int Parm_PDB::ReadParm(std::string const& fname, Topology &TopIn) {
PDBfile infile;
double XYZ[3];
int current_res = 0;
int last_res = -1;
if (infile.OpenRead(fname)) return 1;
// Loop over PDB records
while ( infile.NextLine() != 0 ) {
if (infile.IsPDBatomKeyword()) {
// If this is an ATOM / HETATM keyword, add to topology
infile.pdb_XYZ(XYZ);
NameType pdbresname = infile.pdb_Residue( current_res );
TopIn.AddTopAtom(infile.pdb_Atom(), pdbresname, current_res, last_res, XYZ);
} else if (infile.IsPDB_TER() || infile.IsPDB_END()) {
// Indicate end of molecule for TER/END. Finish if END.
TopIn.StartNewMol();
if (infile.IsPDB_END()) break;
}
}
// If Topology name not set with TITLE etc, use base filename.
// TODO: Read in title.
std::string pdbtitle;
TopIn.SetParmName( pdbtitle, infile.Filename().Base() );
infile.CloseFile();
return 0;
}
/** Initialize and set up pairlist. */
int Ewald::Setup_Pairlist(Box const& boxIn, Vec3 const& recipLengths, double skinnbIn) {
if (pairList_.InitPairList(cutoff_, skinnbIn, debug_)) return 1;
if (pairList_.SetupPairList( boxIn.Type(), recipLengths )) return 1;
# ifdef DEBUG_PAIRLIST
// Write grid PDB
PDBfile gridpdb;
Matrix_3x3 ucell, recip;
boxIn.ToRecip(ucell, recip);
gridpdb.OpenWrite("gridpoints.pdb");
for (int iz = 0; iz != pairList_.NZ(); iz++)
for (int iy = 0; iy != pairList_.NY(); iy++)
for (int ix = 0; ix != pairList_.NX(); ix++) {
double fx = (double)ix / (double)pairList_.NX();
double fy = (double)iy / (double)pairList_.NY();
double fz = (double)iz / (double)pairList_.NZ();
Vec3 cart = ucell.TransposeMult( Vec3(fx,fy,fz) );
gridpdb.WriteHET(1, cart[0], cart[1], cart[2]);
}
gridpdb.CloseFile();
# endif
return 0;
}