Пример #1
0
// Exec_PermuteDihedrals::Execute()
Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn) {
  debug_ = State.Debug();
  mode_ = INTERVAL;
  // Get Keywords - first determine mode
  if (argIn.hasKey("random"))
    mode_ = RANDOM;
  else if (argIn.hasKey("interval"))
    mode_ = INTERVAL;
  // Get input COORDS set
  std::string setname = argIn.GetStringKey("crdset");
  if (setname.empty()) {
    mprinterr("Error: Specify COORDS dataset name with 'crdset'.\n");
    return CpptrajState::ERR;
  }
  DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindCoordsSet( setname );
  if (CRD == 0) {
    mprinterr("Error: Could not find COORDS set '%s'\n", setname.c_str());
    return CpptrajState::ERR;
  }
  mprintf("    PERMUTEDIHEDRALS: Using COORDS '%s'\n", CRD->legend());

  // Get residue range
  Range resRange;
  resRange.SetRange(argIn.GetStringKey("resrange"));
  if (!resRange.Empty())
    resRange.ShiftBy(-1); // User res args start from 1
  mprintf("\tPermutating dihedrals in");
  if (resRange.Empty())
    mprintf(" all solute residues.\n");
  else
    mprintf(" residue range [%s]\n", resRange.RangeArg());

  // Determine which angles to search for
  DihedralSearch dihSearch;
  dihSearch.SearchForArgs(argIn);
  // If nothing is enabled, enable all 
  dihSearch.SearchForAll();
  mprintf("\tSearching for types:");
  dihSearch.PrintTypes();
  mprintf("\n");

  // Setup output trajectory
  outframe_ = 0; 
  std::string outfilename = argIn.GetStringKey("outtraj");
  if (!outfilename.empty()) {
    mprintf("\tCoordinates output to '%s'\n", outfilename.c_str());
    Topology* outtop = State.DSL().GetTopology( argIn );
    if (outtop == 0) {
      mprinterr("Error: No topology for output traj.\n");
      return CpptrajState::ERR;
    }
    // Setup output trajectory FIXME: Correct frames for # of rotations
    if (outtraj_.PrepareTrajWrite(outfilename, argIn, CRD->TopPtr(), CRD->CoordsInfo(),
                                  CRD->Size(), TrajectoryFile::UNKNOWN_TRAJ))
      return CpptrajState::ERR;
  }

  // Setup output coords
  outfilename = argIn.GetStringKey("crdout");
  if (!outfilename.empty()) {
    mprintf("\tCoordinates saved to set '%s'\n", outfilename.c_str());
    crdout_ = (DataSet_Coords_CRD*)State.DSL().AddSet(DataSet::COORDS, outfilename);
    if (crdout_ == 0) return CpptrajState::ERR;
    crdout_->CoordsSetup( CRD->Top(), CRD->CoordsInfo() );
  }

