58 os <<
"METHOD stiff" << std::endl;
60 os <<
"STARTTIME = 0" << std::endl;
67 os <<
"STOPTIME = " << pTrajectoryProblem->
getDuration() << std::endl;
68 os <<
"DT = " << pTrajectoryProblem->
getStepSize() << std::endl;
87 std::ostringstream tmpName;
89 size_t realName_size = realName.size();
94 if (!std::isalpha(ch, C))
98 if (std::isdigit(ch, C)) tmpName << ch;
102 for (i = 1; i < realName_size; i++)
106 if (std::isalpha(ch, C))
108 if (std::isspace(realName[i - 1], C) && std::islower(ch, C))
109 tmpName << (char) toupper(ch);
114 if (std::isdigit(ch, C)) tmpName << ch;
116 if (std::ispunct(ch, C))
163 std::ostringstream newname, tmp;
165 size_t name_size = name.size();
168 for (i = 0; i < name_size; i++)
172 if (std::isalpha(ch, C) && std::islower(ch, C))
173 tmp << (char) toupper(ch);
188 newname << name <<
"_" <<
Frequancy[tmp.str()];
199 return objName +
"_c";
204 return "d/dt(" + objName +
")";
208 const std::string & name,
209 const std::string & expression,
210 const std::string & comments)
212 which << name <<
" = " << expression
213 <<
'\t' <<
'\t' <<
"; " << comments << std::endl;
222 std::ostringstream smKey;
223 smKey <<
"sm_" << metab->
getKey();
361 metab =
dynamic_cast< const CMetab *
>(tmp);
365 std::ostringstream smKey;
366 smKey <<
"sm_" << metab->
getKey();
415 std::ostringstream odeKey;
417 odeKey <<
"ode_" << mentity->
getKey();
440 std::ostringstream localKey;
441 localKey << reac->
getKey() <<
"_root_func";
442 return NameMap[localKey.str()];
450 return "{Initial values:}";
453 return "{Fixed Model Entities: }";
456 return "{Assignment Model Entities: }";
459 return "{Kinetics: }";
465 return "{Equations:}";
Header file of class CExpression.
virtual std::string getDisplayFunctionString(CFunction *func)
std::string testName(const std::string &name)
virtual bool exportSingleODE(const CModelEntity *mentity, std::string &equation, std::string &comments)
virtual bool exportSingleModelEntity(const CModelEntity *tmp, std::string &expression, std::string &comments)
CCopasiProblem * getProblem()
virtual std::string translateTimeVariableName()
virtual const std::string & getKey() const
virtual std::string exportTitleString(const size_t tmp)
virtual void setReservedNames()
std::ostringstream initial
std::string setODEName(const std::string &objName)
std::map< std::string, size_t > Frequancy
const C_FLOAT64 & getStepSize() const
virtual bool exportSingleModVal(const CModelValue *modval, std::string &expression, std::string &comments)
virtual std::string KineticFunction2ODEmember(const CReaction *reac)
const C_FLOAT64 & getDuration() const
virtual const std::string & getKey() const
virtual const std::string & getKey() const
virtual bool exportSingleCompartment(const CCompartment *comp, std::string &expression, std::string &comments)
virtual std::string getDisplayExpressionString(CExpression *tmp)
virtual bool exportTitleData(const CCopasiDataModel *pDataModel, std::ostream &os)
std::set< std::string > NameSet
std::string setConcentrationName(const std::string &objName)
std::map< std::string, std::string > NameMap
virtual std::string translateObjectName(const std::string &realName)
std::ostringstream assignment
The class for handling a chemical kinetic function.
std::string buildBerkeleyMadonnaString() const
const CModelEntity::Status & getStatus() const
virtual bool exportSingleParameter(const CCopasiParameter *param, std::string &expression, std::string &comments)
virtual bool exportSingleObject(std::ostringstream &which, const std::string &name, const std::string &expression, const std::string &comments)
virtual bool exportSingleMetabolite(const CMetab *metab, std::string &expression, std::string &comments)
CEvaluationNode * getRoot()