// Action_Esander::Init()
Action::RetType Action_Esander::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
trajComm_ = init.TrajComm();
# endif
SANDER_.SetDebug( debugIn );
Init_ = init;
// Get keywords
outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
save_forces_ = actionArgs.hasKey("saveforces");
ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
if (REF.error()) return Action::ERR;
if (!REF.empty()) {
refFrame_ = REF.Coord();
currentParm_ = REF.ParmPtr();
}
if (SANDER_.SetInput( actionArgs )) return Action::ERR;
// DataSet name and array
setname_ = actionArgs.GetStringNext();
if (setname_.empty())
setname_ = init.DSL().GenerateDefaultName("ENE");
Esets_.clear();
Esets_.resize( (int)Energy_Sander::N_ENERGYTYPES, 0 );
mprintf(" ESANDER: Calculating energy using Sander.\n");
mprintf("\tTemporary topology file name is '%s'\n", SANDER_.TopFilename().full());
if (save_forces_) mprintf("\tSaving force information to frame.\n");
mprintf("\tReference for initialization");
if (!REF.empty())
mprintf(" is '%s'\n", REF.refName());
else
mprintf(" will be first frame.\n");
return Action::OK;
}
Action::RetType Action_CreateCrd::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Keywords
Topology* parm = init.DSL().GetTopology( actionArgs );
if (parm == 0) {
mprinterr("Error: createcrd: No parm files loaded.\n");
return Action::ERR;
}
pindex_ = parm->Pindex();
check_ = !actionArgs.hasKey("nocheck");
// DataSet
std::string setname = actionArgs.GetStringNext();
if (setname == "_DEFAULTCRD_") {
// Special case: Creation of COORDS DataSet has been requested by an
// analysis and should already be present.
coords_ = (DataSet_Coords_CRD*)init.DSL().FindSetOfType(setname, DataSet::COORDS);
} else
coords_ = (DataSet_Coords_CRD*)init.DSL().AddSet(DataSet::COORDS, setname, "CRD");
if (coords_ == 0) return Action::ERR;
// Do not set topology here since it may be modified later.
mprintf(" CREATECRD: Saving coordinates from Top %s to \"%s\"\n",
parm->c_str(), coords_->legend());
if (!check_)
mprintf("\tNot strictly enforcing that all frames have same # atoms.\n");
# ifdef MPI
if (init.TrajComm().Size() > 1)
mprintf("Warning: Synchronization of COORDS data sets over multiple threads is\n"
"Warning: experimental and may be slower than reading in via a single\n"
"Warning: thread. Users are encouraged to run benchmarks before\n"
"Warning: extensive usage.\n");
# endif
return Action::OK;
}
Action::RetType Action_MultiVector::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
debug_ = debugIn;
// Get keywords
outfile_ = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs);
std::string resrange_arg = actionArgs.GetStringKey("resrange");
if (!resrange_arg.empty())
if (resRange_.SetRange( resrange_arg )) return Action::ERR;
ired_ = actionArgs.hasKey("ired");
// Get atom names
if (SetName(name1_, actionArgs.GetStringKey("name1"), "name1")) return Action::ERR;
if (SetName(name2_, actionArgs.GetStringKey("name2"), "name2")) return Action::ERR;
// Setup DataSet(s) name
dsetname_ = actionArgs.GetStringNext();
mprintf(" MULTIVECTOR: Calculating");
if (ired_) mprintf(" IRED");
if (!resRange_.Empty())
mprintf(" vectors for residues in range %s\n", resRange_.RangeArg());
else
mprintf(" vectors for all solute residues.\n");
mprintf("\tName1='%s' (origin) Name2='%s'\n", *name1_, *name2_);
if (!dsetname_.empty())
mprintf("\tDataSet name: %s\n", dsetname_.c_str());
if (outfile_ != 0) mprintf("\tOutput to %s\n", outfile_->DataFilename().base());
init.DSL().SetDataSetsPending(true);
masterDSL_ = init.DslPtr();
return Action::OK;
}
/** Called once before traj processing. Set up reference info. */
Action::RetType Action_DistRmsd::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Check for keywords
DataFile* outfile = init.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 = 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 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_ = init.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;
}
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(":WAT@O");
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;
}
// Action_Angle::init()
Action::RetType Action_Angle::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Get keywords
DataFile* outfile = init.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_ = init.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;
}
// Action_FilterByData::Init()
Action::RetType Action_FilterByData::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
maxmin_ = init.DSL().AddSet( DataSet::INTEGER, actionArgs.GetStringKey("name"), "Filter" );
if (maxmin_ == 0) return Action::ERR;
DataFile* maxminfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
if (maxminfile != 0)
maxminfile->AddDataSet( maxmin_ );
// Get min and max args.
