Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionargs,
DataSet_Coords* CRD, Action* act,
TrajFrameCounter const& frameCount) const
{
Timer total_time;
total_time.Start();
# ifdef MPI
ActionInit state(State.DSL(), State.DFL(), trajComm_);
# else
ActionInit state(State.DSL(), State.DFL());
# endif
if ( act->Init( actionargs, state, State.Debug() ) != Action::OK )
return CpptrajState::ERR;
actionargs.CheckForMoreArgs();
// Set up frame and parm for COORDS.
ActionSetup originalSetup( CRD->TopPtr(), CRD->CoordsInfo(), CRD->Size() );
Frame originalFrame = CRD->AllocateFrame();
ActionFrame frm( &originalFrame, 0 );
// Set up for this topology
Action::RetType setup_ret = act->Setup( originalSetup );
if ( setup_ret == Action::ERR || setup_ret == Action::SKIP )
return CpptrajState::ERR;
// Loop over all frames in COORDS.
ProgressBar progress( frameCount.TotalReadFrames() );
int set = 0;
for (int frame = frameCount.Start(); frame < frameCount.Stop();
frame += frameCount.Offset(), ++set)
{
progress.Update( set );
CRD->GetFrame( frame, originalFrame );
frm.SetTrajoutNum( set );
Action::RetType ret = act->DoAction( set, frm );
if (ret == Action::ERR) {
mprinterr("Error: crdaction: Frame %i, set %i\n", frame + 1, set + 1);
break;
}
// Check if frame was modified. If so, update COORDS.
if ( ret == Action::MODIFY_COORDS )
CRD->SetCRD( frame, frm.Frm() );
}
# ifdef MPI
act->SyncAction();
# endif
// Check if parm was modified. If so, update COORDS.
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
mprintf("Info: crdaction: Parm for %s was modified by action %s\n",
CRD->legend(), actionargs.Command());
CRD->CoordsSetup( originalSetup.Top(), originalSetup.CoordInfo() );
}
act->Print();
State.MasterDataFileWrite();
total_time.Stop();
mprintf("TIME: Total action execution time: %.4f seconds.\n", total_time.Total());
return CpptrajState::OK;
}
Exec::RetType Exec_Precision::Execute(CpptrajState& State, ArgList& argIn) {
// Next string is DataSet(s)/DataFile that command pertains to.
std::string name1 = argIn.GetStringNext();
if (name1.empty()) {
mprinterr("Error: No filename/setname given.\n");
return CpptrajState::ERR;
}
// This will break if dataset name starts with a digit...
int width = argIn.getNextInteger(12);
if (width < 1) {
mprintf("Error: Cannot set width < 1 (%i).\n", width);
return CpptrajState::ERR;
}
int precision = argIn.getNextInteger(4);
if (precision < 0) precision = 0;
DataFile* df = State.DFL().GetDataFile(name1);
if (df != 0) {
mprintf("\tSetting precision for all sets in %s to %i.%i\n", df->DataFilename().base(),
width, precision);
df->SetDataFilePrecision(width, precision);
} else {
State.DSL().SetPrecisionOfDataSets( name1, width, precision );
}
return CpptrajState::OK;
}
Exec::RetType Exec_DataFilter::Execute(CpptrajState& State, ArgList& argIn) {
Action_FilterByData filterAction;
ActionInit state(State.DSL(), State.DFL());
if (filterAction.Init(argIn, state, State.Debug()) != Action::OK)
return CpptrajState::ERR;
size_t nframes = filterAction.DetermineFrames();
if (nframes < 1) {
mprinterr("Error: No data to filter. All sets must contain some data.\n");
return CpptrajState::ERR;
}
ProgressBar progress( nframes );
ActionFrame frm;
for (size_t frame = 0; frame != nframes; frame++) {
progress.Update( frame );
filterAction.DoAction(frame, frm); // Filter does not need frame.
