/** 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;
}
/** Write file containing only cut atoms and energies as charges. */
int Action_Pairwise::WriteCutFrame(int frameNum, Topology const& Parm, AtomMask const& CutMask,
Darray const& CutCharges,
Frame const& frame, std::string const& outfilename)
{
if (CutMask.Nselected() != (int)CutCharges.size()) {
mprinterr("Error: WriteCutFrame: # of charges (%u) != # mask atoms (%i)\n",
CutCharges.size(), CutMask.Nselected());
return 1;
}
Frame CutFrame(frame, CutMask);
Topology* CutParm = Parm.modifyStateByMask( CutMask );
if (CutParm == 0) return 1;
// Set new charges
for (int i = 0; i != CutParm->Natom(); i++)
CutParm->SetAtom(i).SetCharge( CutCharges[i] );
int err = 0;
Trajout_Single tout;
if (tout.PrepareTrajWrite(outfilename, "multi", CutParm, CoordinateInfo(), 1,
TrajectoryFile::MOL2FILE))
{
mprinterr("Error: Could not set up cut mol2 file %s\n", outfilename.c_str());
err = 1;
} else {
tout.WriteSingle(frameNum, CutFrame);
tout.EndTraj();
}
delete CutParm;
return err;
}
/* * Open the netcdf file, read all dimension and variable IDs, close.
* Return the number of frames in the file.
*/
int Traj_AmberNetcdf::setupTrajin(FileName const& fname, Topology* trajParm)
{
filename_ = fname;
if (openTrajin()) return TRAJIN_ERR;
readAccess_ = true;
// Sanity check - Make sure this is a Netcdf trajectory
if ( GetNetcdfConventions() != NC_AMBERTRAJ ) {
mprinterr("Error: Netcdf file %s conventions do not include \"AMBER\"\n",filename_.base());
return TRAJIN_ERR;
}
// Get global attributes
std::string attrText = GetAttrText("ConventionVersion");
if ( attrText != "1.0")
mprintf("Warning: Netcdf file %s has ConventionVersion that is not 1.0 (%s)\n",
filename_.base(), attrText.c_str());
// Get title
SetTitle( GetAttrText("title") );
// Get Frame info
if ( SetupFrameDim()!=0 ) return TRAJIN_ERR;
if ( Ncframe() < 1 ) {
mprinterr("Error: Netcdf file is empty.\n");
return TRAJIN_ERR;
}
// Setup Coordinates/Velocities
if ( SetupCoordsVelo( useVelAsCoords_ )!=0 ) return TRAJIN_ERR;
// Check that specified number of atoms matches expected number.
if (Ncatom() != trajParm->Natom()) {
mprinterr("Error: Number of atoms in NetCDF file %s (%i) does not\n"
"Error: match number in associated parmtop (%i)!\n",
filename_.base(), Ncatom(), trajParm->Natom());
return TRAJIN_ERR;
}
// Setup Time - FIXME: Allowed to fail silently
SetupTime();
// Box info
double boxcrd[6];
if (SetupBox(boxcrd, NC_AMBERTRAJ) == 1) // 1 indicates an error
return TRAJIN_ERR;
// Replica Temperatures - FIXME: Allowed to fail silently
SetupTemperature();
// Replica Dimensions
ReplicaDimArray remdDim;
if ( SetupMultiD(remdDim) == -1 ) return TRAJIN_ERR;
// Set traj info: FIXME - no forces yet
SetCoordInfo( CoordinateInfo(remdDim, Box(boxcrd), HasVelocities(),
HasTemperatures(), HasTimes(), false) );
// NOTE: TO BE ADDED
// labelDID;
//int cell_spatialDID, cell_angularDID;
//int spatialVID, cell_spatialVID, cell_angularVID;
// Amber Netcdf coords are float. Allocate a float array for converting
// float to/from double.
if (Coord_ != 0) delete[] Coord_;
Coord_ = new float[ Ncatom3() ];
if (debug_>1) NetcdfDebug();
closeTraj();
return Ncframe();
}
/** Prepare trajectory for reading. Determine number of frames. */
int Traj_GmxTrX::setupTrajin(FileName const& fname, Topology* trajParm)
{
int nframes = 0;
if (file_.SetupRead( fname, debug_ )) return TRAJIN_ERR;
// Open and read in header
if ( file_.OpenFile() ) return TRAJIN_ERR;
ReadTrxHeader();
if (debug_ > 0) GmxInfo(); // DEBUG
// Warn if # atoms in parm does not match
if (trajParm->Natom() != natoms_) {
mprinterr("Error: # atoms in TRX file (%i) does not match # atoms in parm %s (%i)\n",
natoms_, trajParm->c_str(), trajParm->Natom());
return TRAJIN_ERR;
}
// If float precision, create temp array. Temp array not needed for double reads.
if (precision_ == sizeof(float)) {
if (farray_ != 0) delete[] farray_;
farray_ = new float[ natom3_ ];
}
// Attempt to determine # of frames in traj
headerBytes_ = (size_t)file_.Tell();
frameSize_ = headerBytes_ + (size_t)box_size_ + (size_t)vir_size_ + (size_t)pres_size_ +
(size_t)x_size_ + (size_t)v_size_ + (size_t)f_size_;
//(size_t)ir_size_ + (size_t)e_size_ + (size_t)top_size_ +
//(size_t)sym_size_;
size_t file_size = (size_t)file_.UncompressedSize();
if (file_size > 0) {
nframes = (int)(file_size / frameSize_);
if ( (file_size % frameSize_) != 0 ) {
mprintf("Warning: %s: Number of frames in TRX file could not be accurately determined.\n"
"Warning: Will attempt to read %i frames.\n", file_.Filename().base(), nframes);
}
} else {
mprintf("Warning: Uncompressed size could not be determined. This is normal for\n");
mprintf("Warning: bzip2 files. Cannot check # of frames. Frames will be read until EOF.\n");
nframes = TRAJIN_UNK;
}
// Load box info so that it can be checked.
