/** Determine what atoms each mask pertains to for the current parm file.
*/
Action::RetType Action_ReplicateCell::Setup(ActionSetup& setup) {
if (setup.Top().SetupIntegerMask( Mask1_ )) return Action::ERR;
mprintf("\t%s (%i atoms)\n",Mask1_.MaskString(), Mask1_.Nselected());
if (Mask1_.None()) {
mprintf("Warning: One or both masks have no atoms.\n");
return Action::SKIP;
}
// Set up imaging info for this parm
image_.SetupImaging( setup.CoordInfo().TrajBox().Type() );
if (!image_.ImagingEnabled()) {
mprintf("Warning: Imaging cannot be performed for topology %s\n", setup.Top().c_str());
return Action::SKIP;
}
// Create combined topology.
if (combinedTop_.Natom() > 0) {
// Topology already set up. Check that # atoms matches.
if (Mask1_.Nselected() * ncopies_ != combinedTop_.Natom()) {
mprintf("Warning: Unit cell can currently only be replicated for"
" topologies with same # atoms.\n");
return Action::SKIP;
}
// Otherwise assume top does not change.
} else {
// Set up topology and frame.
Topology* stripParm = setup.Top().modifyStateByMask( Mask1_ );
if (stripParm == 0) return Action::ERR;
for (int cell = 0; cell != ncopies_; cell++)
combinedTop_.AppendTop( *stripParm );
combinedTop_.Brief("Combined parm:");
delete stripParm;
if (!parmfilename_.empty()) {
ParmFile pfile;
if (pfile.WriteTopology(combinedTop_, parmfilename_, ParmFile::UNKNOWN_PARM, 0)) {
mprinterr("Error: Topology file %s not written.\n", parmfilename_.c_str());
return Action::ERR;
}
}
// Only coordinates for now. FIXME
combinedFrame_.SetupFrameM(combinedTop_.Atoms());
// Set up COORDS / output traj if necessary.
if (coords_ != 0)
coords_->CoordsSetup( combinedTop_, CoordinateInfo() );
if (!trajfilename_.empty()) {
if ( outtraj_.PrepareEnsembleTrajWrite(trajfilename_, trajArgs_,
&combinedTop_, CoordinateInfo(),
setup.Nframes(), TrajectoryFile::UNKNOWN_TRAJ,
ensembleNum_) )
return Action::ERR;
}
}
return Action::OK;
}
/** Process a mask from the command line. */
int Cpptraj::ProcessMask( Sarray const& topFiles, Sarray const& refFiles,
std::string const& maskexpr,
bool verbose, bool residue ) const
{
SetWorldSilent(true);
if (topFiles.empty()) {
mprinterr("Error: No topology file specified.\n");
return 1;
}
ParmFile pfile;
Topology parm;
if (pfile.ReadTopology(parm, topFiles[0], State_.Debug())) return 1;
if (!refFiles.empty()) {
DataSet_Coords_REF refCoords;
if (refCoords.LoadRefFromFile( refFiles[0], parm, State_.Debug())) return 1;
parm.SetDistMaskRef( refCoords.RefFrame() );
}
if (!verbose) {
AtomMask tempMask( maskexpr );
if (parm.SetupIntegerMask( tempMask )) return 1;
loudPrintf("Selected=");
if (residue) {
int res = -1;
for (AtomMask::const_iterator atom = tempMask.begin();
atom != tempMask.end(); ++atom)
{
if (parm[*atom].ResNum() > res) {
loudPrintf(" %i", parm[*atom].ResNum()+1);
res = parm[*atom].ResNum();
}
}
} else
for (AtomMask::const_iterator atom = tempMask.begin();
atom != tempMask.end(); ++atom)
loudPrintf(" %i", *atom + 1);
loudPrintf("\n");
} else {
if (residue)
parm.PrintResidueInfo( maskexpr );
else
parm.PrintAtomInfo( maskexpr );
}
return 0;
}
// Analysis_Hist::Analyze()
Analysis::RetType Analysis_Hist::Analyze() {
// Set up dimensions
// Size of histdata and dimensionArgs should be the same
size_t total_bins = 0UL;
for (unsigned int hd = 0; hd < N_dimensions_; hd++) {
if ( setupDimension(dimensionArgs_[hd], *(histdata_[hd]), total_bins) )
return Analysis::ERR;