}
// Trigger master datafile write just in case
State.MasterDataFileWrite();
return CpptrajState::OK;
}
Exec::RetType Exec_ReadData::Execute(CpptrajState& State, ArgList& argIn) {
DataFile dataIn;
dataIn.SetDebug( State.DFL().Debug() );
std::string filenameIn = argIn.GetStringNext();
File::NameArray fnames = File::ExpandToFilenames( filenameIn );
if (fnames.empty()) {
mprinterr("Error: '%s' matches no files.\n", filenameIn.c_str());
return CpptrajState::ERR;
}
int err = 0;
int idx = -1;
bool useIndex = argIn.hasKey("separate");
for (File::NameArray::const_iterator fn = fnames.begin(); fn != fnames.end(); ++fn) {
if (useIndex) idx++;
if (dataIn.ReadDataIn( *fn, argIn, State.DSL(), idx, fnames.size() )!=0) {
mprinterr("Error: Could not read data file '%s'.\n", fn->full());
err++;
}
}
if (err > 0) return CpptrajState::ERR;
return CpptrajState::OK;
}
Exec::RetType Exec_CrdAction::DoCrdAction(CpptrajState& State, ArgList& actionargs,
DataSet_Coords* CRD, Action* act,
TrajFrameCounter const& frameCount) const
{
Timer total_time;
total_time.Start();
# ifdef MPI
ActionInit state(State.DSL(), State.DFL(), trajComm_);
# else
ActionInit state(State.DSL(), State.DFL());
# endif
if ( act->Init( actionargs, state, State.Debug() ) != Action::OK )
return CpptrajState::ERR;
actionargs.CheckForMoreArgs();
// Set up frame and parm for COORDS.
ActionSetup originalSetup( CRD->TopPtr(), CRD->CoordsInfo(), CRD->Size() );
Frame originalFrame = CRD->AllocateFrame();
// Set up for this topology
Action::RetType setup_ret = act->Setup( originalSetup );
if ( setup_ret == Action::ERR || setup_ret == Action::SKIP )
return CpptrajState::ERR;
// If the topology was modified, we will need a new COORDS set.
DataSet_Coords* crdOut = 0;
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
// This will not work for a TRJ set.
switch ( CRD->Type() ) {
case DataSet::TRAJ : mprinterr("Error: Cannot modify TRAJ data sets.\n"); break;
case DataSet::COORDS : crdOut = (DataSet_Coords*)new DataSet_Coords_CRD(); break;
case DataSet::REF_FRAME : crdOut = (DataSet_Coords*)new DataSet_Coords_REF(); break;
default: crdOut = 0; // SANITY
}
if (crdOut == 0) return CpptrajState::ERR;
mprintf("Info: crdaction: COORDS set '%s' will be modified by action '%s'\n",
CRD->legend(), actionargs.Command());
if (frameCount.TotalReadFrames() != (int)CRD->Size())
mprintf("Info: crdaction: Previous size= %zu, new size is %i\n",
CRD->Size(), frameCount.TotalReadFrames());
// Set up set, copy original metadata
crdOut->SetMeta( CRD->Meta() );
if (crdOut->CoordsSetup( originalSetup.Top(), originalSetup.CoordInfo() ))
return CpptrajState::ERR;
DataSet::SizeArray mfArray(1, frameCount.TotalReadFrames());
if (crdOut->Allocate( mfArray )) return CpptrajState::ERR;
}
// Loop over all frames in COORDS.
ProgressBar* progress = 0;
if (State.ShowProgress())
progress = new ProgressBar( frameCount.TotalReadFrames() );
int set = 0;
for (int frame = frameCount.Start(); frame < frameCount.Stop();
frame += frameCount.Offset(), ++set)
{
// Since Frame can be modified by actions, save original and use currentFrame
ActionFrame frm( &originalFrame, set );
if (progress != 0) progress->Update( set );
CRD->GetFrame( frame, originalFrame );
Action::RetType ret = act->DoAction( set, frm );
if (ret == Action::ERR) {
mprinterr("Error: crdaction: Frame %i, set %i\n", frame + 1, set + 1);
break;
}
// Check if frame was modified. If so, update COORDS.