double box[6];
box[0]=0.0;
box[1]=0.0;
box[2]=0.0;
box[3]=0.0;
box[4]=0.0;
box[5]=0.0;
if ( box_size_ > 0 ) {
if ( ReadBox( box ) ) return TRAJIN_ERR;
}
// Set traj info - No time or temperature
SetCoordInfo( CoordinateInfo(Box(box), (v_size_ > 0), false, false) );
closeTraj();
return nframes;
}
/** Project average coords along eigenvectors */
int Analysis_Modes::ProjectCoords(DataSet_Modes const& modes) {
double scale = factor_;
int max_it = (int)(pcmax_ - pcmin_);
// Check that size of eigenvectors match # coords
int ncoord = tOutParm_->Natom() * 3;
if (ncoord != modes.NavgCrd()) {
mprinterr("Error: # selected coords (%i) != eigenvector size (%i)\n",
ncoord, modes.NavgCrd());
return 1;
}
// Check that mode is valid.
if (tMode_ < 1 || tMode_ > modes.Nmodes() ) {
mprinterr("Error: mode %i is out of bounds.\n", tMode_);
return Analysis::ERR;
}
// Setup frame to hold output coords, initalized to avg coords.
Frame outframe;
outframe.SetupFrameXM( modes.AvgCrd(), modes.Mass() );
// Point to correct eigenvector
const double* Vec = modes.Eigenvector(tMode_-1);
// Initialize coords to pcmin
for (int idx = 0; idx < ncoord; idx++)
outframe[idx] += pcmin_ * Vec[idx];
if (debug_>0) CalculateProjection(0, outframe, tMode_-1);
if (trajout_.SetupTrajWrite( tOutParm_, CoordinateInfo(), max_it )) {
mprinterr("Error: Could not open output modes traj '%s'\n", trajout_.Traj().Filename().full());
return 1;
}
// Write first frame with coords at pcmin.
int set = 0;
trajout_.WriteSingle(set++, outframe);
// Main loop
for (int it = 0; it < max_it; it++) {
double* crd = outframe.xAddress();
// Move coordinates along eigenvector.
for (int idx = 0; idx < ncoord; ++idx)
crd[idx] += scale * Vec[idx];
if (debug_>0) CalculateProjection(set, outframe, tMode_-1);
// DEBUG: calc PC projection for first 3 modes
//for (int m = 0; m < 3; m++)
// CalculateProjection(set, outframe, m);
// Write frame
trajout_.WriteSingle(set++, outframe);
}
trajout_.EndTraj();
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;
}
int SequenceAlign(CpptrajState& State, ArgList& argIn) {
std::string blastfile = argIn.GetStringKey("blastfile");
if (blastfile.empty()) {
mprinterr("Error: 'blastfile' must be specified.\n");
return 1;
}
ReferenceFrame qref = State.DSL()->GetReferenceFrame(argIn);
if (qref.error() || qref.empty()) {
mprinterr("Error: Must specify reference structure for query.\n");
return 1;
}
std::string outfilename = argIn.GetStringKey("out");
if (outfilename.empty()) {
mprinterr("Error: Must specify output file.\n");
return 1;
}
TrajectoryFile::TrajFormatType fmt = TrajectoryFile::GetFormatFromArg(argIn);
if (fmt != TrajectoryFile::PDBFILE && fmt != TrajectoryFile::MOL2FILE)
fmt = TrajectoryFile::PDBFILE; // Default to PDB
int smaskoffset = argIn.getKeyInt("smaskoffset", 0) + 1;
int qmaskoffset = argIn.getKeyInt("qmaskoffset", 0) + 1;
// Load blast file
mprintf("\tReading BLAST alignment from '%s'\n", blastfile.c_str());
BufferedLine infile;
if (infile.OpenFileRead( blastfile )) return 1;
// Seek down to first Query line.
const char* ptr = infile.Line();
bool atFirstQuery = false;
while (ptr != 0) {
if (*ptr == 'Q') {
if ( strncmp(ptr, "Query", 5) == 0 ) {
atFirstQuery = true;
break;
}
}
ptr = infile.Line();
}
if (!atFirstQuery) {
mprinterr("Error: 'Query' not found.\n");
return 1;
}
// Read alignment. Replacing query with subject.
