// Action_MultiVector::Setup();
Action::RetType Action_MultiVector::Setup(Topology* currentParm, Topology** parmAddress) {
Range actualRange;
// If range is empty (i.e. no resrange arg given) look through all
// solute residues.
if (resRange_.Empty())
actualRange = currentParm->SoluteResidues();
else {
// If user range specified, create new range shifted by -1 since internal
// resnums start from 0.
actualRange = resRange_;
actualRange.ShiftBy(-1);
}
// Exit if no residues specified
if (actualRange.Empty()) {
mprinterr("Error: No residues specified for %s\n",currentParm->c_str());
return Action::ERR;
}
// Set default DataSet name if not specified.
if (dsetname_.empty())
dsetname_ = masterDSL_->GenerateDefaultName( "MVEC" );
// Search for specified atom names in each residue in the range
CrdIdx1_.clear();
CrdIdx2_.clear();
for (Range::const_iterator res = actualRange.begin(); res != actualRange.end(); ++res)
{
int atom1 = currentParm->FindAtomInResidue( *res, name1_ );
int atom2 = currentParm->FindAtomInResidue( *res, name2_ );
if (atom1 != -1 && atom2 != -1) {
MetaData md(dsetname_, atom1+1);
md.SetScalarMode( MetaData::M_VECTOR );
if (ired_) md.SetScalarType( MetaData::IREDVEC );
DataSet_Vector* ds = (DataSet_Vector*)masterDSL_->CheckForSet( md );
if (ds == 0) {
// Create DataSet
ds = (DataSet_Vector*)masterDSL_->AddSet( DataSet::VECTOR, md );
if (ds == 0) return Action::ERR;
ds->SetLegend( "v" + currentParm->AtomMaskName(atom1) + "->" +
currentParm->AtomMaskName(atom2) );
if (outfile_ != 0) outfile_->AddDataSet( ds );
}
data_.push_back( ds );
CrdIdx1_.push_back( atom1 * 3 ); // Pre calc coordinate index
CrdIdx2_.push_back( atom2 * 3 );
} else if ((atom1==-1) != (atom2==-1)) {
if (atom1==-1)
mprintf("Warning: '%s' not found but '%s' found for residue %i.\n",
*name1_, *name2_, *res + 1);
else // atom2==-1
mprintf("Warning: '%s' not found but '%s' found for residue %i.\n",
*name2_, *name1_, *res + 1);
}
}
mprintf("\tSelected %zu vectors.\n", CrdIdx1_.size());
for (std::vector<DataSet_Vector*>::const_iterator it = data_.begin();
it != data_.end(); ++it)
mprintf("\t %s\n", (*it)->legend());
return Action::OK;
}
// Action_MultiDihedral::Setup();
Action::RetType Action_MultiDihedral::Setup(Topology* currentParm, Topology** parmAddress) {
Range actualRange;
// If range is empty (i.e. no resrange arg given) look through all
// solute residues.
if (resRange_.Empty())
actualRange.SetRange(0, currentParm->FinalSoluteRes());
else {
// If user range specified, create new range shifted by -1 since internal
// resnums start from 0.
