bool SDFfile::ReadHeader() {
if (!IsOpen()) return true;
// Read title
title_ = GetLine();
RemoveTrailingWhitespace( title_ );
// Read past info and comment
if (NextLine() == 0) return true;
if (NextLine() == 0) return true;
// Read Connection table
const char* ptr = NextLine();
if (ptr == 0) return true;
if (sscanf(ptr, "%i %i", &Natoms_, &Nbonds_) != 2) return true;
return false;
}
bool Traj_Gro::ID_TrajFormat(CpptrajFile& infile) {
// Title line, atoms line, then resnum, resname, atomname, atomnum, X, Y, Z
if (infile.OpenFile()) return false;
int nread = 0;
if (infile.NextLine() != 0) { // Title
const char* ptr = infile.NextLine(); // Natom
if (ptr != 0) {
// Ensure only a single value on # atoms line
std::string natom_str( ptr );
RemoveTrailingWhitespace( natom_str );
if (validInteger(natom_str)) {
ptr = infile.NextLine(); // First atom
if (ptr != 0) {
char resnum[6], resname[6], atname[6], atnum[6];
float XYZ[3];
nread = sscanf(ptr, "%5c%5c%5c%5c%f %f %f", resnum, resname,
atname, atnum, XYZ, XYZ+1, XYZ+2);
}
}
}
}
infile.CloseFile();
return (nread == 7);
}
std::string NoTrailingWhitespace(std::string const& line) {
std::string duplicate(line);
RemoveTrailingWhitespace(duplicate);
return duplicate;
}
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;
}