typedef std::vector<char> Carray;
typedef std::vector<int> Iarray;
Carray Query; // Query residues
Carray Sbjct; // Sbjct residues
Iarray Smap; // Smap[Sbjct index] = Query index
while (ptr != 0) {
const char* qline = ptr; // query line
const char* aline = infile.Line(); // alignment line
const char* sline = infile.Line(); // subject line
if (aline == 0 || sline == 0) {
mprinterr("Error: Missing alignment line or subject line after Query:\n");
mprinterr("Error: %s", qline);
return 1;
}
for (int idx = 12; qline[idx] != ' '; idx++) {
if (qline[idx] == '-') {
// Sbjct does not have corresponding res in Query
Smap.push_back(-1);
Sbjct.push_back( sline[idx] );
} else if (sline[idx] == '-') {
// Query does not have a corresponding res in Sbjct
Query.push_back( qline[idx] );
} else {
// Direct Query to Sbjct map
Smap.push_back( Query.size() );
Sbjct.push_back( sline[idx] );
Query.push_back( qline[idx] );
}
}
// Scan to next Query
ptr = infile.Line();
while (ptr != 0) {
if (*ptr == 'Q') {
if ( strncmp(ptr, "Query", 5) == 0 ) break;
}
ptr = infile.Line();
}
}
// DEBUG
std::string SmaskExp, QmaskExp;
if (State.Debug() > 0) mprintf(" Map of Sbjct to Query:\n");
for (int sres = 0; sres != (int)Sbjct.size(); sres++) {
if (State.Debug() > 0)
mprintf("%-i %3s %i", sres+smaskoffset, Residue::ConvertResName(Sbjct[sres]),
Smap[sres]+qmaskoffset);
const char* qres = "";
if (Smap[sres] != -1) {
qres = Residue::ConvertResName(Query[Smap[sres]]);
if (SmaskExp.empty())
SmaskExp.assign( integerToString(sres+smaskoffset) );
else
SmaskExp.append( "," + integerToString(sres+smaskoffset) );
if (QmaskExp.empty())
QmaskExp.assign( integerToString(Smap[sres]+qmaskoffset) );
else
QmaskExp.append( "," + integerToString(Smap[sres]+qmaskoffset) );
}
if (State.Debug() > 0) mprintf(" %3s\n", qres);
}
mprintf("Smask: %s\n", SmaskExp.c_str());
mprintf("Qmask: %s\n", QmaskExp.c_str());
// Check that query residues match reference.
for (unsigned int sres = 0; sres != Sbjct.size(); sres++) {
int qres = Smap[sres];
if (qres != -1) {
if (Query[qres] != qref.Parm().Res(qres).SingleCharName()) {
mprintf("Warning: Potential residue mismatch: Query %s reference %s\n",
Residue::ConvertResName(Query[qres]), qref.Parm().Res(qres).c_str());
}
}
}
// Build subject using coordinate from reference.
//AtomMask sMask; // Contain atoms that should be in sTop
Topology sTop;
Frame sFrame;
Iarray placeHolder; // Atom indices of placeholder residues.
for (unsigned int sres = 0; sres != Sbjct.size(); sres++) {
int qres = Smap[sres];
NameType SresName( Residue::ConvertResName(Sbjct[sres]) );
if (qres != -1) {
Residue const& QR = qref.Parm().Res(qres);
Residue SR(SresName, sres+1, ' ', QR.ChainID());
if (Query[qres] == Sbjct[sres]) { // Exact match. All non-H atoms.
for (int qat = QR.FirstAtom(); qat != QR.LastAtom(); qat++)
{
if (qref.Parm()[qat].Element() != Atom::HYDROGEN)
sTop.AddTopAtom( qref.Parm()[qat], SR );
sFrame.AddXYZ( qref.Coord().XYZ(qat) );
//sMask.AddAtom(qat);
}
} else { // Partial match. Copy only backbone and CB.
for (int qat = QR.FirstAtom(); qat != QR.LastAtom(); qat++)
{
if ( qref.Parm()[qat].Name().Match("N" ) ||
qref.Parm()[qat].Name().Match("CA") ||
qref.Parm()[qat].Name().Match("CB") ||
qref.Parm()[qat].Name().Match("C" ) ||
qref.Parm()[qat].Name().Match("O" ) )
{
sTop.AddTopAtom( qref.Parm()[qat], SR );
sFrame.AddXYZ( qref.Coord().XYZ(qat) );
}
}
}
} else {
// Residue in query does not exist for subject. Just put placeholder CA for now.
Vec3 Zero(0.0);
placeHolder.push_back( sTop.Natom() );
sTop.AddTopAtom( Atom("CA", "C "), Residue(SresName, sres+1, ' ', ' ') );
sFrame.AddXYZ( Zero.Dptr() );
}
}
//sTop.PrintAtomInfo("*");
mprintf("\tPlaceholder residue indices:");
for (Iarray::const_iterator p = placeHolder.begin(); p != placeHolder.end(); ++p)
mprintf(" %i", *p + 1);
mprintf("\n");
// Try to give placeholders more reasonable coordinates.
if (!placeHolder.empty()) {
Iarray current_indices;
unsigned int pidx = 0;
while (pidx < placeHolder.size()) {
if (current_indices.empty()) {
current_indices.push_back( placeHolder[pidx++] );
// Search for the end of this segment
for (; pidx != placeHolder.size(); pidx++) {
if (placeHolder[pidx] - current_indices.back() > 1) break;
current_indices.push_back( placeHolder[pidx] );
}
// DEBUG
mprintf("\tSegment:");
for (Iarray::const_iterator it = current_indices.begin();
it != current_indices.end(); ++it)
mprintf(" %i", *it + 1);
// Get coordinates of residues bordering segment.
int prev_res = sTop[current_indices.front()].ResNum() - 1;
int next_res = sTop[current_indices.back() ].ResNum() + 1;
mprintf(" (prev_res=%i, next_res=%i)\n", prev_res+1, next_res+1);
Vec3 prev_crd(sFrame.XYZ(current_indices.front() - 1));
Vec3 next_crd(sFrame.XYZ(current_indices.back() + 1));
prev_crd.Print("prev_crd");
next_crd.Print("next_crd");
Vec3 crd_step = (next_crd - prev_crd) / (double)(current_indices.size()+1);
crd_step.Print("crd_step");
double* xyz = sFrame.xAddress() + (current_indices.front() * 3);
for (unsigned int i = 0; i != current_indices.size(); i++, xyz += 3) {
prev_crd += crd_step;
xyz[0] = prev_crd[0];
xyz[1] = prev_crd[1];
xyz[2] = prev_crd[2];
}
current_indices.clear();
}
}
}
//Topology* sTop = qref.Parm().partialModifyStateByMask( sMask );
//if (sTop == 0) return 1;
//Frame sFrame(qref.Coord(), sMask);
// Write output traj
Trajout_Single trajout;
if (trajout.PrepareTrajWrite(outfilename, argIn, &sTop, CoordinateInfo(), 1, fmt)) return 1;
if (trajout.WriteSingle(0, sFrame)) return 1;
trajout.EndTraj();
return 0;
}
// Exec_PermuteDihedrals::RandomizeAngles()
void Exec_PermuteDihedrals::RandomizeAngles(Frame& currentFrame, Topology const& topIn) {
Matrix_3x3 rotationMatrix;
# ifdef DEBUG_PERMUTEDIHEDRALS
// DEBUG
int debugframenum=0;
Trajout_Single DebugTraj;
DebugTraj.PrepareTrajWrite("debugtraj.nc",ArgList(),(Topology*)&topIn,
CoordinateInfo(), BB_dihedrals_.size()*max_factor_,
TrajectoryFile::AMBERNETCDF);
DebugTraj.WriteSingle(debugframenum++,currentFrame);
# endif
int next_resnum;
int bestLoop = 0;
int number_of_rotations = 0;
// Set max number of rotations to try.