while (actionArgs.Contains("min"))
Min_.push_back( actionArgs.getKeyDouble("min", 0.0) );
while (actionArgs.Contains("max"))
Max_.push_back( actionArgs.getKeyDouble("max", 0.0) );
if (Min_.empty()) {
mprinterr("Error: At least one 'min' arg must be specified.\n");
return Action::ERR;
}
if (Max_.empty()) {
mprinterr("Error: At least one 'max' arg must be specified.\n");
return Action::ERR;
}
if (Min_.size() != Max_.size()) {
mprinterr("Error: # of 'min' args (%zu) != # of 'max' args (%zu)\n",
Min_.size(), Max_.size());
return Action::ERR;
}
// Get DataSets from remaining arguments
Dsets_.AddSetsFromArgs( actionArgs.RemainingArgs(), init.DSL() );
if (Dsets_.empty()) {
mprinterr("Error: No data sets specified.\n");
return Action::ERR;
}
if ( Dsets_.size() < Min_.size() ) {
mprinterr("Error: More 'min'/'max' args (%zu) than data sets (%zu).\n",
Min_.size(), Dsets_.size());
return Action::ERR;
}
if ( Dsets_.size() > Min_.size() ) {
unsigned int Nremaining = Dsets_.size() - Min_.size();
double useMin = Min_.back();
double useMax = Max_.back();
mprintf("Warning: More data sets than 'min'/'max' args.\n"
"Warning: Using min=%f and max=%f for last %zu data sets.\n",
useMin, useMax, Nremaining);
for (unsigned int ds = 0; ds < Nremaining; ++ds) {
Min_.push_back( useMin );
Max_.push_back( useMax );
}
}
mprintf(" FILTER: Filtering out frames using %zu data sets.\n", Dsets_.size());
for (unsigned int ds = 0; ds < Dsets_.size(); ds++)
mprintf("\t%.4f < '%s' < %.4f\n", Min_[ds], Dsets_[ds]->legend(), Max_[ds]);
if (maxminfile != 0)
mprintf("\tFilter frame info will be written to %s\n", maxminfile->DataFilename().full());
return Action::OK;
}
// Action_Outtraj::Init()
Action::RetType Action_Outtraj::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Set up output traj
outtraj_.SetDebug(debugIn);
std::string trajfilename = actionArgs.GetStringNext();
if (trajfilename.empty()) {
mprinterr("Error: No filename given.\nError: Usage: ");
Help();
return Action::ERR;
}
associatedParm_ = init.DSL().GetTopology(actionArgs);
if (associatedParm_ == 0) {
mprinterr("Error: Could not get associated topology for %s\n",trajfilename.c_str());
return Action::ERR;
}
// If maxmin, get the name of the dataset as well as the max and min values.
double lastmin = 0.0;
double lastmax = 0.0;
while ( actionArgs.Contains("maxmin") ) {
std::string datasetName = actionArgs.GetStringKey("maxmin");
if (!datasetName.empty()) {
DataSet* dset = init.DSL().GetDataSet(datasetName);
if (dset==0) {
mprintf("Error: maxmin: Could not get dataset %s\n",datasetName.c_str());
return Action::ERR;
} else {
// Currently only allow int, float, or double datasets
if (dset->Type() != DataSet::INTEGER &&
dset->Type() != DataSet::FLOAT &&
dset->Type() != DataSet::DOUBLE)
{
mprinterr("Error: maxmin: Only int, float, or double dataset (%s) supported.\n",
datasetName.c_str());
return Action::ERR;
}
Dsets_.push_back( (DataSet_1D*)dset );
Max_.push_back( actionArgs.getKeyDouble("max",lastmax) );
Min_.push_back( actionArgs.getKeyDouble("min",lastmin) );
lastmax = Max_.back();
lastmin = Min_.back();
}
} else {
mprinterr("Error: maxmin Usage: maxmin <setname> max <max> min <min>\n");
return Action::ERR;
}
}
// Initialize output trajectory with remaining arguments
if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(),
TrajectoryFile::UNKNOWN_TRAJ, init.DSL().EnsembleNum()) )
return Action::ERR;
isSetup_ = false;
mprintf(" OUTTRAJ: Writing frames associated with topology '%s'\n", associatedParm_->c_str());
for (unsigned int ds = 0; ds < Dsets_.size(); ++ds)
mprintf("\tmaxmin: Printing trajectory frames based on %g <= %s <= %g\n",
Min_[ds], Dsets_[ds]->legend(), Max_[ds]);
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;
}
// 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;
// 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;
}
// -----------------------------------------------------------------------------
// 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;
}
// 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;
}
// 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_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_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;