if ( ret == Action::MODIFY_COORDS ) {
if (crdOut != 0)
crdOut->AddFrame( frm.Frm() );
else
CRD->SetCRD( frame, frm.Frm() );
}
}
if (progress != 0) delete progress;
# ifdef MPI
act->SyncAction();
# endif
// If topology was modified, replace old set with new.
if ( setup_ret == Action::MODIFY_TOPOLOGY ) {
mprintf("Info: crdaction: Topology for '%s' was modified by action '%s'\n",
CRD->legend(), actionargs.Command());
State.DSL().RemoveSet( CRD );
State.DSL().AddSet( crdOut );
}
act->Print();
State.MasterDataFileWrite();
total_time.Stop();
mprintf("TIME: Total action execution time: %.4f seconds.\n", total_time.Total());
return CpptrajState::OK;
}
// Exec_PermuteDihedrals::Execute()
Exec::RetType Exec_PermuteDihedrals::Execute(CpptrajState& State, ArgList& argIn) {
debug_ = State.Debug();
mode_ = INTERVAL;
// Get Keywords - first determine mode
if (argIn.hasKey("random"))
mode_ = RANDOM;
else if (argIn.hasKey("interval"))
mode_ = INTERVAL;
// Get input COORDS set
std::string setname = argIn.GetStringKey("crdset");
if (setname.empty()) {
mprinterr("Error: Specify COORDS dataset name with 'crdset'.\n");
return CpptrajState::ERR;
}
DataSet_Coords* CRD = (DataSet_Coords*)State.DSL().FindCoordsSet( setname );
if (CRD == 0) {
mprinterr("Error: Could not find COORDS set '%s'\n", setname.c_str());
return CpptrajState::ERR;
}
mprintf(" PERMUTEDIHEDRALS: Using COORDS '%s'\n", CRD->legend());
// Get residue range
Range resRange;
resRange.SetRange(argIn.GetStringKey("resrange"));
if (!resRange.Empty())
resRange.ShiftBy(-1); // User res args start from 1
mprintf("\tPermutating dihedrals in");
if (resRange.Empty())
mprintf(" all solute residues.\n");
else
mprintf(" residue range [%s]\n", resRange.RangeArg());
// Determine which angles to search for
DihedralSearch dihSearch;
dihSearch.SearchForArgs(argIn);
// If nothing is enabled, enable all
dihSearch.SearchForAll();
mprintf("\tSearching for types:");
dihSearch.PrintTypes();
mprintf("\n");
// Setup output trajectory
outframe_ = 0;
std::string outfilename = argIn.GetStringKey("outtraj");
if (!outfilename.empty()) {
mprintf("\tCoordinates output to '%s'\n", outfilename.c_str());
Topology* outtop = State.DSL().GetTopology( argIn );
if (outtop == 0) {
mprinterr("Error: No topology for output traj.\n");
return CpptrajState::ERR;
}
// Setup output trajectory FIXME: Correct frames for # of rotations
if (outtraj_.PrepareTrajWrite(outfilename, argIn, CRD->TopPtr(), CRD->CoordsInfo(),
CRD->Size(), TrajectoryFile::UNKNOWN_TRAJ))
return CpptrajState::ERR;
}
// Setup output coords
outfilename = argIn.GetStringKey("crdout");
if (!outfilename.empty()) {
mprintf("\tCoordinates saved to set '%s'\n", outfilename.c_str());
crdout_ = (DataSet_Coords_CRD*)State.DSL().AddSet(DataSet::COORDS, outfilename);
if (crdout_ == 0) return CpptrajState::ERR;
crdout_->CoordsSetup( CRD->Top(), CRD->CoordsInfo() );
}
// Get specific mode options.
