int Parm_CharmmPsf::FindTag(char* tag, const char* target, int tgtsize, CpptrajFile& infile) {
int nval = 0;
while (strncmp(tag,target,tgtsize)!=0) {
const char* buffer = infile.NextLine();
if ( buffer == 0 ) return 0;
sscanf(buffer,"%i %10s",&nval,tag);
}
return nval;
}
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;
}
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 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_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");
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;
}
/** Open the Charmm PSF file specified by filename and set up topology data.
* Mask selection requires natom, nres, names, resnames, resnums.
*/
int Parm_CharmmPsf::ReadParm(FileName const& fname, Topology &parmOut) {
const size_t TAGSIZE = 10;
char tag[TAGSIZE];
tag[0]='\0';
CpptrajFile infile;
if (infile.OpenRead(fname)) return 1;
mprintf(" Reading Charmm PSF file %s as topology file.\n",infile.Filename().base());
// Read the first line, should contain PSF...
const char* buffer = 0;
if ( (buffer=infile.NextLine()) == 0 ) return 1;
// Advance to <ntitle> !NTITLE
int ntitle = FindTag(tag, "!NTITLE", 7, infile);
// Only read in 1st title. Skip any asterisks.
std::string psftitle;
if (ntitle > 0) {
buffer = infile.NextLine();
const char* ptr = buffer;
while (*ptr != '\0' && (*ptr == ' ' || *ptr == '*')) ++ptr;
psftitle.assign( ptr );
}
parmOut.SetParmName( NoTrailingWhitespace(psftitle), infile.Filename() );
// Advance to <natom> !NATOM
int natom = FindTag(tag, "!NATOM", 6, infile);
if (debug_>0) mprintf("\tPSF: !NATOM tag found, natom=%i\n", natom);
// If no atoms, probably issue with PSF file
if (natom < 1) {
mprinterr("Error: No atoms in PSF file.\n");
return 1;
}
// Read the next natom lines
int psfresnum = 0;
char psfresname[6];
char psfname[6];
char psftype[6];
double psfcharge;
double psfmass;
for (int atom=0; atom < natom; atom++) {
if ( (buffer=infile.NextLine()) == 0 ) {
mprinterr("Error: ReadParmPSF(): Reading atom %i\n",atom+1);
return 1;
}
// Read line
// ATOM# SEGID RES# RES ATNAME ATTYPE CHRG MASS (REST OF COLUMNS ARE LIKELY FOR CMAP AND CHEQ)
sscanf(buffer,"%*i %*s %i %s %s %s %lf %lf",&psfresnum, psfresname,
psfname, psftype, &psfcharge, &psfmass);
parmOut.AddTopAtom( Atom( psfname, psfcharge, psfmass, psftype),
Residue( psfresname, psfresnum, ' ', ' '), 0 );
} // END loop over atoms
// Advance to <nbond> !NBOND
int bondatoms[9];
int nbond = FindTag(tag, "!NBOND", 6, infile);
if (nbond > 0) {
if (debug_>0) mprintf("\tPSF: !NBOND tag found, nbond=%i\n", nbond);
int nlines = nbond / 4;
if ( (nbond % 4) != 0) nlines++;
for (int bondline=0; bondline < nlines; bondline++) {
if ( (buffer=infile.NextLine()) == 0 ) {
mprinterr("Error: ReadParmPSF(): Reading bond line %i\n",bondline+1);
return 1;
}
// Each line has 4 pairs of atom numbers
int nbondsread = sscanf(buffer,"%i %i %i %i %i %i %i %i",bondatoms,bondatoms+1,
bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5,
bondatoms+6,bondatoms+7);
// NOTE: Charmm atom nums start from 1
for (int bondidx=0; bondidx < nbondsread; bondidx+=2)
parmOut.AddBond(bondatoms[bondidx]-1, bondatoms[bondidx+1]-1);
}
} else
mprintf("Warning: PSF has no bonds.\n");
// Advance to <nangles> !NTHETA
int nangle = FindTag(tag, "!NTHETA", 7, infile);
if (nangle > 0) {
if (debug_>0) mprintf("\tPSF: !NTHETA tag found, nangle=%i\n", nangle);
int nlines = nangle / 3;
if ( (nangle % 3) != 0) nlines++;
for (int angleline=0; angleline < nlines; angleline++) {
if ( (buffer=infile.NextLine()) == 0) {
mprinterr("Error: Reading angle line %i\n", angleline+1);
return 1;
}
// Each line has 3 groups of 3 atom numbers
int nanglesread = sscanf(buffer,"%i %i %i %i %i %i %i %i %i",bondatoms,bondatoms+1,
bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5,
bondatoms+6,bondatoms+7, bondatoms+8);
for (int angleidx=0; angleidx < nanglesread; angleidx += 3)
parmOut.AddAngle( bondatoms[angleidx ]-1,
bondatoms[angleidx+1]-1,
bondatoms[angleidx+2]-1 );
}
} else
mprintf("Warning: PSF has no angles.\n");
// Advance to <ndihedrals> !NPHI
int ndihedral = FindTag(tag, "!NPHI", 5, infile);
if (ndihedral > 0) {
if (debug_>0) mprintf("\tPSF: !NPHI tag found, ndihedral=%i\n", ndihedral);
int nlines = ndihedral / 2;
if ( (ndihedral % 2) != 0) nlines++;
for (int dihline = 0; dihline < nlines; dihline++) {
if ( (buffer=infile.NextLine()) == 0) {
mprinterr("Error: Reading dihedral line %i\n", dihline+1);
return 1;
}
// Each line has 2 groups of 4 atom numbers
int ndihread = sscanf(buffer,"%i %i %i %i %i %i %i %i",bondatoms,bondatoms+1,
bondatoms+2,bondatoms+3, bondatoms+4,bondatoms+5,
bondatoms+6,bondatoms+7);
for (int dihidx=0; dihidx < ndihread; dihidx += 4)
parmOut.AddDihedral( bondatoms[dihidx ]-1,
bondatoms[dihidx+1]-1,
bondatoms[dihidx+2]-1,
bondatoms[dihidx+3]-1 );
}
} else
mprintf("Warning: PSF has no dihedrals.\n");
mprintf("\tPSF contains %i atoms, %i residues.\n", parmOut.Natom(), parmOut.Nres());
infile.CloseFile();
return 0;
}