}
// 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;
}
// 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_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;
}
// 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;
}
// Action_Surf::Init()
Action::RetType Action_Surf::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Get keywords
DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs);
// Get Masks
Mask1_.SetMaskString( actionArgs.GetMaskNext() );
// Dataset to store surface area
surf_ = init.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;
}
// 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;
}
// 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;
}
// 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;
}
// Action_LESsplit::Init()
Action::RetType Action_LESsplit::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
if (init.DSL().EnsembleNum() > -1) {
mprinterr("Error: LESSPLIT currently cannot be used in ensemble mode.\n");
return Action::ERR;
}
trajfilename_ = actionArgs.GetStringKey("out");
avgfilename_ = actionArgs.GetStringKey("average");
lesSplit_ = !trajfilename_.empty();
lesAverage_ = !avgfilename_.empty();
if (!lesSplit_ && !lesAverage_) {
mprinterr("Error: Must specify at least 'out <prefix>' or 'average <name>'.\n");
return Action::ERR;
}
trajArgs_ = actionArgs.RemainingArgs();
mprintf(" LESSPLIT:\n");
if (lesSplit_) mprintf("\tSplit output to '%s.X'\n", trajfilename_.c_str());
if (lesAverage_) mprintf("\tAverage output to '%s'\n", avgfilename_.c_str());
return Action::OK;
}
// Action_Contacts::Init()
Action::RetType Action_Contacts::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
byResidue_ = actionArgs.hasKey("byresidue");
double dist = actionArgs.getKeyDouble("distance", 7.0);
dt_ = actionArgs.getKeyDouble("time", 1.0);
// Square the cutoff
distance_ = dist * dist;
first_ = actionArgs.hasKey("first");
// Get reference
ReferenceFrame REF = init.DSL().GetReferenceFrame( actionArgs );
if (REF.error()) return Action::ERR;
std::string outfilename = actionArgs.GetStringKey("out");
outfile_ = init.DFL().AddCpptrajFile(outfilename, "Contacts", DataFileList::TEXT, true);
if (outfile_ == 0) return Action::ERR;
if (byResidue_) {
if (outfilename.empty()) {
mprinterr("Error: Contacts 'byresidue' requires output filename.\n");
return Action::ERR;
}
outfile2_ = init.DFL().AddCpptrajFile(outfilename + ".native", "Contacts by residue");
if (outfile2_ == 0) return Action::ERR;
}
// Get Mask
std::string mask0 = actionArgs.GetMaskNext();
if (mask0.empty() && byResidue_)
Mask_.SetMaskString("@CA");
else
Mask_.SetMaskString( mask0 );
// Initialize reference. If no reference mask is given mask0 will be used.
// First arg 'nofit' set to true, no fitting with contacts. Allows last arg
// 'RefTrans' to be null.
//if (RefInit(true, false, Mask_.MaskString(), actionArgs, FL, PFL, 0)!=0)
// return 1;
if (!first_ && REF.empty()) {
mprintf("\tNo reference structure specified. Defaulting to first.\n");
first_ = true;
}
if (!first_) {
// TODO: Convert FrameList to return frame reference?
// Set up atom mask for reference frame
if (REF.Parm().SetupIntegerMask(Mask_, REF.Coord())) return Action::ERR;
// Set up reference contacts
SetupContacts(REF.Coord(), REF.Parm());
}
// Output file header - only if not byresidue
if (!byResidue_) {
outfile_->Printf("#time\tContacts\tnative Contacts ");
if (!first_)
outfile_->Printf("(number of natives: %zu)", nativecontacts_.size());
outfile_->Printf("\n");
}
mprintf(" CONTACTS: [%s] Calculating current contacts and comparing results to",
Mask_.MaskString());
if (first_)
mprintf(" first frame.\n");
else
mprintf(" reference structure.\n");
mprintf("\tDistance cutoff is %g angstroms.\n", dist);
mprintf("\tWriting results to %s\n", outfile_->Filename().full());
if (byResidue_)
mprintf("\tResults are output on a per-residue basis to %s.\n", outfile2_->Filename().full());
return Action::OK;
}
// Action_ReplicateCell::Init()
Action::RetType Action_ReplicateCell::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Require imaging.
