Naming Conventions

Naming Conventions The intent of naming conventions is to allow programmers, which are not familiar with the code to easily grasp the meaning and scope of symbols in the source code. Each programmer of COPASI should adhere for its own benefit and to the advantage of the project to the following conventions. Class Names Class names must all start with a capital letter C. This is followed by a descriptive name. This name might be composed by different words. These words must all start with capital letters and are concatenated without underscores. Good examples for class names include: CCopasiXMLParser , CExpatTemplate, and CMathModel. Variable Names In general a variable name should be descriptive. This name might be composed by different words. These words must all start with capital letters and are concatenated without underscores. In addition the following standards should be followed: Counters might be used such as i, k, and l, which may be used in loops. Iterators might be used such as it and end, which may be used in loops. Pointers are prepended with a lower case letter p. Method Parameters must start with a lower case letter. Class Member Variables are prepended with a lower case letter m. Class Member Pointers must have the prefix mp. Method Name Method names should have a descriptive name starting with a lower case letter. This name might be composed by different words. These words beginning with the second must start with capital letters and are concatenated without underscores. Good examples for method names include: createMetabolite, compileIfNecessary, and buildMoieties In addition the following standards should be followed: Retrieval Methods must start with get followed by the member variable name without the prefix. Set Methods must start with set followed by the member variable name without the prefix. Boolean Query Functions should start if applicable with is. Program Code Guidelines Use of #include To minimize compilation problems on the different platforms and with the libraries COPASI depends on it is necessary to define some rules, which need to be followed when specifying include files in the COPASI code. The #include statement distinguishes between two different type of include files. Global Includes: Global include files are indicated by surrounding the filename with < and >, i.e. the statements looks like: #include <filename>. All files not located in the COPASI source tree are considered global includes. Local Includes: Local include files are indicated by surrounding the filename with double quotes, i.e. the statements looks like: #include "filename". All files located in the COPASI source tree are considered local includes. Order of #include in Header Files The number of include statements in header files should be kept to the minimum necessary to compile the header file, i.e., a COPASI code file just containing the following two lines of code must compile successfully: #include "copasi.h" #include "filename" To achieve the minimal list of includes one should replace all not needed includes with forward declarations as often as possible. Please note that it should never be necessary to include copasi.h in a header file. Qt Header Files: Qt header files must appear first. Please note that the Qt header file names are all lowercase. Global Header Files: Other global header files must appear next. COPASI Header Files: All COPASI header files must be included with the full filename starting with the copasi directory, i.e., the include statement looks like #include "copasi/.." Order of #include in Code Files Qt Header Files: Qt header files must appear first. Please note that the Qt header file names are all lowercase. Global Header Files: Other global header files must appear next. copasi.h: This file must precede all other local includes since they depend on the defines of copasi.h to be present. COPASI Header Files: COPASI header files must be included after copasi.h. blaswrap.h or clapackwrap.h: These two wrapper files must appear last as their defines often conflict with other includes. Loops Counter or iterators used in loops must not be declared in the for statement as the scope of the variables declared within is not well defined in C and C++ standard and thus leads to compile problems. The solution is to define those variables prior to the for statement. Code Documentation Class Documentation The COPASI team uses doxygen to generate API documentation. It is therefore necessary that the classes, methods, and variables or documented completely. Variable Documentation Method Documentation Incline Code Documentation COPASI Object Structure COPASI has an object structure which is used to access all objects which can be calculated, plotted, or printed. Objects can be grouped to larger objects called containers. COPASI itself functions as a root container, i.e., it contains all objects which might be of interest for calculation or output. The access to any object is provided with an LDAP like common name (CN) which can be resolved starting from any container. Object The object (class CCopasiObject) is the main building block of the object structure. Each object has the following main attributes: Attribute List std::string mObjectName The name of the object. std::string mObjectType The type of the object, e.g. Compartment. CCopasiContainer * mpObjectParent A pointer to the objects parent container. unsigned int mObjectFlag A flag indicating object properties. In addition to the expected get and set methods the objects provides the following methods: Method List CCopasiContainer * getObjectAncestor(const std::string &type) const This method retrieves the closest ancestor of the object of the specified type. virtual CCopasiObjectName getCN() const This method retrieve the common name (CN) of the object. Container COPASI Vector Parameter Parameter Group Dependencies The Model State State Template Order This section describes whether and in which order the above calculated simulation objects appear in the initial and current state of the model. The order is described by the class CStateTemplate. Please note that all objects with the type "Fixed" are marked "Unused" as there is no need to calculate them during simulation. State Template Order Object Type Status Model Time Used Model Value ODE Used Compartment ODE Used Metabolite ODE Used Metabolite Reaction Independent Metabolite Reaction Dependent Metabolite Assignment Used Compartment Assignment Used Model Value Assignment Used Any Any Unused