}
// dimensionArgs no longer needed
dimensionArgs_.clear();
// Check that the number of data points in each dimension are equal
std::vector<DataSet_1D*>::iterator ds = histdata_.begin();
size_t Ndata = (*ds)->Size();
++ds;
for (; ds != histdata_.end(); ++ds)
{
//mprintf("DEBUG: DS %s size %i\n",histdata[hd]->Name(),histdata[hd]->Xmax()+1);
if (Ndata != (*ds)->Size()) {
mprinterr("Error: Hist: Dataset %s has inconsistent # data points (%zu), expected %zu.\n",
(*ds)->legend(), (*ds)->Size(), Ndata);
return Analysis::ERR;
}
}
mprintf("\tHist: %zu data points in each dimension.\n", Ndata);
if (calcAMD_ && Ndata != amddata_->Size()) {
mprinterr("Error: Hist: AMD data set size (%zu) does not match # expected data points (%zu).\n",
amddata_->Size(), Ndata);
return Analysis::ERR;
}
// Allocate bins
mprintf("\tHist: Allocating histogram, total bins = %zu\n", total_bins);
Bins_.resize( total_bins, 0.0 );
// Bin data
for (size_t n = 0; n < Ndata; n++) {
long int index = 0;
HdimType::const_iterator dim = dimensions_.begin();
OffType::const_iterator bOff = binOffsets_.begin();
for (std::vector<DataSet_1D*>::iterator ds = histdata_.begin();
ds != histdata_.end(); ++ds, ++dim, ++bOff)
{
double dval = (*ds)->Dval( n );
// Check if data is out of bounds for this dimension.
if (dval > dim->Max() || dval < dim->Min()) {
index = -1L;
break;
}
// Calculate index for this particular dimension (idx)
long int idx = (long int)((dval - dim->Min()) / dim->Step());
if (debug_>1) mprintf(" [%s:%f (%li)],", dim->label(), dval, idx);
// Calculate overall index in Bins, offset has already been calcd.
index += (idx * (*bOff));
}
// If index was successfully calculated, populate bin
if (index > -1L && index < (long int)Bins_.size()) {
if (debug_ > 1) mprintf(" |index=%li",index);
if (calcAMD_)
Bins_[index] += exp( amddata_->Dval(n) );
else
Bins_[index]++;
} else {
mprintf("\tWarning: Frame %zu Coordinates out of bounds (%li)\n", n+1, index);
}
if (debug_>1) mprintf("}\n");
}
// Calc free energy if requested
if (calcFreeE_) CalcFreeE();
// Normalize if requested
if (normalize_ != NO_NORM) Normalize();
if (nativeOut_) {
// Use Histogram built-in output
PrintBins();
} else {
// Using DataFileList framework, set-up labels etc.
if (N_dimensions_ == 1) {
DataSet_double& dds = static_cast<DataSet_double&>( *hist_ );
// Since Allocate1D only reserves data, use assignment op.
dds = Bins_;
hist_->SetDim(Dimension::X, dimensions_[0]);
} else if (N_dimensions_ == 2) {
DataSet_MatrixDbl& mds = static_cast<DataSet_MatrixDbl&>( *hist_ );
mds.Allocate2D( dimensions_[0].Bins(), dimensions_[1].Bins() );
std::copy( Bins_.begin(), Bins_.end(), mds.begin() );
hist_->SetDim(Dimension::X, dimensions_[0]);
hist_->SetDim(Dimension::Y, dimensions_[1]);
outfile_->ProcessArgs("noxcol usemap nolabels");
} else if (N_dimensions_ == 3) {
DataSet_GridFlt& gds = static_cast<DataSet_GridFlt&>( *hist_ );
//gds.Allocate3D( dimensions_[0].Bins(), dimensions_[1].Bins(), dimensions_[2].Bins() );
gds.Allocate_N_O_D( dimensions_[0].Bins(), dimensions_[1].Bins(), dimensions_[2].Bins(),
Vec3(dimensions_[0].Min(), dimensions_[1].Min(), dimensions_[2].Min()),
Vec3(dimensions_[0].Step(), dimensions_[1].Step(), dimensions_[2].Step())
);
//std::copy( Bins_.begin(), Bins_.end(), gds.begin() );
// FIXME: Copy will not work since in grids data is ordered with Z
// changing fastest. Should the ordering in grid be changed?