image_.InitImaging( true );
// Set up output traj
std::string trajfilename = actionArgs.GetStringKey("out");
parmfilename_ = actionArgs.GetStringKey("parmout");
bool setAll = actionArgs.hasKey("all");
std::string dsname = actionArgs.GetStringKey("name");
if (!dsname.empty()) {
coords_ = (DataSet_Coords*)init.DSL().AddSet(DataSet::COORDS, dsname, "RCELL");
if (coords_ == 0) return Action::ERR;
}
if (trajfilename.empty() && coords_ == 0) {
mprinterr("Error: Either 'out <traj filename> or 'name <dsname>' must be specified.\n");
return Action::ERR;
}
// Get Mask
Mask1_.SetMaskString( actionArgs.GetMaskNext() );
// Determine which directions to set
if (setAll) {
for (int ix = -1; ix < 2; ix++)
for (int iy = -1; iy < 2; iy++)
for (int iz = -1; iz < 2; iz++) {
directionArray_.push_back( ix );
directionArray_.push_back( iy );
directionArray_.push_back( iz );
}
} else {
std::string dirstring = actionArgs.GetStringKey("dir");
while (!dirstring.empty()) {
std::vector<int> ixyz(3, -2);
std::vector<int>::iterator iptr = ixyz.begin();
for (std::string::const_iterator c = dirstring.begin();
c != dirstring.end(); ++c)
{
if (iptr == ixyz.end()) {
mprinterr("Error: 'dir' string has too many characters.\n");
return Action::ERR;
}
int sign = 1;
if (*c == '+') ++c;
else if (*c == '-') { sign = -1; ++c; }
if (isdigit( *c ))
*iptr = toDigit( *c ) * sign;
else {
mprinterr("Error: illegal character '%c' in 'dir' string '%s'; only numbers allowed.\n",
*c, dirstring.c_str());
return Action::ERR;
}
++iptr;
}
//mprintf("DEBUG: %s = %i %i %i\n", dirstring.c_str(), ixyz[0], ixyz[1], ixyz[2]);
directionArray_.push_back( ixyz[0] );
directionArray_.push_back( ixyz[1] );
directionArray_.push_back( ixyz[2] );
dirstring = actionArgs.GetStringKey("dir");
}
}
ncopies_ = (int)(directionArray_.size() / 3);
if (ncopies_ < 1) {
mprinterr("Error: No directions (or 'all') specified.\n");
return Action::ERR;
}
// Initialize output trajectory with remaining arguments
if (!trajfilename.empty()) {
outtraj_.SetDebug( debugIn );
if ( outtraj_.InitEnsembleTrajWrite(trajfilename, actionArgs.RemainingArgs(),
TrajectoryFile::UNKNOWN_TRAJ, init.DSL().EnsembleNum()) )
return Action::ERR;
writeTraj_ = true;
# ifdef MPI
outtraj_.SetTrajComm( init.TrajComm() );
# endif
} else
writeTraj_ = false;
mprintf(" REPLICATE CELL: Replicating cell in %i directions:\n", ncopies_);
mprintf("\t\t X Y Z\n");
for (unsigned int i = 0; i != directionArray_.size(); i += 3)
mprintf("\t\t%2i %2i %2i\n", directionArray_[i],
directionArray_[i+1], directionArray_[i+2]);
mprintf("\tUsing atoms in mask '%s'\n", Mask1_.MaskString());
if (writeTraj_)
mprintf("\tWriting to trajectory %s\n", outtraj_.Traj().Filename().full());
if (!parmfilename_.empty())
mprintf("\tWriting topology %s\n", parmfilename_.c_str());
if (coords_ != 0)
mprintf("\tSaving coords to data set %s\n", coords_->legend());
return Action::OK;
}
// -----------------------------------------------------------------------------
// Action_NMRrst::Init()
Action::RetType Action_NMRrst::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
if (init.TrajComm().Size() > 1) {
mprinterr("Error: 'nmrrst' action does not work with > 1 thread (%i threads currently).\n",
init.TrajComm().Size());
return Action::ERR;
}
# endif
debug_ = debugIn;
// Get Keywords
Image_.InitImaging( !(actionArgs.hasKey("noimage")) );
useMass_ = !(actionArgs.hasKey("geom"));
findNOEs_ = actionArgs.hasKey("findnoes");
findOutput_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("findout"), "Found NOEs",
DataFileList::TEXT, true);
specOutput_ = init.DFL().AddCpptrajFile(actionArgs.GetStringKey("specout"), "Specified NOEs",
DataFileList::TEXT, true);
if (findOutput_ == 0 || specOutput_ == 0) return Action::ERR;
resOffset_ = actionArgs.getKeyInt("resoffset", 0);
DataFile* outfile = init.DFL().AddDataFile( actionArgs.GetStringKey("out"), actionArgs );
max_cut_ = actionArgs.getKeyDouble("cut", 6.0);
strong_cut_ = actionArgs.getKeyDouble("strongcut", 2.9);
medium_cut_ = actionArgs.getKeyDouble("mediumcut", 3.5);
weak_cut_ = actionArgs.getKeyDouble("weakcut", 5.0);
series_ = actionArgs.hasKey("series");
std::string rstfilename = actionArgs.GetStringKey("file");
viewrst_ = actionArgs.GetStringKey("viewrst");
setname_ = actionArgs.GetStringKey("name");
if (setname_.empty())
setname_ = init.DSL().GenerateDefaultName("NMR");
nframes_ = 0;
// Atom Mask
Mask_.SetMaskString( actionArgs.GetMaskNext() );
// Pairs specified on command line.
