/** \return true if TRR/TRJ file. */
bool Traj_GmxTrX::ID_TrajFormat(CpptrajFile& infile) {
// File must already be set up for read
if (infile.OpenFile()) return false;
bool istrx = IsTRX(infile);
infile.CloseFile();
return istrx;
}
bool Parm_CharmmPsf::ID_ParmFormat(CpptrajFile& fileIn) {
// Assumes already set up
if (fileIn.OpenFile()) return false;
std::string nextLine = fileIn.GetLine();
if (nextLine.empty()) return false;
bool isPSF = ( nextLine.compare(0, 3, "PSF") == 0 );
fileIn.CloseFile();
return isPSF;
}
bool DataIO_OpenDx::ID_DataFormat( CpptrajFile& infile ) {
bool isDX = false;
if (!infile.OpenFile()) {
std::string firstLine = infile.GetLine();
if (!firstLine.empty())
isDX = (firstLine.compare(0, 28, "object 1 class gridpositions") == 0);
infile.CloseFile();
}
return isDX;
}
// PDBfile::ID_PDB()
bool PDBfile::ID_PDB(CpptrajFile& fileIn) {
// NOTE: ASSUME FILE SET UP FOR READ
if (fileIn.OpenFile()) return false;
std::string line1 = fileIn.GetLine();
std::string line2 = fileIn.GetLine();
fileIn.CloseFile();
if (!IsPDBkeyword( line1 )) return false;
if (!IsPDBkeyword( line2 )) return false;
return true;
}
// DataIO_CCP4::ID_DataFormat()
bool DataIO_CCP4::ID_DataFormat( CpptrajFile& infile ) {
bool isCCP4 = false;
if (!infile.OpenFile()) {
unsigned char MAP[4];
if (infile.Seek(52 * wSize) == 0) {
infile.Read( MAP, wSize );
isCCP4 = MapCharsValid( MAP );
}
infile.CloseFile();
}
return isCCP4;
}
/** Determine if fileIn is a CIF file. Look for entries beginning with
* an underscore (indicating data block), and a 'loop_' keyword or
* '_entry.id' block.
*/
bool CIFfile::ID_CIF(CpptrajFile& fileIn) {
// NOTE: ASSUME FILE SET UP FOR READ
if (fileIn.OpenFile()) return false;
int ndata = 0; // Number of '_XXX' entries seen
bool foundLoop = false;
bool foundEntryID = false;
for (int i = 0; i < 10; i++) {
std::string lineIn = fileIn.GetLine();
if (lineIn[0] == '_') ndata++;
if (lineIn.compare(0,5,"loop_")==0) foundLoop = true;
if (lineIn.compare(0,9,"_entry.id")==0) foundEntryID = true;
}
fileIn.CloseFile();
return ( ndata > 2 && (foundLoop || foundEntryID) );
}
// DataIO_Mdout::ID_DataFormat()
bool DataIO_Mdout::ID_DataFormat(CpptrajFile& infile) {
if (infile.OpenFile()) return false;
bool isMdout = false;
std::string line = infile.GetLine();
if (line[0] == '\n') {
line = infile.GetLine();
if (line.compare(0, 15, " -----") == 0) {
line = infile.GetLine();
if (line.compare(0, 15, " Amber") == 0)
isMdout = true;
}
}
infile.CloseFile();
return isMdout;
}
bool SDFfile::ID_SDF(CpptrajFile& fileIn) {
// NOTE: ASSUMES FILE IS ALREADY SETUP!
if (fileIn.OpenFile()) return false;
// Search for V2000 somewhere in line 4
const char* ptr = 0;
for (int i = 0; i < 4; i++)
if ( (ptr = fileIn.NextLine()) == 0 ) {
fileIn.CloseFile();
return false;
}
fileIn.CloseFile();
std::string line( ptr ); // Line 4, Connection table
if ( line.find( "V2000" ) != std::string::npos ) return true;
return false;
}
bool Traj_CharmmCor::ID_TrajFormat(CpptrajFile& fileIn) {
// File must already be set up for read.
if (fileIn.OpenFile()) return false;
bool isCor = false;
const char* ptr = fileIn.NextLine();
// Must be at least 1 title line denoted with '*'
if (ptr != 0 && *ptr == '*') {
// Scan past all title lines
while (ptr != 0 && *ptr == '*') ptr = fileIn.NextLine();
if (ptr != 0) {
// Next line must be # atoms ONLY
int ibuf[2];
if (sscanf(ptr, "%i %i", ibuf, ibuf+1) == 1)
// make sure it was a valid integer
isCor = (ibuf[0] > 0);
}
}
fileIn.CloseFile();
return isCor;
}
// 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;
}
bool DataIO_XVG::ID_DataFormat(CpptrajFile& infile) {
if (infile.OpenFile()) return false;
const char* ptr = infile.NextLine();
while (ptr != 0 && ptr[0] == '#') {
const char* cc = ptr;
while (*cc != '\0') {
if (*cc == 'G') {
if ( cc[2] == 'R' && cc[4] == 'O' && cc[6] == 'M' &&
cc[8] == 'A' && cc[10] == 'A' && cc[12] == 'C' )
{
infile.CloseFile();
mprintf("DEBUG:\tFound G R O M A C\n");
return true;
}
}
++cc;
}
ptr = infile.NextLine();
}
infile.CloseFile();
return false;
}
bool TinkerFile::ID_Tinker(CpptrajFile& fileIn) {
// NOTE: ASSUME FILE SET UP FOR READ
if (fileIn.OpenFile()) return false;
ArgList firstLine( fileIn.NextLine() );
ArgList secondLine( fileIn.NextLine() );
ArgList thirdLine( fileIn.NextLine() );
fileIn.CloseFile();
// First line should have <natom> <title> only
int natom = 0;
std::string title;
if ( SetNatomAndTitle(firstLine, natom, title) != 0 )
return false;
//mprinterr("Past SetNatomAndTitle\n");
if (secondLine.Nargs() == 6) {
bool isBoxLine = true;
for (int i = 0; i < 6; i++) {
// It is a box line if all 6 tokens are doubles
try {
convertToDouble( secondLine.GetStringNext() );
}
catch (std::runtime_error e) {
if (i != 1) return false;
// We found a non-double on the second character -- it could be an atom
// name. Check that the rest of the line matches an atom record
isBoxLine = false;
break;
}
}
// If we are here it is not a box line, so make sure
if (!isBoxLine) {
return IsAtomLine(secondLine);
} else { // our second line WAS a box, now check the 3rd line
return IsAtomLine(thirdLine);
}
}
// There is no box, check that the second line is an atom line
return IsAtomLine(secondLine);
}
/** Check for an integer (I5) followed by 0-2 scientific floats (E15.7) */
bool Traj_AmberRestart::ID_TrajFormat(CpptrajFile& fileIn) {
// Assume file set up for read
if (fileIn.OpenFile()) return false;
bool isRestart = false;
if ( fileIn.NextLine() !=0 ) { // Title
const char* ptr = fileIn.NextLine(); // Natom [time [temp]]
if (ptr != 0) {
int i0;
double D[3];
int nread = sscanf(ptr, "%5i%15lf%15lf%lf", &i0, D, D+1, D+2);
if (nread > 0 && nread < 4) {
// Read at least 3 12.7 coordinates from next line.
ptr = fileIn.NextLine();
if (ptr != 0) {
nread = sscanf(ptr, "%12lf%12lf%12lf", D, D+1, D+2);
if (nread == 3)
isRestart = true;
}
}
}
}
fileIn.CloseFile();
return isRestart;
}
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);
}
// 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;
}