actualRange = resRange_;
actualRange.ShiftBy(-1);
}
// Exit if no residues specified
if (actualRange.Empty()) {
mprinterr("Error: multidihedral: No residues specified for %s\n",currentParm->c_str());
return Action::ERR;
}
// Search for specified dihedrals in each residue in the range
if (dihSearch_.FindDihedrals(*currentParm, actualRange))
return Action::ERR;
mprintf("\tResRange=[%s]", resRange_.RangeArg());
dihSearch_.PrintTypes();
mprintf(", %i dihedrals.\n", dihSearch_.Ndihedrals());
// Print selected dihedrals, set up DataSets
data_.clear();
if (dsetname_.empty())
dsetname_ = masterDSL_->GenerateDefaultName("MDIH");
for (DihedralSearch::mask_it dih = dihSearch_.begin();
dih != dihSearch_.end(); ++dih)
{
int resNum = (*dih).ResNum() + 1;
// See if Dataset already present
DataSet* ds = masterDSL_->GetSet(dsetname_, resNum, (*dih).Name());
if (ds == 0) {
// Create new DataSet
ds = masterDSL_->AddSetIdxAspect( DataSet::DOUBLE, dsetname_, resNum, (*dih).Name());
// Add to outfile
if (outfile_ != 0)
outfile_->AddSet( ds );
}
// TODO: SetScalar
if (ds != 0)
data_.push_back( ds );
if (debug_ > 0) {
mprintf("\tDIH [%s]:", ds->Legend().c_str());
mprintf(" :%i@%i", (*currentParm)[(*dih).A0()].ResNum()+1, (*dih).A0() + 1);
mprintf(" :%i@%i", (*currentParm)[(*dih).A1()].ResNum()+1, (*dih).A1() + 1);
mprintf(" :%i@%i", (*currentParm)[(*dih).A2()].ResNum()+1, (*dih).A2() + 1);
mprintf(" :%i@%i\n", (*currentParm)[(*dih).A3()].ResNum()+1, (*dih).A3() + 1);
}
}
return Action::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;
}
void dirSeedsReg2::dirSweep(Datareg2& reg2)
{
u_int i, j;
Range resp;
float min, max, t;
float gradx;
float grad1ya, grad1yb;
float grad2ya, grad2yb;
int keepflat;
int prev;
for(i=0; i<reg2.dim[0]-1; i++)
{
keepflat = 1;
prev = -1;
for(j=0; j<reg2.dim[1]-1; j++)
{
resp.MakeEmpty();
// test responsiblity for each face
// left
if(i == 0)
{
min = max = reg2.getValue(reg2.index2vert(i,j));
if((t=reg2.getValue(reg2.index2vert(i,j+1))) < min)
{
min = t;
}
if(t > max)
{
max = t;
}
if(min != max)
{
resp += Range(min,max);
}
}
else
{
// never do anything other than on boundary
}
// right
if(i == reg2.dim[0]-2)
{
// never keep a right boundary seed
}
else
{
// never keep a right boundary seed
}
// general case: bottom edge in middle
// cell (i,j) and (i,j-1) share this x-grad
gradx = reg2.getValue(reg2.index2vert(i+1,j)) -
reg2.getValue(reg2.index2vert(i,j));
// compute y-grad at (i,j) and (i+1,j)
grad1ya = reg2.getValue(reg2.index2vert(i,j+1)) -
reg2.getValue(reg2.index2vert(i,j));
grad1yb = reg2.getValue(reg2.index2vert(i+1,j+1)) -
reg2.getValue(reg2.index2vert(i+1,j));
if(keepflat)
{
// check to see if gradient has 'turned'
// only a seed if gradx & grady disagree in sign
// note that 0 gradient is not considered opposite
if(sgn(grad1ya) == 0 && sgn(grad1yb) == 0)
{
// flat cell (in y dim) - continue
}
else if(sgn(gradx) == -sgn(grad1ya) || sgn(gradx) == -sgn(grad1yb))
{
// extreme occurs if y components oppose each other
// note that 0 gradient is not considered opposite
min = max = reg2.getValue(reg2.index2vert(i,j));
if((t=reg2.getValue(reg2.index2vert(i+1,j))) < min)
{
min = t;
}
if(t > max)
{
max = t;
}
resp += Range(min,max);
keepflat = 0;
}
}
// top
if(j == reg2.dim[1]-2)
{
if(keepflat)
{
min = max = reg2.getValue(reg2.index2vert(i,j+1));
if((t=reg2.getValue(reg2.index2vert(i+1,j+1))) < min)
{
min = t;
}
if(t > max)
{
