void MoleculePopulateProcess::populateUniformDense(Species* aSpecies,
unsigned int aList[],
unsigned int* aCount)
{
std::cout << " Populating:" << getIDString(aSpecies) << std::endl;
Comp* aComp(aSpecies->getComp());
if(!aSpecies->getIsPopulated())
{
if(UniformRadiusX == 1 && UniformRadiusY == 1 && UniformRadiusZ == 1 &&
!OriginX && !OriginY && !OriginZ)
{
unsigned int aSize(aSpecies->getPopulateMoleculeSize());
for(unsigned int j(0); j != aSize; ++j)
{
Voxel* aVoxel;
do
{
aVoxel = theSpatiocyteStepper->coord2voxel(
aComp->coords[aList[(*aCount)++]]);
}
while(aVoxel->id != aComp->vacantID);
aSpecies->addMolecule(aVoxel);
}
}
else
{
populateUniformRanged(aSpecies);
}
aSpecies->setIsPopulated();
}
}
void Core::saveConfiguration()
{
if (QThread::currentThread() != coreThread)
return (void) QMetaObject::invokeMethod(this, "saveConfiguration");
if (!isReady())
return;
ProfileLocker::assertLock();
QString dir = Settings::getSettingsDirPath();
QDir directory(dir);
if (!directory.exists() && !directory.mkpath(directory.absolutePath()))
{
qCritical() << "Error while creating directory " << dir;
return;
}
QString profile = Settings::getInstance().getCurrentProfile();
if (profile == "")
{ // no profile active; this should only happen on startup, if at all
profile = sanitize(getUsername());
if (profile == "") // happens on creation of a new Tox ID
profile = getIDString();
Settings::getInstance().switchProfile(profile);
}
QString path = directory.filePath(profile + TOX_EXT);
saveConfiguration(path);
}
void MoleculePopulateProcess::populateUniformOnDiffuseVacant(Species* aSpecies)
{
std::cout << " Populating:" << getIDString(aSpecies) << std::endl;
if(!aSpecies->getIsPopulated())
{
if(UniformRadiusX == 1 && UniformRadiusY == 1 && UniformRadiusZ == 1 &&
!OriginX && !OriginY && !OriginZ)
{
Species* aVacantSpecies(aSpecies->getVacantSpecies());
aVacantSpecies->updateDiffuseVacantMolecules();
unsigned int aSize(aSpecies->getPopulateMoleculeSize());
if(aVacantSpecies->size() < aSize)
{
THROW_EXCEPTION(ValueError, String(
getPropertyInterface().getClassName()) +
"[" + getFullID().asString() + "]: There are " +
int2str(aSize) + " " + getIDString(aSpecies) +
" molecules that must be uniformly populated," +
"\nbut there are only " +
int2str(aVacantSpecies->size()) +
" diffuse vacant voxels of " +
getIDString(aSpecies->getVacantSpecies()) +
" that can be populated on.");
}
for(unsigned int i(0); i != aSize; ++i)
{
Voxel* aMolecule(aVacantSpecies->getRandomMolecule());
aVacantSpecies->softRemoveMolecule(aMolecule);
aSpecies->addMolecule(aMolecule);
}
}
else
{
populateUniformRanged(aSpecies);
}
aSpecies->setIsPopulated();
}
}
virtual void initialize()
{
if(isInitialized)
{
return;
}
SpatiocyteProcess::initialize();
for(VariableReferenceVector::iterator
i(theVariableReferenceVector.begin());
i != theVariableReferenceVector.end(); ++i)
{
Species* aSpecies(theSpatiocyteStepper->variable2species(
(*i).getVariable()));
if((*i).getCoefficient())
{
if((*i).getCoefficient() == -1)
{
if(theVacantSpecies)
{
THROW_EXCEPTION(ValueError, String(
getPropertyInterface().getClassName()) +
"[" + getFullID().asString() +
"]: A MicrotubuleProcess requires only " +
"one vacant variable reference with -1 " +
"coefficient as the vacant species of " +
"the microtubule compartment, but " +
getIDString(theVacantSpecies) + " and " +
getIDString(aSpecies) + " are given.");
}
theVacantSpecies = aSpecies;
}
else if((*i).getCoefficient() == -2)
{
if(theMinusSpecies)
{
THROW_EXCEPTION(ValueError, String(
getPropertyInterface().getClassName()) +
"[" + getFullID().asString() +
"]: A MicrotubuleProcess requires only " +
"one variable reference with -2 " +
"coefficient as the minus end species " +
"of the microtubule compartment, but " +
getIDString(theMinusSpecies) + " and " +
getIDString(aSpecies) + " are given.");