Setting the Initial State The initial state of a COPASI model is due to the introduction of assignments for all model entities no longer determined through fixed values. To calculate the current initial values those assignments have to be evaluated at t = T 0 . These evaluation will effect in many cases other initial values. For example the initial particle numbers of metabolites will change when a compartment's initial volume changes. To detemine the initial values, which need to be recalculated as well as the functions used for their calculation COPASI uses a dependecy system. In this system each initial value stores the information on which values it depends and which method to call to recalculated its value. Since the change of one initial value may now result in a complicated chain of updates for other initial values it no longer suffices to use its update method to set its value. We need to add an additional step which will update all values effected by the change. To retrive the list of needed refreshes in the proper order the class CModel provides the following method. vector<Refresh *> buildInitialRefreshSequence(set<const CCopasiObject *> &changedObjects); This method retrieves a vector of refresh methods, which must be called to update all other initial values given a set of changed objects. If the set of changed objects is empty the method will return a vector of refresh method, which suffices to synchronize all initial values. e Setting the State Applying Assignments Calculating Current Values Dependency Specifications Initial Values Metabolite with Assignment Metabolite with Assignment Attribute Dependencies Refresh Method Initial Particle Number Initial Concentration, parent compartment Volume refreshInititalValue Initial Concentration all objects in implicit expression refreshInitialConcentration

Metabolite without Assignment Metabolite without Assignment Attribute Dependencies Refresh Method Initial Particle Number initial concentration, parent compartment volume refreshInitialValue Initial Concentration parent compartment Volume refreshInititalConcentration

The initial concentration is of course dependent on the initial particle number. This must be taken into account manually to avoid circular depencies. However, this is straight forward as the initial particle number may only be set directly, in which case no further dependencies are encountered or calculated from the initial concentration in the case the concentration is given the normal dependecies take care of the problem. Compartment, Global Quantity with Assignment Compartment, Global Quantity with Assignment Attribute Dependencies Refresh Method Initial Value all objects in implicit expression refreshInitialValue

Compartment, Global Quantity without Assignment Compartment, Global Quantity without Assignment Attribute Dependencies Refresh Method Initial Value none none

Moiety Moiety Attribute Dependencies Refresh Method Initial Number Particle numbers of all involved metabolites refreshInitialValue

Transient Values Metabolite Reaction (Independent) Metabolite Reaction (Independent) Attribute Dependencies Refresh Method Self none none Particle Number Self (state controlled) none Concentration Particle Number, parent compartment Volume refreshConcentration Particle Rate All particle fluxes of reactions the metabolites participates in refreshRate Concentration Rate Particle Rate, Concentration, parent compartment Volume and Rate refreshConcentrationRate Transition Time All particle fluxes of reactions the metabolites participates in refreshTransitionTime

Metabolite Reaction (Dependent) Metabolite Reaction (Dependent) Attribute Dependencies Refresh Method Self none none Particle Number none none Concentration Particle Number, parent compartment Volume refreshConcentration Particle Rate All particle fluxes of reactions the metabolites participates in refreshRate Concentration Rate Particle Rate, Concentration, parent compartment Volume and Rate refreshConcentrationRate Transition Time All particle fluxes of reactions the metabolites participates in refreshTransitionTime

Metabolite Assignment (Concentration) Metabolite Assignment (Concentration) Attribute Dependencies Refresh Method Self none none Particle Number Concentration, parent compartment Volume refreshNumber Concentration all objects in expression calculate Particle Rate (NA) none none Concentration Rate (NA) none none Transition Time (NA) none none

This will be implemented later Metabolite ODE (Concentration) Metabolite ODE (Concentration) Attribute Dependencies Refresh Method Self none none Particle Number Self (state controlled) none Concentration Particle Number, parent compartment Volume refreshConcentration Particle Rate all objects in expression, parent compartment Volume calculate Concentration Rate Particle Rate, Concentration, parent compartment Volume and Rate refreshConcentrationRate Transition Time Particle Number, Particle Rate refreshTransitionTime

This will be implemented later Moiety Moiety Attribute Dependencies Refresh Method Self Particle number of participating independent metabolites none Dependent Number Self none

Reaction Reaction Attribute Dependencies Refresh Method Self all variables of the kinetic function, associated compartment Volume, kinetic function, all metabolites involved calculate ParticleFlux all variables of the kinetic function, associated compartment Volume calculate Flux all variables of the kinetic function, associated compartment Volume calculate

Model Value Assignment Model Value Assignment Attribute Dependencies Refresh Method Self none none Value all objects in expression calculate Rate (not available) none none

Model Value ODE Model Value ODE Attribute Dependencies Refresh Method Self none none Value Self (state controlled) none Rate all objects in expression calculate

Compartment Assignment Compartment Assignment Attribute Dependencies Refresh Method Self none none Volume all objects in expression calculate Rate (not available) none none

This will be implemented later Compartment ODE Compartment ODE Attribute Dependencies Refresh Method Self none none Volume Self (state controlled) none Rate all objects in expression calculate