void ASENSOR_DAQFT_FT( ASENSOR *asensor, matrix &f, matrix &t )
{
matrix D;
asensor->CurrentValues(D);
matrix_dim(f,AXIS_XYZ,1);
f(1,1) = D(1,1);
f(2,1) = D(2,1);
f(3,1) = D(3,1);
matrix_dim(t,AXIS_XYZ,1);
t(1,1) = D(4,1);
t(2,1) = D(5,1);
t(3,1) = D(6,1);
}
int Action_NativeContacts::DetermineNativeContacts(Topology const& parmIn, Frame const& fIn)
#endif
{
# ifdef MPI
Frame fIn = frameIn;
if (trajComm_.Size() > 1) {
// Ensure all threads use same reference
if (trajComm_.Master())
for (int rank = 1; rank < trajComm_.Size(); rank++)
fIn.SendFrame( rank, trajComm_ );
else
fIn.RecvFrame( 0, trajComm_ );
}
# endif
if (pfile_ != 0 || nfile_ != 0) {
refFrame_ = fIn; // Save frame for later PDB output.
refParm_ = &parmIn; // Save parm for later PDB output.
}
if ( SetupContactLists(parmIn, fIn) ) return 1;
// If specified, set up contacts maps; base size on atom masks.
if (nativeMap_ != 0) {
int matrix_max;
if (Mask2_.MaskStringSet()) {
matrix_min_ = std::min( Mask1_[0], Mask2_[0] );
matrix_max = std::max( Mask1_.back(), Mask2_.back() );
} else {
matrix_min_ = Mask1_[0];
matrix_max = Mask1_.back();
}
std::string label("Atom");
if (byResidue_) {
matrix_min_ = parmIn[matrix_min_].ResNum();
matrix_max = parmIn[matrix_max].ResNum();
label.assign("Residue");
}
int matrix_cols = matrix_max - matrix_min_ + 1;
if (nativeMap_->AllocateHalf( matrix_cols )) return 1;
if (nonnatMap_->AllocateHalf( matrix_cols )) return 1;
Dimension matrix_dim( matrix_min_+1, 1, label );
nativeMap_->SetDim(Dimension::X, matrix_dim);
nativeMap_->SetDim(Dimension::Y, matrix_dim);
nonnatMap_->SetDim(Dimension::X, matrix_dim);
nonnatMap_->SetDim(Dimension::Y, matrix_dim);
}
double maxDist2 = 0.0;
double minDist2 = DBL_MAX;
nativeContacts_.clear();
std::pair<contactListType::iterator, bool> ret;
if (determineNativeContacts_) {
if ( Mask2_.MaskStringSet() ) {
for (AtomMask::const_iterator c1 = Mask1_.begin(); c1 != Mask1_.end(); ++c1)
for (AtomMask::const_iterator c2 = Mask2_.begin(); c2 != Mask2_.end(); ++c2)
{
SetNativeContact();
}
} else {
for (AtomMask::const_iterator c1 = Mask1_.begin(); c1 != Mask1_.end(); ++c1)
for (AtomMask::const_iterator c2 = c1 + 1; c2 != Mask1_.end(); ++c2)
{
SetNativeContact();
}
}
}
//mprintf("\tMinimum observed distance= %f, maximum observed distance= %f\n",
// sqrt(minDist2), sqrt(maxDist2));
// Print contacts
mprintf("\tSetup %zu native contacts:\n", nativeContacts_.size());
for (contactListType::const_iterator contact = nativeContacts_.begin();
contact != nativeContacts_.end(); ++contact)
{
int a1 = contact->first.first;
int a2 = contact->first.second;
mprintf("\t\tAtom '%s' to '%s'\n", parmIn.AtomMaskName(a1).c_str(),
parmIn.AtomMaskName(a2).c_str());
}
return 0;
}
