/** Called once before traj processing. Set up reference info. */
Action::RetType Action_DistRmsd::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Check for keywords
  DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  // Reference keywords
  // TODO: Can these just be put in the InitRef call?
  bool first = actionArgs.hasKey("first");
  ReferenceFrame REF = DSL->GetReferenceFrame( actionArgs );
  std::string reftrajname = actionArgs.GetStringKey("reftraj");
  Topology* RefParm = PFL->GetParm( actionArgs );
  // Get the RMS mask string for target 
  std::string mask0 = actionArgs.GetMaskNext();
  TgtMask_.SetMaskString(mask0);
  // Get the RMS mask string for reference
  std::string mask1 = actionArgs.GetMaskNext();
  if (mask1.empty())
    mask1 = mask0;

  // Initialize reference
  if (refHolder_.InitRef(false, first, false, false, reftrajname, REF, RefParm,
                         mask1, actionArgs, "distrmsd"))
    return Action::ERR;
 
  // Set up the RMSD data set
  drmsd_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(),"DRMSD");
  if (drmsd_==0) return Action::ERR;
  // Add dataset to data file list
  if (outfile != 0) outfile->AddDataSet( drmsd_ );

  mprintf("    DISTRMSD: (%s), reference is %s\n",TgtMask_.MaskString(),
          refHolder_.RefModeString());

  return Action::OK;
}
Example #2
0
Action::RetType Action_Channel::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Keywords.
  DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  dxyz_[0] = actionArgs.getKeyDouble("dx", 0.35);
  dxyz_[1] = actionArgs.getKeyDouble("dy", dxyz_[0]);
  dxyz_[2] = actionArgs.getKeyDouble("dz", dxyz_[1]);
  // solute mask
  std::string sMask = actionArgs.GetMaskNext();
  if (sMask.empty()) {
    mprinterr("Error: No solute mask specified.\n");
    return Action::ERR;
  }
  soluteMask_.SetMaskString( sMask );
  // solvent mask
  sMask = actionArgs.GetMaskNext();
  if (sMask.empty())
    sMask.assign(":[email protected]");
  solventMask_.SetMaskString( sMask );

  // Grid Data Set
  grid_ = init.DSL().AddSet(DataSet::GRID_FLT, actionArgs.GetStringNext(), "Channel");
  if (grid_ == 0) return Action::ERR;
  if (outfile != 0) outfile->AddDataSet( grid_ );

  mprintf("Warning: *** THIS ACTION IS EXPERIMENTAL AND NOT FULLY IMPLEMENTED. ***\n");
  mprintf("    CHANNEL: Solute mask [%s], solvent mask [%s]\n",
          soluteMask_.MaskString(), solventMask_.MaskString());
  mprintf("\tSpacing: XYZ={ %g %g %g }\n", dxyz_[0], dxyz_[1], dxyz_[2]);
  return Action::OK;
}
Example #3
0
// Action_Angle::init()
Action::RetType Action_Angle::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Get keywords
  DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  useMass_ = actionArgs.hasKey("mass");

  // Get Masks
  std::string mask1 = actionArgs.GetMaskNext();
  std::string mask2 = actionArgs.GetMaskNext();
  std::string mask3 = actionArgs.GetMaskNext();
  if (mask1.empty() || mask2.empty() || mask3.empty()) {
    mprinterr("Error: angle: Requires 3 masks\n");
    return Action::ERR;
  }
  Mask1_.SetMaskString(mask1);
  Mask2_.SetMaskString(mask2);
  Mask3_.SetMaskString(mask3);

  // Dataset to store angles
  ang_ = DSL->AddSet(DataSet::DOUBLE, MetaData(actionArgs.GetStringNext(),MetaData::M_ANGLE),"Ang");
  if (ang_==0) return Action::ERR;
  // Add dataset to data file list
  if (outfile != 0) outfile->AddDataSet( ang_ );

  mprintf("    ANGLE: [%s]-[%s]-[%s]\n",Mask1_.MaskString(), Mask2_.MaskString(), 
          Mask3_.MaskString());
  if (useMass_)
    mprintf("\tUsing center of mass of atoms in masks.\n");

  return Action::OK;
}
Example #4
0
// Action_Center::Init()
Action::RetType Action_Center::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Get keywords
  useMass_ = actionArgs.hasKey("mass");
  ReferenceFrame refFrm = init.DSL().GetReferenceFrame( actionArgs );
  if (refFrm.error()) return Action::ERR;
  // Determine center mode.
  if (!refFrm.empty())
    centerMode_ = REF;
  else if (actionArgs.hasKey("origin"))
    centerMode_ = ORIGIN;
  else if (actionArgs.hasKey("point")) {
    centerMode_ = POINT;
    refCenter_[0] = actionArgs.getNextDouble(0.0);
    refCenter_[1] = actionArgs.getNextDouble(0.0);
    refCenter_[2] = actionArgs.getNextDouble(0.0);
  } else
    centerMode_ = BOXCTR;

  // Get Masks
  Mask_.SetMaskString( actionArgs.GetMaskNext() );
  // Get reference mask if reference specified.
  AtomMask refMask;
  if (centerMode_ == REF) {
    std::string rMaskExpr = actionArgs.GetMaskNext();
    if (rMaskExpr.empty())
      rMaskExpr = Mask_.MaskExpression();
    refMask.SetMaskString( rMaskExpr );
    if (refFrm.Parm().SetupIntegerMask( refMask, refFrm.Coord() ))
      return Action::ERR;
    // Get center of mask in reference
    if (useMass_)
      refCenter_ = refFrm.Coord().VCenterOfMass( refMask );
    else
      refCenter_ = refFrm.Coord().VGeometricCenter( refMask );
  }

  mprintf("    CENTER: Centering coordinates using");
  if (useMass_)
    mprintf(" center of mass");
  else
    mprintf(" geometric center");
  mprintf(" of atoms in mask (%s) to\n", Mask_.MaskString());
  switch (centerMode_) {
    case ORIGIN: mprintf("\tcoordinate origin.\n"); break;
    case BOXCTR: mprintf("\tbox center.\n"); break;
    case REF:
      mprintf("\tcenter of mask (%s) in reference '%s'.\n", refMask.MaskString(),
              refFrm.refName());
      break;
    case POINT:  mprintf("\tpoint (%g, %g, %g).\n",
                         refCenter_[0], refCenter_[1], refCenter_[2]);
      break;
  }
  return Action::OK;
}
Example #5
0
// Action_Dihedral::init()
Action::RetType Action_Dihedral::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL,
                          DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Get keywords
  DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  useMass_ = actionArgs.hasKey("mass");
  DataSet::scalarType stype = DataSet::UNDEFINED;
  range360_ = actionArgs.hasKey("range360");
  std::string stypename = actionArgs.GetStringKey("type");
  if      ( stypename == "alpha"   ) stype = DataSet::ALPHA;
  else if ( stypename == "beta"    ) stype = DataSet::BETA;
  else if ( stypename == "gamma"   ) stype = DataSet::GAMMA;
  else if ( stypename == "delta"   ) stype = DataSet::DELTA;
  else if ( stypename == "epsilon" ) stype = DataSet::EPSILON;
  else if ( stypename == "zeta"    ) stype = DataSet::ZETA;
  else if ( stypename == "chi"     ) stype = DataSet::CHI;
  else if ( stypename == "c2p"     ) stype = DataSet::C2P;
  else if ( stypename == "h1p"     ) stype = DataSet::H1P;
  else if ( stypename == "phi"     ) stype = DataSet::PHI;
  else if ( stypename == "psi"     ) stype = DataSet::PSI;
  else if ( stypename == "pchi"    ) stype = DataSet::PCHI;

