void updateCOM() {
DataStorage& data = snapshotMan_->getCurrentSnapshot()->*storage_;
bool needsVel = false;
if (data.getStorageLayout() & DataStorage::dslVelocity) needsVel = true;
if (cutoffAtomList.size() == 1) {
data.position[localIndex_] = cutoffAtomList[0]->getPos();
if (needsVel)
data.velocity[localIndex_] = cutoffAtomList[0]->getVel();
} else {
std::vector<Atom *>::iterator i;
Atom * atom;
RealType totalMass = getMass();
data.position[localIndex_] = V3Zero;
if (needsVel) data.velocity[localIndex_] = V3Zero;
for(atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
data.position[localIndex_] += atom->getMass() * atom->getPos();
if (needsVel)
data.velocity[localIndex_] += atom->getMass() * atom->getVel();
}
data.position[localIndex_] /= totalMass;
if (needsVel) data.velocity[localIndex_] /= totalMass;
}
}
RealType getMass() {
if (!haveTotalMass) {
totalMass = 0.0;
std::vector<Atom *>::iterator i;
for(Atom* atom = beginAtom(i); atom != NULL; atom = nextAtom(i)) {
RealType mass = atom->getMass();
totalMass += mass;
}
haveTotalMass = true;
}
return totalMass;
}
Angle Residue::getTorsionPhi() const
{
Angle result(0.0);
if (hasTorsionPhi())
{
const Residue* previous = getPrevious(RTTI::getDefault<Residue>());
if (previous != 0)
{
const Atom* C = 0;
const Atom* N = 0;
const Atom* CA = 0;
AtomConstIterator it;
for (it = beginAtom(); +it; ++it)
{
if (it->getName() == "C") C = &*it;
if (it->getName() == "CA") CA = &*it;
if (it->getName() == "N") N = &*it;
}
const Atom* last_C = 0;
for (it = previous->beginAtom(); +it; ++it)
{
if (it->getName() == "C")
{
last_C = &*it;
break;
}
}
if ((N != 0) && (C != 0) && (CA != 0) && (last_C != 0))
{
result = calculateTorsionAngle(*last_C, *N, *CA, *C);
}
else
{
Log.error() << "Atoms not found:" << last_C << "/" << N << "/" << CA << "/" << C << " in residue " << getFullName() << " " << getID() << endl;
}
}
else
{
Log.error() << "No previous residue!" << endl;
}
}
return result;
}
Angle Residue::getTorsionPsi() const
{
Angle result(0.0);
if (hasTorsionPsi())
{
const Residue* next = getNext(RTTI::getDefault<Residue>());
if (next != 0)
{
const Atom* C = 0;
const Atom* N = 0;
const Atom* CA = 0;
AtomConstIterator it;
for (it = beginAtom(); +it; ++it)
{
if (it->getName() == "C") C = &*it;
if (it->getName() == "CA") CA = &*it;
if (it->getName() == "N") N = &*it;
}
const Atom* next_N = 0;
for (it = next->beginAtom(); +it; ++it)
{
if (it->getName() == "N")
{
next_N = &*it;
break;
}
}
if ((N != 0) && (C != 0) && (CA != 0) && (next_N != 0))
{
result = calculateTorsionAngle(*N, *CA, *C, *next_N);
}
else
{
Log.error() << "Atoms not found:" << N << "/" << CA << "/" << C << "/" << next_N << " in residue " << getFullName() << " " << getID() << endl;
}
}
else
{
Log.error() << "No next residue!" << endl;
}
}
return result;
}