  // Get specific mode options.
  double interval_in_deg = 60.0;
  if ( mode_ == INTERVAL ) {
    interval_in_deg = argIn.getNextDouble(60.0);
    mprintf("\tDihedrals will be rotated at intervals of %.2f degrees.\n", interval_in_deg);
  } else if (mode_ == RANDOM) {
    check_for_clashes_ = argIn.hasKey("check");
    checkAllResidues_ = argIn.hasKey("checkallresidues");
    cutoff_ = argIn.getKeyDouble("cutoff",0.8);
    rescutoff_ = argIn.getKeyDouble("rescutoff",10.0);
    backtrack_ = argIn.getKeyInt("backtrack",4);
    increment_ = argIn.getKeyInt("increment",1);
    max_factor_ = argIn.getKeyInt("maxfactor",2);
    int iseed = argIn.getKeyInt("rseed",-1);
    // Output file for # of problems
    DataFile* problemFile = State.DFL().AddDataFile(argIn.GetStringKey("out"), argIn);
    // Dataset to store number of problems
    number_of_problems_ = State.DSL().AddSet(DataSet::INTEGER, argIn.GetStringNext(),"Nprob");
    if (number_of_problems_==0) return CpptrajState::ERR;
   // Add dataset to data file list
    if (problemFile != 0) problemFile->AddDataSet(number_of_problems_);
    // Check validity of args
    if (cutoff_ < Constants::SMALL) {
      mprinterr("Error: cutoff too small.\n");
      return CpptrajState::ERR;
    }
    if (rescutoff_ < Constants::SMALL) {
      mprinterr("Error: rescutoff too small.\n");
      return CpptrajState::ERR;
    }
    if (backtrack_ < 0) {
      mprinterr("Error: backtrack value must be >= 0\n");
      return CpptrajState::ERR;
    }
    if ( increment_<1 || (360 % increment_)!=0 ) {
      mprinterr("Error: increment must be a factor of 360.\n");
      return CpptrajState::ERR;
    }
    // Calculate max increment
    max_increment_ = 360 / increment_;
    // Seed random number gen
    RN_.rn_set( iseed );
    // Print info
    mprintf("\tDihedrals will be rotated to random values.\n");
    if (iseed==-1)
      mprintf("\tRandom number generator will be seeded using time.\n");
    else
      mprintf("\tRandom number generator will be seeded using %i\n",iseed);
    if (check_for_clashes_) {
      mprintf("\tWill attempt to recover from bad steric clashes.\n");
      if (checkAllResidues_)
        mprintf("\tAll residues will be checked.\n");
      else
        mprintf("\tResidues up to the currenly rotating dihedral will be checked.\n");
      mprintf("\tAtom cutoff %.2f, residue cutoff %.2f, backtrack = %i\n",
              cutoff_, rescutoff_, backtrack_);
      mprintf("\tWhen clashes occur dihedral will be incremented by %i\n",increment_);
      mprintf("\tMax # attempted rotations = %i times number dihedrals.\n",
              max_factor_);
    }
    // Square cutoffs to compare to dist^2 instead of dist
    cutoff_ *= cutoff_;
    rescutoff_ *= rescutoff_;
    // Increment backtrack by 1 since we need to skip over current res
    ++backtrack_;
    // Initialize CheckStructure
    if (checkStructure_.SetOptions( false, false, false, State.Debug(), "*", "", 0.8, 1.15, 4.0 )) {
      mprinterr("Error: Could not set up structure check.\n");
      return CpptrajState::ERR;
    }
    // Set up CheckStructure for this parm (false = nobondcheck)
    if (checkStructure_.Setup(CRD->Top(), CRD->CoordsInfo().TrajBox()))
      return CpptrajState::ERR;
  }