int max_rotations = (int)BB_dihedrals_.size();
max_rotations *= max_factor_;
// Loop over all dihedrals
std::vector<PermuteDihedralsType>::const_iterator next_dih = BB_dihedrals_.begin();
next_dih++;
for (std::vector<PermuteDihedralsType>::const_iterator dih = BB_dihedrals_.begin();
dih != BB_dihedrals_.end();
++dih, ++next_dih)
{
++number_of_rotations;
// Get the residue atom of the next dihedral. Residues up to and
// including this residue will be checked for bad clashes
if (next_dih != BB_dihedrals_.end())
next_resnum = next_dih->resnum;
else
next_resnum = dih->resnum - 1;
// Set axis of rotation
Vec3 axisOfRotation = currentFrame.SetAxisOfRotation(dih->atom1, dih->atom2);
// Generate random value to rotate by in radians
// Guaranteed to rotate by at least 1 degree.
// NOTE: could potentially rotate 360 - prevent?
// FIXME: Just use 2PI and rn_gen, get everything in radians
double theta_in_degrees = ((int)(RN_.rn_gen()*100000) % 360) + 1;
double theta_in_radians = theta_in_degrees * Constants::DEGRAD;
// Calculate rotation matrix for random theta
rotationMatrix.CalcRotationMatrix(axisOfRotation, theta_in_radians);
int loop_count = 0;
double clash = 0;
double bestClash = 0;
if (debug_>0) mprintf("DEBUG: Rotating dihedral %zu res %8i:\n", dih - BB_dihedrals_.begin(),
dih->resnum+1);
bool rotate_dihedral = true;
while (rotate_dihedral) {
if (debug_>0) {
mprintf("\t%8i %12s %12s, +%.2lf degrees (%i).\n",dih->resnum+1,
topIn.AtomMaskName(dih->atom1).c_str(),
topIn.AtomMaskName(dih->atom2).c_str(),
theta_in_degrees,loop_count);
}
// Rotate around axis
currentFrame.Rotate(rotationMatrix, dih->Rmask);
# ifdef DEBUG_PERMUTEDIHEDRALS
// DEBUG
DebugTraj.WriteSingle(debugframenum++,currentFrame);
# endif
// If we dont care about sterics exit here
if (!check_for_clashes_) break;
// Check resulting structure for issues
int checkresidue;
if (!checkAllResidues_)
checkresidue = CheckResidue(currentFrame, topIn, *dih, next_resnum, clash);
else
checkresidue = CheckResidue(currentFrame, topIn, *dih, topIn.Nres(), clash);
if (checkresidue==0)
rotate_dihedral = false;
else if (checkresidue==-1) {
if (dih - BB_dihedrals_.begin() < 2) {
mprinterr("Error: Cannot backtrack; initial structure already has clashes.\n");
number_of_rotations = max_rotations + 1;
} else {
dih--; // 0
dih--; // -1
next_dih = dih;
next_dih++;
if (debug_>0)
mprintf("\tCannot resolve clash with further rotations, trying previous again.\n");
}
break;
}
if (clash > bestClash) {bestClash = clash; bestLoop = loop_count;}
//n_problems = CheckResidues( currentFrame, second_atom );
//if (n_problems > -1) {
// mprintf("%i\tCheckResidues: %i problems.\n",frameNum,n_problems);
// rotate_dihedral = false;
//} else if (loop_count==0) {
if (loop_count==0 && rotate_dihedral) {
if (debug_>0)
mprintf("\tTrying dihedral increments of +%i\n",increment_);
// Instead of a new random dihedral, try increments
theta_in_degrees = (double)increment_;
theta_in_radians = theta_in_degrees * Constants::DEGRAD;
// Calculate rotation matrix for new theta
rotationMatrix.CalcRotationMatrix(axisOfRotation, theta_in_radians);
}
++loop_count;
if (loop_count == max_increment_) {
if (debug_>0)
mprintf("%i iterations! Best clash= %.3lf at %i\n",max_increment_,
sqrt(bestClash),bestLoop);
if (dih - BB_dihedrals_.begin() < backtrack_) {
mprinterr("Error: Cannot backtrack; initial structure already has clashes.\n");
number_of_rotations = max_rotations + 1;
} else {
for (int bt = 0; bt < backtrack_; bt++)
dih--;
next_dih = dih;
next_dih++;
if (debug_>0)
mprintf("\tCannot resolve clash with further rotations, trying previous %i again.\n",
backtrack_ - 1);
}
break;
