/home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFinput/NFinput.cpp File Reference

#include "NFinput.hh"

Functions
System *	NFinput::initializeFromXML (string filename, bool blockSameComplexBinding, int globalMoleculeLimit, bool verbose, int &suggestedTraversalLimit)
	Maintains information about a component of a TemplateMolecule.
bool	NFinput::initParameters (TiXmlElement *pListOfParameters, System *s, map< string, double > &parameter, bool verbose)
	Reads the parameter XML block and puts them in the parameter map.
bool	NFinput::initMoleculeTypes (TiXmlElement *pListOfMoleculeTypes, System *system, map< string, int > &allowedStates, bool verbose)
	Reads the MoleculeType XML block and adds the MoleculeTypes to the system.
bool	NFinput::initStartSpecies (TiXmlElement *pListOfSpecies, System *system, map< string, double > &parameter, map< string, int > &allowedStates, bool verbose)
	Reads a Species XML block, creates the molecules and adds them to the system.
bool	NFinput::initReactionRules (TiXmlElement *pListOfReactionRules, System *system, map< string, double > &parameter, map< string, int > &allowedStates, bool blockSameComplexBinding, bool verbose, int &suggestedTraversalLimit)
	Reads a reactionRule XML block and adds the rules to the system.
bool	NFinput::readObservableForTemplateMolecules (TiXmlElement *pObs, string observableName, vector< TemplateMolecule * > &tmList, vector< string > &stochRelation, vector< int > &stochQuantity, System *s, map< string, double > &parameter, map< string, int > &allowedStates, int obsType, bool verbose, int &suggestedTraversalLimit)
bool	NFinput::initObservables (TiXmlElement *pListOfObservables, System *system, map< string, double > &parameter, map< string, int > &allowedStates, bool verbose, int &suggestedTraversalLimit)
	Reads an observable XML block and adds the new observables to the system.
TemplateMolecule *	NFinput::readPattern (TiXmlElement *pListOfMol, System *s, map< string, double > &parameter, map< string, int > &allowedStates, string patternName, map< string, TemplateMolecule * > &templates, map< string, component > &comps, map< string, component > &symMap, bool verbose, int &suggestedTraversalLimit)
	Reads a pattern XML block and returns the set of new TemplateMolecule objects.
bool	NFinput::readProductPattern (TiXmlElement *pListOfMol, System *s, map< string, double > &parameter, map< string, int > &allowedStates, string patternName, vector< MoleculeType * > &productMoleculeTypes, vector< vector< int > > &stateInformation, vector< vector< int > > &bindingSiteInformation, bool verbose)
	Reads a pattern XML block and returns the set of new TemplateMolecule objects.

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