/** Called every time the trajectory changes. Set up FrameMask for the new
* parmtop and allocate space for selected atoms from the Frame.
*/
Action::RetType Action_Rmsd::Setup(Topology* currentParm, Topology** parmAddress) {
// Target setup
if (SetupRmsMask(*currentParm, "rmsd")) return Action::ERR;
// Reference setup
if (SetupRef(*currentParm, TgtMask().Nselected(), "rmsd"))
return Action::ERR;
// Per residue rmsd setup
if (perres_) {
// If RefParm is still NULL probably 'first', set now.
if (RefParm_ == 0)
RefParm_ = currentParm;
if (perResSetup(currentParm, RefParm_)) return Action::ERR;
}
return Action::OK;
}
/** Called every time the trajectory changes. Set up FrameMask for the new
* parmtop and allocate space for selected atoms from the Frame.
*/
Action::RetType Action_Rmsd::Setup(ActionSetup& setup) {
// Target setup
if ( setup.Top().SetupIntegerMask( tgtMask_ ) ) return Action::ERR;
mprintf("\tTarget mask:");
tgtMask_.BriefMaskInfo();
mprintf("\n");
if ( tgtMask_.None() ) {
mprintf("Warning: No atoms in mask '%s'.\n", tgtMask_.MaskString());
return Action::SKIP;
}
// Allocate space for selected atoms in the frame. This will also put the
// correct masses in based on the mask.
tgtFrame_.SetupFrameFromMask(tgtMask_, setup.Top().Atoms());
// Reference setup
if (REF_.SetupRef(setup.Top(), tgtMask_.Nselected(), "rmsd"))
return Action::SKIP;
// Per residue rmsd setup
if (perres_) {
// If RefParm is still NULL probably 'first', set now.
if (RefParm_ == 0)
RefParm_ = setup.TopAddress();
int err = perResSetup(setup.Top(), *RefParm_);
if (err == 1) return Action::SKIP;
else if (err == 2) return Action::ERR;
}
// Warn if PBC and rotating
if (rotate_ && setup.CoordInfo().TrajBox().Type() != Box::NOBOX) {
mprintf("Warning: Coordinates are being rotated and box coordinates are present.\n"
"Warning: Unit cell vectors are NOT rotated; imaging will not be possible\n"
"Warning: after the RMS-fit is performed.\n");
}
return Action::OK;
}