NFsim: NFinput Namespace Reference

This is a very straightforward set of functions and simple classes that together parse and handle all the major input into NFsim. The raw XML parsing code comes from the TinyXML project and can be found in its unedited form in the TinyXML directory. Thanks TinyXML! You perform great and you are definitely tiny!


Classes
class	component
	Maintains information about a component of a TemplateMolecule. More...
Functions
bool	parseArguments (int argc, const char *argv[], map< string, string > &argMap)
	Parses command line arguments from the console nicely.
int	parseAsInt (map< string, string > &argMap, string argName, int defaultValue)
	Looks up the argument in the argMap and tries to parse the value as an integer.
void	parseAsCommaSeparatedSequence (map< string, string > &argMap, string argName, vector< int > &sequence)
	Looks up the argument in the argMap and tries to parse the value as a comma delimited sequence of ints.
double	parseAsDouble (map< string, string > &argMap, string argName, double defaultValue)
	Looks up the argument in the argMap and tries to parse the value as a double.
bool	parseSequence (string numString, vector< double > &outputTimes)
	Parses a matlab style sequence (ie startValue:step:endValue) into the vector.
bool	createSystemDumper (string paramStr, System *s, bool verbose)
	Parses the cmd line arg that specifies system dumps, and schedules them.
System *	initializeFromXML (string filename, bool blockSameComplexBinding, int globalMoleculeLimit, bool verbose, int &suggestedTraversalLimit)
	Maintains information about a component of a TemplateMolecule.
bool	initParameters (TiXmlElement pListOfParameters, System s, map< string, double > &parameter, bool verbose)
	Reads the parameter XML block and puts them in the parameter map.
bool	initMoleculeTypes (TiXmlElement pListOfMoleculeTypes, System system, map< string, int > &allowedStates, bool verbose)
	Reads the MoleculeType XML block and adds the MoleculeTypes to the system.
bool	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	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	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	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 *	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	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.
bool	initFunctions (TiXmlElement pListOfFunctions, System system, map< string, double > &parameter, TiXmlElement *pListOfObservables, map< string, int > &allowedStates, bool verbose)
	Reads the Function XML block and adds the Functions to the system.
bool	FindReactionRuleSymmetry (TiXmlElement pRxnRule, System s, map< string, double > &parameter, map< string, int > &allowedStates, map< string, component > &symComps, map< string, component > &symRxnCenter, bool verbose)
bool	readPatternForSymmetry (TiXmlElement pListOfMol, System s, string patternName, map< string, component > &comps, map< string, component > &symComps, bool verbose)
bool	generateRxnPermutations (vector< map< string, component > > &permutations, map< string, component > &symComps, map< string, component > &symRxnCenter, bool verbose)
bool	lookup (component *&c, string id, map< string, component > &comps, map< string, component > &symMap)
void	walk (System *s)
	Allows the user to walk through the system with an interactive text-based program.
bool	readRNFfile (map< string, string > &argMap, vector< string > &commands, bool verbose)
bool	runRNFcommands (System *s, map< string, string > &argMap, vector< string > &commands, bool verbose)

Function Documentation

bool NFinput::createSystemDumper	(	string	paramStr,
		System *	s,
		bool	verbose
	)

Parses the cmd line arg that specifies system dumps, and schedules them.

This method works by parsing the argument, initializing the class DumpSystem defined in the file NFoutput.hh, and adding the DumpSystem to the System.

Author:: Michael Sneddon

bool NFinput::FindReactionRuleSymmetry	(	TiXmlElement *	pRxnRule,
		System *	s,
		map< string, double > &	parameter,
		map< string, int > &	allowedStates,
		map< string, component > &	symComps,
		map< string, component > &	symRxnCenter,
		bool	verbose
	)

bool NFinput::generateRxnPermutations	(	vector< map< string, component > > &	permutations,
		map< string, component > &	symComps,
		map< string, component > &	symRxnCenter,
		bool	verbose
	)

Output for debugging

bool NFinput::initFunctions	(	TiXmlElement *	pListOfFunctions,
		System *	system,
		map< string, double > &	parameter,
		TiXmlElement *	pListOfObservables,
		map< string, int > &	allowedStates,
		bool	verbose
	)

Reads the Function XML block and adds the Functions to the system.

Author:: Michael Sneddon

System * NFinput::initializeFromXML	(	string	filename,
		bool	blockSameComplexBinding,
		int	globalMoleculeLimit,
		bool	verbose,
		int &	suggestedTraversalLimit
	)

Maintains information about a component of a TemplateMolecule.

Author:: Michael Sneddon

bool NFinput::initMoleculeTypes	(	TiXmlElement *	pListOfMoleculeTypes,
		System *	s,
		map< string, int > &	allowedStates,
		bool	verbose
	)

Reads the MoleculeType XML block and adds the MoleculeTypes to the system.

The strategy is to look at one MoleculeType at a time, make sure that moleculeType contains valid information, then, and only then, create it.

Author:: Michael Sneddon

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.

Author:: Michael Sneddon

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.

Author:: Michael Sneddon

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.

Author:: Michael Sneddon

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.

Author:: Michael Sneddon

bool NFinput::lookup	(	component *&	c,
		string	id,
		map< string, component > &	comps,
		map< string, component > &	symMap
	)

bool NFinput::parseArguments	(	int	argc,
		const char *	argv[],
		map< string, string > &	argMap
	)

Parses command line arguments from the console nicely.

Author:: Michael Sneddon

void NFinput::parseAsCommaSeparatedSequence	(	map< string, string > &	argMap,
		string	argName,
		vector< int > &	sequence
	)

Looks up the argument in the argMap and tries to parse the value as a comma delimited sequence of ints.

Author:: Michael Sneddon

double NFinput::parseAsDouble	(	map< string, string > &	argMap,
		string	argName,
		double	defaultValue
	)

Looks up the argument in the argMap and tries to parse the value as a double.

Author:: Michael Sneddon

int NFinput::parseAsInt	(	map< string, string > &	argMap,
		string	argName,
		int	defaultValue
	)

Looks up the argument in the argMap and tries to parse the value as an integer.

Author:: Michael Sneddon

bool NFinput::parseSequence	(	string	numString,
		vector< double > &	outputTimes
	)

Parses a matlab style sequence (ie startValue:step:endValue) into the vector.

Author:: Michael Sneddon

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
	)

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.

Author:: Michael Sneddon

bool NFinput::readPatternForSymmetry	(	TiXmlElement *	pListOfMol,
		System *	s,
		string	patternName,
		map< string, component > &	comps,
		map< string, component > &	symComps,
		bool	verbose
	)

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.

Author:: Michael Sneddon

bool NFinput::readRNFfile	(	map< string, string > &	argMap,
		vector< string > &	commands,
		bool	verbose
	)

bool NFinput::runRNFcommands	(	System *	s,
		map< string, string > &	argMap,
		vector< string > &	commands,
		bool	verbose
	)

void NFinput::walk ( System * s )

Allows the user to walk through the system with an interactive text-based program.

Author:: Michael Sneddon

NFinput Namespace Reference

Detailed Description

Classes

Functions

Function Documentation