  // Get Masks
  std::string mask1 = actionArgs.GetMaskNext();
  std::string mask2 = actionArgs.GetMaskNext();
  std::string mask3 = actionArgs.GetMaskNext();
  std::string mask4 = actionArgs.GetMaskNext();
  if (mask1.empty() || mask2.empty() || mask3.empty() || mask4.empty()) {
    mprinterr("Error: dihedral: Requires 4 masks\n");
    return Action::ERR;
  }
  M1_.SetMaskString(mask1);
  M2_.SetMaskString(mask2);
  M3_.SetMaskString(mask3);
  M4_.SetMaskString(mask4);

  // Setup dataset
  dih_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(),"Dih");
  if (dih_==0) return Action::ERR;
  dih_->SetScalar( DataSet::M_TORSION, stype );
  // Add dataset to datafile list
  if (outfile != 0) outfile->AddSet( dih_ );

  mprintf("    DIHEDRAL: [%s]-[%s]-[%s]-[%s]\n", M1_.MaskString(), 
          M2_.MaskString(), M3_.MaskString(), M4_.MaskString());
  if (useMass_)
    mprintf("              Using center of mass of atoms in masks.\n");
  if (range360_)
    mprintf("              Output range is 0 to 360 degrees.\n");
  else
    mprintf("              Output range is -180 to 180 degrees.\n");

  return Action::OK;
}
// Action_SymmetricRmsd::Init()
Action::RetType Action_SymmetricRmsd::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Check for keywords
  bool fit = !actionArgs.hasKey("nofit");
  bool useMass = actionArgs.hasKey("mass");
  DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
  remap_ = actionArgs.hasKey("remap");
  // Reference keywords
  bool previous = actionArgs.hasKey("previous");
  bool first = actionArgs.hasKey("first");
  ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
  std::string reftrajname = actionArgs.GetStringKey("reftraj");
  Topology* RefParm = init.DSL().GetTopology( actionArgs );
  // Get the RMS mask string for target
  std::string tMaskExpr = actionArgs.GetMaskNext();
  if (tgtMask_.SetMaskString( tMaskExpr )) return Action::ERR;
  // Initialize Symmetric RMSD calc.
  if (SRMSD_.InitSymmRMSD( fit, useMass, debugIn )) return Action::ERR;
  // Initialize reference
  std::string rMaskExpr = actionArgs.GetMaskNext();
  if (rMaskExpr.empty())
    rMaskExpr = tMaskExpr;
  if (REF_.InitRef(previous, first, useMass, fit, reftrajname, REF, RefParm,
                   rMaskExpr, actionArgs, "symmrmsd"))
    return Action::ERR;
  // Set up the RMSD data set.
  MetaData md(actionArgs.GetStringNext(), MetaData::M_RMS); 
  rmsd_ = init.DSL().AddSet(DataSet::DOUBLE, md, "RMSD");
  if (rmsd_==0) return Action::ERR;
  // Add dataset to data file list
  if (outfile != 0) outfile->AddDataSet( rmsd_ );
  if (remap_ || SRMSD_.Fit())
    action_return_ = Action::MODIFY_COORDS;
  else
    action_return_ = Action::OK;
  
  mprintf("    SYMMRMSD: (%s), reference is %s", tgtMask_.MaskString(),
          REF_.RefModeString());
  if (!SRMSD_.Fit())
    mprintf(", no fitting");
  else
    mprintf(", with fitting");
  if (SRMSD_.UseMass())
    mprintf(", mass-weighted");
  mprintf(".\n");
  if (remap_) mprintf("\tAtoms will be re-mapped for symmetry.\n");
  return Action::OK;
}
// Action_Closest::Init()
Action_Closest::RetType Action_Closest::Init(ArgList& actionArgs, int debugIn)
{
  debug_ = debugIn;
  // Get Keywords
  closestWaters_ = actionArgs.getNextInteger(-1);
  if (closestWaters_ < 0) {
    mprinterr("Error: Invalid # solvent molecules to keep (%i).\n",
              closestWaters_);
    return Action_Closest::ERR;
  }
  if ( actionArgs.hasKey("oxygen") || actionArgs.hasKey("first") )
    firstAtom_=true;
  useMaskCenter_ = actionArgs.hasKey("center");
  image_.InitImaging( !(actionArgs.hasKey("noimage")) );

  // Get Masks
  std::string mask1 = actionArgs.GetMaskNext();
  if (mask1.empty()) {
    mprinterr("Error: No mask specified.\n");
    return Action_Closest::ERR;
  }
  distanceMask_.SetMaskString(mask1);

  mprintf("    CLOSEST: Finding closest %i solvent molecules to atoms in mask %s\n",
          closestWaters_, distanceMask_.MaskString());
  if (useMaskCenter_)
    mprintf("\tGeometric center of atoms in mask will be used.\n");
  if (!image_.UseImage()) 
    mprintf("\tImaging will be turned off.\n");
  if (firstAtom_)
    mprintf("\tOnly first atom of solvent molecule used for distance calc.\n");
  return Action_Closest::OK;
}
Example #8
0
// Action_Average::init()
Action::RetType Action_Average::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL,
                          DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  debug_ = debugIn;
  // Get Keywords
  avgfilename_ = actionArgs.GetStringNext();
  if (avgfilename_.empty()) {
    mprinterr("Error: average: No filename given.\n");
    return Action::ERR;
  }
  // Get start/stop/offset args
  if (InitFrameCounter(actionArgs)) return Action::ERR;

  // Get Masks
  Mask1_.SetMaskString( actionArgs.GetMaskNext() );

  // Save all remaining arguments for setting up the trajectory at the end.
  trajArgs_ = actionArgs.RemainingArgs();

  mprintf("    AVERAGE: Averaging over coordinates in mask [%s]\n",Mask1_.MaskString());
  FrameCounterInfo();
  mprintf("\tWriting averaged coords to [%s]\n",avgfilename_.c_str());

  Nframes_ = 0;

  return Action::OK;
}
// Action_AreaPerMol::Init()
Action::RetType Action_AreaPerMol::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Get keywords
  DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  if (actionArgs.hasKey("xy")) areaType_ = XY;
  else if (actionArgs.hasKey("xz")) areaType_ = XZ;
  else if (actionArgs.hasKey("yz")) areaType_ = YZ;
  else areaType_ = XY;