std::string pair1 = actionArgs.GetStringKey("pair");
while (!pair1.empty()) {
std::string pair2 = actionArgs.GetStringNext();
if (pair2.empty()) {
mprinterr("Error: Only one mask specified for pair (%s)\n", pair1.c_str());
return Action::ERR;
}
Pairs_.push_back( MaskPairType(AtomMask(pair1), AtomMask(pair2)) );
pair1 = actionArgs.GetStringKey("pair");
}
// Check that something will be done
if (!findNOEs_ && rstfilename.empty() && Pairs_.empty()) {
mprinterr("Error: Must specify restraint file, 'pair', and/or 'findnoes'.\n");
return Action::ERR;
}
// Read in NMR restraints.
if (!rstfilename.empty()) {
if (ReadNmrRestraints( rstfilename )) return Action::ERR;
}
// Set up distances.
int num_noe = 1;
for (noeDataArray::iterator noe = NOEs_.begin(); noe != NOEs_.end(); ++noe, ++num_noe) {
// Translate any ambiguous atom names
TranslateAmbiguous( noe->aName1_ );
TranslateAmbiguous( noe->aName2_ );
// Create mask expressions from resnum/atom name
noe->dMask1_.SetMaskString( MaskExpression( noe->resNum1_, noe->aName1_ ) );
noe->dMask2_.SetMaskString( MaskExpression( noe->resNum2_, noe->aName2_ ) );
// Dataset to store distances
AssociatedData_NOE noeData(noe->bound_, noe->boundh_, noe->rexp_);
MetaData md(setname_, "NOE", num_noe);
md.SetLegend( noe->dMask1_.MaskExpression() + " and " + noe->dMask2_.MaskExpression());
md.SetScalarMode( MetaData::M_DISTANCE );
md.SetScalarType( MetaData::NOE );
noe->dist_ = init.DSL().AddSet(DataSet::DOUBLE, md);
if (noe->dist_==0) return Action::ERR;
noe->dist_->AssociateData( &noeData );
// Add dataset to data file
if (outfile != 0) outfile->AddDataSet( noe->dist_ );
}
masterDSL_ = init.DslPtr();
mprintf("Warning: *** THIS ACTION IS EXPERIMENTAL. ***\n");
mprintf(" NMRRST: %zu NOEs from NMR restraint file.\n", NOEs_.size());
mprintf("\tShifting residue numbers in restraint file by %i\n", resOffset_);
// DEBUG - print NOEs
for (noeDataArray::const_iterator noe = NOEs_.begin(); noe != NOEs_.end(); ++noe)
mprintf("\t'%s' %f < %f < %f\n", noe->dist_->legend(),
noe->bound_, noe->rexp_, noe->boundh_);
if (findNOEs_) {
mprintf("\tSearching for potential NOEs. Max cutoff is %g Ang.\n", max_cut_);
mprintf("\tNOE distance criteria (Ang.): S= %g, M= %g, W= %g\n",
strong_cut_, medium_cut_, weak_cut_);
if (series_)
mprintf("\tDistance data for NOEs less than cutoff will be saved as '%s[foundNOE]'.\n",
setname_.c_str());
mprintf("\tFound NOEs will be written to '%s'\n", findOutput_->Filename().full());
}
if (!Pairs_.empty()) {
mprintf("\tSpecified NOE pairs:\n");
for (MaskPairArray::const_iterator mp = Pairs_.begin(); mp != Pairs_.end(); ++mp)
mprintf("\t\t[%s] to [%s]\n", mp->first.MaskString(), mp->second.MaskString());
mprintf("\tSpecified NOE data will be written to '%s'\n", specOutput_->Filename().full());
}
if (!Image_.UseImage())
mprintf("\tNon-imaged");
else
mprintf("\tImaged");
if (useMass_)
mprintf(", center of mass.\n");
else
mprintf(", geometric center.\n");
if (!viewrst_.empty())
mprintf("\tTopologies corresponding to found NOEs will be written to '%s'\n", viewrst_.c_str());
return Action::OK;
}
// Action_LIE::init()
Action::RetType Action_LIE::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
// Always use imaged distances
InitImaging(true);
double cut;
// Get Keywords
doelec_ = !(actionArgs.hasKey("noelec"));
dovdw_ = !(actionArgs.hasKey("novdw"));
DataFile* datafile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
