// Traj_AmberCoord::ID_TrajFormat()
bool Traj_AmberCoord::ID_TrajFormat(CpptrajFile& fileIn) {
// File must already be set up for read
if (fileIn.OpenFile()) return false;
if (fileIn.NextLine()==0) return false; // Title
std::string buffer2 = fileIn.GetLine(); // REMD header/coords
fileIn.CloseFile();
// Check if second line contains REMD/HREMD, Amber Traj with REMD header
if ( IsRemdHeader( buffer2.c_str() ) ) {
if (debug_>0) mprintf(" AMBER TRAJECTORY with (H)REMD header.\n");
hasREMD_ = REMD_HEADER_SIZE + (size_t)fileIn.IsDos();
return true;
}
// Check if we can read at least 3 coords of width 8, Amber trajectory
float TrajCoord[3];
if ( sscanf(buffer2.c_str(), "%8f%8f%8f", TrajCoord, TrajCoord+1, TrajCoord+2) == 3 )
{
if (debug_>0) mprintf(" AMBER TRAJECTORY file\n");
return true;
}
return false;
}
// Traj_AmberCoord::ID_TrajFormat()
bool Traj_AmberCoord::ID_TrajFormat(CpptrajFile& fileIn) {
// File must already be set up for read
if (fileIn.OpenFile()) return false;
if (fileIn.NextLine()==0) return false; // Title
std::string buffer2 = fileIn.GetLine(); // REMD header/coords
fileIn.CloseFile();
// Check if second line contains REMD/HREMD, Amber Traj with REMD header
if ( IsRemdHeader( buffer2.c_str() ) ) {
if (debug_>0) mprintf(" AMBER TRAJECTORY with (H)REMD header.\n");
headerSize_ = REMD_HEADER_SIZE + (size_t)fileIn.IsDos();
tStart_ = 33; // 42 - 8 - 1
tEnd_ = 41; // 42 - 1
return true;
}
// TODO: Read these in as indices instead of temperatures
if ( IsRxsgldHeader( buffer2.c_str() ) ) {
mprintf(" AMBER TRAJECTORY with RXSGLD header.\n");
headerSize_ = RXSGLD_HEADER_SIZE + (size_t)fileIn.IsDos();
tStart_ = 35; // 44 - 8 - 1
tEnd_ = 43; // 44 - 1
return true;
}
// Check if we can read 3, 6, 9, or 10 coords (corresponding to 1, 2, 3 or
// > 3 atoms) of width 8; Amber trajectory.
float TrajCoord[10];
int nscan = sscanf(buffer2.c_str(), "%8f%8f%8f%8f%8f%8f%8f%8f%8f%8f",
TrajCoord, TrajCoord+1, TrajCoord+2, TrajCoord+3,
TrajCoord+4, TrajCoord+5, TrajCoord+6, TrajCoord+7,
TrajCoord+8, TrajCoord+9);
if (nscan == 3 || nscan == 6 || nscan == 9 || nscan == 10)
{
if (debug_>0) mprintf(" AMBER TRAJECTORY file\n");
return true;
}
return false;
}
// Traj_AmberCoord::setupTrajin()
int Traj_AmberCoord::setupTrajin(std::string 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, hasREMD_, title.size() );
if (debug_ > 0) {
mprintf("Each frame is %u bytes", file_.FrameSize());
if (hasREMD_ != 0) mprintf(" (including REMD header)");
mprintf(".\n");
}
// Read the first frame of coordinates
if ( file_.ReadFrame() == -1 ) {
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.
Box boxInfo;
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()) ) {
// 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.",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.
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: Expect only 3 or 6 box coords, got %i\n", numBoxCoords_);
mprinterr("Error: Box line=[%s]\n", 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_size * 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",
file_.Filename().base());
mprintf(" Frames will be read until EOF.\n");
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",
file_.Filename().base());
mprintf(" indicates a corrupted trajectory. Will attempt to read %i frames.\n",
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
SetBox( boxInfo );
SetTemperature( hasREMD_ != 0 );
SetTitle( title );
SetSeekable( seekable );
return Frames;
}