  Nmols_ = (double)actionArgs.getKeyInt("nmols", -1);

  // Get Masks
  if (Nmols_ < 0.0) {
    Nlayers_ = (double)actionArgs.getKeyInt("nlayers", 1);
    if (Nlayers_ < 1.0) {
      mprinterr("Error: Number of layers must be > 0\n");
      return Action::ERR;
    }
    Mask1_.SetMaskString( actionArgs.GetMaskNext() );
  }

  // DataSet
  area_per_mol_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(),"APM");
  if (area_per_mol_==0) return Action::ERR;
  // Add DataSet to DataFileList
  if (outfile != 0) outfile->AddDataSet( area_per_mol_ );

  mprintf("    AREAPERMOL: Calculating %s area per molecule", APMSTRING[areaType_]);
  if (Mask1_.MaskStringSet())
    mprintf(" using mask '%s', %.0f layers.\n", Mask1_.MaskString(), Nlayers_);
  else
    mprintf(" for %.0f mols\n", Nmols_);

  return Action::OK;
}
Example #10
0
// Action_Grid::Init()
Action::RetType Action_Grid::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  debug_ = debugIn;
  nframes_ = 0;
  // Get output filename
  std::string filename = actionArgs.GetStringKey("out");
  // Get grid options
  grid_ = GridInit( "GRID", actionArgs, init.DSL() );
  if (grid_ == 0) return Action::ERR;
# ifdef MPI
  if (ParallelGridInit(init.TrajComm(), grid_)) return Action::ERR;
# endif
  // Get extra options
  max_ = actionArgs.getKeyDouble("max", 0.80);
  madura_ = actionArgs.getKeyDouble("madura", 0);
  smooth_ = actionArgs.getKeyDouble("smoothdensity", 0);
  invert_ = actionArgs.hasKey("invert");
  pdbfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("pdb"),"Grid PDB",DataFileList::PDB,true);
  density_ = actionArgs.getKeyDouble("density",0.033456);
  if (actionArgs.hasKey("normframe")) normalize_ = TO_FRAME;
  else if (actionArgs.hasKey("normdensity")) normalize_ = TO_DENSITY;
  else normalize_ = NONE;
  if (normalize_ != NONE && (smooth_ > 0.0 || madura_ > 0.0)) {
    mprinterr("Error: Normalize options are not compatible with smoothdensity/madura options.\n");
    init.DSL().RemoveSet( grid_ );
    return Action::ERR;
  }
  // Get mask
  std::string maskexpr = actionArgs.GetMaskNext();
  if (maskexpr.empty()) {
    mprinterr("Error: GRID: No mask specified.\n");
    init.DSL().RemoveSet( grid_ );
    return Action::ERR;
  }
  mask_.SetMaskString(maskexpr);

  // Setup output file
  // For backwards compat., if no 'out' assume next string is filename
  if (filename.empty() && actionArgs.Nargs() > 1 && !actionArgs.Marked(1))
    filename = actionArgs.GetStringNext();
  DataFile* outfile = init.DFL().AddDataFile(filename, actionArgs);
  if (outfile != 0) outfile->AddDataSet((DataSet*)grid_);

  // Info
  mprintf("    GRID:\n");
  GridInfo( *grid_ );
  if (outfile != 0) mprintf("\tGrid will be printed to file %s\n", outfile->DataFilename().full());
  mprintf("\tGrid data set: '%s'\n", grid_->legend());
  mprintf("\tMask expression: [%s]\n",mask_.MaskString());
  if (pdbfile_ != 0)
      mprintf("\tPseudo-PDB will be printed to %s\n", pdbfile_->Filename().full());
  if (normalize_ == TO_FRAME)
    mprintf("\tGrid will be normalized by number of frames.\n");
  else if (normalize_ == TO_DENSITY)
    mprintf("\tGrid will be normalized to a density of %g molecules/Ang^3.\n", density_);
  // TODO: print extra options

  return Action::OK;
}
Example #11
0
// Action_Center::Init()
Action::RetType Action_Center::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Get keywords
  if (actionArgs.hasKey("origin"))
    centerMode_ = ORIGIN;
  else
    centerMode_ = BOXCTR;
  useMass_ = actionArgs.hasKey("mass");
  ReferenceFrame refFrm = DSL->GetReferenceFrame( actionArgs );
  if (refFrm.error()) return Action::ERR;

  // Get Masks
  Mask_.SetMaskString( actionArgs.GetMaskNext() );
  // Get reference mask if reference specified.
  AtomMask refMask;
  if (!refFrm.empty()) {
    std::string rMaskExpr = actionArgs.GetMaskNext();
    if (rMaskExpr.empty())
      rMaskExpr = Mask_.MaskExpression();
    refMask.SetMaskString( rMaskExpr );
    if (refFrm.Parm().SetupIntegerMask( refMask, refFrm.Coord() ))
      return Action::ERR;
    // Get center of mask in reference
    if (useMass_)
      refCenter_ = refFrm.Coord().VCenterOfMass( refMask );
    else
      refCenter_ = refFrm.Coord().VGeometricCenter( refMask );
    centerMode_ = POINT; 
  }

  mprintf("    CENTER: Centering coordinates using");
  if (useMass_)
    mprintf(" center of mass");
  else
    mprintf(" geometric center");
  mprintf(" of atoms in mask (%s) to\n", Mask_.MaskString());
  if (centerMode_ == POINT)
    mprintf("\tcenter of mask (%s) in reference '%s'.\n", refMask.MaskString(),
            refFrm.refName());
  else if (centerMode_ == ORIGIN)
    mprintf("\tcoordinate origin.\n");
  else
    mprintf("\tbox center.\n");

