cvm::atom::atom(atom const &a)
: index(a.index)
{
id = (cvm::proxy)->get_atom_id(index);
update_mass();
reset_data();
}
cvm::atom::atom(int atom_number)
{
colvarproxy *p = cvm::proxy;
index = p->init_atom(atom_number);
if (cvm::debug()) {
cvm::log("The index of this atom in the colvarproxy arrays is "+
cvm::to_str(index)+".\n");
}
id = p->get_atom_id(index);
update_mass();
reset_data();
}
cvm::atom::atom(cvm::residue_id const &residue,
std::string const &atom_name,
std::string const &segment_id)
{
colvarproxy *p = cvm::proxy;
index = p->init_atom(residue, atom_name, segment_id);
if (cvm::debug()) {
cvm::log("The index of this atom in the colvarproxy_namd arrays is "+
cvm::to_str(index)+".\n");
}
id = p->get_atom_id(index);
update_mass();
reset_data();
}
void insert(int j, int i) {
update_mass(j, i);
if (nodes_type[j] == NODE_INTERNAL) {
insert_recursive(j, i);
} else if (nodes_body[j] > -1) {
nodes_type[j] = NODE_INTERNAL;
branch(j);
insert_recursive(j, nodes_body[j]);
insert_recursive(j, i);
nodes_body[j] = -1;
} else {
nodes_body[j] = i;
}
}