#include <iostream>
#include <map>
#include <vector>
#include <stdio.h>
#include <limits.h>
#include <exception>
#include "../NFcore/NFcore.hh"
#include "../NFoutput/NFoutput.hh"
#include "../NFfunction/NFfunction.hh"
#include "../NFreactions/reactions/reaction.hh"
#include "TinyXML/tinyxml.h"
Go to the source code of this file.
Namespaces | |
| namespace | NFinput |
Classes | |
| class | NFinput::component |
| Maintains information about a component of a TemplateMolecule. More... | |
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 > ¶meter, bool verbose) |
| Reads the parameter XML block and puts them in the parameter map. | |
| bool | NFinput::initFunctions (TiXmlElement *pListOfFunctions, System *system, map< string, double > ¶meter, TiXmlElement *pListOfObservables, map< string, int > &allowedStates, bool verbose) |
| Reads the Function XML block and adds the Functions to the system. | |
| 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::FindReactionRuleSymmetry (TiXmlElement *pRxnRule, System *s, map< string, double > ¶meter, map< string, int > &allowedStates, map< string, component > &symComps, map< string, component > &symRxnCenter, bool verbose) |
| bool | NFinput::readPatternForSymmetry (TiXmlElement *pListOfMol, System *s, string patternName, map< string, component > &comps, map< string, component > &symComps, bool verbose) |
| bool | NFinput::generateRxnPermutations (vector< map< string, component > > &permutations, map< string, component > &symComps, map< string, component > &symRxnCenter, bool verbose) |
| bool | NFinput::readObservableForTemplateMolecules (TiXmlElement *pObs, string observableName, vector< TemplateMolecule * > &tmList, vector< string > &stochRelation, vector< int > &stochQuantity, System *s, map< string, double > ¶meter, map< string, int > &allowedStates, int obsType, bool verbose, int &suggestedTraversalLimit) |
| bool | NFinput::initStartSpecies (TiXmlElement *pListOfSpecies, System *system, map< string, double > ¶meter, 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 > ¶meter, map< string, int > &allowedStates, bool blockSameComplexBinding, bool verbose, int &suggestedTraversalLimit) |
| Reads a reactionRule XML block and adds the rules to the system. | |
| bool | NFinput::initObservables (TiXmlElement *pListOfObservables, System *system, map< string, double > ¶meter, 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 > ¶meter, 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 > ¶meter, 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 | 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. | |
| 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. | |
| 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. | |
| 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. | |
| void | NFinput::walk (System *s) |
| Allows the user to walk through the system with an interactive text-based program. | |
| bool | NFinput::createSystemDumper (string paramStr, System *s, bool verbose) |
| Parses the cmd line arg that specifies system dumps, and schedules them. | |
| bool | NFinput::parseSequence (string numString, vector< double > &outputTimes) |
| Parses a matlab style sequence (ie startValue:step:endValue) into the vector. | |
| 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) |
1.5.4