  return Action::OK;
}
// Action_VelocityAutoCorr::Init()
Action::RetType Action_VelocityAutoCorr::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  if (actionArgs.hasKey("usevelocity")) {
    mprinterr("Error: The 'usevelocity' keyword is deprecated. Velocity information\n"
              "Error:   is now used by default if present. To force cpptraj to use\n"
              "Error:   coordinates to estimate velocities (not recommended) use the\n"
              "Error:   'usecoords' keyword.\n");
    return Action::ERR;
  }
  useVelInfo_ = !actionArgs.hasKey("usecoords");
  if (mask_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;
  DataFile* outfile =  init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  diffout_ = init.DFL().AddCpptrajFile( actionArgs.GetStringKey("diffout"),
                                        "VAC diffusion constants", DataFileList::TEXT, true );
  maxLag_ = actionArgs.getKeyInt("maxlag", -1);
  tstep_ = actionArgs.getKeyDouble("tstep", 1.0);
  useFFT_ = !actionArgs.hasKey("direct");
  normalize_ = actionArgs.hasKey("norm");
  // Set up output data set
  VAC_ = init.DSL().AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "VAC");
  if (VAC_ == 0) return Action::ERR;
  // TODO: This should just be a scalar
  diffConst_ = init.DSL().AddSet(DataSet::DOUBLE,
                                 MetaData(VAC_->Meta().Name(), "D", MetaData::NOT_TS));
  if (diffConst_ == 0) return Action::ERR;
  if (outfile != 0) outfile->AddDataSet( VAC_ );
# ifdef MPI
  trajComm_ = init.TrajComm(); 
  if (trajComm_.Size() > 1 && !useVelInfo_)
    mprintf("\nWarning: When calculating velocities between consecutive frames,\n"
            "\nWarning:   'velocityautocorr' in parallel will not work correctly if\n"
            "\nWarning:   coordinates have been modified by previous actions (e.g. 'rms').\n\n");
  diffConst_->SetNeedsSync( false );
# endif
  mprintf("    VELOCITYAUTOCORR:\n"
          "\tCalculate velocity auto-correlation function for atoms in mask '%s'\n",
          mask_.MaskString());
  if (useVelInfo_)
    mprintf("\tUsing velocity information present in frames.\n");
  else
    mprintf("\tCalculating velocities between consecutive frames from coordinates.\n");
  if (outfile != 0)
    mprintf("\tOutput velocity autocorrelation function '%s' to '%s'\n", VAC_->legend(), 
            outfile->DataFilename().full());
  mprintf("\tWriting diffusion constants to '%s'\n", diffout_->Filename().full());
  if (maxLag_ < 1)
    mprintf("\tMaximum lag will be half total # of frames");
  else
    mprintf("\tMaximum lag is %i frames", maxLag_);
  mprintf(", time step between frames is %f ps\n", tstep_);
  if (useFFT_)
    mprintf("\tUsing FFT to calculate autocorrelation function.\n");
  else
    mprintf("\tUsing direct method to calculate autocorrelation function.\n");
  if (normalize_)
    mprintf("\tNormalizing autocorrelation function to 1.0\n");
  return Action::OK;
}
// Analysis_Wavelet::Setup
Analysis::RetType Analysis_Wavelet::Setup(ArgList& analyzeArgs, DataSetList* datasetlist,
        TopologyList* PFLin, DataFileList* DFLin, int debugIn)
{
    // Attempt to get COORDS DataSet from DataSetList. If none specified the
    // default COORDS set will be used.
    std::string setname = analyzeArgs.GetStringKey("crdset");
    coords_ = (DataSet_Coords*)datasetlist->FindCoordsSet( setname );
    if (coords_ == 0) {
        mprinterr("Error: Could not locate COORDS set corresponding to %s\n", setname.c_str());
        return Analysis::ERR;
    }
    // Get keywords
    DataFile* outfile = DFLin->AddDataFile( analyzeArgs.GetStringKey("out"), analyzeArgs );
    setname = analyzeArgs.GetStringKey("name");
    // TODO: Check defaults
    nb_ = analyzeArgs.getKeyInt("nb", 0); // FIXME: Should be more descriptive? nscale?
    if (nb_ < 1) {
        mprinterr("Error: Scaling number must be > 0\n");
        return Analysis::ERR;
    }
    S0_ = analyzeArgs.getKeyDouble("s0", 0.2);
    ds_ = analyzeArgs.getKeyDouble("ds", 1.0/3.0);
    correction_ = analyzeArgs.getKeyDouble("correction", 1.01);
    chival_ = analyzeArgs.getKeyDouble("chival", 0.2231);
    // Wavelet type: default to Morlet
    std::string wavelet_name = analyzeArgs.GetStringKey("type");
    if (wavelet_name.empty())
        wavelet_type_ = W_MORLET;
    else {
        wavelet_type_ = W_NONE;
        for (int itoken = 0; itoken != (int)W_NONE; itoken++)
            if (wavelet_name.compare(Tokens_[itoken].key_) == 0) {
                wavelet_type_ = (WaveletType)itoken;
                break;
            }
        if (wavelet_type_ == W_NONE) {
            mprinterr("Error: Unrecognized wavelet type: %s\n", wavelet_name.c_str());
            return Analysis::ERR;
        }
    }
    // Atom mask
    mask_.SetMaskString( analyzeArgs.GetMaskNext() );
    // Set up output data set
    output_ = datasetlist->AddSet( DataSet::MATRIX_FLT, setname, "WAVELET" );
    if (output_ == 0) return Analysis::ERR;
    if (outfile != 0) outfile->AddDataSet( output_ );

    mprintf("    WAVELET: Using COORDS set '%s', wavelet type %s\n",
            coords_->legend(), Tokens_[wavelet_type_].description_);
    mprintf("\tCalculating for atoms in mask '%s'\n", mask_.MaskString());
    mprintf("\tScaling wavelet %i times starting from %g with delta of %g\n",
            nb_, S0_, ds_);
    mprintf("\tCorrection: %g\n", correction_);
    mprintf("\tChiVal:     %g\n", chival_);
    if (outfile != 0) mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());

    return Analysis::OK;
}
// Action_AtomicFluct::Init()
Action::RetType Action_AtomicFluct::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
    // Get frame # keywords
    if (InitFrameCounter(actionArgs)) return Action::ERR;
    // Get other keywords
    bfactor_ = actionArgs.hasKey("bfactor");
    calc_adp_ = actionArgs.hasKey("calcadp");
    adpoutfile_ = DFL->AddCpptrajFile(actionArgs.GetStringKey("adpout"), "PDB w/ADP",
                                      DataFileList::PDB);;
    if (adpoutfile_!=0) calc_adp_ = true; // adpout implies calcadp
    if (calc_adp_ && !bfactor_) bfactor_ = true;
    DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
    if (actionArgs.hasKey("byres"))
        outtype_ = BYRES;
    else if (actionArgs.hasKey("bymask"))
        outtype_ = BYMASK;
    else if (actionArgs.hasKey("byatom") || actionArgs.hasKey("byatm"))
        outtype_ = BYATOM;
    // Get Mask
    Mask_.SetMaskString( actionArgs.GetMaskNext()  );
    // Get DataSet name
    std::string setname = actionArgs.GetStringNext();
    // Add output dataset
    MetaData md( setname );
    md.SetTimeSeries( MetaData::NOT_TS );
    if (bfactor_)
        md.SetLegend("B-factors");
    else
        md.SetLegend("AtomicFlx");
    dataout_ = DSL->AddSet( DataSet::XYMESH, md, "Fluct" );
    if (dataout_ == 0) {
        mprinterr("Error: AtomicFluct: Could not allocate dataset for output.\n");
        return Action::ERR;
    }
    if (outfile != 0)
        outfile->AddDataSet( dataout_ );

    mprintf("    ATOMICFLUCT: calculating");
    if (bfactor_)
        mprintf(" B factors");
    else
        mprintf(" atomic positional fluctuations");
    if (outfile != 0)
        mprintf(", output to file %s", outfile->DataFilename().full());
    mprintf("\n                 Atom mask: [%s]\n",Mask_.MaskString());
    FrameCounterInfo();
    if (calc_adp_) {
        mprintf("\tCalculating anisotropic displacement parameters.\n");
        if (adpoutfile_!=0) mprintf("\tWriting PDB with ADP to '%s'\n", adpoutfile_->Filename().full());
    }
    if (!setname.empty())
        mprintf("\tData will be saved to set named %s\n", setname.c_str());

    return Action::OK;
}
Example #15
0
// Action_Energy::Init()
Action::RetType Action_Energy::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  ENE_.SetDebug( debugIn );
  // Get keywords
  DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  // Which terms will be calculated?
  Ecalcs_.clear();
  if (actionArgs.hasKey("bond"))     Ecalcs_.push_back(BND);
  if (actionArgs.hasKey("angle"))    Ecalcs_.push_back(ANG);
  if (actionArgs.hasKey("dihedral")) Ecalcs_.push_back(DIH);
  if (actionArgs.hasKey("nb14"))     Ecalcs_.push_back(N14);
  if (actionArgs.hasKey("nonbond"))  Ecalcs_.push_back(NBD);
  // If nothing is selected, select all.
  if (Ecalcs_.empty()) {
    for (int c = 0; c <= (int)NBD; c++)
      Ecalcs_.push_back( (CalcType)c );
  }