// Calculate how much to rotate back in order to get to best clash
/*int num_back = bestLoop - 359;
theta_in_degrees = (double) num_back;
theta_in_radians = theta_in_degrees * Constants::DEGRAD;
// Calculate rotation matrix for theta
calcRotationMatrix(rotationMatrix, axisOfRotation, theta_in_radians);
// Rotate back to best clash
frm.Frm().RotateAroundAxis(rotationMatrix, theta_in_radians, dih->Rmask);
// DEBUG
DebugTraj.WriteFrame(debugframenum++,currentParm,*currentFrame);
// Sanity check
CheckResidue(currentFrame, *dih, second_atom, &clash);
rotate_dihedral=false;*/
//DebugTraj.EndTraj();
//return 1;
}
} // End dihedral rotation loop
// Safety valve - number of defined dihedrals times * maxfactor
if (number_of_rotations > max_rotations) {
mprinterr("Error: # of rotations (%i) exceeds max rotations (%i), exiting.\n",
number_of_rotations, max_rotations);
//# ifdef DEBUG_PERMUTEDIHEDRALS
// DebugTraj.EndTraj();
//# endif
// Return gracefully for now
break;
//return 1;
}
} // End loop over dihedrals
# ifdef DEBUG_PERMUTEDIHEDRALS
DebugTraj.EndTraj();
mprintf("\tNumber of rotations %i, expected %u\n",number_of_rotations,BB_dihedrals_.size());
# endif
}
// Action_LESsplit::Setup()
Action::RetType Action_LESsplit::Setup(ActionSetup& setup) {
if ( !setup.Top().LES().HasLES() ) {
mprintf("Warning: No LES parameters in '%s', skipping.\n", setup.Top().c_str());
return Action::SKIP;
}
if (lesParm_ == 0) { // First time setup
// Set up masks for all copies
lesMasks_.clear();
lesMasks_.resize( setup.Top().LES().Ncopies() );
unsigned int atom = 0;
for (LES_Array::const_iterator les = setup.Top().LES().Array().begin();
les != setup.Top().LES().Array().end(); ++les, ++atom)
{
// Copy 0 is in all copies
if ( les->Copy() == 0 ) {
for (MaskArray::iterator mask = lesMasks_.begin(); mask != lesMasks_.end(); ++mask)
mask->AddAtom( atom );
} else
lesMasks_[ les->Copy() - 1 ].AddAtom( atom );
}
for (unsigned int i = 0; i < lesMasks_.size(); i++) {
mprintf("\t%i atoms in LES copy %u\n", lesMasks_[i].Nselected(), i+1);
if ( lesMasks_[i].Nselected() != lesMasks_[0].Nselected() ) {
mprinterr("Error: Currently all LES copies MUST have same # atoms.\n");
return Action::ERR;
}
}
// Create topology for first copy
lesParm_ = setup.Top().modifyStateByMask( lesMasks_[0] );
if (lesParm_ == 0) return Action::ERR;
// Set up frames to hold individual copies
lesFrames_.resize( lesMasks_.size() );
lesFrames_.SetupFrames(lesParm_->Atoms(), setup.CoordInfo());
lesPtrs_.resize( lesMasks_.size() );
for (unsigned int i = 0; i != lesMasks_.size(); i++)
lesPtrs_[i] = &lesFrames_[i];
if (lesSplit_) {
// Set up output ensemble FIXME check overwrites TODO combine init/setup?
if (lesTraj_.InitEnsembleWrite(trajfilename_, trajArgs_, lesMasks_.size(),
TrajectoryFile::UNKNOWN_TRAJ))
return Action::ERR;
if (lesTraj_.SetupEnsembleWrite(lesParm_, setup.CoordInfo(), setup.Nframes()))
return Action::ERR;
lesTraj_.PrintInfo(0);
}
if (lesAverage_) {
// For average only care about coords.
avgFrame_.SetupFrame( lesParm_->Natom() );
if (avgTraj_.PrepareTrajWrite( avgfilename_, trajArgs_, lesParm_,
CoordinateInfo(), setup.Nframes(),
TrajectoryFile::UNKNOWN_TRAJ ))
return Action::ERR;
avgTraj_.PrintInfo(0);
}
} else {
if (lesParm_->Pindex() != setup.Top().Pindex()) {
mprintf("Warning: Already set up for LES parm '%s'. Skipping '%s'\n",
lesParm_->c_str(), setup.Top().c_str());
return Action::SKIP;
}
}
return Action::OK;
}
/** Set up and read Amber restart file. Coordinate/velocities will be saved
* here to avoid having to open the file again. Check that number of atoms
* matches number of atoms in associated parmtop. Check for box/velocity info.
