copyobj

R2026b

Copy SimBiology object and its children

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Syntax

copiedObj = copyobj(modelObj)
copiedObj = copyobj(object,parentObj)
copiedObj = copyobj(object,parentObj,conflictOption)

Description

copiedObj = copyobj(modelObj) makes a copy of a SimBiology model object modelObj and returns the copied model object copiedObj. The function also sets the Parent property of the copied model object to the root object. Use this function to create a copy of a model that you can then add as a submodel to build a model hierarchy.

copiedObj = copyobj(object,parentObj) makes a copy of a SimBiology object and returns the copied object. The function also sets the Parent property of the copied object to parentObj.

One exception is that if both object and parentObj are compartments, the Owner property of the copied object is set to parentObj instead.

example

copiedObj = copyobj(object,parentObj,conflictOption) specifies how to handle naming conflicts. (since R2024a)

example

Examples

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Open Live Script

Create a model object and add a reaction.

m1 = sbiomodel("m1");
c1 = addcompartment(m1,"c1");
r1 = addreaction(m1,"a -> b");

Create a copy of the reaction object and add it to another model. 

m2 = sbiomodel("m2");
r1copy = copyobj(r1,m2);

Create a copy of species a in the same compartment using the "force" option. The function adds the postfix "_1" to the name of the copied species to resolve the naming conflict.

a = m1.Species(1);
a_copy = copyobj(a,c1,"force")
a_copy = 
   SimBiology Species Array

   Index:    Compartment:    Name:    Value:    Units:    ParentModel:
   1         c1              a_1      0                   m1
Open Live Script

Build a PBPK model from a generic organ template using submodels, then use sbioselect and addequivalence to connect shared compartments and species across organ submodels.

Create a generic organ model with venous blood, arterial blood, and organ compartments, each containing a Drug species.

genericOrganModel = sbiomodel("Generic Organ");
venousComp = addcompartment(genericOrganModel,"Venous Blood",3000,Units="milliliter");
arterialComp = addcompartment(genericOrganModel,"Arterial Blood",1500,Units="milliliter");
organComp = addcompartment(genericOrganModel,"Organ",0.5e-10,Units="milliliter");
addspecies(venousComp,"Drug",0,Units="milligram/milliliter");
addspecies(arterialComp,"Drug",0,Units="milligram/milliliter");
addspecies(organComp,"Drug",0,Units="milligram/milliliter");
addparameter(genericOrganModel,"DrugBloodPlasmaRatio",0.8,Units="dimensionless");
addparameter(genericOrganModel,"DrugFractionUnbound",0.6,Units="dimensionless");

Build the PBPK model hierarchy by copying the generic organ model into multiple organ submodels using copyobj.

pbpkModel = sbiomodel("PBPK");
for organ = ["Gut","Liver","Lung","Heart","Brain","Kidney"]
    organModel = copyobj(genericOrganModel,pbpkModel);
    organModel.Name = organ + " submodel";
    organCompartment = sbioselect(organModel.Compartments,Name="Organ");
    rename(organCompartment,organ);
end

Inspect the submodel hierarchy.

pbpkModel.Models
ans = 
   SimBiology Model Array

   Index:    Name:              ParentModel:
   1         Gut submodel       PBPK        
   2         Liver submodel     PBPK        
   3         Lung submodel      PBPK        
   4         Heart submodel     PBPK        
   5         Brain submodel     PBPK        
   6         Kidney submodel    PBPK

Use sbioselect to find all Venous Blood compartments across submodels.

venousComps = sbioselect(pbpkModel,"Type","compartment","Name","Venous Blood")
venousComps = 
   SimBiology Compartment Array

   Index:    Name:           Value:    Units:        ParentModel:   
   1         Venous Blood    3000      milliliter    Gut submodel   
   2         Venous Blood    3000      milliliter    Liver submodel 
   3         Venous Blood    3000      milliliter    Lung submodel  
   4         Venous Blood    3000      milliliter    Heart submodel 
   5         Venous Blood    3000      milliliter    Brain submodel 
   6         Venous Blood    3000      milliliter    Kidney submodel

Use addequivalence to create an equivalence set grouping all Venous Blood compartments. During simulation, these compartments share a single resolved value.

eqVenous = addequivalence(pbpkModel,venousComps)
eqVenous = 
  EquivalenceSet with properties:

          ModelScope: [1×1 SimBiology.Model]
          Quantities: [6×1 SimBiology.Compartment]
    ResolvedQuantity: [1×1 SimBiology.Compartment]
            SuperSet: []
             SubSets: [6×1 SimBiology.EquivalenceSet]
         TopLevelSet: [1×1 SimBiology.EquivalenceSet]

Check which compartment is the resolved quantity. This is the quantity used in simulation and analysis workflows.

eqVenous.ResolvedQuantity
ans = 
   SimBiology Compartment - Venous Blood 

   Compartment Components:
     Value:             3000
     Units:             milliliter
     Compartments:      0
     Constant:          true
     Owner:             
     Species:           1
     ParentModel:       Gut submodel

Similarly, create an equivalence set for Arterial Blood compartments.

arterialComps = sbioselect(pbpkModel,"Type","compartment","Name","Arterial Blood");
eqArterial = addequivalence(pbpkModel,arterialComps);

Making compartments equivalent does not automatically make their species equivalent. Create equivalence sets for the Drug species in the Venous Blood and Arterial Blood compartments.

venousDrugSpecies = sbioselect(venousComps,"Type","species","Name","Drug");
eqVenousDrug = addequivalence(pbpkModel,venousDrugSpecies);

arterialDrugSpecies = sbioselect(arterialComps,"Type","species","Name","Drug");
eqArterialDrug = addequivalence(pbpkModel,arterialDrugSpecies);

Verify the equivalence sets on the model.

pbpkModel.EquivalenceSets
ans = 
  4×1 EquivalenceSet array with properties:

    ModelScope
    Quantities
    ResolvedQuantity
    SuperSet
    SubSets
    TopLevelSet

Input Arguments

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SimBiology model component, specified as a Model, Compartment, Reaction, KineticLaw, or Root object.

If the input object is...parentObj must be...

Configset, Event, Reaction, Rule, RepeatDose, ScheduleDose, Variant, or Observable object

Model object

Compartment object

Compartment or Model object

Species object

Compartment object

Parameter object

Model or KineticLaw object

KineticLaw object

Reaction object

Model object

Root or Model object

SimBiology model, specified as a Model object.

Method to resolve naming conflicts, specified as a character vector or string. Valid options are:

  • "force" — The function copies the model component but renames the copied component if there is a naming conflict by appending "_N", where N is a positive integer. For example, when you try to make a copy of a species inside the same compartment, the "force" option creates a copied species, which has the same name as the original species with a postfix "_N". For details, see Guidelines for Naming Model Components.

  • "strict" — The function throws an error and will not copy the model component if there is a naming conflict.

Note

There are some exceptions for this option, and it works for a subset of model components.

  • Compartment, dose, event, observable, parameter, rule, species, and variant objects support this option.

  • Configset and reaction objects do not have this option, but the copied object and any reaction-scoped parameters are always renamed as needed.

  • KineticLaw objects do not have or need this option.

Version History

Introduced in R2006a

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See Also

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