  // Determine from selected mask atoms which dihedrals will be rotated.
  PermuteDihedralsType dst;
  // If range is empty (i.e. no resrange arg given) look through all 
  // solute residues.
  Range actualRange;
  if (resRange.Empty())
    actualRange = CRD->Top().SoluteResidues();
  else 
    actualRange = resRange;
  // Search for dihedrals
  if (dihSearch.FindDihedrals(CRD->Top(), actualRange))
    return CpptrajState::ERR;
  // For each found dihedral, set up mask of atoms that will move upon 
  // rotation. Also set up mask of atoms in this residue that will not
  // move, including atom2.
  if (debug_>0)
    mprintf("DEBUG: Dihedrals:\n");
  for (DihedralSearch::mask_it dih = dihSearch.begin();
                               dih != dihSearch.end(); ++dih)
  {
    dst.checkAtoms.clear();
    // Set mask of atoms that will move during dihedral rotation.
    dst.Rmask = DihedralSearch::MovingAtoms(CRD->Top(), dih->A1(), dih->A2());
    // If randomly rotating angles, check for atoms that are in the same
    // residue as A1 but will not move. They need to be checked for clashes
    // since further rotations will not help them.
    if (mode_ == RANDOM && check_for_clashes_) {
      CharMask cMask( dst.Rmask.ConvertToCharMask(), dst.Rmask.Nselected() );
      int a1res = CRD->Top()[dih->A1()].ResNum();
      for (int maskatom = CRD->Top().Res(a1res).FirstAtom();
               maskatom < CRD->Top().Res(a1res).LastAtom(); ++maskatom)
        if (!cMask.AtomInCharMask(maskatom))
          dst.checkAtoms.push_back( maskatom );
      dst.checkAtoms.push_back(dih->A1()); // TODO: Does this need to be added first?
      // Since only the second atom and atoms it is bonded to move during 
      // rotation, base the check on the residue of the second atom.
      dst.resnum = a1res;
    }
    dst.atom0 = dih->A0(); // FIXME: This duplicates info
    dst.atom1 = dih->A1();
    dst.atom2 = dih->A2();
    dst.atom3 = dih->A3();
    BB_dihedrals_.push_back(dst);
    // DEBUG: List dihedral info.
    if (debug_ > 0) {
      mprintf("\t%s-%s-%s-%s\n", 
              CRD->Top().TruncResAtomName(dih->A0()).c_str(),
              CRD->Top().TruncResAtomName(dih->A1()).c_str(),
              CRD->Top().TruncResAtomName(dih->A2()).c_str(),
              CRD->Top().TruncResAtomName(dih->A3()).c_str() );
      if (debug_ > 1 && mode_ == RANDOM && check_for_clashes_) {
        mprintf("\t\tCheckAtoms=");
        for (std::vector<int>::const_iterator ca = dst.checkAtoms.begin();
                                              ca != dst.checkAtoms.end(); ++ca)
          mprintf(" %i", *ca + 1);
        mprintf("\n");
      }
      if (debug_ > 2) {
        mprintf("\t\t");
        dst.Rmask.PrintMaskAtoms("Rmask:");
      }
    }
  }

  // Set up simple structure check. First step is coarse; check distances 
  // between a certain atom in each residue (first, COM, CA, some other atom?)
  // to see if residues are in each others neighborhood. Second step is to 
  // check the atoms in each close residue.
  if (check_for_clashes_) {
    ResidueCheckType rct;
    int res = 0;
    for (Topology::res_iterator residue = CRD->Top().ResStart();
                                residue != CRD->Top().ResEnd(); ++residue)
    {
      rct.resnum = res++;
      rct.start = residue->FirstAtom();
      rct.stop = residue->LastAtom();
      rct.checkatom = rct.start;
      ResCheck_.push_back(rct);
    }
  }

