MoleculeType * NFtest_tlbr::createL(System * s, int count)
{
vector <string> compName;
vector <string> defaultCompState;
vector < vector <string> > possibleCompStates;
compName.push_back("r0");
defaultCompState.push_back("No State");
vector <string> possibleR0states;
possibleCompStates.push_back(possibleR0states);
compName.push_back("r1");
defaultCompState.push_back("No State");
vector <string> possibleR1states;
possibleCompStates.push_back(possibleR1states);
compName.push_back("r2");
defaultCompState.push_back("No State");
vector <string> possibleR2states;
possibleCompStates.push_back(possibleR2states);
MoleculeType *L = new MoleculeType("L", compName, defaultCompState, possibleCompStates, s);
L->populateWithDefaultMolecules(count);
return L;
}
/*!
*/
void clearMoleculeComplexIds(System *s) {
for(int i=0; i<s->getNumOfMoleculeTypes(); i++) {
MoleculeType *mt = s->getMoleculeType(i);
for(int j=0; j<mt->getMoleculeCount(); j++) {
mt->getMolecule(j)->setComplexID(-1);
}
}
}
std::string formula(const MoleculeType &mol)
{
// Adapted from chemkit:
// A map of atomic symbols to their quantity.
std::map<unsigned char, size_t> composition;
for (Array<unsigned char>::const_iterator it = mol.atomicNumbers().begin(),
itEnd = mol.atomicNumbers().end(); it != itEnd; ++it) {
composition[*it]++;
}
std::stringstream result;
std::map<unsigned char, size_t>::iterator iter;
// Carbons first
iter = composition.find(6);
if (iter != composition.end()) {
result << "C";
if (iter->second > 1)
result << iter->second;
composition.erase(iter);
// If carbon is present, hydrogens are next.
iter = composition.find(1);
if (iter != composition.end()) {
result << "H";
if (iter->second > 1)
result << iter->second;
composition.erase(iter);
}
}
// The rest:
iter = composition.begin();
while (iter != composition.end()) {
result << Avogadro::Core::Elements::symbol(iter->first);
if (iter->second > 1)
result << iter->second;
++iter;
}
return result.str();
}
MoleculeType * NFtest_tlbr::createR(System * s, int count)
{
vector <string> compName;
vector <string> defaultCompState;
vector < vector <string> > possibleCompStates;
compName.push_back("l0");
defaultCompState.push_back("No State");
vector <string> possibleL0states;
possibleCompStates.push_back(possibleL0states);
compName.push_back("l1");
defaultCompState.push_back("No State");
vector <string> possibleL1states;
possibleCompStates.push_back(possibleL1states);
MoleculeType *R = new MoleculeType("R", compName, defaultCompState, possibleCompStates, s);
R->populateWithDefaultMolecules(count);
return R;
}
void DumpSystem::dumpHeaderFile(double dumpTime) {
string dumpFileName = pathToFolder + s->getName()+"_nf."+Util::toString(dumpTime)+".dump.head";
//cout<<"writing file: "<<dumpFileName<<endl;;
ofstream ofs;
//ios_base::out -- Set for output only, instead of for input/output
//ios_base::trunc -- Truncate the file - that is overwrite anything that was already there
ofs.open((dumpFileName).c_str(), ios_base::out | ios_base::trunc);
//Make sure we could open the stream (this is really the only thing that can go around)
if(!ofs.is_open()) {
cout<<"--------"<<endl;
cout<<"-Error dumping header file.";
cout<<"-Could not open stream to file: '"<<dumpFileName<<"'"<<endl;
cout<<"-The path is probably incorrect or does not exist."<<endl;
return;
}
ofs<<"## Automatically generated file from NFsim. Do not edit manually.\n";
ofs<<"## To read this file and the associated information, use the\n";
ofs<<"## included Matlab script readNFdump.m.\n\n";
ofs<<"\n>> Time #######################################\n";
ofs<<dumpTime<<"\n";
ofs<<"\n>> MoleculeTypeDef ############################\n";
ofs<<"##\tindex\tname\tnumOfInstances\tnumOfComponents\n";
for(int i=0; i<s->getNumOfMoleculeTypes(); i++) {
MoleculeType *mt = s->getMoleculeType(i);
ofs<<"\t"<<i<<"\t"<<mt->getName()<<"\t"<<mt->getMoleculeCount()<<"\t";