double interval_in_deg = 60.0;
if ( mode_ == INTERVAL ) {
interval_in_deg = argIn.getNextDouble(60.0);
mprintf("\tDihedrals will be rotated at intervals of %.2f degrees.\n", interval_in_deg);
} else if (mode_ == RANDOM) {
check_for_clashes_ = argIn.hasKey("check");
checkAllResidues_ = argIn.hasKey("checkallresidues");
cutoff_ = argIn.getKeyDouble("cutoff",0.8);
rescutoff_ = argIn.getKeyDouble("rescutoff",10.0);
backtrack_ = argIn.getKeyInt("backtrack",4);
increment_ = argIn.getKeyInt("increment",1);
max_factor_ = argIn.getKeyInt("maxfactor",2);
int iseed = argIn.getKeyInt("rseed",-1);
// Output file for # of problems
DataFile* problemFile = State.DFL().AddDataFile(argIn.GetStringKey("out"), argIn);
// Dataset to store number of problems
number_of_problems_ = State.DSL().AddSet(DataSet::INTEGER, argIn.GetStringNext(),"Nprob");
if (number_of_problems_==0) return CpptrajState::ERR;
// Add dataset to data file list
if (problemFile != 0) problemFile->AddDataSet(number_of_problems_);
// Check validity of args
if (cutoff_ < Constants::SMALL) {
mprinterr("Error: cutoff too small.\n");
return CpptrajState::ERR;
}
if (rescutoff_ < Constants::SMALL) {
mprinterr("Error: rescutoff too small.\n");
return CpptrajState::ERR;
}
if (backtrack_ < 0) {
mprinterr("Error: backtrack value must be >= 0\n");
return CpptrajState::ERR;
}
if ( increment_<1 || (360 % increment_)!=0 ) {
mprinterr("Error: increment must be a factor of 360.\n");
return CpptrajState::ERR;
}
// Calculate max increment
max_increment_ = 360 / increment_;
// Seed random number gen
RN_.rn_set( iseed );
// Print info
mprintf("\tDihedrals will be rotated to random values.\n");
if (iseed==-1)
mprintf("\tRandom number generator will be seeded using time.\n");
else
mprintf("\tRandom number generator will be seeded using %i\n",iseed);
if (check_for_clashes_) {
mprintf("\tWill attempt to recover from bad steric clashes.\n");
if (checkAllResidues_)
mprintf("\tAll residues will be checked.\n");
else
mprintf("\tResidues up to the currenly rotating dihedral will be checked.\n");
mprintf("\tAtom cutoff %.2f, residue cutoff %.2f, backtrack = %i\n",
cutoff_, rescutoff_, backtrack_);
mprintf("\tWhen clashes occur dihedral will be incremented by %i\n",increment_);
mprintf("\tMax # attempted rotations = %i times number dihedrals.\n",
max_factor_);
}
// Square cutoffs to compare to dist^2 instead of dist
cutoff_ *= cutoff_;
rescutoff_ *= rescutoff_;
// Increment backtrack by 1 since we need to skip over current res
++backtrack_;
// Initialize CheckStructure
if (checkStructure_.SetOptions( false, false, false, State.Debug(), "*", "", 0.8, 1.15, 4.0 )) {
mprinterr("Error: Could not set up structure check.\n");
return CpptrajState::ERR;
}
// Set up CheckStructure for this parm (false = nobondcheck)
if (checkStructure_.Setup(CRD->Top(), CRD->CoordsInfo().TrajBox()))
return CpptrajState::ERR;
}
// Determine from selected mask atoms which dihedrals will be rotated.
PermuteDihedralsType dst;
// If range is empty (i.e. no resrange arg given) look through all
// solute residues.
Range actualRange;
if (resRange.Empty())
actualRange = CRD->Top().SoluteResidues();
else
actualRange = resRange;
// Search for dihedrals
if (dihSearch.FindDihedrals(CRD->Top(), actualRange))
return CpptrajState::ERR;
// For each found dihedral, set up mask of atoms that will move upon
// rotation. Also set up mask of atoms in this residue that will not
// move, including atom2.
if (debug_>0)
mprintf("DEBUG: Dihedrals:\n");
for (DihedralSearch::mask_it dih = dihSearch.begin();
dih != dihSearch.end(); ++dih)
{
dst.checkAtoms.clear();
// Set mask of atoms that will move during dihedral rotation.