  // Get Masks
  Mask1_.SetMaskString( actionArgs.GetMaskNext() );

  // DataSet
  std::string setname = actionArgs.GetStringNext();
  if (setname.empty())
    setname = init.DSL().GenerateDefaultName("ENE");
  Energy_.clear();
  Energy_.resize( (int)TOTAL + 1, 0 );
  for (calc_it calc = Ecalcs_.begin(); calc != Ecalcs_.end(); ++calc)
  {
    switch (*calc) {
      case BND: if (AddSet(BOND, init.DSL(), outfile, setname)) return Action::ERR; break;
      case ANG: if (AddSet(ANGLE, init.DSL(), outfile, setname)) return Action::ERR; break;
      case DIH: if (AddSet(DIHEDRAL, init.DSL(), outfile, setname)) return Action::ERR; break;
      case N14:
        if (AddSet(V14, init.DSL(), outfile, setname)) return Action::ERR;
        if (AddSet(Q14, init.DSL(), outfile, setname)) return Action::ERR;
        break;
      case NBD:
        if (AddSet(VDW, init.DSL(), outfile, setname)) return Action::ERR;
        if (AddSet(ELEC, init.DSL(), outfile, setname)) return Action::ERR;
        break;
    }
  }
//  if (Ecalcs_.size() > 1) {
    if (AddSet(TOTAL, init.DSL(), outfile, setname)) return Action::ERR;
//  }
      
  mprintf("    ENERGY: Calculating energy for atoms in mask '%s'\n", Mask1_.MaskString());
  mprintf("\tCalculating terms:");
  for (calc_it calc = Ecalcs_.begin(); calc != Ecalcs_.end(); ++calc)
    mprintf(" %s", Cstring[*calc]);
  mprintf("\n");

  return Action::OK;
}
Example #16
0
// -----------------------------------------------------------------------------
// Action_Jcoupling::Init()
Action::RetType Action_Jcoupling::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  debug_ = debugIn;
  outfile_ = 0;
  // Get Keywords
  outputfile_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("outfile"), "J-coupling");
  outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  std::string karpluspath = actionArgs.GetStringKey("kfile");
  setname_ = actionArgs.GetStringKey("name");
  // Get Masks
  if (Mask1_.SetMaskString( actionArgs.GetMaskNext() )) return Action::ERR;

  // If no Karplus params specified check environment vars. 
  if (karpluspath.empty()) {
    // Check if the KARPLUS env var is set.
    const char* env = getenv("KARPLUS");
    if (env != 0) {
      mprintf("Info: Using parameter file defined by $KARPLUS environment variable.\n");
      karpluspath.assign(env);
    } else {
      // If KARPLUS not set check for $AMBERHOME/dat/Karplus.txt
      env = getenv("AMBERHOME");
      if (env == 0) {
        mprinterr("Error: Either AMBERHOME must be set or KARPLUS must point\n"
                  "Error:   to the file containing Karplus parameters.\n");
        return Action::ERR;
      }
      mprintf("Info: Using parameter file in '$AMBERHOME/dat/'.\n");
      karpluspath.assign(env);
      karpluspath += "/dat/Karplus.txt";
    }
  }
  // Load Karplus parameters
  if (loadKarplus(karpluspath)) 
    return Action::ERR;

  mprintf("    J-COUPLING: Searching for dihedrals in mask [%s].\n"
          "\tUsing Karplus parameters in \"%s\"\n"
          "\t%i parameters found for %zu residues.\n",
          Mask1_.MaskString(), karpluspath.c_str(), Nconstants_, KarplusConstants_.size());
  if (outfile_ != 0)
    mprintf("\tDataSets will be written to %s\n", outfile_->DataFilename().full());
  if (outputfile_ != 0)
    mprintf("\tWriting fixed-format output to %s\n",outputfile_->Filename().full());
  mprintf("# Citations: Chou et al. JACS (2003) 125 p.8959-8966\n"
          "#            Perez et al. JACS (2001) 123 p.7081-7093\n");
  init.DSL().SetDataSetsPending(true);
  masterDSL_ = init.DslPtr();
  return Action::OK;
}
Example #17
0
Exec::RetType Exec_ParmSolvent::Execute(CpptrajState& State, ArgList& argIn) {
  std::string maskexpr;
  if (!argIn.hasKey("none")) {
    maskexpr = argIn.GetMaskNext();
    if ( maskexpr.empty() ) {
      mprinterr("Error: solvent: No mask specified.\n");
      return CpptrajState::ERR;
    }
  }
  // Get parm index
  Topology* parm = State.DSL().GetTopByIndex( argIn );
  if (parm == 0) return CpptrajState::ERR;
  parm->SetSolvent( maskexpr );
  return CpptrajState::OK;
}
Example #18
0
Action::RetType Action_Rotate::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL,
                          DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  double xrot = actionArgs.getKeyDouble("x",0.0);
  double yrot = actionArgs.getKeyDouble("y",0.0);
  double zrot = actionArgs.getKeyDouble("z",0.0);
  mask_.SetMaskString( actionArgs.GetMaskNext() );