dielc_ = actionArgs.getKeyDouble("diel", 1.0);
cut = actionArgs.getKeyDouble("cutvdw", 12.0);
cut2vdw_ = cut * cut; // store square of cut for computational efficiency
cut = actionArgs.getKeyDouble("cutelec", 12.0);
cut2elec_ = cut * cut; // store square of cut for computational efficiency
onecut2_ = 1 / cut2elec_;
bool has_mask2 = false;
if (!doelec_ && !dovdw_) {
mprinterr("Error: LIE: Cannot skip both ELEC and VDW calcs\n");
return Action::ERR;
}
// Get Masks
Mask1_.SetMaskString( actionArgs.GetMaskNext() );
std::string refmask = actionArgs.GetMaskNext();
if (!refmask.empty()) {
Mask2_.SetMaskString(refmask);
has_mask2 = true;
}
else {
Mask2_ = Mask1_;
Mask2_.InvertMaskExpression();
}
// Get data set name
std::string ds_name = actionArgs.GetStringNext();
if (ds_name.empty())
ds_name = init.DSL().GenerateDefaultName("LIE");
// Datasets
if (doelec_) {
elec_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(ds_name, "EELEC"));
if (elec_ == 0) return Action::ERR;
if (datafile != 0) datafile->AddDataSet(elec_);
}
if (dovdw_) {
vdw_ = init.DSL().AddSet(DataSet::DOUBLE, MetaData(ds_name, "EVDW"));
if (vdw_ == 0) return Action::ERR;
if (datafile != 0) datafile->AddDataSet(vdw_);
}
mprintf(" LIE: Ligand mask is %s. Surroundings are ", Mask1_.MaskString());
if (!has_mask2)
mprintf("everything else. ");
else
mprintf("atoms in mask %s. ", Mask2_.MaskString());
mprintf("Cutoff is %.3lf Ang. ", cut);
if (!doelec_)
mprintf("Skipping Electrostatic Calc. ");
if (!dovdw_)
mprintf("Skipping VDW Calc. ");
mprintf("\n");
return Action::OK;
}
// Action_Radial::Init()
Action::RetType Action_Radial::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
debug_ = debugIn;
// Get Keywords
image_.InitImaging( !(actionArgs.hasKey("noimage")) );
std::string outfilename = actionArgs.GetStringKey("out");
// Default particle density (mols/Ang^3) for water based on 1.0 g/mL
density_ = actionArgs.getKeyDouble("density",0.033456);
if (actionArgs.hasKey("center1"))
rmode_ = CENTER1;
else if (actionArgs.hasKey("center2"))
rmode_ = CENTER2;
else if (actionArgs.hasKey("nointramol"))
rmode_ = NO_INTRAMOL;
else
rmode_ = NORMAL;
useVolume_ = actionArgs.hasKey("volume");
DataFile* intrdfFile = init.DFL().AddDataFile(actionArgs.GetStringKey("intrdf"));
DataFile* rawrdfFile = init.DFL().AddDataFile(actionArgs.GetStringKey("rawrdf"));
spacing_ = actionArgs.getNextDouble(-1.0);
if (spacing_ < 0) {
mprinterr("Error: Radial: No spacing argument or arg < 0.\n");
Help();
return Action::ERR;
}
double maximum = actionArgs.getNextDouble(-1.0);
if (maximum < 0) {
mprinterr("Error: Radial: No maximum argument or arg < 0.\n");
Help();
return Action::ERR;
}
// Store max^2, distances^2 greater than max^2 do not need to be
// binned and therefore do not need a sqrt calc.
maximum2_ = maximum * maximum;
// Get First Mask
std::string mask1 = actionArgs.GetMaskNext();
if (mask1.empty()) {
mprinterr("Error: Radial: No mask given.\n");
return Action::ERR;
}
Mask1_.SetMaskString(mask1);
// Check for second mask - if none specified use first mask
std::string mask2 = actionArgs.GetMaskNext();
if (!mask2.empty())
Mask2_.SetMaskString(mask2);
else
Mask2_.SetMaskString(mask1);
// If filename not yet specified check for backwards compat.
if (outfilename.empty() && actionArgs.Nargs() > 1 && !actionArgs.Marked(1))
outfilename = actionArgs.GetStringNext();
// Set up output dataset.