dst.Rmask = DihedralSearch::MovingAtoms(CRD->Top(), dih->A1(), dih->A2());
// If randomly rotating angles, check for atoms that are in the same
// residue as A1 but will not move. They need to be checked for clashes
// since further rotations will not help them.
if (mode_ == RANDOM && check_for_clashes_) {
CharMask cMask( dst.Rmask.ConvertToCharMask(), dst.Rmask.Nselected() );
int a1res = CRD->Top()[dih->A1()].ResNum();
for (int maskatom = CRD->Top().Res(a1res).FirstAtom();
maskatom < CRD->Top().Res(a1res).LastAtom(); ++maskatom)
if (!cMask.AtomInCharMask(maskatom))
dst.checkAtoms.push_back( maskatom );
dst.checkAtoms.push_back(dih->A1()); // TODO: Does this need to be added first?
// Since only the second atom and atoms it is bonded to move during
// rotation, base the check on the residue of the second atom.
dst.resnum = a1res;
}
dst.atom0 = dih->A0(); // FIXME: This duplicates info
dst.atom1 = dih->A1();
dst.atom2 = dih->A2();
dst.atom3 = dih->A3();
BB_dihedrals_.push_back(dst);
// DEBUG: List dihedral info.
if (debug_ > 0) {
mprintf("\t%s-%s-%s-%s\n",
CRD->Top().TruncResAtomName(dih->A0()).c_str(),
CRD->Top().TruncResAtomName(dih->A1()).c_str(),
CRD->Top().TruncResAtomName(dih->A2()).c_str(),
CRD->Top().TruncResAtomName(dih->A3()).c_str() );
if (debug_ > 1 && mode_ == RANDOM && check_for_clashes_) {
mprintf("\t\tCheckAtoms=");
for (std::vector<int>::const_iterator ca = dst.checkAtoms.begin();
ca != dst.checkAtoms.end(); ++ca)
mprintf(" %i", *ca + 1);
mprintf("\n");
}
if (debug_ > 2) {
mprintf("\t\t");
dst.Rmask.PrintMaskAtoms("Rmask:");
}
}
}
// Set up simple structure check. First step is coarse; check distances
// between a certain atom in each residue (first, COM, CA, some other atom?)
// to see if residues are in each others neighborhood. Second step is to
// check the atoms in each close residue.
if (check_for_clashes_) {
ResidueCheckType rct;
int res = 0;
for (Topology::res_iterator residue = CRD->Top().ResStart();
residue != CRD->Top().ResEnd(); ++residue)
{
rct.resnum = res++;
rct.start = residue->FirstAtom();
rct.stop = residue->LastAtom();
rct.checkatom = rct.start;
ResCheck_.push_back(rct);
}
}
// Perform dihedral permute
Frame currentFrame = CRD->AllocateFrame();
for (unsigned int set = 0; set != CRD->Size(); set++)
{
CRD->GetFrame(set, currentFrame);
int n_problems = 0;
switch (mode_) {
case RANDOM:
RandomizeAngles(currentFrame, CRD->Top());
// Check the resulting structure
n_problems = checkStructure_.CheckOverlaps( currentFrame );
//mprintf("%i\tResulting structure has %i problems.\n",frameNum,n_problems);
number_of_problems_->Add(set, &n_problems);
if (outtraj_.IsInitialized()) outtraj_.WriteSingle(outframe_++, currentFrame);
if (crdout_ != 0) crdout_->AddFrame( currentFrame );
break;
case INTERVAL: IntervalAngles(currentFrame, CRD->Top(), interval_in_deg); break;
}
}
if (outtraj_.IsInitialized()) outtraj_.EndTraj();
return CpptrajState::OK;
}
// Exec_ParallelAnalysis::Execute()
Exec::RetType Exec_ParallelAnalysis::Execute(CpptrajState& State, ArgList& argIn)
{
Timer t_total;
t_total.Start();
Timer t_sync;
bool syncToMaster = argIn.hasKey("sync");
std::vector<unsigned int> setSizesBefore;
if (syncToMaster) {
t_sync.Start();
setSizesBefore.reserve( State.DSL().size() );
for (DataSetList::const_iterator it = State.DSL().begin(); it != State.DSL().end(); ++it)
setSizesBefore.push_back( (*it)->Size() );
t_sync.Stop();
}
// DEBUG - Have each thread report what analyses it knows about and what
// data sets it has.