  // Calc rotation matrix
  RotMatrix_.CalcRotationMatrix( xrot * DEGRAD, yrot * DEGRAD, zrot * DEGRAD );

  mprintf("    ROTATE: Rotating atoms in mask %s\n", mask_.MaskString());
  mprintf("\t%f degrees around X, %f degrees around Y, %f degrees around Z\n",
          xrot, yrot, zrot);
  return Action::OK;
};
Example #19
0
Exec::RetType Exec_ParmStrip::Execute(CpptrajState& State, ArgList& argIn) {
    Topology* parm = State.DSL().GetTopByIndex( argIn );
  if (parm == 0) return CpptrajState::ERR;
  // Check if this topology has already been used to set up an input
  // trajectory, as this will break the traj read.
  bool topology_in_use = false;
  const char* fname = 0;
  for (TrajinList::trajin_it tIn = State.InputTrajList().trajin_begin();
                             tIn != State.InputTrajList().trajin_end(); ++tIn)
    if ( (*tIn)->Traj().Parm() == parm ) {
      topology_in_use = true;
      fname = (*tIn)->Traj().Filename().full();
      break;
    }
  if (!topology_in_use) {
    for (TrajinList::ensemble_it eIn = State.InputTrajList().ensemble_begin();
                                 eIn != State.InputTrajList().ensemble_end(); ++eIn)
      if ( (*eIn)->Traj().Parm() == parm ) {
        topology_in_use = true;
        fname = (*eIn)->Traj().Filename().full();
        break;
      }
  }
  if (topology_in_use) {
    mprinterr("Error: Topology '%s' has already been used to set up trajectory '%s'.\n"
              "Error:   To strip this topology use the 'strip' action.\n",
              parm->c_str(), fname);
    return CpptrajState::ERR;
  }
  AtomMask tempMask( argIn.GetMaskNext() );
  // Since want to keep atoms outside mask, invert selection
  tempMask.InvertMaskExpression();
  if (parm->SetupIntegerMask( tempMask )) return CpptrajState::ERR;
  mprintf("\tStripping atoms in mask [%s] (%i) from %s\n",tempMask.MaskString(),
           parm->Natom() - tempMask.Nselected(), parm->c_str());
  Topology* tempParm = parm->modifyStateByMask(tempMask);
  if (tempParm==0) {
    mprinterr("Error: %s: Could not strip parm.\n", argIn.Command());
    return CpptrajState::ERR;
  } else {
    // Replace parm with stripped version
    *parm = *tempParm;
    parm->Brief("Stripped parm:");
    delete tempParm;
  }
  return CpptrajState::OK;
}
Example #20
0
// Action_Unwrap::Init()
Action::RetType Action_Unwrap::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Get Keywords
  center_ = actionArgs.hasKey("center");
  if (actionArgs.hasKey("bymol"))
    imageMode_ = Image::BYMOL;
  else if (actionArgs.hasKey("byres"))
    imageMode_ = Image::BYRES;
  else if (actionArgs.hasKey("byatom")) {
    imageMode_ = Image::BYATOM;
    // Unwrapping to center by atom makes no sense
    if (center_) center_ = false;
  } else
    imageMode_ = Image::BYATOM;
  // Get reference
  ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
  if (REF.error()) return Action::ERR;
  if (!REF.empty()) {
    RefFrame_ = REF.Coord();
    // Get reference parm for frame
    RefParm_ = REF.ParmPtr();
  }

  // Get mask string
  maskExpression_ = actionArgs.GetMaskNext();

  mprintf("    UNWRAP: By %s", Image::ModeString(imageMode_));
  if (!maskExpression_.empty())
    mprintf(" using mask '%s'", maskExpression_.c_str());
  else
    mprintf(" using all atoms");
  if (imageMode_ != Image::BYATOM) {
    if (center_)
      mprintf(" based on center of mass.");
    else
      mprintf(" based on first atom position.");
  }
  mprintf("\n");
  if ( !REF.empty())
    mprintf("\tReference is %s", REF.refName());
  else
    mprintf("\tReference is first frame.");
  mprintf("\n");

  return Action::OK;
}
Example #21
0
// Action_AtomicCorr::Init()
Action::RetType Action_AtomicCorr::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  debug_ = debugIn;
  outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  cut_ = actionArgs.getKeyDouble("cut", 0.0);
  if (cut_ < 0.0 || cut_ > 1.0) {
    mprinterr("Error: cut value must be between 0 and 1.\n");
    return Action::ERR;
  }
  min_ = actionArgs.getKeyInt("min",0);
  if (actionArgs.hasKey("byatom"))
    acorr_mode_ = ATOM;
  else if (actionArgs.hasKey("byres"))
    acorr_mode_ = RES;
  mask_.SetMaskString( actionArgs.GetMaskNext() );
  
  // Set up DataSet
  dset_ = init.DSL().AddSet( DataSet::MATRIX_FLT, actionArgs.GetStringNext(), "ACorr" );
  if (dset_ == 0) {
    mprinterr("Error: Could not allocate output data set.\n");
    return Action::ERR;
  }
  // Add DataSet to output file
  if (outfile_ != 0) outfile_->AddDataSet( dset_ );

  mprintf("    ATOMICCORR: Correlation of %s motions will be calculated for\n",
          ModeString[acorr_mode_]);
  mprintf("\tatoms in mask [%s]", mask_.MaskString());
  if (outfile_ != 0) mprintf(", output to file %s", outfile_->DataFilename().full());
  mprintf("\n\tData saved in set '%s'\n", dset_->legend());
  if (cut_ != 0)
    mprintf("\tOnly correlations greater than %.2f or less than -%.2f will be printed.\n",
            cut_,cut_);
  if (min_!=0)
    mprintf("\tOnly correlations for %ss > %i apart will be calculated.\n",
            ModeString[acorr_mode_],min_);
# ifdef MPI
  trajComm_ = init.TrajComm();
  if (trajComm_.Size() > 1)
    mprintf("\nWarning: 'atomiccorr' in parallel will not work correctly if coordinates have\n"
              "Warning:   been modified by previous actions (e.g. 'rms').\n\n");
  // Since matrix calc only happens in Print(), no sync needed.
  dset_->SetNeedsSync( false );
# endif
  return Action::OK;
}
// Action_CheckStructure::Init()
Action::RetType Action_CheckStructure::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Get Keywords
  std::string around = actionArgs.GetStringKey("around");
  SeparateInit( !(actionArgs.hasKey("noimage")), actionArgs.GetMaskNext(),
                around, actionArgs.GetStringKey("reportfile"),
                actionArgs.getKeyDouble("cut",0.8),
                actionArgs.getKeyDouble("offset",1.15),
                actionArgs.hasKey("silent"), init.DFL() );
  // DoAction-only keywords.
  bondcheck_ = !actionArgs.hasKey("nobondcheck");
  skipBadFrames_ = actionArgs.hasKey("skipbadframes");