Dset_ = init.DSL().AddSet( DataSet::DOUBLE, actionArgs.GetStringNext(), "g(r)");
if (Dset_ == 0) return RDF_ERR("Could not allocate RDF data set.");
DataFile* outfile = init.DFL().AddDataFile(outfilename, actionArgs);
if (outfile != 0) outfile->AddDataSet( Dset_ );
// Make default precision a little higher than normal
Dset_->SetupFormat().SetFormatWidthPrecision(12,6);
// Set DataSet legend from mask strings.
Dset_->SetLegend(Mask1_.MaskExpression() + " => " + Mask2_.MaskExpression());
// TODO: Set Yaxis label in DataFile
// Calculate number of bins
one_over_spacing_ = 1 / spacing_;
double temp_numbins = maximum * one_over_spacing_;
temp_numbins = ceil(temp_numbins);
numBins_ = (int) temp_numbins;
// Setup output datafile. Align on bin centers instead of left.
// TODO: Use Rdim for binning?
Dimension Rdim( spacing_ / 2.0, spacing_, "Distance (Ang)" );
Dset_->SetDim(Dimension::X, Rdim);
// Set up output for integral of mask2 if specified.
if (intrdfFile != 0) {
intrdf_ = init.DSL().AddSet( DataSet::DOUBLE, MetaData(Dset_->Meta().Name(), "int" ));
if (intrdf_ == 0) return RDF_ERR("Could not allocate RDF integral data set.");
intrdf_->SetupFormat().SetFormatWidthPrecision(12,6);
intrdf_->SetLegend("Int[" + Mask2_.MaskExpression() + "]");
intrdf_->SetDim(Dimension::X, Rdim);
intrdfFile->AddDataSet( intrdf_ );
} else
intrdf_ = 0;
// Set up output for raw rdf
if (rawrdfFile != 0) {
rawrdf_ = init.DSL().AddSet( DataSet::DOUBLE, MetaData(Dset_->Meta().Name(), "raw" ));
if (rawrdf_ == 0) return RDF_ERR("Could not allocate raw RDF data set.");
rawrdf_->SetupFormat().SetFormatWidthPrecision(12,6);
rawrdf_->SetLegend("Raw[" + Dset_->Meta().Legend() + "]");
rawrdf_->SetDim(Dimension::X, Rdim);
rawrdfFile->AddDataSet( rawrdf_ );
} else
rawrdf_ = 0;
// Set up histogram
RDF_ = new int[ numBins_ ];
std::fill(RDF_, RDF_ + numBins_, 0);
# ifdef _OPENMP
// Since RDF is shared by all threads and we cant guarantee that a given
// bin in RDF wont be accessed at the same time by the same thread,
// each thread needs its own bin space.
#pragma omp parallel
{
if (omp_get_thread_num()==0)
numthreads_ = omp_get_num_threads();
}
rdf_thread_ = new int*[ numthreads_ ];
for (int i=0; i < numthreads_; i++) {
rdf_thread_[i] = new int[ numBins_ ];
std::fill(rdf_thread_[i], rdf_thread_[i] + numBins_, 0);
}
# endif
mprintf(" RADIAL: Calculating RDF for atoms in mask [%s]",Mask1_.MaskString());
if (!mask2.empty())
mprintf(" to atoms in mask [%s]",Mask2_.MaskString());
mprintf("\n");
if (outfile != 0)
mprintf(" Output to %s.\n", outfile->DataFilename().full());
if (intrdf_ != 0)
mprintf(" Integral of mask2 atoms will be output to %s\n",
intrdfFile->DataFilename().full());
if (rawrdf_ != 0)
mprintf(" Raw RDF bin values will be output to %s\n",
rawrdfFile->DataFilename().full());
if (rmode_==CENTER1)
mprintf(" Using center of atoms in mask1.\n");
else if (rmode_==CENTER2)
mprintf(" Using center of atoms in mask2.\n");
mprintf(" Histogram max %f, spacing %f, bins %i.\n",maximum,
spacing_,numBins_);
if (useVolume_)
mprintf(" Normalizing based on cell volume.\n");
else
mprintf(" Normalizing using particle density of %f molecules/Ang^3.\n",density_);
if (!image_.UseImage())
mprintf(" Imaging disabled.\n");
if (numthreads_ > 1)
mprintf(" Parallelizing RDF calculation with %i threads.\n",numthreads_);
return Action::OK;
}
// Action_Density::Init()
Action::RetType Action_Density::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