*/
int Traj_AmberRestart::setupTrajin(FileName const& fname, Topology* trajParm)
{
BufferedFrame infile;
if (infile.SetupRead( fname, debug_ )) return TRAJIN_ERR;
if (infile.OpenFile()) return TRAJIN_ERR;
readAccess_ = true;
// Read in title
std::string title = infile.GetLine();
SetTitle( NoTrailingWhitespace(title) );
// Read in natoms, time, and Replica Temp if present
std::string nextLine = infile.GetLine();
if (nextLine.empty()) {
mprinterr("Error: Could not read restart atoms/time.\n");
return TRAJIN_ERR;
}
int restartAtoms = 0;
bool hasTemp = false;
bool hasTime = false;
int nread = sscanf(nextLine.c_str(),"%i %lE %lE",&restartAtoms,&restartTime_,&restartTemp_);
if (nread < 1) {
mprinterr("Error: Unable to read restart atoms/time.\n");
return TRAJIN_ERR;
} else if (nread == 1) { // # atoms only
restartTime_ = 0.0;
restartTemp_ = -1.0;
} else if (nread == 2) { // # atoms and time
hasTime = true;
restartTemp_ = -1.0;
} else { // # atoms, time, and temperature
hasTime = true;
hasTemp = true;
}
if (debug_ > 0)
mprintf("\tAmber restart: Atoms=%i Time=%lf Temp=%lf\n",restartAtoms,
restartTime_, restartTemp_);
// Check that natoms matches parm natoms
if (restartAtoms != trajParm->Natom()) {
mprinterr("Error: Number of atoms in Amber Restart %s (%i) does not\n",
infile.Filename().base(), restartAtoms);
mprinterr(" match number in associated parmtop (%i)\n",trajParm->Natom());
return TRAJIN_ERR;
}
natom3_ = restartAtoms * 3;
// Calculate the length of coordinate frame in bytes
infile.SetupFrameBuffer( natom3_, 12, 6 );
// Read past restart coords
if ( infile.ReadFrame() ) {
mprinterr("Error: AmberRestart::setupTrajin(): Error reading coordinates.\n");
return TRAJIN_ERR;
}
// Save coordinates
CRD_.resize( natom3_ );
infile.BufferBegin();
infile.BufferToDouble(&CRD_[0], natom3_);
// Attempt a second read to get velocities or box coords
bool hasVel = false;
boxInfo_.SetNoBox();
nread = infile.AttemptReadFrame();
if ( nread < 0 ) {
mprinterr("Error: Error attempting to read box line of Amber restart file.\n");
return TRAJIN_ERR;
}
size_t readSize = (size_t)nread;
//mprintf("DEBUG: Restart readSize on second read = %i\n",readSize);
// If 0 no box or velo
if (readSize > 0) {
if (readSize == infile.FrameSize()) {
// If filled framebuffer again, has velocity info.
hasVel = true;
VEL_.resize( natom3_ );
infile.BufferBegin();
infile.BufferToDouble(&VEL_[0], natom3_);
// If we can read 1 more line after velocity, should be box info.
nextLine = infile.GetLine();
if (!nextLine.empty()) {
if (getBoxAngles(nextLine, boxInfo_)) return TRAJIN_ERR;
}
} else if (readSize<82) {
// If we read something but didnt fill framebuffer, should have box coords.
nextLine.assign(infile.Buffer(), readSize);
if (getBoxAngles(nextLine, boxInfo_)) return TRAJIN_ERR;
} else {
// Otherwise, who knows what was read?
mprinterr("Error: AmberRestart::setupTrajin(): When attempting to read in\n"
"Error: box coords/velocity info got %lu chars, expected 0, 37,\n"
"Error: 73, or %lu.\n", readSize, infile.FrameSize());
mprinterr("Error: This usually indicates a malformed or corrupted restart file.\n");
return TRAJIN_ERR;
}
}
if (useVelAsCoords_ && !hasVel) {
mprinterr("Error: 'usevelascoords' specified but no velocities in this restart.\n");
return TRAJIN_ERR;
}
infile.CloseFile();
// Set coordinate info
SetCoordInfo( CoordinateInfo(boxInfo_, hasVel, hasTemp, hasTime) );
// Only 1 frame in restart by definition
return 1;
}
// Traj_NcEnsemble::setupTrajin()
int Traj_NcEnsemble::setupTrajin(FileName const& fname, Topology* trajParm)
{
# ifdef MPI
if (NoPnetcdf()) return TRAJIN_ERR;
# endif
readAccess_ = true;
filename_ = fname;
//if (openTrajin()) return TRAJIN_ERR;
// Open single thread for now
if (NC_openRead( filename_.Full() )) return TRAJIN_ERR;
// Sanity check - Make sure this is a Netcdf ensemble trajectory
if ( GetNetcdfConventions() != NC_AMBERENSEMBLE ) {
mprinterr("Error: Netcdf file %s conventions do not include \"AMBERENSEMBLE\"\n",
filename_.base());
return TRAJIN_ERR;
}
// This will warn if conventions are not 1.0
CheckConventionsVersion();
// Get title
SetTitle( GetNcTitle() );
// Get Frame info
if ( SetupFrameDim()!=0 ) return TRAJIN_ERR;
if ( Ncframe() < 1 ) {
mprinterr("Error: Netcdf file is empty.\n");
return TRAJIN_ERR;
}
// Get ensemble info
int ensembleSize = SetupEnsembleDim();
if (ensembleSize < 1) {
mprinterr("Error: Could not get ensemble dimension info.\n");
return TRAJIN_ERR;
}
// Setup Coordinates/Velocities
if ( SetupCoordsVelo( useVelAsCoords_, useFrcAsCoords_ )!=0 ) return TRAJIN_ERR;
// Check that specified number of atoms matches expected number.
if (Ncatom() != trajParm->Natom()) {
mprinterr("Error: Number of atoms in NetCDF file %s (%i) does not\n"
"Error: match number in associated parmtop (%i)!\n",
filename_.base(), Ncatom(), trajParm->Natom());
return TRAJIN_ERR;
}
// Setup Time - FIXME: Allowed to fail silently
SetupTime();
// Box info
Box nc_box;
if (SetupBox(nc_box, NC_AMBERENSEMBLE) == 1) // 1 indicates an error
return TRAJIN_ERR;
// Replica Temperatures - FIXME: Allowed to fail silently
SetupTemperature();
// Replica Dimensions
ReplicaDimArray remdDim;
if ( SetupMultiD(remdDim) == -1 ) return TRAJIN_ERR;
// Set traj info: FIXME - no forces yet
SetCoordInfo( CoordinateInfo(ensembleSize, remdDim, nc_box, HasVelocities(),
HasTemperatures(), HasTimes(), false) );
if (debug_>1) NetcdfDebug();
//closeTraj();
// Close single thread for now
NC_close();
// Set up local ensemble parameters
# ifdef MPI
ensembleStart_ = Parallel::World().Rank();
ensembleEnd_ = Parallel::World().Rank() + 1;
# else
ensembleStart_ = 0;
ensembleEnd_ = ensembleSize;
# endif
// DEBUG: Print info for all ranks
WriteVIDs();
// Allocate float array
if (Coord_ != 0) delete[] Coord_;
Coord_ = new float[ Ncatom3() ];
return Ncframe();
}
int Traj_Gro::setupTrajin(FileName const& fnameIn, Topology* trajParm)
{
float fXYZ[9];
fname_ = fnameIn; // TODO SetupRead for BufferedLine
// Open file for reading
if (file_.OpenFileRead( fname_ )) return TRAJIN_ERR;
// Read the title. May contain time value, 't= <time>'
const char* ptr = file_.Line();
if (ptr == 0) {
mprinterr("Error: Reading title.\n");
return TRAJIN_ERR;
}
std::string title( ptr );
RemoveTrailingWhitespace(title);
mprintf("DBG: Title: %s\n", title.c_str());
bool hasTime = true;
// TODO Is it OK to assume there will never be a negative time value?