  // Perform dihedral permute
  Frame currentFrame = CRD->AllocateFrame();
  for (unsigned int set = 0; set != CRD->Size(); set++)
  {
    CRD->GetFrame(set, currentFrame);
    int n_problems = 0;
    switch (mode_) {
      case RANDOM:
        RandomizeAngles(currentFrame, CRD->Top());
        // Check the resulting structure
        n_problems = checkStructure_.CheckOverlaps( currentFrame );
        //mprintf("%i\tResulting structure has %i problems.\n",frameNum,n_problems);
        number_of_problems_->Add(set, &n_problems);
        if (outtraj_.IsInitialized()) outtraj_.WriteSingle(outframe_++, currentFrame);
        if (crdout_ != 0) crdout_->AddFrame( currentFrame );
        break;
      case INTERVAL: IntervalAngles(currentFrame, CRD->Top(), interval_in_deg); break;
    }
  }
  if (outtraj_.IsInitialized()) outtraj_.EndTraj();
  return CpptrajState::OK;
}
Пример #2
0
/** Determine from selected mask atoms which dihedrals will be rotated. */
Action::RetType Action_DihedralScan::Setup(ActionSetup& setup) {
  DihedralScanType dst;
  // If range is empty (i.e. no resrange arg given) look through all 
  // solute residues.
  Range actualRange;
  if (resRange_.Empty())
    actualRange = setup.Top().SoluteResidues();
  else 
    actualRange = resRange_;
  // Search for dihedrals
  if (dihSearch_.FindDihedrals(setup.Top(), actualRange))
    return Action::ERR;
  // For each found dihedral, set up mask of atoms that will move upon 
  // rotation. Also set up mask of atoms in this residue that will not
  // move, including atom2.
  if (debug_>0)
    mprintf("DEBUG: Dihedrals:\n");
  for (DihedralSearch::mask_it dih = dihSearch_.begin();
                               dih != dihSearch_.end(); ++dih)
  {
    dst.checkAtoms.clear();
    // Set mask of atoms that will move during dihedral rotation.
    dst.Rmask = DihedralSearch::MovingAtoms(setup.Top(), dih->A1(), dih->A2());
    // If randomly rotating angles, check for atoms that are in the same
    // residue as A1 but will not move. They need to be checked for clashes
    // since further rotations will not help them.
    if (mode_ == RANDOM && check_for_clashes_) {
      CharMask cMask( dst.Rmask.ConvertToCharMask(), dst.Rmask.Nselected() );
      int a1res = setup.Top()[dih->A1()].ResNum();
      for (int maskatom = setup.Top().Res(a1res).FirstAtom();
               maskatom < setup.Top().Res(a1res).LastAtom(); ++maskatom)
        if (!cMask.AtomInCharMask(maskatom))
          dst.checkAtoms.push_back( maskatom );
      dst.checkAtoms.push_back(dih->A1()); // TODO: Does this need to be added first?
      // Since only the second atom and atoms it is bonded to move during 
      // rotation, base the check on the residue of the second atom.
      dst.resnum = a1res;
    }
    dst.atom0 = dih->A0(); // FIXME: This duplicates info
    dst.atom1 = dih->A1();
    dst.atom2 = dih->A2();
    dst.atom3 = dih->A3();
    BB_dihedrals_.push_back(dst);
    // DEBUG: List dihedral info.
    if (debug_ > 0) {
      mprintf("\t%s-%s-%s-%s\n", 
              setup.Top().TruncResAtomName(dih->A0()).c_str(),
              setup.Top().TruncResAtomName(dih->A1()).c_str(),
              setup.Top().TruncResAtomName(dih->A2()).c_str(),
              setup.Top().TruncResAtomName(dih->A3()).c_str() );
      if (debug_ > 1 && mode_ == RANDOM && check_for_clashes_) {
        mprintf("\t\tCheckAtoms=");
        for (std::vector<int>::const_iterator ca = dst.checkAtoms.begin();
                                              ca != dst.checkAtoms.end(); ++ca)
          mprintf(" %i", *ca + 1);
        mprintf("\n");
      }
      if (debug_ > 2) {
        mprintf("\t\t");
        dst.Rmask.PrintMaskAtoms("Rmask:");
      }
    }
  }

  // Set up CheckStructure for this parm (false = nobondcheck)
  if (checkStructure_.SeparateSetup(setup.Top(),
                                    setup.CoordInfo().TrajBox().Type(), false) != Action::OK)
    return Action::ERR;

  // Set the overall max number of rotations to try
  max_rotations_ = (int) BB_dihedrals_.size();
  max_rotations_ *= max_factor_;

  // Set up simple structure check. First step is coarse; check distances 
  // between a certain atom in each residue (first, COM, CA, some other atom?)
  // to see if residues are in each others neighborhood. Second step is to 
  // check the atoms in each close residue.
  if (check_for_clashes_) {
    ResidueCheckType rct;
    int res = 0;
    for (Topology::res_iterator residue = setup.Top().ResStart();
                                residue != setup.Top().ResEnd(); ++residue)
    {
      rct.resnum = res++;
      rct.start = residue->FirstAtom();
      rct.stop = residue->LastAtom();
      rct.checkatom = rct.start;
      ResCheck_.push_back(rct);
    }
  }

  if (!outfilename_.empty() && CurrentParm_ == 0) // FIXME: Correct frames for # of rotations
    outtraj_.SetupTrajWrite(setup.TopAddress(), setup.CoordInfo(), setup.Nframes());