/*
for (int rank = 0; rank < Parallel::World().Size(); rank++) {
if (rank == Parallel::World().Rank()) {
printf("Rank %i, %u analyses, %zu data sets:\n", rank, State.Analyses().size(),
State.DSL().size());
for (DataSetList::const_iterator it = State.DSL().begin(); it != State.DSL().end(); ++it)
printf("\t'%s' (%zu)\n", (*it)->Meta().PrintName().c_str(), (*it)->Size());
}
Parallel::World().Barrier();
}
Parallel::World().Barrier();
*/
mprintf(" PARALLELANALYSIS: Will attempt to run current Analyses in parallel.\n\n"
"*** THIS COMMAND IS STILL EXPERIMENTAL! ***\n\n");
if (syncToMaster)
mprintf("\tResulting data sets will be synced back to master.\n");
// Naively divide up all analyses among threads.
int my_start, my_stop;
int nelts = Parallel::World().DivideAmongProcesses( my_start, my_stop, State.Analyses().size() );
rprintf("Dividing %zu analyses among %i threads: %i to %i (%i)\n",
State.Analyses().size(), Parallel::World().Size(), my_start, my_stop, nelts);
// Each thread runs the analyses they are responsible for.
int nerr = 0;
for (int na = my_start; na != my_stop; na++) {
// TODO check setup status
if (State.Analyses().Ana(na).Analyze() != Analysis::OK) {
rprinterr("Error: Analysis failed: '%s'\n", State.Analyses().Args(na).ArgLine());
nerr++;
}
}
// This error check serves as a barrier
if (Parallel::World().CheckError( nerr )) return CpptrajState::ERR;
State.DFL().AllThreads_WriteAllDF();
State.Analyses().Clear();
if (syncToMaster) {
t_sync.Start();
// Check which sizes have changed.
if (setSizesBefore.size() != State.DSL().size()) {
mprintf("Warning: Number of sets have changed. Not attempting to sync sets to master.\n");
} else {
for (unsigned int idx = 0; idx != State.DSL().size(); idx++) {
int setHasChanged = 0;
if (!Parallel::World().Master()) {
if (setSizesBefore[idx] != State.DSL()[idx]->Size()) {
if (State.Debug() > 0)
rprintf("Set '%s' size has changed from %u to %zu\n",
State.DSL()[idx]->legend(), setSizesBefore[idx], State.DSL()[idx]->Size());
setHasChanged = 1;
}
}
int totalChanged;
Parallel::World().AllReduce(&totalChanged, &setHasChanged, 1, MPI_INT, MPI_SUM);
if (totalChanged > 0) {
if (totalChanged == 1) {
int sourceRank = 0;
if (setHasChanged == 1)
setHasChanged = Parallel::World().Rank();
Parallel::World().ReduceMaster(&sourceRank, &setHasChanged, 1, MPI_INT, MPI_SUM);
if (State.Debug() > 0)
mprintf("DEBUG: Need to sync '%s' from %i\n", State.DSL()[idx]->legend(), sourceRank);
if (Parallel::World().Master())
State.DSL()[idx]->RecvSet( sourceRank, Parallel::World() );
else if (setHasChanged == Parallel::World().Rank())
State.DSL()[idx]->SendSet( 0, Parallel::World() );
} else
mprintf("Warning: '%s' exists on multiple threads. Not syncing.\n",
State.DSL()[idx]->legend());
}
}
}
t_sync.Stop();
}
t_total.Stop();
if (syncToMaster)
t_sync.WriteTiming(2, "Sync:", t_total.Total());
t_total.WriteTiming(1, "Total:");
return CpptrajState::OK;
}
/** Syntax: dataset invert <set arg0> ... name <new name> */
Exec::RetType Exec_DataSetCmd::InvertSets(CpptrajState& State, ArgList& argIn) {
DataSetList& DSL = State.DSL();
// Get keywords
DataSet* inputNames = 0;
std::string dsname = argIn.GetStringKey("legendset");