double timeVal = GetTimeValue( ptr );
if (timeVal < 0.0) hasTime = false;
mprintf("DBG: Timeval= %g HasTime= %i\n", timeVal, (int)hasTime);
// Read number of atoms
ptr = file_.Line();
if (ptr == 0) return TRAJIN_ERR;
natom_ = atoi(ptr);
if (natom_ < 1) {
mprinterr("Error: Reading number of atoms.\n");
return TRAJIN_ERR;
}
if (natom_ != trajParm->Natom()) {
mprinterr("Error: Number of atoms %i does not match associated parm %s (%i)\n",
natom_, trajParm->c_str(), trajParm->Natom());
return TRAJIN_ERR;
}
// Read first atom to see if there are velocities
ptr = file_.Line();
int nread = sscanf(ptr, "%*5c%*5c%*5c%*5c%f %f %f %f %f %f",
fXYZ, fXYZ+1, fXYZ+2, fXYZ+3, fXYZ+4, fXYZ+5);
bool hasV = false;
if (nread == 6)
hasV = true;
else if (nread != 3) {
mprinterr("Error: Reading first atom, expected 3 or 6 coordinates, got %i\n", nread);
return TRAJIN_ERR;
}
// Read past the rest of the atoms
for (int i = 1; i != natom_; i++)
if (file_.Line() == 0) {
mprinterr("Error: Reading atom %i of first frame.\n", i+1);
return TRAJIN_ERR;
}
// Attempt to read box line
// v1(x) v2(y) v3(z) [v1(y) v1(z) v2(x) v2(z) v3(x) v3(y)]
ptr = file_.Line();
Box groBox;
if (ptr != 0)
groBox = GetBox( ptr );
// Set trajectory information. No temperature info.
SetCoordInfo( CoordinateInfo(groBox, hasV, false, hasTime) );
SetTitle( title );
// Check for multiple frames. If nothing was read above, 1 frame, no box. If
// box info was read but nothing more can be read, 1 frame. Otherwise there
// are more frames.
bool hasMultipleFrames = false;
if (ptr != 0) {
if (groBox.Type() == Box::NOBOX) // Assume another title read.
hasMultipleFrames = true;
else {
ptr = file_.Line(); // Read line after box info
if (ptr != 0)
hasMultipleFrames = true;
}
}
// Set up some info for performing blank reads.
linesToRead_ = natom_;
if (groBox.Type() != Box::NOBOX)
linesToRead_ += 1;
int nframes = 1;
if (hasMultipleFrames) {
// Since there is no guarantee that each frame is the same size we cannot
// just seek. Blank reads for as many times as possible. Should currently
// be positioned at the title line of the next frame.
while (ptr != 0 ) {
ptr = file_.Line(); // Natoms
int Nat = atoi(ptr);
if (Nat != natom_) {
mprinterr("Error: Frame %i # atoms (%i) does not match first frame (%i).\n"
"Error: Only reading %i frames.\n", nframes+1, Nat, natom_, nframes);
break;
}
for (int i = 0; i != linesToRead_; i++)
ptr = file_.Line();
if (ptr == 0) break;
nframes++;
ptr = file_.Line(); // Next title or EOF
}
}
file_.CloseFile();
return nframes;
}
// Traj_AmberCoord::setupTrajin()
int Traj_AmberCoord::setupTrajin(FileName const& fname, Topology* trajParm)
{
// Set up file for reading
if (file_.SetupRead( fname, debug_ )) return TRAJIN_ERR;
// Attempt to open the file. Read and set the title and titleSize
if ( file_.OpenFile() ) return TRAJIN_ERR;
std::string title = file_.GetLine();
// Allocate mem to read in frame (plus REMD header if present). REMD
// header is checked for when file is IDd. Title size is used in seeking.
natom3_ = trajParm->Natom() * 3;
file_.SetupFrameBuffer( natom3_, 8, 10, headerSize_, title.size() );
if (debug_ > 0) {
mprintf("Each frame is %zu bytes", file_.FrameSize());
if (headerSize_ != 0) mprintf(" (including REMD header)");
mprintf(".\n");
}
// Read the first frame of coordinates
if ( file_.ReadFrame() ) {
mprinterr("Error: in read of Coords frame 1 of trajectory %s.\n", file_.Filename().base());
return TRAJIN_ERR;
}
// Check for box coordinates. If present, update the frame size and
// reallocate the frame buffer. If less than 3 atoms there is no way
// to tell if a line is a box line or coordinates, so skip.
