TrialMol::TrialMol(const MoleculeKind& k, const BoxDimensions& ax,
uint box)
: kind(&k), axes(&ax), box(box), tCoords(k.NumAtoms()),
totalWeight(1.0)
{
atomBuilt = new bool[k.NumAtoms()];
std::fill_n(atomBuilt, k.NumAtoms(), false);
growthToWorld.LoadIdentity();
}
DCLinear::DCLinear(System& sys, const Forcefield& ff,
const MoleculeKind& kind, const Setup& set) :
data(sys, ff, set)
{
mol_setup::MolMap::const_iterator it = set.mol.kindMap.find(kind.name);
assert(it != set.mol.kindMap.end());
const mol_setup::MolKind setupKind = it->second;
//assuming the molecule's ends are 0 and Length - 1
uint size = kind.NumAtoms();
forward.push_back(new DCSingle(&data, 0));
backward.push_back(new DCSingle(&data, size - 1));
if (size < 2) return;
forward.push_back(new DCOnSphere(&data, setupKind, 1, 0));
backward.push_back(new DCOnSphere(&data, setupKind, size - 2, size - 1));
if (size < 3) return;
forward.push_back(new DCLinkNoDih(&data, setupKind, 2, 1));
backward.push_back(new DCLinkNoDih(&data, setupKind, size - 3, size - 2));
for (uint i = 3; i < size; ++i)
{
forward.push_back(new DCLink(&data, setupKind, i, i - 1));
backward.push_back(new DCLink(&data, setupKind, size - i - 1, size - i));
}
}
