virtual void initializeThird()
{
for(std::vector<Species*>::const_iterator i(theProcessSpecies.begin());
i != theProcessSpecies.end(); ++i)
{
if((*i)->getIsDiffusing())
{
THROW_EXCEPTION(ValueError,
String(getPropertyInterface().getClassName()) +
"[" + getFullID().asString() +
"]: All polymer subunit species must be" +
" immobile. " +
(*i)->getVariable()->getFullID().asString() +
" is a diffusing species.");
}
if((*i)->getIsVolume())
{
THROW_EXCEPTION(ValueError,
String(getPropertyInterface().getClassName()) +
"[" + getFullID().asString() +
"]: All polymer subunit species must be on a " +
"surface. " +
(*i)->getVariable()->getFullID().asString() +
" is a volume species.");
}
}
}
virtual void initialize()
{
if(isInitialized)
{
return;
}
ReactionProcess::initialize();
isPriorityQueued = true;
if(getOrder() != 1 && getOrder() != 2)
{
THROW_EXCEPTION(ValueError,
String(getPropertyInterface().getClassName()) +
"[" + getFullID().asString() +
"]: This PolymerFragmentationProcess requires " +
"two substrates.");
}
if(p == -1)
{
p = k;
}
else
{
k = p;
}
}
void setSpatiocyteStepper()
{
Model::StepperMap aStepperMap(getModel()->getStepperMap());
for(Model::StepperMap::const_iterator i(aStepperMap.begin());
i != aStepperMap.end(); ++i )
{
theSpatiocyteStepper = dynamic_cast<SpatiocyteStepper*>(i->second);
if(theSpatiocyteStepper)
{
return;
}
}
THROW_EXCEPTION(ValueError, getPropertyInterface().getClassName() +
": " + getFullID().asString() +
" SpatiocyteStepper has not been declared.");
}
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();
}
}
String Entity::asString() const
{
return getPropertyInterface().getClassName() + "["
+ ( theSuperSystem ? getFullID().asString():
"unbound: " + getID() ) + "]";
}
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]));
}
}
