/** Element access. Use this whenever possible to avoid the virtual function overhead of get(). */
T const & operator()(long row, long col) const
{
ConstIterator existing = m.find(IndexPair(row, col));
if (existing == m.end())
return ZERO;
else
return existing->second;
}
int FF_Restraint_NativeContact::createContacts()
{
printf("Searching for native contacts\n");
// Proxies
WorkSpace& wspace = RestraintForcefieldBase::getWSpace();
int i, j = 0;
double dist;
// delete all previous forces
contact.clear();
for(i = 0; i < wspace.atom.size(); i++) {
// Does this atom need to be part of the restraint set ?
if(!m_Picker->matches(wspace.atom[i])) continue;
for(j = i + 1; j < wspace.atom.size(); j++)
{
// Does this atom need to be part of the restraint set ?
if(!m_Picker->matches(wspace.atom[j])) continue;
// get the distance between atoms i and j - this will be assumed to be their "native" distance.
dist = wspace.calcAtomDistance(i, j);
if(dist > (NativeDist - (log(1.0/0.1 - 1)/Steepness)) ) continue;
// only accept contacts that are will at least score 0.9 out of 1.0 on
// the sigmoidal function
//printf("Native Contact: %d %d %d \n",contact.size(), i ,j );
contact.push_back(IndexPair(i, j));
}
}
if(contact.size() == 0){
throw(ProcedureException("No native contacts found! Are you sure there isnt an error somewhere ?"));
}
return 0;
}
/** Constructor. */
ConstIterator(AddressableMatrix const & m_, long r = 0, long c = 0)
: m(m_), nrows(m_.numRows()), ncols(m_.numColumns()), entry(IndexPair(r, c), 0)
{}
/** Unset an element by removing it from the underlying map. Its value is now identically zero. */
void unset(long row, long col) {
m.erase(IndexPair(row, col));
}
void set(long row, long col, T const & value)
{
m[IndexPair(row, col)] = value;
}
/**
* {@inheritDoc}
*
* For mapped matrices, this function will always add the (row, col) element to the matrix if it doesn't yet exist, setting
* it to an initial value of zero. This may destroy the sparsity of the matrix.
*/
T & getMutable(long row, long col)
{
// See documentation of std::map::insert()
return m.insert(typename Map::value_type(IndexPair(row, col), static_cast<T>(0))).first->second;
}
/** Check if an element has an explicitly set value. */
bool isSet(long row, long col) const
{
return m.find(IndexPair(row, col)) != m.end();
}
IndexPair DirichletProblem::getLastPoint(Index nx, Index ny) const
{
return IndexPair(nx-1,ny-1);
}
IndexPair DirichletProblem::getFirstPoint(Index, Index) const
{
return IndexPair(1,1);
}