  CurrentParm_ = setup.TopAddress();
  return Action::OK;  
}
Пример #3
0
// Exec_RotateDihedral::Execute()
Exec::RetType Exec_RotateDihedral::Execute(CpptrajState& State, ArgList& argIn) {
  // Get input COORDS set
  std::string setname = argIn.GetStringKey("crdset");
  if (setname.empty()) {
    mprinterr("Error: Specify COORDS dataset name with 'crdset'.\n");
    return CpptrajState::ERR;
  }
  DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindCoordsSet( setname );
  if (CRD == 0) {
    mprinterr("Error: Could not find COORDS set '%s'\n", setname.c_str());
    return CpptrajState::ERR;
  }
  if (CRD->Size() < 1) {
    mprinterr("Error: COORDS set is empty.\n");
    return CpptrajState::ERR;
  }
  int frame = argIn.getKeyInt("frame", 0);
  if (frame < 0 || frame >= (int)CRD->Size()) {
    mprinterr("Error: Specified frame %i is out of range.\n", frame+1);
    return CpptrajState::ERR;
  }
  mprintf("    ROTATEDIHEDRAL: Using COORDS '%s', frame %i\n", CRD->legend(), frame+1);
  // Get target frame
  Frame FRM = CRD->AllocateFrame();
  CRD->GetFrame(frame, FRM);
  // Save as reference
  Frame refFrame = FRM;

  // Create output COORDS set if necessary
  DataSet_Coords* OUT = 0;
  int outframe = 0;
  std::string outname = argIn.GetStringKey("name");
  if (outname.empty()) {
    // This will not work for TRAJ data sets
    if (CRD->Type() == DataSet::TRAJ) {
      mprinterr("Error: Using TRAJ as input set requires use of 'name' keyword for output.\n");
      return CpptrajState::ERR;
    }
    OUT = CRD;
    outframe = frame;
  } else {
    // Create new output set with 1 empty frame.
    OUT = (DataSet_Coords*)State.DSL().AddSet( DataSet::COORDS, outname );
    if (OUT == 0) return CpptrajState::ERR;
    OUT->Allocate( DataSet::SizeArray(1, 1) );
    OUT->CoordsSetup( CRD->Top(), CRD->CoordsInfo() );
    OUT->AddFrame( CRD->AllocateFrame() );
    mprintf("\tOutput to set '%s'\n", OUT->legend());
  }

  // Determine whether we are setting or incrementing.
  enum ModeType { SET = 0, INCREMENT };
  ModeType mode = SET;
  if (argIn.Contains("value"))
    mode = SET;
  else if (argIn.Contains("increment"))
    mode = INCREMENT;
  else {
    mprinterr("Error: Specify 'value <value>' or 'increment <increment>'\n");
    return CpptrajState::ERR;
  }
  double value = argIn.getKeyDouble(ModeStr[mode], 0.0);
  switch (mode) {
    case SET: mprintf("\tDihedral will be set to %g degrees.\n", value); break;
    case INCREMENT: mprintf("\tDihedral will be incremented by %g degrees.\n", value); break;
  }
  // Convert to radians
  value *= Constants::DEGRAD;

