pycotools3.model.Model¶

class pycotools3.model.Model(copasi_file, quantity_type='concentration', new=False, **kwargs)[source]¶

Construct a pycotools3 model from a copasi file

The Model object is of central importance in pycotools as it extracts relevant information from a copasi file file into python.

These are Model attributes and properties:

Examples

>>> from pycotools3.model import Model
>>> model_path = r'/full/path/to/model.cps'
>>> model = Model(model_path) ##work in concentration units
>>> model = Model(model_path, quantity_type='particle_numbers') ## work in particle numbers

Property	Description
copasi_file	Full path to model
root	Full path directory containing model
reference	Copasi model reference
time_unit	Time unit
name	Model name
volume_unit	Volume unit
quantity_unit	Quantity unit
area_unit	Area Unit
length_unit	Length unit
avagadro	Avagadro’s number
key	Model key
states	List of states in correct order defined by copasi StateTemplate element.
fit_item_order	Order in which fit items appear
all_variable_names	List of reactions, metabolites, global_quantities local_parameters, compartment names as string
number_of_reactions	Number of reactions in `model.Model`

__init__(copasi_file, quantity_type='concentration', new=False, **kwargs)[source]¶

Parameters:	copasi_file (str) – full path to a copasi file quantity_type (str) – either ‘concentration’ (default) or ‘particle_numbers’ new (bool) – True when constructing a new model

Methods

__init__(copasi_file[, quantity_type, new])

param copasi_file:
	full path to a copasi file

add(component_name, **kwargs) add a model component to the model

add_compartment(compartment) Add compartment to model

add_component(component_name, component[, …]) add a model component to the model

add_function(function) Add function to model

add_global_quantity(global_quantity) Add global quantity to model

add_local_parameter(local_parameter) Add a local parameter to the model, specifically into the String=’kinetic Parameters’ section of parameter sets

add_metabolite(metab) Add a metabolite to the model xml

add_reaction(reaction[, expression, rate_law])

param reaction:	py:class:Reaction or str. If str then

add_state(state, value) Append state on to end of state template.

convert_molar_to_particles(moles, mol_unit, …) Convert molarity to particle numbers

convert_particles_to_molar(particles, …) Converts particle numbers to Molarity.

get(component, value[, by]) Factory method for getting a model component by a value of a certain type

get_variable_names([which, …]) Get the names of variables in the model.

insert_parameters(**kwargs) Wrapper around the InsetParameters class

open([copasi_file, as_temp]) Open model with the gui.

refresh() Save the file then reload the Model.

remove(component, name) General factor method for removing model components

remove_compartment(value[, by]) Remove a compartment with the attribute given as the ‘by’ and value arguments

remove_function(value[, by]) remove a function from model

remove_global_quantity(value[, by]) Remove a global quantity from your model

remove_metabolite(value[, by]) Remove metabolite from model.

remove_reaction(value[, by]) Remove reaction

remove_state(state) Remove state from StateTemplate and InitialState fields.

reset_cache(prop) Delete property from cache then reset it

save([copasi_file]) Save copasiML to copasi_filename.

scan([inplace]) Perform a parameter scan on model

set(component, match_value, new_value[, …]) Set a model components attribute to a new value

simulate(start, stop, by[, variables])

to_antimony() Args:

to_df() Convert kwargs to 1D df :return: pandas.DataFrame

to_dict() get kwargs as dictionary :return: dict

to_sbml([sbml_file]) convert model to sbml

to_string() Produce kwargs as string format for using in __str__ methods in subclasses.

Attributes

`active_parameter_set`	get active parameter set
`all_variable_names`	The names of all compartments, metabolites, global quantities, reactions and local parameters in the model.
`area_unit`	str. The currently defined area unit.
`avagadro`	Not really needed but good to check the consistancy of avagadros number.
`compartments`	Get list of model compartments
`constants`	Get list of constants from xml attribute `cn=”String=Kinetic Parameters”
`copasi_file`	`Model`
`fit_item_order`	Get names of parameters being fitted in the order they appear
`functions`	get model functions
`global_quantities`	list each element is `GlobalQuantity`
`key`	Get the model reference - the ‘key’ from self.get_model_units
`length_unit`	str
`local_parameters`	Get local parameters in model.
`metabolites`	list. Each element is `Metabolite`
`name`	str. The model name
`number_of_reactions`	int number of reactions
`parameter_descriptions`	list. Each element a `ParameterDescription`
`parameter_sets`	Here for potential future implementation of easy switching between parameter sets :return:
`parameters`	get all locals, globals and metabs as pandas dataframe
`quantity_unit`	str. The currently defined quantity unit
`reactions`	assemble a list of reactions
`reference`	Get model reference from xml
`root`	Root directory for model.
`states`	The states (metabolites, globals, compartments) in the order they are read by Copasi from the StateTemplate element.
`time_unit`	str current time unit defined by copasi
`volume_unit`	str. The currently defined volume unit

active_parameter_set¶

get active parameter set

Not really in use

Returns:	`etree.Element`

Args:

Returns:

add(component_name, **kwargs)[source]¶

add a model component to the model

Parameters:

component_name – str`. i.e. ‘reaction’, ‘function’, ‘metabolite
component – py:class:model.<component>. The component class to add i.e. Metabolite
reaction_expression – When adding reaction using string as first arg, this argument takes the reaction expression (i.e. A -> B)
reaction_rate_law – When adding reaction using string as first argument this argument takes the reaction rate law (i.e. k*A)
**kwargs –

Returns:

py:class:`Model

add_compartment(compartment)[source]¶

Add compartment to model

Parameters:	compartment – py:class:Compartment
Returns:	py:class:Model

add_component(component_name, component, reaction_expression=None, reaction_rate_law=None)[source]¶

add a model component to the model

Parameters:	component_name – str`. i.e. ‘reaction’, ‘function’, ‘metabolite component – py:class:model.<component>. The component class to add i.e. Metabolite reaction_expression – When adding reaction using string as first arg, this argument takes the reaction expression (i.e. A -> B) (Default value = None) reaction_rate_law – When adding reaction using string as first argument this argument takes the reaction rate law (i.e. k*A) (Default value = None)
Returns:	class:`Model
Return type:	py

add_function(function)[source]¶

Add function to model

Parameters:	function – py:class:Function.
Returns:	py:class:Model

add_global_quantity(global_quantity)[source]¶

Add global quantity to model

Parameters:	global_quantity – str` or `GlobalQuantity`. If str

is the name of global_quantity to add and default GlobalQuantity properties are adopted. If GlobalQuantity, a GlobalQuantity instance must be prebuilt and passes as arg.

Returns:	py:class:Model

add_local_parameter(local_parameter)[source]¶

Add a local parameter to the model, specifically into the String=’kinetic Parameters’ section of parameter sets

Parameters:	local_parameter – py:class:LocalParameter
Returns:	py:class:Model

add_metabolite(metab)[source]¶

Add a metabolite to the model xml

Parameters:	metab – str` or `Metabolite`. If str

is the name of metabolite to add and default Metabolite properties are adopted. If Metabolite, a Metabolite instance must be prebuilt and passes as arg.

Returns:	py:class:Model

add_reaction(reaction, expression=None, rate_law=None)[source]¶

Parameters:	reaction – py:class:Reaction or str. If str then

must be the name of the reaction.: expression: (Default value = None) rate_law: (Default value = None)

Returns:	py:class:Model

add_state(state, value)[source]¶

Append state on to end of state template. Used within add_metabolite and add_global_quantity. Shouldn’t need to use manually

Parameters:	state – str`. A valid key value – int`, float. Value for state

Returns:

all_variable_names¶

The names of all compartments, metabolites, global quantities, reactions and local parameters in the model.

Returns:	list. Each element is str

Args:

Returns:

area_unit¶

str. The currently defined area unit.

Args:

Returns:

Type:	return

avagadro¶

Not really needed but good to check the consistancy of avagadros number.

This number was changed between version 16 and 19 and caused a bug

Args:

Returns:

compartments¶

Get list of model compartments

Returns:	list. Each element is `Compartment`

Args:

Returns:

constants¶

Get list of constants from xml attribute `cn=”String=Kinetic Parameters”

Returns:	list each element `LocalParameter`

static convert_molar_to_particles(moles, mol_unit, compartment_volume)[source]¶

Convert molarity to particle numbers

Parameters:	moles – int` or float. Number of moles in mol_unit to convert mol_unit – str`. Mole unit to convert from.

suppoerted: fmol, pmol, nmol, umol, mmol or mol: compartment_volume: int` or float. Volume of compartment containing specie to convert

Returns:	int`. number of particles

static convert_particles_to_molar(particles, mol_unit, compartment_volume)[source]¶

Converts particle numbers to Molarity.