size_t idx = 0;
for (size_t z = 0; z < gds.NZ(); z++)
for (size_t y = 0; y < gds.NY(); y++)
for (size_t x = 0; x < gds.NX(); x++)
gds.SetElement( x, y, z, (float)Bins_[idx++] );
hist_->SetDim(Dimension::X, dimensions_[0]);
hist_->SetDim(Dimension::Y, dimensions_[1]);
hist_->SetDim(Dimension::Z, dimensions_[2]);
outfile_->ProcessArgs("noxcol usemap nolabels");
// Create pseudo-topology/trajectory
if (!traj3dName_.empty()) {
Topology pseudo;
pseudo.AddTopAtom(Atom("H3D", 0), Residue("H3D", 1, ' ', ' '));
pseudo.CommonSetup();
if (!parmoutName_.empty()) {
ParmFile pfile;
if (pfile.WriteTopology( pseudo, parmoutName_, ParmFile::UNKNOWN_PARM, 0 ))
mprinterr("Error: Could not write pseudo topology to '%s'\n", parmoutName_.c_str());
}
Trajout_Single out;
if (out.PrepareTrajWrite(traj3dName_, ArgList(), &pseudo, CoordinateInfo(),
Ndata, traj3dFmt_) == 0)
{
Frame outFrame(1);
for (size_t i = 0; i < Ndata; ++i) {
outFrame.ClearAtoms();
outFrame.AddVec3( Vec3(histdata_[0]->Dval(i),
histdata_[1]->Dval(i),
histdata_[2]->Dval(i)) );
out.WriteSingle(i, outFrame);
}
out.EndTraj();
} else
mprinterr("Error: Could not set up '%s' for write.\n", traj3dName_.c_str());
}
}
}
return Analysis::OK;
}
// ----- M A I N ---------------------------------------------------------------
int main(int argc, char** argv) {
SetWorldSilent(true); // No STDOUT output from cpptraj routines.
std::string topname, crdname, title, bres, pqr, sybyltype, writeconect;
std::string aatm(" pdbatom"), ter_opt(" terbyres"), box(" sg \"P 1\"");
TrajectoryFile::TrajFormatType fmt = TrajectoryFile::PDBFILE;
bool ctr_origin = false;
bool useExtendedInfo = false;
int res_offset = 0;
int debug = 0;
int numSoloArgs = 0;
for (int i = 1; i < argc; ++i) {
std::string arg( argv[i] );
if (arg == "-p" && i+1 != argc && topname.empty()) // Topology
topname = std::string( argv[++i] );
else if (arg == "-c" && i+1 != argc && crdname.empty()) // Coords
crdname = std::string( argv[++i] );
else if (arg == "-tit" && i+1 != argc && title.empty()) // Title
title = " title " + std::string( argv[++i] );
else if (arg == "-offset" && i+1 != argc) // Residue # offset
res_offset = convertToInteger( argv[++i] );
else if ((arg == "-d" || arg == "--debug") && i+1 != argc) // Debug level
debug = convertToInteger( argv[++i] );
else if (arg == "-h" || arg == "--help") { // Help
Help(argv[0], true);
return 0;
} else if (arg == "-v" || arg == "--version") { // Version info
WriteVersion();
return 0;
} else if (arg == "-aatm") // Amber atom names, include extra pts
aatm.assign(" include_ep");
else if (arg == "-sybyl") // Amber atom types to SYBYL
sybyltype.assign(" sybyltype");
else if (arg == "-conect") // Write CONECT records from bond info
writeconect.assign(" conect");
else if (arg == "-ep") // PDB atom names, include extra pts
aatm.append(" include_ep");
else if (arg == "-bres") // PDB residue names
bres.assign(" pdbres");
else if (arg == "-ext") // Use extended PDB info from Topology
useExtendedInfo = true;
else if (arg == "-ctr") // Center on origin
ctr_origin = true;
else if (arg == "-noter") // No TER cards
ter_opt.assign(" noter");
else if (arg == "-nobox") // No CRYST1 record
box.assign(" nobox");
else if (arg == "-pqr") { // Charge/Radii in occ/bfactor cols
pqr.assign(" dumpq");
++numSoloArgs;
} else if (arg == "-mol2") { // output as mol2
fmt = TrajectoryFile::MOL2FILE;
++numSoloArgs;
} else if (Unsupported(arg)) {
mprinterr("Error: Option '%s' is not yet supported.\n\n", arg.c_str());
return 1;
} else {
mprinterr("Error: Unrecognized option '%s'\n", arg.c_str());
Help(argv[0], false);
return 1;
}
}
if (debug > 0) WriteVersion();
// Check command line for errors.
