C++ Molecule::getComponentState方法代码示例

bool System::saveSpecies(string filename)
{
	bool debugOut = false;

	//open the output filestream
	ofstream speciesFile;
	speciesFile.open(filename.c_str());
	if(!speciesFile.is_open()) {
		cerr<<"Error in System when calling System::saveSpecies(string)!  Cannot open output stream to file "<<filename<<". "<<endl;
		cerr<<"quitting."<<endl;
		exit(1);
	}

	cout<<"\n\nsaving list of final molecular species..."<<endl;

	// create a couple data structures to store results as we go
	list <Molecule *> molecules;
	list <Molecule *>::iterator iter;
	map <int,bool> reportedMolecules;
    map <string,int> reportedSpecies;


	// loop over all the types of molecules that exist
	for( unsigned int k=0; k<allMoleculeTypes.size(); k++)
	{
		// retrieve the MoleculeType
		MoleculeType *mt = allMoleculeTypes.at(k);

		// loop over every individual molecule
		for(int j=0; j<mt->getMoleculeCount(); j++)
		{
			// check if we have looked this molecule before, and skip it if we have
			if(reportedMolecules.find(mt->getMolecule(j)->getUniqueID())!=reportedMolecules.end()) {
				continue;
			}



			//otherwise, we have not visited this particular species before, so loop over the molecules
			//that make up the species
			string speciesString = "";
			molecules.clear();
			mt->getMolecule(j)->traverseBondedNeighborhood(molecules,ReactionClass::NO_LIMIT);

			// key: partnerID1, bsiteID1, partnerID2, bsiteID2
			vector <vector <int> * > bondNumberMap;

			bool isFirst = true;
			for( iter = molecules.begin(); iter != molecules.end(); iter++ )
			{
				Molecule *m = (*iter);
				reportedMolecules.insert(pair <int,bool> (m->getUniqueID(),true));

				//Fist, output the molecule name
				if(isFirst) { speciesString += m->getMoleculeTypeName()+"("; isFirst=false; }
				else { speciesString += "."+m->getMoleculeTypeName()+"("; }

				//Go through each component of the molecule
				for(int s=0; s<m->getMoleculeType()->getNumOfComponents(); s++)
				{
					// output the component name
					string compName = m->getMoleculeType()->getComponentName(s);
					if(m->getMoleculeType()->isEquivalentComponent(s)) {
						// symmetric site, so we need to look up its sym name
						compName = m->getMoleculeType()->getEquivalenceClassComponentNameFromComponentIndex(s);
					}
					if(s==0) speciesString += compName;
					else speciesString += ","+compName;


					//output the state of the component, if it is set
					if(m->getComponentState(s)>=0) {
						speciesString += "~" + m->getMoleculeType()->getComponentStateName(s,m->getComponentState(s));
					}


					// check if the component is bound, if so we have to output a bond
					// we will label the bond incrementally, but we have to check to make
					// sure the bond wasn't declared earlier.  that's what the vector of int vectors is for.
					if(m->isBindingSiteBonded(s)) {
						if(debugOut) cout<<"binding site is bonded"<<endl;
						int partnerID = m->getBondedMolecule(s)->getUniqueID();
						int partnerSite = m->getBondedMoleculeBindingSiteIndex(s);
						int thisBondNumber = -1;

						// create the key
						vector <int> *key = new vector<int>(4);
						if(partnerID<m->getUniqueID()) {
							key->at(0) = partnerID; key->at(1) = partnerSite;
							key->at(2) = m->getUniqueID(); key->at(3)=s;
						} else {
							key->at(2) = partnerID; key->at(3) = partnerSite;
							key->at(0) = m->getUniqueID(); key->at(1)=s;
						}

						//search if that key was already inserted
						bool foundExistingBond = false;
						for(unsigned int bnmIndex =0; bnmIndex < bondNumberMap.size(); bnmIndex++) {
							if( key->at(0)==bondNumberMap.at(bnmIndex)->at(0) &&
								key->at(1)==bondNumberMap.at(bnmIndex)->at(1) &&
//.........这里部分代码省略.........