Exemplo n.º 1
0
/** 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;
}
Exemplo n.º 2
0
/** 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;
}