# ifdef MPI
trajComm_ = init.TrajComm();
# endif
DataFile* outfile = init.DFL().AddDataFile(actionArgs.GetStringKey("out"), actionArgs);
std::string dsname = actionArgs.GetStringKey("name");
if (actionArgs.hasKey("x") ) {
axis_ = DX;
area_coord_[0] = DY;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("y") ) {
axis_ = DY;
area_coord_[0] = DX;
area_coord_[1] = DZ;
} else if (actionArgs.hasKey("z") ) {
axis_ = DZ;
area_coord_[0] = DX;
area_coord_[1] = DY;
}
property_ = NUMBER;
if (actionArgs.hasKey("number") ) property_ = NUMBER;
else if (actionArgs.hasKey("mass") ) property_ = MASS;
else if (actionArgs.hasKey("charge") ) property_ = CHARGE;
else if (actionArgs.hasKey("electron") ) property_ = ELECTRON;
binType_ = CENTER;
if (actionArgs.hasKey("bincenter")) binType_ = CENTER;
else if (actionArgs.hasKey("binedge") ) binType_ = EDGE;
delta_ = actionArgs.getKeyDouble("delta", 0.01);
if (delta_ <= 0) {
mprinterr("Error: Delta must be > 0.0\n");
return Action::ERR;
}
// for compatibility with ptraj, ignored because we rely on the atom code to
// do the right thing, see Atom.{h,cpp}
if (actionArgs.hasKey("efile"))
mprintf("Warning: The 'efile' keyword is deprecated.\n");
// read the rest of the command line as a series of masks
std::string maskstr;
unsigned int idx = 1;
while ( (maskstr = actionArgs.GetMaskNext() ) != emptystring) {
masks_.push_back( AtomMask(maskstr) );
if (dsname.empty())
dsname = init.DSL().GenerateDefaultName("DENSITY");
MetaData MD(dsname, "avg", idx);
MD.SetTimeSeries( MetaData::NOT_TS );
// Hold average density
DataSet* ads = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (ads == 0) return Action::ERR;
ads->SetLegend( NoWhitespace(masks_.back().MaskExpression()) );
AvSets_.push_back( ads );
if (outfile != 0) outfile->AddDataSet( ads );
// Hold SD density
MD.SetAspect("sd");
DataSet* sds = init.DSL().AddSet( DataSet::DOUBLE, MD );
if (sds == 0) return Action::ERR;
sds->SetLegend( NoWhitespace("sd(" + masks_.back().MaskExpression() + ")") );
SdSets_.push_back( sds );
if (outfile != 0) outfile->AddDataSet( sds );
# ifdef MPI
ads->SetNeedsSync( false ); // Populated in Print()
sds->SetNeedsSync( false );
# endif
idx++;
}
if (masks_.empty()) {
// If no masks assume we want total system density.
if (dsname.empty())
dsname = actionArgs.GetStringNext();
density_ = init.DSL().AddSet(DataSet::DOUBLE, dsname, "DENSITY");
if (density_ == 0) return Action::ERR;
if (outfile != 0) outfile->AddDataSet( density_ );
image_.InitImaging( true );
// Hijack delta for storing sum of masses
delta_ = 0.0;
} else {
// Density selected by mask(s) along an axis
density_ = 0;
histograms_.resize(masks_.size() );
}
mprintf(" DENSITY:");
if (density_ == 0) {
const char* binStr[] = {"center", "edge"};
mprintf(" Determining %s density for %zu masks.\n", PropertyStr_[property_], masks_.size());
mprintf("\troutine version: %s\n", ROUTINE_VERSION_STRING);
mprintf("\tDelta is %f\n", delta_);
mprintf("\tAxis is %s\n", AxisStr_[axis_]);
mprintf("\tData set name is '%s'\n", dsname.c_str());
mprintf("\tData set aspect [avg] holds the mean, aspect [sd] holds standard deviation.\n");
mprintf("\tBin coordinates will be to bin %s.\n", binStr[binType_]);
} else {
mprintf(" No masks specified, calculating total system density in g/cm^3.\n");
mprintf("\tData set name is '%s'\n", density_->legend());
}
if (outfile != 0)
mprintf("\tOutput to '%s'\n", outfile->DataFilename().full());
return Action::OK;
}
