/** Called every time a frame is read in. Calc RMSD. If not first and not
* RefTraj SetRefStructure has already been called. When fitting,
* SetRefStructure pre-centers the reference coordinates at the origin
* and puts the translation from origin to reference in Trans[3-5].
*/
Action::RetType Action_Rmsd::DoAction(int frameNum, Frame* currentFrame, Frame** frameAddress) {
// Perform any needed reference actions
ActionRef( *currentFrame, Fit(), UseMass() );
// Calculate RMSD
double rmsdval = CalcRmsd( *currentFrame, SelectedRef(), RefTrans() );
rmsd_->Add(frameNum, &rmsdval);
// ---=== Per Residue RMSD ===---
// Set reference and selected frame for each residue using the previously
// set-up masks in refResMask and tgtResMask. Use SetFrame instead
// of SetCoordinates since each residue can be a different size.
if (perres_) {
for (int N=0; N < NumResidues_; ++N) {
if (!resIsActive_[N]) {
//mprintf("DEBUG: [%4i] Not Active.\n",N);
continue;
}
ResRefFrame_->SetFrame(RefFrame(), refResMask_[N]);
ResFrame_->SetFrame(*currentFrame, tgtResMask_[N]);
if (perrescenter_) {
ResFrame_->CenterOnOrigin(false);
ResRefFrame_->CenterOnOrigin(false);
}
double R = ResFrame_->RMSD_NoFit(*ResRefFrame_, UseMass());
//mprintf("DEBUG: [%4i] Res [%s] nofit RMSD to [%s] = %lf\n",N,
// tgtResMask[N]->MaskString(),refResMask[N]->MaskString(),R);
PerResRMSD_[N]->Add(frameNum, &R);
}
}
if (Previous())
SetRefStructure( *currentFrame, Fit(), UseMass() );
return Action::OK;
}
// ReferenceAction::InitRef()
int ReferenceAction::InitRef(bool previousIn, bool firstIn, bool massIn, bool fitIn,
std::string const& reftrajname, ReferenceFrame const& REF,
Topology* RefParm, std::string const& refmaskIn,
ArgList& actionArgs, const char* call)
{
refmode_ = UNKNOWN_REF;
previous_ = previousIn;
if (firstIn || previous_)
refmode_ = FIRST;
else {
if (REF.error()) return 1;
if (REF.empty()) {
if (!reftrajname.empty()) {
if (RefParm == 0) {
mprinterr("Error: %s: No parm found for reftraj %s. Make sure parm has been loaded.\n",
call, reftrajname.c_str());
return 1;
}
refmode_ = REFTRAJ;
} else {
// No reference keywords specified. Default to first.
mprintf("Warning: %s: No reference structure given. Defaulting to first.\n",call);
refmode_ = FIRST;
}
} else
refmode_ = REFFRAME;
}
// Set the reference mask expression
refMask_.SetMaskString(refmaskIn);
// Initialize reference if not 'first'
if (refmode_ != FIRST) {
if ( !reftrajname.empty() ) {
// Reference trajectory
if (SetRefMask( *RefParm, call )!=0) return 1;
// Attempt to open reference traj.
if (refTraj_.SetupTrajRead( reftrajname, actionArgs, RefParm)) {
mprinterr("Error: %s: Could not set up reftraj %s\n", call, reftrajname.c_str());
return 1;
}
refFrame_.SetupFrameV(RefParm->Atoms(), refTraj_.TrajCoordInfo());
if (refTraj_.BeginTraj()) {
mprinterr("Error: %s: Could not open reftraj %s\n", call, reftrajname.c_str());
return 1;
}
} else {
// Reference Frame
if (SetRefMask( REF.Parm(), call ) != 0) return 1;
SetRefStructure( REF.Coord(), fitIn, massIn );
}
}
// Set reference mode string
if (previous_)
modeString_ = "previous frame";
else if (refmode_ == FIRST)
modeString_ = "first frame";
else if (refmode_==REFTRAJ)
modeString_ = "trajectory " + refTraj_.Traj().Filename().Full();
else // REFFRAME
modeString_ = "\"" + REF.RefName() + "\"";
modeString_ += " (" + refMask_.MaskExpression() + ")";
return 0;
}