  // Select dihedral atoms
  int A1, A2, A3, A4;
  if (argIn.Contains("type")) {
    // By type
    ArgList typeArg = argIn.GetStringKey("type");
    if (typeArg.empty()) {
      mprinterr("Error: No dihedral type specified after 'type'\n");
      return CpptrajState::ERR;
    }
    DihedralSearch dihSearch;
    dihSearch.SearchForArgs( typeArg );
    if (dihSearch.NoDihedralTokens()) {
      mprinterr("Error: Specified dihedral type not recognized.\n");
      return CpptrajState::ERR;
    }
    // Get residue
    int res = argIn.getKeyInt("res", -1);
    if (res <= 0) {
      mprinterr("Error: If 'type' specified 'res' must be specified and > 0.\n");
      return CpptrajState::ERR;
    }
    // Search for dihedrals. User residue #s start from 1.
    if (dihSearch.FindDihedrals(CRD->Top(), Range(res-1)))
      return CpptrajState::ERR;
    DihedralSearch::mask_it dih = dihSearch.begin();
    A1 = dih->A0();
    A2 = dih->A1();
    A3 = dih->A2();
    A4 = dih->A3();
  } else {
    // By masks
    AtomMask m1( argIn.GetMaskNext() );
    AtomMask m2( argIn.GetMaskNext() );
    AtomMask m3( argIn.GetMaskNext() );
    AtomMask m4( argIn.GetMaskNext() );
    if (CRD->Top().SetupIntegerMask( m1 )) return CpptrajState::ERR;
    if (CRD->Top().SetupIntegerMask( m2 )) return CpptrajState::ERR;
    if (CRD->Top().SetupIntegerMask( m3 )) return CpptrajState::ERR;
    if (CRD->Top().SetupIntegerMask( m4 )) return CpptrajState::ERR;
    if (m1.Nselected() != 1) return MaskError( m1 );
    if (m2.Nselected() != 1) return MaskError( m2 );
    if (m3.Nselected() != 1) return MaskError( m3 );
    if (m4.Nselected() != 1) return MaskError( m4 );
    A1 = m1[0];
    A2 = m2[0];
    A3 = m3[0];
    A4 = m4[0];
  }
  mprintf("\tRotating dihedral defined by atoms '%s'-'%s'-'%s'-'%s'\n",
          CRD->Top().AtomMaskName(A1).c_str(),
          CRD->Top().AtomMaskName(A2).c_str(),
          CRD->Top().AtomMaskName(A3).c_str(),
          CRD->Top().AtomMaskName(A4).c_str());
  // Set mask of atoms that will move during dihedral rotation
  AtomMask Rmask = DihedralSearch::MovingAtoms(CRD->Top(), A2, A3);
  // Calculate current value of dihedral
  double torsion = Torsion( FRM.XYZ(A1), FRM.XYZ(A2), FRM.XYZ(A3), FRM.XYZ(A4) );
  // Calculate delta needed to get to target value.
  double delta;
  switch (mode) {
    case SET:       delta = value - torsion; break;
    case INCREMENT: delta = value; break;
  }
  mprintf("\tOriginal torsion is %g, rotating by %g degrees.\n",
          torsion*Constants::RADDEG, delta*Constants::RADDEG);
  // Set axis of rotation
  Vec3 axisOfRotation = FRM.SetAxisOfRotation( A2, A3 );
  // Calculate rotation matrix for delta.
  Matrix_3x3 rotationMatrix;
  rotationMatrix.CalcRotationMatrix(axisOfRotation, delta);
  // Rotate around axis
  FRM.Rotate(rotationMatrix, Rmask);
  // RMS-fit the non-moving part of the coords back on original
  AtomMask refMask = Rmask;
  refMask.InvertMask();
  FRM.Align( refFrame, refMask );
  // Update coords
  OUT->SetCRD( outframe, FRM );

  return CpptrajState::OK;
}
// Action_MakeStructure::Init()
Action::RetType Action_MakeStructure::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  debug_ = debugIn;
  secstruct_.clear();
  // Get all arguments 
  std::string ss_expr = actionArgs.GetStringNext();
  while ( !ss_expr.empty() ) {
    ArgList ss_arg(ss_expr, ":");
    if (ss_arg.Nargs() < 2) {
      mprinterr("Error: Malformed SS arg.\n");
      Help();
      return Action::ERR;
    }
    // Type is 1st arg, range is 2nd arg.
    SecStructHolder ss_holder(ss_arg[1], FindSStype(ss_arg[0]));

    if (ss_arg.Nargs() == 2) {
    // Find SS type: <ss type>:<range>
      if (ss_holder.sstype_idx == SS_EMPTY) {
        mprinterr("Error: SS type %s not found.\n", ss_arg[0].c_str());
        return Action::ERR;
      } 
      ss_holder.dihSearch_.SearchFor(MetaData::PHI);
      ss_holder.dihSearch_.SearchFor(MetaData::PSI);
      secstruct_.push_back( ss_holder );