  mprintf("    CHECKSTRUCTURE: Checking atoms in mask '%s'",Mask1_.MaskString());
  if (Mask2_.MaskStringSet())
    mprintf(" around mask '%s'", Mask2_.MaskString());
  if (!image_.UseImage())
    mprintf(", imaging off");
  if (outfile_ != 0)
    mprintf(", output to %s", outfile_->Filename().full());
  mprintf(".\n");
  if (!bondcheck_) {
    mprintf("\tChecking inter-atomic distances only.\n");
    mprintf("\tWarnings will be printed for non-bond distances < %.2f Ang.\n", sqrt(nonbondcut2_));
  } else {
    mprintf("\tChecking inter-atomic and bond distances.\n");
    mprintf("\tWarnings will be printed for bond lengths > eq + %.2f Ang\n",
            bondoffset_);
    mprintf("\tand non-bond distances < %.2f Ang.\n", sqrt(nonbondcut2_));
  }
  if (skipBadFrames_)
    mprintf("\tFrames with problems will be skipped.\n");
  if (silent_)
    mprintf("\tWarning messages will be suppressed.\n");
# ifdef _OPENMP
# pragma omp parallel
  {
#   pragma omp master
    {
    mprintf("\tParallelizing calculation with %i threads.\n", omp_get_num_threads());
    }
  }
# endif
  return Action::OK;
}
Example #23
0
// Action_Distance::Init()
Action::RetType Action_Distance::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  AssociatedData_NOE noe;
  // Get Keywords
  image_.InitImaging( !(actionArgs.hasKey("noimage")) );
  useMass_ = !(actionArgs.hasKey("geom"));
  DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  MetaData::scalarType stype = MetaData::UNDEFINED;
  std::string stypename = actionArgs.GetStringKey("type");
  if ( stypename == "noe" ) {
    stype = MetaData::NOE;
    if (noe.NOE_Args( actionArgs )) return Action::ERR;
  }
  // Get Masks
  std::string mask1 = actionArgs.GetMaskNext();
  std::string mask2 = actionArgs.GetMaskNext();
  if (mask1.empty() || mask2.empty()) {
    mprinterr("Error: distance requires 2 masks\n");
    return Action::ERR;
  }
  Mask1_.SetMaskString(mask1);
  Mask2_.SetMaskString(mask2);

  // Dataset to store distances TODO store masks in data set?
  dist_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(actionArgs.GetStringNext(),
                                                MetaData::M_DISTANCE, stype), "Dis");
  if (dist_==0) return Action::ERR;
  if ( stype == MetaData::NOE ) {
    dist_->AssociateData( &noe );
    dist_->SetLegend(Mask1_.MaskExpression() + " and " + Mask2_.MaskExpression());
  }
  // Add dataset to data file
  if (outfile != 0) outfile->AddDataSet( dist_ );

  mprintf("    DISTANCE: %s to %s",Mask1_.MaskString(), Mask2_.MaskString());
  if (!image_.UseImage()) 
    mprintf(", non-imaged");
  if (useMass_) 
    mprintf(", center of mass");
  else
    mprintf(", geometric center");
  mprintf(".\n");

  return Action::OK;
}
Example #24
0
// Action_Principal::Init()
Action::RetType Action_Principal::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  debug_ = debugIn;
  // Keywords
  std::string dsname = actionArgs.GetStringKey("name");
  doRotation_ = actionArgs.hasKey("dorotation");
  // CPPTRAJ always uses mass no matter what this keyword says.
  useMass_ = actionArgs.hasKey("mass");
  std::string filename = actionArgs.GetStringKey("out");
  if (!doRotation_ && filename.empty() && dsname.empty()) {
    mprinterr("Error: At least one of 'dorotation', 'out <filename>', or 'name <dsname>' must be specified.\n");
    return Action::ERR;
  }
  // Masks
  mask_.SetMaskString( actionArgs.GetMaskNext() );
  // Set up data
  if (!dsname.empty()) {
     vecData_ = (DataSet_Mat3x3*)init.DSL().AddSet(DataSet::MAT3X3, MetaData(dsname, "evec"));
     valData_ = (DataSet_Vector*)init.DSL().AddSet(DataSet::VECTOR, MetaData(dsname, "eval"));
     if (vecData_ == 0 || valData_ == 0) return Action::ERR;
  }

  mprintf("    PRINCIPAL:");
  if (!filename.empty()) {
    outfile_ = init.DFL().AddCpptrajFile(filename, "Eigenvectors/Eigenvalues");
    if (outfile_ == 0) return Action::ERR;
    mprintf(" output eigenvectors/eigenvalues to %s,", outfile_->Filename().full());
  }
  if (doRotation_)
    mprintf(" with rotation by");
  else
    mprintf(" without rotation by");
  if (useMass_)
    mprintf(" center of mass");
  else
    mprintf(" center of geometry");
  mprintf(", atoms selected by [%s]\n", mask_.MaskString());
  if (vecData_ != 0)
    mprintf("\tSaving eigenvectors to '%s' (in rows of 3x3 matrices).\n"
            "\tSaving eigenvalues to '%s'\n", vecData_->legend(), valData_->legend());

  return Action::OK;
}
Example #25
0
// Action_VelocityAutoCorr::Init()
Action::RetType Action_VelocityAutoCorr::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  useVelInfo_ = actionArgs.hasKey("usevelocity");
  mask_.SetMaskString( actionArgs.GetMaskNext() );
  DataFile* outfile =  init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  maxLag_ = actionArgs.getKeyInt("maxlag", -1);
  tstep_ = actionArgs.getKeyDouble("tstep", 1.0);
  useFFT_ = !actionArgs.hasKey("direct");
  normalize_ = actionArgs.hasKey("norm");
  // Set up output data set
  VAC_ = init.DSL().AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "VAC");
  if (VAC_ == 0) return Action::ERR;
  if (outfile != 0) outfile->AddDataSet( VAC_ );
# ifdef MPI
  trajComm_ = init.TrajComm(); 
  if (trajComm_.Size() > 1 && !useVelInfo_)
    mprintf("\nWarning: When calculating velocities between consecutive frames,\n"
            "\nWarning:   'velocityautocorr' in parallel will not work correctly if\n"
            "\nWarning:   coordinates have been modified by previous actions (e.g. 'rms').\n\n");
# endif
  mprintf("    VELOCITYAUTOCORR:\n"
          "\tCalculate velocity auto-correlation function for atoms in mask '%s'\n",
          mask_.MaskString());
  if (useVelInfo_)
    mprintf("\tUsing velocity information present in frames.\n");
  else
    mprintf("\tCalculating velocities between consecutive frames.\n");
  if (outfile != 0)
    mprintf("\tOutput data set '%s' to '%s'\n", VAC_->legend(), 
            outfile->DataFilename().full());
  if (maxLag_ < 1)
    mprintf("\tMaximum lag will be half total # of frames");
  else
    mprintf("\tMaximum lag is %i frames", maxLag_);
  mprintf(", time step is %f ps\n", tstep_);
  if (useFFT_)
    mprintf("\tUsing FFT to calculate autocorrelation function.\n");
  else
    mprintf("\tUsing direct method to calculate autocorrelation function.\n");
  if (normalize_)
    mprintf("\tNormalizing autocorrelation function to 1.0\n");
  return Action::OK;
}
// Action_GridFreeEnergy::init()
Action::RetType Action_GridFreeEnergy::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Get output filename
  DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringNext(), actionArgs);
  if (outfile == 0) {
    mprinterr("Error: GridFreeEnergy: no output filename specified.\n");
    return Action::ERR;
  }
  // Get grid options (<nx> <dx> <ny> <dy> <nz> <dz> [box|origin] [negative])
  grid_ = GridInit( "GridFreeEnergy", actionArgs, init.DSL() );
  if (grid_ == 0) return Action::ERR;
# ifdef MPI
  if (ParallelGridInit(init.TrajComm(), grid_)) return Action::ERR;
# endif
  //grid_.PrintXplor( filename_, "", "REMARKS Change in Free energy from bulk solvent with bin normalisation of " + integerToString(currentLargestVoxelOccupancyCount) );