max = t;
}
resp += Range(min,max);
}
}
else
{
// only consider the top at the boundary
if(!keepflat)
{
gradx = reg2.getValue(reg2.index2vert(i+1,j+1)) -
reg2.getValue(reg2.index2vert(i,j+1));
grad2ya = reg2.getValue(reg2.index2vert(i,j+1)) -
reg2.getValue(reg2.index2vert(i,j));
grad2yb = reg2.getValue(reg2.index2vert(i+1,j+1)) -
reg2.getValue(reg2.index2vert(i+1,j));
if(sgn(gradx) != 0 && (sgn(gradx) == sgn(grad2ya) || sgn(gradx) == sgn(grad2yb)))
{
keepflat=1;
}
}
else
{
gradx = reg2.getValue(reg2.index2vert(i+1,j+1)) -
reg2.getValue(reg2.index2vert(i,j+1));
grad2ya = reg2.getValue(reg2.index2vert(i,j+1)) -
reg2.getValue(reg2.index2vert(i,j));
grad2yb = reg2.getValue(reg2.index2vert(i+1,j+1)) -
reg2.getValue(reg2.index2vert(i+1,j));
if(sgn(gradx) == -sgn(grad2ya) || sgn(gradx) == -sgn(grad2yb))
{
keepflat=0;
}
}
}
if(!resp.Empty())
{
if(prev == -1)
{
if(i!=0)
prev = seeds.AddSeed(reg2.index2cell(i,j), resp.MinAll(),
resp.MaxAll());
else
seeds.AddSeed(reg2.index2cell(i,j), resp.MinAll(),
resp.MaxAll());
}
else
{
seeds.AddToRange(prev, resp.MinAll(), resp.MaxAll());
prev = -1;
}
}
else
{
prev = -1;
}
}
}
}
// Preprocess() - build a segment tree for O(log n) queries
void regProp2::compSeeds(void)
{
Datareg2& reg2 = (Datareg2&)data;
int i, j;
int xdim, ydim;
float val[4];
Range* _prop_x, *prop_x;
Range prop_y;
Range propagated;
Range c_prop;
Range responsibility, c_respons;
Range delay;
Range y_comp;
float min_x, min_y, max_x, max_y;
float min_in, max_in, min4, max4;
int nseed;
xdim = reg2.dim[0];
ydim = reg2.dim[1];
_prop_x = new Range[ydim];
// proceed through the slices computing seeds
nseed=0;
// process the k'th slab
for(i=0; i<xdim-1; i++)
for(j=0; j<ydim-1; j++)
{
prop_x = &_prop_x[j];
// load the voxel data
reg2.getCellValues(i, j, val);
min_x = MIN2(val[0], val[3]);
max_x = MAX2(val[0], val[3]);
min_y = MIN2(val[0], val[1]);
max_y = MAX2(val[0], val[1]);
// set the incoming values if on a border
if(i==0)
{
prop_x->Set(min_x, max_x);
}
if(j==0)
{
prop_y.Set(min_y, max_y);
}
// merge incoming information
y_comp = prop_y.Complement(min_y, max_y);
propagated = prop_y + ((*prop_x)-y_comp);
// compute complement of incoming ranges
min_in = MIN2(min_x, min_y);
max_in = MAX2(max_x, max_y);
c_prop.Set(min_in,max_in);
c_prop -= propagated;
// compute responsibility ranges
min4 = MIN2(min_in, val[2]);
max4 = MAX2(max_in, val[2]);
responsibility.Set(min4, max4);
responsibility-=c_prop;
c_respons = responsibility.Complement(min4, max4);
// determine range which can be delayed
delay.MakeEmpty();
if(i < xdim-2)
delay+=Range(MIN2(val[1], val[2]),
MAX2(val[1], val[2]));
if(j < ydim-2)
delay+=Range(MIN2(val[2], val[3]),
MAX2(val[2], val[3]));
// test for propagation of entire responsibility range
if(responsibility.Empty() || (!delay.Empty() &&
delay.MinAll() <= responsibility.MinAll() &&
delay.MaxAll() >= responsibility.MaxAll()))
{
// propagate first to the next x-slice
if(i == xdim-2)
{
prop_x->MakeEmpty();
}
else
{
prop_x->Set(MIN2(val[1], val[2]), MAX2(val[1], val[2]));
*prop_x-=c_respons;
}
c_respons += *prop_x;
// all remaining propagated in y-dir
if(j == ydim-2)
{
prop_y.MakeEmpty();
}
else
{
prop_y.Set(MIN2(val[2], val[3]), MAX2(val[2], val[3]));
prop_y-= c_respons;
}
}
else
{
// can't propagate all responsiblity, cell must be a seed
seeds.AddSeed(reg2.index2cell(i,j), responsibility.MinAll(),
responsibility.MaxAll());
nseed++;
