//using dist for no image
// and kernel for when we use solute molecule center
void Action_Closest::Action_NoImage_Center(Frame&, double maxD)
{
double Dist;
int solventMol;
AtomMask::const_iterator solute_atom;
Iarray::const_iterator solvent_atom;
Vec3 maskCenter = frmIn.VGeometricCenter( distanceMask_ );
for (solventMol=0; solventMol < NsolventMolecules_; solventMol++) { //standard loop
SolventMols_[solventMol].D = maxD;
for (solvent_atom = SolventMols_[solventMol].solventAtoms.begin();
solvent_atom != SolventMols_[solventMol].solventAtoms.end(); ++solvent_atom)
{
//main dist2_noImage code
double *a1 = maskCenter.Dptr(); //center of solute molecule
double *a2 = frmIn.XYZ(*solvent_atom);
double x = a1[0] - a2[0];
double y = a1[1] - a2[1];
double z = a1[2] - a2[2];
Dist = (x*x + y*y + z*z);
if (Dist < SolventMols_[solventMol].D)
SolventMols_[solventMol].D = Dist;
}
}
}
//pulling out the dist control statement
void Action_Closest::Action_NoImage(Frame& frmIn,double maxD)
{
double Dist;
int solventMol;
AtomMask::const_iterator solute_atom;
Iarray::const_iterator solvent_atom;
// Loop over all solvent molecules in original frame
if (useMaskCenter_) {
Vec3 maskCenter = frmIn.VGeometricCenter( distanceMask_ );
for (solventMol=0; solventMol < NsolventMolecules_; solventMol++) {
SolventMols_[solventMol].D = maxD;
for (solvent_atom = SolventMols_[solventMol].solventAtoms.begin();
solvent_atom != SolventMols_[solventMol].solventAtoms.end(); ++solvent_atom)
{
Dist = DIST2_NoImage( maskCenter.Dptr(),
frmIn.XYZ(*solvent_atom));
//printf("DIST = %f\n", Dist);
if (Dist < SolventMols_[solventMol].D)
SolventMols_[solventMol].D = Dist;
}
}
} else {
for (solventMol=0; solventMol < NsolventMolecules_; solventMol++) {
if (debug_ > 1)
mprintf("DEBUG: Calculating distance for molecule %i\n", solventMol);
// Set the initial minimum distance for this solvent mol to be the
// max possible distance.
SolventMols_[solventMol].D = maxD;
// Calculate distance between each atom in distanceMask and atoms in solvent Mask
for (solvent_atom = SolventMols_[solventMol].solventAtoms.begin();
solvent_atom != SolventMols_[solventMol].solventAtoms.end(); ++solvent_atom)
{
for (solute_atom = distanceMask_.begin();
solute_atom != distanceMask_.end(); ++solute_atom)
{
Dist = DIST2_NoImage(frmIn.XYZ(*solute_atom),
frmIn.XYZ(*solvent_atom));
//printf("no center DIST = %f\n", Dist);
if (Dist < SolventMols_[solventMol].D)
SolventMols_[solventMol].D = Dist;
if (debug_ > 2)
mprintf("DEBUG: SolvMol %i, soluteAtom %i, solventAtom %i, D= %f, minD= %f\n",
solventMol, *solute_atom, *solvent_atom, Dist,
sqrt(SolventMols_[solventMol].D));
}
}
if (debug_ > 1) mprintf("DEBUG:\tMol %8i minD= %lf\n",solventMol, SolventMols_[solventMol].D);
} // END for loop over solventMol
}
}
/** Find the minimum distance between atoms in distanceMask and each
* solvent Mask.
*/
Action_Closest::RetType Action_Closest::DoAction(int frameNum, Frame& frmIn) {
int solventMol;
double Dist, maxD;
Matrix_3x3 ucell, recip;
AtomMask::const_iterator solute_atom;
Iarray::const_iterator solvent_atom;
if (image_.ImagingEnabled()) {
frmIn.BoxCrd().ToRecip(ucell, recip);
// Calculate max possible imaged distance
maxD = frmIn.BoxCrd().BoxX() + frmIn.BoxCrd().BoxY() +
frmIn.BoxCrd().BoxZ();
maxD *= maxD;
} else {
// If not imaging, set max distance to an arbitrarily large number
maxD = DBL_MAX;
}
// Loop over all solvent molecules in original frame
if (useMaskCenter_) {
Vec3 maskCenter = frmIn.VGeometricCenter( distanceMask_ );
for (solventMol=0; solventMol < NsolventMolecules_; solventMol++) {
SolventMols_[solventMol].D = maxD;
for (solvent_atom = SolventMols_[solventMol].solventAtoms.begin();
solvent_atom != SolventMols_[solventMol].solventAtoms.end(); ++solvent_atom)
{
Dist = DIST2( maskCenter.Dptr(),
frmIn.XYZ(*solvent_atom), image_.ImageType(),
frmIn.BoxCrd(), ucell, recip);
if (Dist < SolventMols_[solventMol].D)
SolventMols_[solventMol].D = Dist;
}
}
} else {
for (solventMol=0; solventMol < NsolventMolecules_; solventMol++) {
if (debug_ > 1)
mprintf("DEBUG: Calculating distance for molecule %i\n", solventMol);
// Set the initial minimum distance for this solvent mol to be the
// max possible distance.
SolventMols_[solventMol].D = maxD;
// Calculate distance between each atom in distanceMask and atoms in solvent Mask
for (solvent_atom = SolventMols_[solventMol].solventAtoms.begin();
solvent_atom != SolventMols_[solventMol].solventAtoms.end(); ++solvent_atom)
{
for (solute_atom = distanceMask_.begin();
solute_atom != distanceMask_.end(); ++solute_atom)
{
Dist = DIST2(frmIn.XYZ(*solute_atom),
frmIn.XYZ(*solvent_atom), image_.ImageType(),
frmIn.BoxCrd(), ucell, recip);
if (Dist < SolventMols_[solventMol].D)
SolventMols_[solventMol].D = Dist;
if (debug_ > 2)
mprintf("DEBUG: SolvMol %i, soluteAtom %i, solventAtom %i, D= %f, minD= %f\n",
solventMol, *solute_atom, *solvent_atom, Dist,
sqrt(SolventMols_[solventMol].D));
}
}
if (debug_ > 1) mprintf("DEBUG:\tMol %8i minD= %lf\n",solventMol, SolventMols_[solventMol].D);
} // END for loop over solventMol
}
// Sort distances
std::sort( SolventMols_.begin(), SolventMols_.end(), moldist_cmp() );
// Add first closestWaters solvent atoms to stripMask
std::vector<MolDist>::iterator solventend = SolventMols_.begin() + closestWaters_;
for ( std::vector<MolDist>::const_iterator solvent = SolventMols_.begin();
solvent != solventend;
++solvent )
{
solvent_atom = solvent->mask.begin();
mprintf("\tMol= %8i Atom= %8i Dist= %10.4f\n", solvent->mol,
*solvent_atom + 1, sqrt( solvent->D ));
}
return Action_Closest::OK;
}