bool PDBFileWriter::writeAtomLine(int nserial, const ResidIndex &rindex,
const char *resnam, char chainch,
MolAtomPtr pa, qlib::PrintStream &prs)
{
int resind = rindex.first;
char inscode = rindex.second;
LString atomnam = pa->getName().c_str();
// atomnam = atomnam.toUpperCase();
// conv ILE's CD name
// (CD is converted to CD1 in PDBFileReader, so this should not occur)
if (LChar::equals(resnam, "ILE") && atomnam.equals("CD"))
atomnam = "CD1";
#ifdef QTL_CONV
// conv nucl's prime to aster
atomnam.replace('\'', '*');
// convert THY's C5A to C5M
if (LChar::equals(resnam, "THY") &&
atomnam.equals("C5A")) {
atomnam = "C5M";
}
// conv nucl name
if (LChar::equals(resnam, "ADE")) {
resnam = " A";
}
else if (LChar::equals(resnam, "THY")) {
resnam = " T";
}
else if (LChar::equals(resnam, "GUA")) {
resnam = " G";
}
else if (LChar::equals(resnam, "CYT")) {
resnam = " C";
}
else if (LChar::equals(resnam, "URI")) {
resnam = " U";
}
#endif
LString shead;
shead = LString::format("%5d ", nserial);
// format atom name
shead += formatAtomName(pa);
shead += LString::format("%3s "
"%c"
"%4d"
"%c",
resnam,
chainch,
resind,
(inscode=='\0') ? ' ' : inscode);
//////////
// output to the stream
prs.print("ATOM ");
prs.print(shead);
// Get atom position before applying xformMat, if xformMat is set
Vector4D pos = pa->getRawPos();
prs.formatln(" "
"%8.3f"
"%8.3f"
"%8.3f"
"%6.2f"
"%6.2f"
" "
" ",
pos.x(),
pos.y(),
pos.z(),
pa->getOcc(),
pa->getBfac());
if (pa->hasAnIsoU()) {
prs.print("ANISOU");
prs.print(shead);
int u11 = int(pa->getU(0,0) * 1.0e4);
int u22 = int(pa->getU(1,1) * 1.0e4);
int u33 = int(pa->getU(2,2) * 1.0e4);
int u12 = int(pa->getU(0,1) * 1.0e4);
int u13 = int(pa->getU(0,2) * 1.0e4);
int u23 = int(pa->getU(1,2) * 1.0e4);
prs.formatln(" "
" %6d"
" %6d"
" %6d"
" %6d"
" %6d"
" %6d"
" ",
u11, u22, u33, u12, u13, u23);
}
return true;
}