}
theMinusSpecies = aSpecies;
}
else if((*i).getCoefficient() == -3)
{
if(thePlusSpecies)
{
THROW_EXCEPTION(ValueError, String(
getPropertyInterface().getClassName()) +
"[" + getFullID().asString() +
"]: A MicrotubuleProcess requires only " +
"one variable reference with -3 " +
"coefficient as the plus end species " +
"of the microtubule compartment, but " +
getIDString(thePlusSpecies) + " and " +
getIDString(aSpecies) + " are given.");
}
thePlusSpecies = aSpecies;
}
}
else
{
theKinesinSpecies.push_back(aSpecies);
}
}
if(!theKinesinSpecies.size())
{
THROW_EXCEPTION(ValueError, String(
getPropertyInterface().getClassName()) +
"[" + getFullID().asString() +
"]: A MicrotubuleProcess requires at least one " +
"nonHD variable reference with zero coefficient " +
"as the kinesin species, but none is given.");
}
if(!theVacantSpecies)
{
THROW_EXCEPTION(ValueError, String(
getPropertyInterface().getClassName()) +
"[" + getFullID().asString() +
"]: A MicrotubuleProcess requires one " +
"nonHD variable reference with negative " +
"coefficient as the vacant species, " +
"but none is given.");
}
if(!theMinusSpecies)
{
theMinusSpecies = theVacantSpecies;
}
if(!thePlusSpecies)
{
thePlusSpecies = theVacantSpecies;
}
VoxelDiameter = theSpatiocyteStepper->getVoxelRadius()*2;
DimerPitch /= VoxelDiameter;
Length /= VoxelDiameter;
MonomerPitch /= VoxelDiameter;
Radius /= VoxelDiameter;
theVacantSpecies->setIsOffLattice();
theMinusSpecies->setIsOffLattice();
thePlusSpecies->setIsOffLattice();
for(unsigned int i(0); i != theKinesinSpecies.size(); ++i)
{
theKinesinSpecies[i]->setIsOffLattice();
}
}
void MoleculePopulateProcess::populateUniformRanged(Species* aSpecies)
{
Comp* aComp(aSpecies->getComp());
double delta(0);
// Increase the compartment dimensions by delta if it is a surface
// compartment:
if(aComp->dimension == 2)
{
delta = 0.1;
}
double maxX(std::min(1.0, OriginX+UniformRadiusX));
double minX(std::max(-1.0, OriginX-UniformRadiusX));
double maxY(std::min(1.0, OriginY+UniformRadiusY));
double minY(std::max(-1.0, OriginY-UniformRadiusY));
double maxZ(std::min(1.0, OriginZ+UniformRadiusZ));
double minZ(std::max(-1.0, OriginZ-UniformRadiusZ));
maxX = aComp->centerPoint.x + maxX*aComp->lengthX/2*(1+delta);
minX = aComp->centerPoint.x + minX*aComp->lengthX/2*(1+delta);
maxY = aComp->centerPoint.y + maxY*aComp->lengthY/2*(1+delta);
minY = aComp->centerPoint.y + minY*aComp->lengthY/2*(1+delta);
maxZ = aComp->centerPoint.z + maxZ*aComp->lengthZ/2*(1+delta);
minZ = aComp->centerPoint.z + minZ*aComp->lengthZ/2*(1+delta);
std::vector<unsigned int> aCoords;
for(std::vector<unsigned int>::iterator i(aComp->coords.begin());
i != aComp->coords.end(); ++i)
{
Voxel* aVoxel(theSpatiocyteStepper->coord2voxel(*i));
Point aPoint(theSpatiocyteStepper->coord2point(aVoxel->coord));
if(aVoxel->id == aSpecies->getVacantID() &&
aPoint.x < maxX && aPoint.x > minX &&
aPoint.y < maxY && aPoint.y > minY &&
aPoint.z < maxZ && aPoint.z > minZ)
{
aCoords.push_back(*i);
}
}
unsigned int aSize(aSpecies->getPopulateMoleculeSize());
if(aCoords.size() < aSize)
{
THROW_EXCEPTION(ValueError, String(
getPropertyInterface().getClassName()) +
"[" + getFullID().asString() + "]: There are " +
int2str(aSize) + " " + getIDString(aSpecies) +
" molecules that must be uniformly populated in a " +
"given range,\n but there are only " +
int2str(aCoords.size()) + " vacant voxels of " +
getIDString(aSpecies->getVacantSpecies()) +
" that can be populated.");
}
unsigned int aCoordsArray[aCoords.size()];
for(unsigned int i(0); i != aCoords.size(); ++i)
{
aCoordsArray[i] = aCoords[i];
}
gsl_ran_shuffle(getStepper()->getRng(), aCoordsArray, aCoords.size(),
sizeof(unsigned int));
for(unsigned int i(0); i != aSize; ++i)
{
aSpecies->addMolecule(theSpatiocyteStepper->coord2voxel(aCoordsArray[i]));
}
}