##TODO build support for copasi’s newest units

Parameters:	particles – int` Number of particles to convert mol_unit – str`. The quantity unit, i.e:

fmol, pmol, nmol, umol, mmol or mol: compartment_volume: int`, float. Volume of compartment containing specie to convert

Returns:	float`. Molarity

copasi_file¶

Model

Type:	Returns

fit_item_order¶

Get names of parameters being fitted in the order they appear

Returns:	list

Args:

Returns:

functions¶

get model functions

Returns:	list each element a py:class:`Function

get(component, value, by='name')[source]¶

Factory method for getting a model component by a value of a certain type

Parameters:

component – str`. The component i.e. metabolite or local_parameter
value – str`. Value of the attribute to match by i.e. metabolite called A
by – str`. Which attribute to search by. i.e. name or key or value (Default value = ‘name’)

Returns:

py:class:Model.<component>`

Get reaction called A2B:

Get metabolite called A:

Get all reactions which have a fixed simulation_type:

Get all compartments with an initial value of 15 (concentration or particles depending on quantity_type):

Get metabolites in the nucleus compartment:

Return type:

Instance of `

>>> model.get('reaction', 'A2B', by='name')

>>> model.get('metabolite', 'A', by='name')

>>> model.get('global_quantity', 'fixed', by='simulation_type')

>>> model.get('compartment', 15, by='initial_value')

>>> model.get('metabolite', 'nuc', by='compartment')

get_model_object(string)[source]¶

Retrieve a model object, such as a parameter or metabolite :param string: name of parameter :type string: str

Returns:	correct model object

get_parameters_as_antimony()[source]¶: get parametes as antimony string Returns (string):

get_parameters_as_dict()[source]¶: Uses :py:meth:`model.Model.get_parameters_as_antimony then converts into a dict. Returns:

get_variable_names(which='a', include_assignments=True, prefix=None)[source]¶

Get the names of variables in the model. If include_assignments is off these are ommited from the results (this is useful for ParameterEstimation) as they are not generally estimated. Prefix provides a way of filtering the returned list

Parameters:

which – string. Default=’a’. A string containing any or all of characters ‘a’, ‘m’, ‘g’, ‘l’, ‘c’ for all, metabolites, global_quantities, local_parameters and compartments respectively
include_assignments – Boolean. Default=True. If True, return global variables with assignments
prefix – str. Default=None. If given, returned parameter names are filtered to only include parameter with prerfix at the begining.

Returns:

‘list’ of variable names

global_quantities¶

list each element is GlobalQuantity

Args:

Returns:

Type:	return

insert_parameters(**kwargs)[source]¶

Wrapper around the InsetParameters class

Parameters:	kwargs – Arguments for InsertParameters **kwargs –
Returns:	py:class:Model

key¶

Get the model reference - the ‘key’ from self.get_model_units

Returns:	str

Args:

Returns:

length_unit¶

str

Args:

Returns:

Type:	return

local_parameters¶

Get local parameters in model. local_parameters are those which are actively used in reactions and do not have a global variable assigned to them. The constant property returns all local parameters regardless of simulation type (fixed or assignment)

Returns:	list. Each element is `LocalParameter`

Args:

Returns:

metabolites¶

list. Each element is Metabolite

Args:

Returns:

Type:	return

name¶

str. The model name

Args:

Returns:

Type:	return

number_of_reactions¶

int number of reactions

Args:

Returns:

Type:	return

open(copasi_file=None, as_temp=False)[source]¶

Open model with the gui. In order to work the environment variables must be properly set so that the command CopasiUI in the terminal or command prompt opens the model.

First Model.save() the model to copasi_file then open with CopasiUI. Optionally open with a temporary filename.

Parameters:	copasi_file – str` or None. Same as `model.Save()` (Default value = None) as_temp – bool`. Use temp file to open the model and remove

afterwards (Default value = False)

Returns:	None`

parameter_descriptions¶

list. Each element a ParameterDescription

Args:

Returns:

Type:	return

parameter_sets¶

Here for potential future implementation of easy switching between parameter sets :return:

Args:

Returns:

parameters¶

get all locals, globals and metabs as pandas dataframe

Returns:	`pandas.DataFrame`

Args:

Returns:

quantity_unit¶

str. The currently defined quantity unit

Args:

Returns:

Type:	return

reactions¶

assemble a list of reactions

Returns:	list each element a `Reaction`

reference¶

Get model reference from xml

Returns:	str

Args:

Returns:

refresh()[source]¶

Save the file then reload the Model. Can’t use the save method though because the save method uses the refresh method. :return:

Args:

Returns:

remove(component, name)[source]¶

General factor method for removing model components

Parameters:	component – str` which component to remove (i.e. metabolite) name – str` name of component to remove
Returns:	py:class:Model

remove_compartment(value, by='name')[source]¶

Remove a compartment with the attribute given as the ‘by’ and value arguments

Parameters:	value – str`. Value of attribute to match i.e. ‘Nucleus’ by – str` which attribute to match i.e. ‘name’ or ‘key’ (Default value = ‘name’)
Returns:	py:class:Model

remove_function(value, by='name')[source]¶

remove a function from model

Parameters:	value – str` value of attribute to match (i.e the functions name) by – str` which attribute to match by. default=’name’
Returns:	py:class:model.Model

remove_global_quantity(value, by='name')[source]¶

Remove a global quantity from your model

Parameters:	value – value to match by (i.e. ProteinA or ProteinB) by – attribute to match (i.e. name or key) (Default value = ‘name’)
Returns:	py:class:model.Model

remove_metabolite(value, by='name')[source]¶

Remove metabolite from model.

Parameters:

value – str`. Attribute value to remove
by – str` Any metabolite attribute type to match (Default value = ‘name’)

Returns:

py:class:Model

Usage: ## Remove attribute called ‘A’

## Remove metabolites with initial concentration of 0

>>> model.remove_metabolite('A', by='name')

>>> model.remove_metabolite(0, by='concentration')

remove_reaction(value, by='name')[source]¶

Remove reaction

Parameters:	value – str`. Value of attibute by – attribute of reaction to match default=’name

str which :py:class`Reaction` atrribute to match

Returns:	py:class:Model

remove_state(state)[source]¶

Remove state from StateTemplate and InitialState fields. USed for deleting metabolites and global quantities.

Parameters:	state – str`. key of state to remove (i.e. Metabolite_1)
Returns:	py:class:Model

reset_cache(prop)[source]¶

Delete property from cache then reset it

Parameters:	prop – str`. property to reset
Returns:	py:class:Model

root¶

Root directory for model. The directory where copasi_file is saved.

Does not need a setter since root is derived from copasi_file property

Returns:	str

Args:

Returns:

save(copasi_file=None)[source]¶

Save copasiML to copasi_filename.

Parameters:	copasi_filename – str` or None. Deafult is None. When None defaults to same filepath the model came from. If another path, saves to that path. copasi_file: (Default value = None)
Returns:	py:class:Model

scan(inplace=False, **kwargs)[source]¶

Perform a parameter scan on model

This is a wrapper around tasks.Scan and accepts all of the same arguments, except the model which is already provided.

Parameters:	**kwargs –

Returns:

sensitivities(inplace=False, **kwargs)[source]¶

Perform a sensitivity analysis on model

This is a wrapper around tasks.Sensitivities and accepts all of the same arguments, except the model which is already provided.

Parameters:	**kwargs –

Returns:

set(component, match_value, new_value, match_field='name', change_field='name')[source]¶

Set a model components attribute to a new value

Parameters:	component – str` type of component to change (i.e. metbaolite) match_value – str`, int, float depending on value of match_field.

The value to match.: new_value: str`, int or float depending on value of match_field
new value for component attribute: match_field: str`. The attribute of component to match by. (Default value = ‘name’) change_field: str` The attribute of the component matched that you want to change? (Default value = ‘name’)

Returns:

py:class:Model

Set initial concentration of metabolite called ‘X’ to 50:

Set name of global quantity called ‘G’ to ‘H’:

>>> model.set('metabolite', 'X', 50, match_field='name', change_field='concentration')

>>> model.set('global_quantity', 'G', 'H', match_field='name', change_field='name')

states¶

The states (metabolites, globals, compartments) in the order they are read by Copasi from the StateTemplate element.

Returns:	OrderedDict

Args:

Returns:

time_unit¶

str current time unit defined by copasi

Args:

Returns:

Type:	return

to_antimony()[source]¶

Args:

Returns:	return:

to_sbml(sbml_file=None)[source]¶

convert model to sbml

Parameters:	sbml_file – str`. Path for SBML. Defaults to same as copasi filename
Returns:	str`. Path to smbl file

to_tellurium()[source]¶: return a roadrunner model via the tellurium package Returns:

volume_unit¶

str. The currently defined volume unit

Args:

Returns:

Type:	return