if (topname.empty()) topname.assign("prmtop");
if (debug > 0 && crdname.empty())
mprinterr("| Reading Amber restart from STDIN\n");
if (numSoloArgs > 1) {
mprinterr("Error: Only one alternate output format option may be specified (found %i)\n",
numSoloArgs);
Help(argv[0], true);
return 1;
}
if (!sybyltype.empty() && fmt != TrajectoryFile::MOL2FILE) {
mprinterr("Warning: -sybyl is only valid for MOL2 file output.\n");
sybyltype.clear();
}
if (debug > 0) {
mprinterr("Warning: debug is %i; debug info will be written to STDOUT.\n", debug);
SetWorldSilent(false);
}
// Topology
ParmFile pfile;
Topology parm;
if (pfile.ReadTopology(parm, topname, debug)) {
if (topname == "prmtop") Help(argv[0], false);
return 1;
}
if (!useExtendedInfo)
parm.ResetPDBinfo();
if (res_offset != 0)
for (int r = 0; r < parm.Nres(); r++)
parm.SetRes(r).SetOriginalNum( parm.Res(r).OriginalResNum() + res_offset );
ArgList trajArgs;
// Input coords
Frame TrajFrame;
CoordinateInfo cInfo;
if (!crdname.empty()) {
Trajin_Single trajin;
if (trajin.SetupTrajRead(crdname, trajArgs, &parm)) return 1;
cInfo = trajin.TrajCoordInfo();
TrajFrame.SetupFrameV(parm.Atoms(), cInfo);
trajin.BeginTraj();
if (trajin.ReadTrajFrame(0, TrajFrame)) return 1;
trajin.EndTraj();
} else {
// Assume Amber restart from STDIN
// Check that input is from a redirect.
if ( isatty(fileno(stdin)) ) {
mprinterr("Error: No coordinates specified with '-c' and no STDIN '<'.\n");
return 1;
}
Traj_AmberRestart restartIn;
restartIn.SetDebug( debug );
//restartIn.processReadArgs( trajArgs );
int total_frames = restartIn.setupTrajin("", &parm);
if (total_frames < 1) return 1;
cInfo = restartIn.CoordInfo();
TrajFrame.SetupFrameV(parm.Atoms(), cInfo);
if (restartIn.openTrajin()) return 1;
if (restartIn.readFrame(0, TrajFrame)) return 1;
restartIn.closeTraj();
}
if (ctr_origin)
TrajFrame.CenterOnOrigin(false);
// Output coords
Trajout_Single trajout;
trajArgs.SetList( aatm + bres + pqr + title + ter_opt + box + sybyltype + writeconect, " " );
if ( trajout.PrepareStdoutTrajWrite(trajArgs, &parm, cInfo, 1, fmt) ) return 1;
trajout.WriteSingle(0, TrajFrame);
trajout.EndTraj();
return 0;
}