  // Get mask
  std::string maskexpr = actionArgs.GetMaskNext();
  if (maskexpr.empty()) {
    mprinterr("Error: GridFreeEnergy: No mask specified.\n");
    init.DSL().RemoveSet( grid_ );
    return Action::ERR;
  }
  mask_.SetMaskString(maskexpr);

  // Get extra args
  tempInKevin_ = actionArgs.getKeyDouble("temp", 293.0);
  outfile->AddDataSet( grid_ );

  // Info
  mprintf("Warning: DNAIONTRACKER is experimental code!\n");
  mprintf("    GridFreeEnergy\n");
  GridInfo( *grid_ );
  mprintf("\tGrid will be printed to file %s\n",outfile->DataFilename().full());
  mprintf("\tMask expression: [%s]\n",mask_.MaskString());
  mprintf("\tTemp is : %f K\n",tempInKevin_);

  // Allocate grid
  //if (GridAllocate()) return 1;

  return Action::OK;
}
Example #27
0
// Action_Surf::Init()
Action::RetType Action_Surf::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Get keywords
  DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs);

  // Get Masks
  Mask1_.SetMaskString( actionArgs.GetMaskNext() );

  // Dataset to store surface area 
  surf_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "SA");
  if (surf_==0) return Action::ERR;
  // Add dataset to data file list
  if (outfile != 0) outfile->AddDataSet( surf_ );

  mprintf("    SURF: Calculating surface area for atoms in mask [%s]\n",Mask1_.MaskString());
  mprintf("#Citation: Weiser, J.; Shenkin, P. S.; Still, W. C.; \"Approximate atomic\n"
          "#          surfaces from linear combinations of pairwise overlaps (LCPO).\"\n"
          "#          J. Comp. Chem. (1999), V.20, pp.217-230.\n");

  return Action::OK;
}
Example #28
0
// Action_Distance::init()
Action::RetType Action_Distance::Init(ArgList& actionArgs, TopologyList* PFL, FrameList* FL,
                          DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Get Keywords
  InitImaging( !(actionArgs.hasKey("noimage")) );
  useMass_ = !(actionArgs.hasKey("geom"));
  DataFile* outfile = DFL->AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  DataSet::scalarType stype = DataSet::UNDEFINED;
  std::string stypename = actionArgs.GetStringKey("type");
  if      ( stypename == "hbond" ) stype = DataSet::HBOND;
  else if (stypename == "noe"    ) stype = DataSet::NOE; // TODO: Grab bound and boundh

  // Get Masks
  std::string mask1 = actionArgs.GetMaskNext();
  std::string mask2 = actionArgs.GetMaskNext();
  if (mask1.empty() || mask2.empty()) {
    mprinterr("Error: distance: Requires 2 masks\n");
    return Action::ERR;
  }
  Mask1_.SetMaskString(mask1);
  Mask2_.SetMaskString(mask2);

  // Dataset to store distances
  dist_ = DSL->AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "Dis");
  if (dist_==0) return Action::ERR;
  dist_->SetScalar( DataSet::M_DISTANCE, stype );
  // Add dataset to data file
  if (outfile != 0) outfile->AddSet( dist_ );

  mprintf("    DISTANCE: %s to %s",Mask1_.MaskString(), Mask2_.MaskString());
  if (!UseImage()) 
    mprintf(", non-imaged");
  if (useMass_) 
    mprintf(", center of mass");
  else
    mprintf(", geometric center");
  mprintf(".\n");

  return Action::OK;
}
Example #29
0
// Action_AtomicCorr::Init()
Action::RetType Action_AtomicCorr::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  debug_ = debugIn;
  outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
  cut_ = actionArgs.getKeyDouble("cut", 0.0);
  if (cut_ < 0.0 || cut_ > 1.0) {
    mprinterr("Error: cut value must be between 0 and 1.\n");
    return Action::ERR;
  }
  min_ = actionArgs.getKeyInt("min",0);
  if (actionArgs.hasKey("byatom"))
    acorr_mode_ = ATOM;
  else if (actionArgs.hasKey("byres"))
    acorr_mode_ = RES;
  mask_.SetMaskString( actionArgs.GetMaskNext() );
  
  // Set up DataSet
  dset_ = init.DSL().AddSet( DataSet::MATRIX_FLT, actionArgs.GetStringNext(), "ACorr" );
  if (dset_ == 0) {
    mprinterr("Error: Could not allocate output data set.\n");
    return Action::ERR;
  }
  // Add DataSet to output file
  if (outfile_ != 0) outfile_->AddDataSet( dset_ );

  mprintf("    ATOMICCORR: Correlation of %s motions will be calculated for\n",
          ModeString[acorr_mode_]);
  mprintf("\tatoms in mask [%s]", mask_.MaskString());
  if (outfile_ != 0) mprintf(", output to file %s", outfile_->DataFilename().full());
  mprintf("\n\tData saved in set '%s'\n", dset_->legend());
  if (cut_ != 0)
    mprintf("\tOnly correlations greater than %.2f or less than -%.2f will be printed.\n",
            cut_,cut_);
  if (min_!=0)
    mprintf("\tOnly correlations for %ss > %i apart will be calculated.\n",
            ModeString[acorr_mode_],min_);

  return Action::OK;
}
Example #30
0
// Action_RandomizeIons::Init()
Action::RetType Action_RandomizeIons::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  debug_ = debugIn;
  // Get first mask
  std::string ionmask = actionArgs.GetMaskNext();
  if (ionmask.empty()) {
    mprinterr("Error: randomizeions: No mask for ions specified.\n");
    return Action::ERR;
  }
  ions_.SetMaskString( ionmask );

  // Get Keywords
  image_.InitImaging( !actionArgs.hasKey("noimage") );
  int seed = actionArgs.getKeyInt("seed", -1);
  overlap_ = actionArgs.getKeyDouble("overlap", 3.5);
  min_ = actionArgs.getKeyDouble("by", 3.5);
  // Pre-square overlap and min
  overlap_ *= overlap_;
  min_ *= min_;
  // If no around mask specified, leave blank
  std::string aroundmask = actionArgs.GetStringKey("around");
  if (!aroundmask.empty())
    around_.SetMaskString( aroundmask );
  
  // INFO
  mprintf("    RANDOMIZEIONS: Swapping postions of ions in mask '%s' with solvent.\n",
          ions_.MaskString());
  mprintf("\tNo ion can get closer than %.2f angstroms to another ion.\n", sqrt( overlap_ ));
  if (around_.MaskStringSet())
    mprintf("\tNo ion can get closer than %.2f angstroms to atoms in mask '%s'\n",
            sqrt( min_ ), around_.MaskString());
  if (!image_.UseImage())
    mprintf("\tImaging of the coordinates will not be performed.\n");
  if (seed > 0)
    mprintf("\tRandom number generator seed is %i\n", seed);
  RN_.rn_set( seed );

  return Action::OK;
}