kinetics from the root models annotation and writes them into a dictionary

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bool

checkReactionIds(self, ids)
Checks if all given ids have the correct form as it is given in the SBML definition.

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list

checkPartOfModel(self, model, ids)
Checks if reaction ids are part of a given model.

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getInvalidIds(self)

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getNonModelIds(self)

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Method Details

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getKinetics(self, string, document, macros)

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Reads and processes 'string' for alternative kinetics from commandline. Or if 'string' is empty reads the kinetics from the annotation of the root model. The string must follow the conventions of the parameter -k: "reaction(kinetic)"

Parameters:

string (str) - string of the form "reaction(kinetic)"
document (sbml.SBMLDocument) - the SBML document containing the root model

Returns: {str:[str]}

alternate kinetics for each reaction in the root model

__getKineticsFromString(self, string, macros)

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Reads different kinetics from the commandline argument -k/--kinetics

Returns: {str:[str]}: alternate kinetics for each reaction in the root model

__getKineticsFromModel(self, document)

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Reads different kinetics from the root models annotation and writes them into a dictionary

Returns: {str:[str]}: alternate kinetics for each reaction in the root model

checkReactionIds(self, ids)

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Checks if all given ids have the correct form as it is given in the SBML definition.

Parameters:

ids (list) - list of ids

Returns: bool

true if all ids match the right pattern, false otherwise

checkPartOfModel(self, model, ids)

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Checks if reaction ids are part of a given model.

Parameters:

model (sbml.SBMLModel) - the root model
ids (list) - list of ids

Returns: list

list of reactions that are in the model and in 'ids'