ofs<<mt->getNumOfComponents()<<"\t"<<mt->getNumOfTypeIFunctions()<<"\n";
}
ofs<<"\n>> MoleculeTypeComponents #####################\n";
ofs<<"##\ttype\tindex\tname\n";
for(int i=0; i<s->getNumOfMoleculeTypes(); i++) {
MoleculeType *mt = s->getMoleculeType(i);
for(int k=0; k<mt->getNumOfComponents(); k++) {
ofs<<"\t"<<i<<"\t"<<k<<"\t"<<mt->getComponentName(k)<<"\n";
}
}
ofs<<"\n>> MoleculeTypeFunctions ######################\n";
ofs<<"##\ttype\tindex\tname\n";
for(int i=0; i<s->getNumOfMoleculeTypes(); i++) {
MoleculeType *mt = s->getMoleculeType(i);
for(int k=0; k<mt->getNumOfTypeIFunctions(); k++) {
ofs<<"\t"<<i<<"\t"<<k<<"\t"<<mt->getTypeILocalFunction(k)->getName()<<"\n";
}
}
ofs<<"\n>> EOF ##########################################\n";
ofs.flush();
ofs.close();
}
void DumpSystem::dumpMoleculeTypeFiles(double dumpTime) {
double complexCount = 0;
for(int i=0; i<s->getNumOfMoleculeTypes(); i++) {
MoleculeType *mt = s->getMoleculeType(i);
string dumpFileName = pathToFolder+s->getName() + "_nf."+Util::toString(dumpTime)+".dump."+Util::toString(i);
ofstream ofs;
//ios_base::out -- Set for output only, instead of for input/output
//ios_base::binary -- Set output to binary
//ios_base::trunc -- Truncate the file - that is overwrite anything that was already there
ofs.open((dumpFileName).c_str(), ios_base::out | ios_base::binary | ios_base::trunc);
//Make sure we could open the stream (this is really the only thing that can go around)
if(!ofs.is_open()) {
cout<<"--------"<<endl;
cout<<"-Error dumping header file.";
cout<<"-Could not open stream to file: '"<<dumpFileName<<"'"<<endl;
cout<<"-The path is probably incorrect or does not exist."<<endl;
return;
}
double NOBOND = -1;
list <Molecule *> molList; list <Molecule *>::iterator molIter;
for(int j=0; j<mt->getMoleculeCount(); j++) {
//First, write out this molecules unique ID
Molecule *m=mt->getMolecule(j);
double uId = (double)m->getUniqueID();
ofs.write((char *)&uId,sizeof(double));
//Second, output the complex number so we can quickly recover
//the complexes
if(!s->isUsingComplex()) {
if(m->getComplexID()==-1) { //if we haven't visited this guy yet...
m->traverseBondedNeighborhood(molList,ReactionClass::NO_LIMIT);
for(molIter=molList.begin(); molIter!=molList.end(); molIter++) {
(*molIter)->setComplexID((int)complexCount);
}
ofs.write((char *)&complexCount,sizeof(double));
complexCount++;
molList.clear();
} else {
double thisUid = m->getComplexID();
ofs.write((char *)&thisUid,sizeof(double));
}
} else {
complexCount = m->getComplexID();
ofs.write((char *)&complexCount,sizeof(double));
}
//Now export all the components, marking its state and
//binding partner if any
for(int k=0; k<mt->getNumOfComponents(); k++) {
double stateValue = (double)m->getComponentState(k);
ofs.write((char *)&stateValue,sizeof(double));
if(!m->isBindingSiteBonded(k)) {
ofs.write((char *)&NOBOND,sizeof(double));
} else {
Molecule *m2=m->getBondedMolecule(k);
double uId2 = (double)m2->getUniqueID();
ofs.write((char *)&uId2,sizeof(double));
}
}
for(int k=0; k<mt->getNumOfTypeIFunctions(); k++) {
double val = m->getLocalFunctionValue(k);
LocalFunction *lf = m->getLocalFunction(k);
double localValue = lf->evaluateOn(m,LocalFunction::MOLECULE);
ofs.write((char *)&val,sizeof(double));
ofs.write((char *)&localValue,sizeof(double));
// ofs<<"\t"<<i<<"\t"<<k<<"\t"<<mt->getTypeIILocalFunction(k)->getName()<<"\n";
}
}
ofs.flush();
ofs.close();
}
}
void NFtest_transcription::run()
{
cout<<"Running the transcription system"<<endl;
// 1)
System *s = new System("Transcription System");
// 2)
MoleculeType *molRNA = createRNA(s);
// 3) Instantiate the actual molecules (this populate function is the easiest way, but you can do it
// manually as well by creating each molecule separately - see the MoleculeType::populate function for
// an example on how this can be done).