prop_y.MakeEmpty();
prop_x->MakeEmpty();
}
}
if(verbose)
{
printf("computed %d seeds\n", nseed);
}
}
// Exec_DataSetCmd::ModifyPoints()
Exec::RetType Exec_DataSetCmd::ModifyPoints(CpptrajState& State, ArgList& argIn, bool drop) {
const char* mode;
if (drop)
mode = "Drop";
else
mode = "Kee";
// Keywords
std::string name = argIn.GetStringKey("name");
int start = argIn.getKeyInt("start", 0) - 1;
int stop = argIn.getKeyInt("stop", -1);
int offset = argIn.getKeyInt("offset", -1);
Range points;
if (start < 0 && stop < 0 && offset < 0) {
std::string rangearg = argIn.GetStringKey("range");
if (rangearg.empty()) {
mprinterr("Error: Must specify range or start/stop/offset.\n");
return CpptrajState::ERR;
}
points.SetRange( rangearg );
if (points.Empty()) {
mprinterr("Error: Range '%s' is empty.\n", rangearg.c_str());
return CpptrajState::ERR;
}
mprintf("\t%sping points in range %s\n", mode, rangearg.c_str());
// User args start from 1
points.ShiftBy(-1);
}
// Get data set to drop/keep points from
// Loop over all DataSet arguments
std::string ds_arg = argIn.GetStringNext();
while (!ds_arg.empty()) {
DataSetList dsl = State.DSL().GetMultipleSets( ds_arg );
for (DataSetList::const_iterator it = dsl.begin(); it != dsl.end(); ++it)
{
DataSet* DS = *it;
if (DS->Size() < 1) {
mprinterr("Error: Set '%s' is empty.\n", DS->legend());
return CpptrajState::ERR;
}
// Restrict to 1D sets for now TODO more types
if (DS->Group() != DataSet::SCALAR_1D) {
mprinterr("Error: Currently only works for 1D scalar data sets.\n");
return CpptrajState::ERR;
}
DataSet_1D* ds1 = (DataSet_1D*)DS;
// Output data set
DataSet* out = 0;
if (name.empty()) {
// Modifying this set. Create new temporary set.
out = State.DSL().Allocate( ds1->Type() );
if (out == 0) return CpptrajState::ERR;
*out = *ds1;
mprintf("\tOverwriting set '%s'\n", ds1->legend());
} else {
// Write to new set
MetaData md = ds1->Meta();
md.SetName( name );
out = State.DSL().AddSet(ds1->Type(), md);
if (out == 0) return CpptrajState::ERR;
mprintf("\tNew set is '%s'\n", out->Meta().PrintName().c_str());
}
out->Allocate(DataSet::SizeArray(1, ds1->Size()));
if (points.Empty()) {
// Drop by start/stop/offset. Set defaults if needed
if (start < 0) start = 0;
if (stop < 0) stop = ds1->Size();
if (offset < 0) offset = 1;
mprintf("\t%sping points from %i to %i, step %i\n", mode, start+1, stop, offset);
for (int idx = start; idx < stop; idx += offset)
points.AddToRange( idx );
} // TODO check that range values are valid?
if (State.Debug() > 0) mprintf("DEBUG: Keeping points:");
Range::const_iterator pt = points.begin();
int idx = 0;
int odx = 0;
if (drop) {
// Drop points
for (; idx < (int)ds1->Size(); idx++) {
if (pt == points.end()) break;
if (*pt != idx) {
if (State.Debug() > 0) mprintf(" %i", idx + 1);
KeepPoint(ds1, out, idx, odx);
} else
++pt;
}
// Keep all remaining points
for (; idx < (int)ds1->Size(); idx++) {
if (State.Debug() > 0) mprintf(" %i", idx + 1);
KeepPoint(ds1, out, idx, odx);
}
} else {
// Keep points
for (; pt != points.end(); pt++) {
if (*pt >= (int)ds1->Size()) break;
if (State.Debug() > 0) mprintf(" %i", *pt + 1);
KeepPoint(ds1, out, *pt, odx);
}
}
if (State.Debug() > 0) mprintf("\n");
if (name.empty()) {
// Replace old set with new set
State.DSL().RemoveSet( ds1 );
State.DSL().AddSet( out );
}
} // END loop over sets
ds_arg = argIn.GetStringNext();
} // END loop over set args
return CpptrajState::OK;
}