if (!dsname.empty()) {
inputNames = DSL.GetDataSet( dsname );
if (inputNames == 0) {
mprinterr("Error: Name set '%s' not found.\n", dsname.c_str());
return CpptrajState::ERR;
}
if (inputNames->Type() != DataSet::STRING) {
mprinterr("Error: Set '%s' does not contain strings.\n", inputNames->legend());
return CpptrajState::ERR;
}
mprintf("\tUsing names from set '%s' as legends for inverted sets.\n", inputNames->legend());
}
dsname = argIn.GetStringKey("name");
if (dsname.empty()) {
mprinterr("Error: 'invert' requires that 'name <new set name>' be specified.\n");
return CpptrajState::ERR;
}
mprintf("\tNew sets will be named '%s'\n", dsname.c_str());
DataFile* outfile = State.DFL().AddDataFile( argIn.GetStringKey("out"), argIn );
if (outfile != 0)
mprintf("\tNew sets will be output to '%s'\n", outfile->DataFilename().full());
// TODO determine type some other way
DataSet::DataType outtype = DataSet::DOUBLE;
// Get input DataSets
std::vector<DataSet_1D*> input_sets;
std::string dsarg = argIn.GetStringNext();
while (!dsarg.empty()) {
DataSetList sets = DSL.GetMultipleSets( dsarg );
for (DataSetList::const_iterator ds = sets.begin(); ds != sets.end(); ++ds)
{
if ( (*ds)->Group() != DataSet::SCALAR_1D ) {
mprintf("Warning: '%s': Inversion only supported for 1D scalar data sets.\n",
(*ds)->legend());
} else {
if (!input_sets.empty()) {
if ( (*ds)->Size() != input_sets.back()->Size() ) {
mprinterr("Error: Set '%s' has different size (%zu) than previous set (%zu)\n",
(*ds)->legend(), (*ds)->Size(), input_sets.back()->Size());
return CpptrajState::ERR;
}
}
input_sets.push_back( (DataSet_1D*)*ds );
}
}
dsarg = argIn.GetStringNext();
}
if (input_sets.empty()) {
mprinterr("Error: No sets selected.\n");
return CpptrajState::ERR;
}
if (inputNames != 0 && inputNames->Size() != input_sets.front()->Size()) {
mprinterr("Error: Name set '%s' size (%zu) differs from # data points (%zu).\n",
inputNames->legend(), inputNames->Size(), input_sets.front()->Size());
return CpptrajState::ERR;
}
mprintf("\t%zu input sets; creating %zu output sets.\n",
input_sets.size(), input_sets.front()->Size());
// Need an output data set for each point in input sets
std::vector<DataSet*> output_sets;
int column = 1;
for (int idx = 0; idx != (int)input_sets[0]->Size(); idx++, column++) {
DataSet* ds = 0;
ds = DSL.AddSet(outtype, MetaData(dsname, column));
if (ds == 0) return CpptrajState::ERR;
if (inputNames != 0)
ds->SetLegend( (*((DataSet_string*)inputNames))[idx] );
output_sets.push_back( ds );
if (outfile != 0) outfile->AddDataSet( ds );
}
// Create a data set containing names of each input data set
DataSet* nameset = DSL.AddSet(DataSet::STRING, MetaData(dsname, column));
if (nameset == 0) return CpptrajState::ERR;
if (inputNames != 0)
nameset->SetLegend("Names");
if (outfile != 0) outfile->AddDataSet( nameset );
// Populate output data sets
for (int jdx = 0; jdx != (int)input_sets.size(); jdx++)
{
DataSet_1D const& INP = static_cast<DataSet_1D const&>( *(input_sets[jdx]) );
nameset->Add( jdx, INP.legend() );
for (unsigned int idx = 0; idx != INP.Size(); idx++)
{
double dval = INP.Dval( idx );
output_sets[idx]->Add( jdx, &dval );
}
}
return CpptrajState::OK;
}