Detector::Detector(int s, double t, char *td){
totalPixelSkin = 0;
totalPixelNonSkinBase = 0;
totalPixelSkinBase = 0;
totalPixelNonSkin = 0;
scale = s;
threshold = t;
testDir = td;
getHistogramSkin();
getHistogramNonSkin();
writeHistogram();
}
void HBondGeometric::process() {
Molecule* mol1;
Molecule* mol2;
RigidBody* rb1;
Molecule::HBondDonor* hbd1;
Molecule::HBondDonor* hbd2;
std::vector<Molecule::HBondDonor*>::iterator hbdi;
std::vector<Molecule::HBondDonor*>::iterator hbdj;
std::vector<Atom*>::iterator hbai;
std::vector<Atom*>::iterator hbaj;
Atom* hba1;
Atom* hba2;
SimInfo::MoleculeIterator mi;
Molecule::RigidBodyIterator rbIter;
Vector3d dPos;
Vector3d aPos;
Vector3d hPos;
Vector3d DH;
Vector3d DA;
RealType DAdist, DHdist, theta, ctheta;
int ii, jj;
int nHB, nA, nD;
DumpReader reader(info_, dumpFilename_);
int nFrames = reader.getNFrames();
frameCounter_ = 0;
for (int istep = 0; istep < nFrames; istep += step_) {
reader.readFrame(istep);
frameCounter_++;
currentSnapshot_ = info_->getSnapshotManager()->getCurrentSnapshot();
// update the positions of atoms which belong to the rigidbodies
for (mol1 = info_->beginMolecule(mi); mol1 != NULL;
mol1 = info_->nextMolecule(mi)) {
for (rb1 = mol1->beginRigidBody(rbIter); rb1 != NULL;
rb1 = mol1->nextRigidBody(rbIter)) {
rb1->updateAtoms();
}
}
if (evaluator1_.isDynamic()) {
seleMan1_.setSelectionSet(evaluator1_.evaluate());
}
if (evaluator2_.isDynamic()) {
seleMan2_.setSelectionSet(evaluator2_.evaluate());
}
for (mol1 = seleMan1_.beginSelectedMolecule(ii);
mol1 != NULL; mol1 = seleMan1_.nextSelectedMolecule(ii)) {
// We're collecting statistics on the molecules in selection 1:
nHB = 0;
nA = 0;
nD = 0;
for (mol2 = seleMan2_.beginSelectedMolecule(jj);
mol2 != NULL; mol2 = seleMan2_.nextSelectedMolecule(jj)) {
// loop over the possible donors in molecule 1:
for (hbd1 = mol1->beginHBondDonor(hbdi); hbd1 != NULL;
hbd1 = mol1->nextHBondDonor(hbdi)) {
dPos = hbd1->donorAtom->getPos();
hPos = hbd1->donatedHydrogen->getPos();
DH = hPos - dPos;
currentSnapshot_->wrapVector(DH);
DHdist = DH.length();
// loop over the possible acceptors in molecule 2:
for (hba2 = mol2->beginHBondAcceptor(hbaj); hba2 != NULL;
hba2 = mol2->nextHBondAcceptor(hbaj)) {
aPos = hba2->getPos();
DA = aPos - dPos;
currentSnapshot_->wrapVector(DA);
DAdist = DA.length();
// Distance criteria: are the donor and acceptor atoms
// close enough?
if (DAdist < rCut_) {
ctheta = dot(DH, DA) / (DHdist * DAdist);
theta = acos(ctheta) * 180.0 / M_PI;
// Angle criteria: are the D-H and D-A and vectors close?
if (theta < thetaCut_) {
// molecule 1 is a Hbond donor:
nHB++;
nD++;
}
}
}
}
// now loop over the possible acceptors in molecule 1:
for (hba1 = mol1->beginHBondAcceptor(hbai); hba1 != NULL;
hba1 = mol1->nextHBondAcceptor(hbai)) {
aPos = hba1->getPos();
// loop over the possible donors in molecule 2:
for (hbd2 = mol2->beginHBondDonor(hbdj); hbd2 != NULL;
hbd2 = mol2->nextHBondDonor(hbdj)) {
dPos = hbd2->donorAtom->getPos();
DA = aPos - dPos;
currentSnapshot_->wrapVector(DA);
DAdist = DA.length();
// Distance criteria: are the donor and acceptor atoms
// close enough?
if (DAdist < rCut_) {
hPos = hbd2->donatedHydrogen->getPos();
DH = hPos - dPos;
currentSnapshot_->wrapVector(DH);
DHdist = DH.length();
ctheta = dot(DH, DA) / (DHdist * DAdist);
theta = acos(ctheta) * 180.0 / M_PI;
// Angle criteria: are the D-H and D-A and vectors close?
if (theta < thetaCut_) {
// molecule 1 is a Hbond acceptor:
nHB++;
nA++;
}
}
}
}
}
collectHistogram(nHB, nA, nD);
}
}
writeHistogram();
}
bool rspfHistogramWriter::execute()
{
writeHistogram();
return true;
}
