/** Perform setup required for per residue rmsd calculation.
* Need to set up a target mask, reference mask, and dataset for each
* residue specified in ResRange.
* NOTE: Residues in the range arguments from user start at 1, internal
* res nums start from 0.
*/
int Action_Rmsd::perResSetup(Topology const& currentParm, Topology const& refParm) {
Range tgt_range; // Selected target residues
Range ref_range; // Selected reference residues
// If no target range previously specified do all solute residues
if (TgtRange_.Empty()) {
tgt_range = currentParm.SoluteResidues();
tgt_range.ShiftBy(1); // To match user range arg which would start from 1
} else
tgt_range = TgtRange_;
// If the reference range is empty, set it to match the target range
if (RefRange_.Empty())
ref_range = tgt_range;
else
ref_range = RefRange_;
// Check that the number of reference residues matches number of target residues
if (tgt_range.Size() != ref_range.Size()) {
mprintf("Warning: Number of target residues %i does not match\n"
"Warning: number of reference residues %i.\n",
tgt_range.Size(), ref_range.Size());
return 1;
}
// Setup a dataset, target mask, and reference mask for each residue.
int maxNatom = 0;
Range::const_iterator ref_it = ref_range.begin();
MetaData md(rmsd_->Meta().Name(), "res");
md.SetScalarMode( MetaData::M_RMS );
for (Range::const_iterator tgt_it = tgt_range.begin();
tgt_it != tgt_range.end(); ++tgt_it, ++ref_it)
{
int tgtRes = *tgt_it;
int refRes = *ref_it;
// Check if either the residue num or the reference residue num out of range.
if ( tgtRes < 1 || tgtRes > currentParm.Nres()) {
mprintf("Warning: Specified residue # %i is out of range.\n", tgtRes);
continue;
}
if ( refRes < 1 || refRes > refParm.Nres() ) {
mprintf("Warning: Specified reference residue # %i is out of range.\n", refRes);
continue;
}
// Check if a perResType has been set for this residue # yet.
perResArray::iterator PerRes;
for (PerRes = ResidueRMS_.begin(); PerRes != ResidueRMS_.end(); ++PerRes)
if ( PerRes->data_->Meta().Idx() == tgtRes ) break;
// If necessary, create perResType for residue
if (PerRes == ResidueRMS_.end()) {
perResType p;
md.SetIdx( tgtRes );
md.SetLegend( currentParm.TruncResNameNum(tgtRes-1) );
p.data_ = (DataSet_1D*)masterDSL_->AddSet(DataSet::DOUBLE, md);
if (p.data_ == 0) {
mprinterr("Internal Error: Could not set up per residue data set.\n");
return 2;
}
if (perresout_ != 0) perresout_->AddDataSet( p.data_ );
// Setup mask strings. Note that masks are based off user residue nums
p.tgtResMask_.SetMaskString(":" + integerToString(tgtRes) + perresmask_);
p.refResMask_.SetMaskString(":" + integerToString(refRes) + perresmask_);
ResidueRMS_.push_back( p );
PerRes = ResidueRMS_.end() - 1;
}
PerRes->isActive_ = false;
// Setup the reference mask
if (refParm.SetupIntegerMask(PerRes->refResMask_)) {
mprintf("Warning: Could not setup reference mask for residue %i\n",refRes);
continue;
}
if (PerRes->refResMask_.None()) {
mprintf("Warning: No atoms selected for reference residue %i\n",refRes);
continue;
}
// Setup the target mask
if (currentParm.SetupIntegerMask(PerRes->tgtResMask_)) {
mprintf("Warning: Could not setup target mask for residue %i\n",tgtRes);
continue;
}
if (PerRes->tgtResMask_.None()) {
mprintf("Warning: No atoms selected for target residue %i\n",tgtRes);
continue;
}
// Check that # atoms in target and reference masks match
if (PerRes->tgtResMask_.Nselected() != PerRes->refResMask_.Nselected()) {
mprintf("Warning: Res %i: # atoms in Tgt (%i) != # atoms in Ref (%i)\n",
tgtRes, PerRes->tgtResMask_.Nselected(), PerRes->refResMask_.Nselected());
if (debug_ > 0) {
mprintf(" Target Atoms:\n");
for (AtomMask::const_iterator t = PerRes->tgtResMask_.begin();
t != PerRes->tgtResMask_.end(); ++t)
mprintf("\t%s\n", currentParm.AtomMaskName(*t).c_str());
mprintf(" Ref Atoms:\n");
for (AtomMask::const_iterator r = PerRes->refResMask_.begin();
r != PerRes->refResMask_.end(); ++r)
mprintf("\t%s\n", refParm.AtomMaskName(*r).c_str());
}
continue;
}
if ( PerRes->tgtResMask_.Nselected() > maxNatom ) maxNatom = PerRes->tgtResMask_.Nselected();
// Indicate that these masks were properly set up
PerRes->isActive_ = true;
}
mprintf("\tMax # selected atoms in residues: %i\n", maxNatom);
// Allocate memory for target and reference residue frames.
// Although initial masses are wrong this is OK since the number of atoms
// and masses will be assigned when residue RMSD is actually being calcd.
if (maxNatom > 0) {
std::vector<Atom> temp( maxNatom );
ResTgtFrame_.SetupFrameM( temp );
ResRefFrame_.SetupFrameM( temp );
} else {
mprintf("Warning: No residues selected for per-residue calculation.\n");
return 1;
}
return 0;
}