    } else if (ss_arg[0] == "ref") {
    // Use dihedrals from reference structure
      if (ss_arg.Nargs() < 3) {
        mprinterr("Error: Invalid 'ref' arg. Requires 'ref:<range>:<refname>[:<ref range>]'\n");
        return Action::ERR;
      }
      ss_arg.MarkArg(0);
      ss_arg.MarkArg(1);
      // Sanity check: Currently only unique args of this type are allowed
      if (ss_holder.sstype_idx != SS_EMPTY) {
        mprinterr("Error: Ref backbone types must be unique [%s]\n", ss_arg[0].c_str());
        return Action::ERR;
      }
      // Use backbone phi/psi from reference structure
      ss_holder.dihSearch_.SearchFor(MetaData::PHI);
      ss_holder.dihSearch_.SearchFor(MetaData::PSI);
      // Get reference structure
      DataSet_Coords_REF* REF = (DataSet_Coords_REF*)
                                DSL->FindSetOfType(ss_arg.GetStringNext(),
                                                   DataSet::REF_FRAME); // ss_arg[2]
      if (REF == 0) {
        mprinterr("Error: Could not get reference structure [%s]\n", ss_arg[2].c_str());
        return Action::ERR;
      }
      // Get reference residue range, or use resRange
      Range refRange(ss_arg.GetStringNext(), -1); // ss_arg[3]
      if (!refRange.Empty()) {
        if (ss_holder.resRange.Size() != refRange.Size()) {
          mprinterr("Error: Reference range [%s] must match residue range [%s]\n",
                    refRange.RangeArg(), ss_holder.resRange.RangeArg());
          return Action::ERR;
        }
      } else
        refRange = ss_holder.resRange;
      // Look for phi/psi only in reference
      DihedralSearch refSearch;
      refSearch.SearchFor(MetaData::PHI);
      refSearch.SearchFor(MetaData::PSI);
      if (refSearch.FindDihedrals( REF->Top(), refRange )) return Action::ERR;
      // For each found dihedral, set theta 
      for (DihedralSearch::mask_it dih = refSearch.begin(); dih != refSearch.end(); ++dih)
      {
        double torsion = Torsion( REF->RefFrame().XYZ(dih->A0()),
                                  REF->RefFrame().XYZ(dih->A1()),
                                  REF->RefFrame().XYZ(dih->A2()),
                                  REF->RefFrame().XYZ(dih->A3()) );
        ss_holder.thetas_.push_back( (float)torsion );
      }
      secstruct_.push_back( ss_holder );

    } else if (ss_arg.Nargs() == 4 && isalpha(ss_arg[2][0])) {
    // Single dihedral type: <name>:<range>:<dih type>:<angle>
      DihedralSearch::DihedralType dtype = DihedralSearch::GetType(ss_arg[2]);
      if (ss_holder.sstype_idx == SS_EMPTY) {
        // Type not yet defined. Create new type. 
        if (dtype == MetaData::UNDEFINED) {
          mprinterr("Error: Dihedral type %s not found.\n", ss_arg[2].c_str());
          return Action::ERR;
        }
        if (!validDouble(ss_arg[3])) {
          mprinterr("Error: 4th arg (angle) is not a valid number.\n");
          return Action::ERR;
        }
        SS.push_back( SS_TYPE(convertToDouble(ss_arg[3]), 0.0, 0.0, 0.0, 2, ss_arg[0]) );
        ss_holder.sstype_idx = (int)(SS.size() - 1);
      }
      ss_holder.dihSearch_.SearchFor( dtype ); 
      secstruct_.push_back( ss_holder );