molRNA->populateWithDefaultMolecules(500);
// 4) Create the reactions and add them to the system. These are calls to specific functions
// below where I set up the details of the reactions. The numbers are the rates and are in
// arbitrary units here. In general, the rates should be in units of per second.
ReactionClass * rna_degrade = createReactionRNAdegrades(molRNA, 0.5);
ReactionClass *rna_transcribe = createReactionRNAtranscribed(molRNA, 100.0);
s->addReaction(rna_degrade);
s->addReaction(rna_transcribe);
// 5) Add the observables that we want to track throughout the simulation. Again, to
// see how this is done, see the function below.
addObs(s, molRNA);
// 6) Prepare the system for simulation (this adds molecules to reactionLists
// and counts up the observables)
s->prepareForSimulation();
s->printAllReactions();
// 7) Register the output file name (This will put the file in your working directory)
// Here, you also want to output the header to the file, which is not done automatically
// because you can run a simulation with multiple calls to the sim functions.
s->registerOutputFileLocation("transcription_system_output.txt");
s->outputAllObservableNames();
//8) Run the simulation!
//You can optionally equilibrate the system for a set amount of time where output is not
//recorded (all times are in seconds) using this function where the first parameter is the
//length of the equilibration, and the second is the number of times we want to print a
//message that says how we are doing. After it equilibrates, the simulation time is reset to zero.
//The first parameter is the number of seconds we want to equilibrate. The second (optional) parameter
//is the number of times you want to print an 'ok' output message. If the second parameter is not
//given, nothing is outputted to the console.
s->equilibrate(0,10);
//There are two ways to run a simulation. First, you can just call the function sim as in:
s->sim(50,50);
//Calling this sim function is the easist way to run a simulation. The first parameter is the
//number of seconds you want to run for, the second is the number of times you want to output
//the results to the outputfile. So in this example, we run for 500 seconds and output 500 times,
//so we output once per second.
//The second way to run a simulation is to call this stepTo function:
cout<<endl<<endl<<"Calling the stepTo function and stepping to the system time t=600 seconds"<<endl;
double stoppingTime = s->stepTo(600);
cout<<"The last reaction was fired at simulation time: "<<stoppingTime<<endl<<endl;
//This function runs the simulation until the given time is reached, and it also returns the
//time of the simulation when the last reaction fired (which is now the current time in the
//system. This function does not output to a file automatically, so to output using this function,
//so to get results, you will have to use a call to this function:
s->outputAllObservableCounts();
//The stepTo function will have to be written as part of a loop where you decide when it should
//output. This gives you more control, but of course requires more work.
//Here we can print out the list of reactions. This is nice because it tells us how many times
//a reaction fired, and how many molecules are in each list at the end of the simulation
s->printAllReactions();
//Be nice and clean up when we are done. Deleting the system (should) delete everything else
//associated with the system, so we don't ever have to remember to delete individual reactions, molecules
//moleculeTypes, etc...
delete s;
}
void NFtest_tlbr::runSystem(int n_L, int n_R, double cTot, double beta, double koff,
string outputFileName, double simTime, double dt,
bool outputObservables, bool outputAvg, bool outputFinalDist)
{
double freeBindRate = (cTot*koff)/(3.0*(double)n_L);
double crossLinkRate = (beta*koff)/(double)n_R;
cout<<"beta: " <<beta<<endl;
cout<<"cTot: " <<cTot<<endl;
cout<<"kOff: " <<koff<<endl;
cout<<"N_l: " <<n_L<<endl;
cout<<"N_r: " <<n_R<<endl;
//Create the system with ligands, receptors, and reactions
System * s = new System("TLBR",true);
vector<vector<string> > v;
MoleculeType * L = createL(s,n_L);
L->addEquivalentComponents(v);
MoleculeType * R = createR(s,n_R);
R->addEquivalentComponents(v);
createUnbindingRxns(s,R,koff);
createFreeBindingRxns(s,L,R,freeBindRate);
createCrossLinkingRxns(s,L,R,crossLinkRate);
//add the observables if we so choose
//if(outputObservables) addObservables(s,L,R);
//Prepare to run
s->printAllMoleculeTypes();
s->prepareForSimulation();
s->registerOutputFileLocation(outputFileName.c_str());
///////////////// added here for calculating scalling...