Box boxInfo;
if ( trajParm->Natom() < 3 ) {
mprintf("Warning: Less than 3 atoms, skipping box check.\n");
numBoxCoords_ = 0;
} else {
std::string nextLine = file_.GetLine();
if ( !nextLine.empty() ) {
if (debug_>0) rprintf("DEBUG: Line after first frame: (%s)\n", nextLine.c_str());
if ( IsRemdHeader(nextLine.c_str()) || IsRxsgldHeader(nextLine.c_str()) ) {
// REMD header - no box coords
numBoxCoords_ = 0;
} else {
double box[8];
numBoxCoords_ = sscanf(nextLine.c_str(), "%8lf%8lf%8lf%8lf%8lf%8lf%8lf%8lf",
box, box+1, box+2, box+3, box+4, box+5, box+6, box+7);
if (numBoxCoords_ == -1) {
mprinterr("Error: Could not read Box coord line of trajectory %s.\n",
file_.Filename().base());
return TRAJIN_ERR;
} else if (numBoxCoords_ == 8) {
// Full line of coords was read, no box coords.
numBoxCoords_ = 0;
} else if (numBoxCoords_ == 3) {
// Box lengths only, ortho. or truncated oct. Use default parm angles.
if (trajParm->ParmBox().Type() == Box::NOBOX)
mprintf("Warning: Trajectory only contains box lengths and topology has no box info.\n"
"Warning: To set box angles for topology use the 'parmbox' command.\n");
box[3] = boxAngle_[0] = trajParm->ParmBox().Alpha();
box[4] = boxAngle_[1] = trajParm->ParmBox().Beta();
box[5] = boxAngle_[2] = trajParm->ParmBox().Gamma();
boxInfo.SetBox( box );
} else if (numBoxCoords_ == 6) {
// General triclinic. Set lengths and angles.
boxInfo.SetBox( box );
} else {
mprinterr("Error: In %s, expect only 3 or 6 box coords, got %i\n"
"Error: Box line=[%s]\n",
file_.Filename().base(), numBoxCoords_, nextLine.c_str());
return TRAJIN_ERR;
}
}
}
// Reallocate frame buffer accordingly
file_.ResizeBuffer( numBoxCoords_ );
}
// Calculate Frames and determine seekable. If not possible and this is not a
// compressed file the trajectory is probably corrupted. Frames will
// be read until EOF.
int Frames = 0;
if (debug_>0)
rprintf("Title offset=%lu FrameSize=%lu UncompressedFileSize=%lu\n",
title.size(), file_.FrameSize(), file_.UncompressedSize());
off_t title_size = (off_t) title.size();
off_t frame_size = (off_t) file_.FrameSize();
off_t uncompressed_size = file_.UncompressedSize();
off_t file_size = uncompressed_size - title_size;
bool seekable = false;
if (file_.Compression() != CpptrajFile::NO_COMPRESSION) {
// -----==== AMBER TRAJ COMPRESSED ====------
// If the uncompressed size of compressed file is reported as <= 0,
// uncompressed size cannot be determined. Read coordinates until
// EOF.
if (uncompressed_size <= 0) {
mprintf("Warning: %s: Uncompressed size of trajectory could not be determined.\n",
file_.Filename().base());
if (file_.Compression() == CpptrajFile::BZIP2)
mprintf(" (This is normal for bzipped files)\n");
mprintf(" Number of frames could not be calculated.\n");
mprintf(" Frames will be read until EOF.\n");
Frames = TRAJIN_UNK;
seekable = false;
} else {
// Frame calculation for large gzip files
if (file_.Compression() == CpptrajFile::GZIP) {
// Since this is gzip compressed, if the file_size % frame size != 0,
// it could be that the uncompressed filesize > 4GB. Since
// ISIZE = uncompressed % 2^32,
// try ((file_size + (2^32 * i)) % frame_size) and see if any are 0.
if ( (file_size % frame_size) != 0) {
// Determine the maximum number of iterations to try based on the
// fact that Amber trajectories typically compress about 3x with
// gzip.
off_t tmpfsize = ((file_.FileSize() * 4) - uncompressed_size) / 4294967296LL;
int maxi = (int) tmpfsize;
++maxi;
if (debug_>1)
mprintf("\tLooking for uncompressed gzip size > 4GB, %i iterations.\n",maxi);
tmpfsize = 0;
bool sizeFound = false;
for (int i = 0; i < maxi; i++ ) {
tmpfsize = (4294967296LL * i) + file_size;
if ( (tmpfsize % frame_size) == 0) {sizeFound=true; break;}
}
if (sizeFound) file_size = tmpfsize;
}
}
if ((file_size % frame_size) == 0) {
Frames = (int) (file_size / frame_size);
seekable = true;
} else {
mprintf("Warning: %s: Number of frames in compressed traj could not be determined.\n"
"Warning: Frames will be read until EOF.\n", file_.Filename().base());
Frames = TRAJIN_UNK;
seekable = false;
}
}
} else {
// ----==== AMBER TRAJ NOT COMPRESSED ====----
Frames = (int) (file_size / frame_size);
if ( (file_size % frame_size) == 0 ) {
seekable = true;
} else {
mprintf("Warning: %s: Could not accurately predict # frames. This usually\n"
"Warning: indicates a corrupted trajectory or trajectory/topology\n"
"Warning: mismatch. Will attempt to read %i frames.\n",
file_.Filename().base(), Frames);
seekable = false;
}
}
if (debug_>0)
rprintf("Atoms: %i FrameSize: %lu TitleSize: %lu NumBox: %i Seekable: %i Frames: %i\n\n",
trajParm->Natom(), frame_size, title_size, numBoxCoords_, (int)seekable, Frames);
// Close the file
file_.CloseFile();
// Set trajectory info: no velocity, no time.
SetCoordInfo( CoordinateInfo(boxInfo, false, (headerSize_ != 0), false) );
SetTitle( title );
return Frames;
}