    } else if (ss_arg.Nargs() == 7 || ss_arg.Nargs() == 8) {
    // Single custom dihedral type: <name>:<range>:<at0>:<at1>:<at2>:<at3>:<angle>[:<offset>]
      if (ss_holder.sstype_idx == SS_EMPTY) {
        // Type not yet defined. Create new type.
        if (!validDouble(ss_arg[6])) {
          mprinterr("Error: 7th arg (angle) is not a valid number.\n");
          return Action::ERR;
        }
        SS.push_back( SS_TYPE(convertToDouble(ss_arg[6]), 0.0, 0.0, 0.0, 2, ss_arg[0]) );
        ss_holder.sstype_idx = (int)(SS.size() - 1);
      }
      int offset = 0;
      if (ss_arg.Nargs() == 8) {
        if (!validInteger(ss_arg[7])) {
          mprinterr("Error: 8th arg (offset) is not a valid number.\n");
          return Action::ERR;
        }
        offset = convertToInteger(ss_arg[7]);
      }
      ss_holder.dihSearch_.SearchForNewType(offset,ss_arg[2],ss_arg[3],ss_arg[4],ss_arg[5],
                                            ss_arg[0]);
      secstruct_.push_back( ss_holder );

    } else if (ss_arg.Nargs() == 4 || ss_arg.Nargs() == 6) {
    // Custom SS/turn type: <name>:<range>:<phi1>:<psi1>[:<phi2>:<psi2>]
      if (ss_holder.sstype_idx == SS_EMPTY) {
        // Type not yet defined. Create new type.
        if (!validDouble(ss_arg[2]) || !validDouble(ss_arg[3])) {
          mprinterr("Error: 3rd or 4th arg (phi1/psi1) is not a valid number.\n");
          return Action::ERR;
        }
        double phi1 = convertToDouble(ss_arg[2]);
        double psi1 = convertToDouble(ss_arg[3]);
        int isTurn = 0;
        double phi2 = 0.0;
        double psi2 = 0.0;
        if (ss_arg.Nargs() == 6) {
          isTurn = 1;
          if (!validDouble(ss_arg[4]) || !validDouble(ss_arg[5])) {
            mprinterr("Error: 5th or 6th arg (phi2/psi2) is not a valid number.\n");
            return Action::ERR;
          }
          phi2 = convertToDouble(ss_arg[4]);
          psi2 = convertToDouble(ss_arg[5]);
        }
        SS.push_back(SS_TYPE(phi1, psi1, phi2, psi2, isTurn, ss_arg[0] ));
        ss_holder.sstype_idx = (int)(SS.size() - 1);
      }
      ss_holder.dihSearch_.SearchFor(MetaData::PHI);
      ss_holder.dihSearch_.SearchFor(MetaData::PSI);
      secstruct_.push_back( ss_holder );

    } else {
      mprinterr("Error: SS arg type [%s] not recognized.\n", ss_arg[0].c_str());
      return Action::ERR;
    }
    ss_expr = actionArgs.GetStringNext();
  } // End loop over args
  if (secstruct_.empty()) {
    mprinterr("Error: No SS types defined.\n");
    return Action::ERR;
  }
  mprintf("    MAKESTRUCTURE:\n");
  for (std::vector<SecStructHolder>::iterator ss = secstruct_.begin();
                                              ss != secstruct_.end(); ++ss)
  {
    if (ss->sstype_idx != SS_EMPTY) {
      const SS_TYPE& myType = SS[ss->sstype_idx];
      switch ( myType.isTurn ) {
        case 0:
          mprintf("\tSS type %s will be applied to residue(s) %s\n",
                 myType.type_arg.c_str(), ss->resRange.RangeArg());
          break;
        case 1:
          mprintf("\tTurn type %s will be applied to residue(s) %s\n",
                  myType.type_arg.c_str(), ss->resRange.RangeArg());
          break;
        case 2:
          mprintf("\tDihedral value of %.2f will be applied to %s dihedrals in residue(s) %s\n",
                  myType.phi, myType.type_arg.c_str(), ss->resRange.RangeArg());
      }
    } else 
      mprintf("\tBackbone angles from reference will be applied to residue(s) %s\n",
              ss->resRange.RangeArg());
  }
  return Action::OK;
}