//s->equilibriate(200,20);
s->sim(simTime,3);
string x = "";
cout<<"waiting for you to enter something."<<endl;
cin>>x;
s->printAllReactions();
// NETGEN -- redirected call to the ComplexList object at s->allComplexes
cout << "Finished... avg complex size: " << (s->getAllComplexes()).calculateMeanCount(R) << " receptors" << endl;
delete s;
return;
/////////////////////////////////////
if(outputObservables || outputAvg) s->outputAllObservableNames();
double currentTime = 0;
double nextStoppingTime = dt;
double avg=-1;
// NETGEN -- redirected call to the ComplexList object at s->allComplexes
if(outputAvg) avg = (s->getAllComplexes()).outputMeanCount(R);
if(outputObservables) s->outputAllObservableCounts();
int step=0;
while(currentTime<simTime)
{
currentTime = s->stepTo(nextStoppingTime);
if(outputAvg) avg = (s->getAllComplexes()).outputMeanCount(R);
if(step%((int)(100/dt))==0)cout<<"at time: "<<currentTime<<" avg: "<<avg<<endl;
if(outputObservables) s->outputAllObservableCounts();
nextStoppingTime += dt;
step++;
}
s->printAllReactions();
// NETGEN -- redirected call to the ComplexList object at s->allComplexes
avg = (s->getAllComplexes()).calculateMeanCount(R);
cout<<"Finished... avg complex size: "<<avg<<" receptors"<<endl;
//(s->allComplexes).printAllComplexes();
//If we aren't outputting the trajectory, make sure that we output the
//final aggregate size distribution
// NETGEN -- redirected call to the ComplexList object at s->allComplexes
if(outputFinalDist) (s->getAllComplexes()).outputMoleculeTypeCountPerComplex(R);
if(outputFinalDist) (s->getAllComplexes()).outputMoleculeTypeCountPerComplex(R);
delete s;
}
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) &&
key->at(2)==bondNumberMap.at(bnmIndex)->at(2) &&
key->at(3)==bondNumberMap.at(bnmIndex)->at(3) ) {
thisBondNumber = bnmIndex+1;
foundExistingBond = true;
if(debugOut) cout<<"Found bond number: "<<thisBondNumber<<endl;
break;
}
}
//If it was not found, then insert it
if(!foundExistingBond) {
bondNumberMap.push_back(key);
thisBondNumber = bondNumberMap.size();
if(debugOut) cout<<"Creating bond number: "<<bondNumberMap.size()<<endl;
}
speciesString += "!" + NFutil::toString(thisBondNumber);
}
}
speciesString += ")";
}
if(reportedSpecies.find(speciesString) != reportedSpecies.end()) {
reportedSpecies[speciesString] = reportedSpecies[speciesString] + mt->getMolecule(j)->getPopulation();
} else {
reportedSpecies.insert(pair <string,int> (speciesString, mt->getMolecule(j)->getPopulation()));
}
//speciesString += " 1";
//cout<<speciesString<<endl;
if(debugOut) cout<<endl<<endl;
//delete elements of the map
while(bondNumberMap.size()>0) {
vector <int> *v = bondNumberMap.at(bondNumberMap.size()-1);
bondNumberMap.pop_back();
delete v;
}
if(debugOut) cout<<endl<<endl;
}
}
speciesFile<<"# nfsim generated species list for system: '"<< this->name <<"'\n";
speciesFile<<"# warning! this feature is not yet fully tested! \n";
for ( map<string,int>::iterator it=reportedSpecies.begin() ; it != reportedSpecies.end(); it++ )
speciesFile << (*it).first << " " << (*it).second << "\n";
speciesFile.flush();
speciesFile.close();
return true;
}