// write PDB file to stream
bool PDBFileWriter::write(qlib::OutStream &outs)
{
m_pMol = getTarget<MolCoord>();
if (m_pMol==NULL) {
LOG_DPRINTLN("PDBWriter> MolCoord is not attached !!");
return false;
}
// check extension record handlers
PDBFileReader::HndlrTab &htab = PDBFileReader::m_htab;
bool bUseHndlr = htab.size()>0;
MolCoord *pMol = m_pMol;
qlib::PrintStream prs(outs);
//
// write header
//
//LString sbuf = pqsys->getVersion();
//prs.formatln("REMARK PDB File Generated by CueMol (ver %s)", sbuf.c_str());
prs.formatln("REMARK PDB File Generated by CueMol2");
//
// write SSBOND record
//
writeSSBonds(prs);
//
// write LINK record
//
writeLinks(prs);
writeSecstr(prs);
//
// write extension records (CRYST1)
//
if (bUseHndlr) {
LString sbuf;
PDBFileReader::HndlrTab::const_iterator iter = htab.begin();
for (; iter!=htab.end(); ++iter) {
PDBFileReader::RecordHandler *ph = iter->second;
if (ph!=NULL && ph->write(sbuf, pMol)) {
prs.println(sbuf);
}
}
}
//
// write body (ATOM/ANISOU records)
//
int nserial = 1;
// Sort chain names by ASCII order
// take care of '_' (empty) chain
std::list<LString> chnames;
{
MolCoord::ChainIter iter = pMol->begin();
bool bHasEmptyChain = false;
for (; iter!=pMol->end(); ++iter) {
MolChainPtr pChn = iter->second;
LString chnam = (pChn->getName().c_str());
if (chnam.equals("_")) {
bHasEmptyChain = true;
continue;
}
chnames.push_back(chnam);
}
chnames.sort();
if (bHasEmptyChain)
chnames.push_back("_");
}
std::list<LString>::const_iterator cniter = chnames.begin();
for (; cniter!=chnames.end(); ++cniter) {
LString chnam = *cniter;
MolChainPtr pChn = pMol->getChain(chnam);
// format chain name
char cch = convChainName(chnam);
LString resnam;
MolChain::ResidCursor2 riter = pChn->begin2();
// int nlastres = 0;
for (; riter!=pChn->end2(); ++riter) {
//MolResiduePtr pRes = *riter;
MolResiduePtr pRes = riter->second;
if (pRes.isnull()) continue;
ResidIndex rindex = pRes->getIndex();
resnam = pRes->getName();
// format residue name
// resnam = resnam.toUpperCase();
resnam = resnam.substr(0,3);
// sort atom by AID
std::list<int> atmlist;
{
MolResidue::AtomCursor aiter = pRes->atomBegin();
for (; aiter!=pRes->atomEnd(); ++aiter) {
atmlist.push_back(aiter->second);
}
atmlist.sort();
}
std::list<int>::const_iterator iter = atmlist.begin();
for (; iter!=atmlist.end(); ++iter) {
int aid = *iter;
MolAtomPtr pAtm = pMol->getAtom(aid);
if (pAtm.isnull())
continue;
if (!m_pSel.isnull()) {
if (!m_pSel->isSelected(pAtm))
continue; // skip nonselected atom
}
writeAtomLine(nserial, rindex, resnam,
cch, pAtm, prs);
nserial++;
}
// nlastres = rindex.first;
}
// print TER record
/*prs.formatln("TER "
"%5d"
" "
"%3s "
"%1s"
"%4d"
" ",
nserial, resnam.c_str(), chnam.c_str(), nlastres);*/
prs.println("TER");
nserial ++;
}
//prs.println("END ");
prs.println("END");
return true;
}
void PDBFileWriter::writeSecstr(qlib::PrintStream &prs)
{
MolResiduePtr pRes1;
int nhx = 1;
MolCoordPtr pMol(m_pMol);
ResidIterator riter(pMol); //(MolCoordPtr(m_pMol));
// Write HELIX records
for (riter.first(); riter.hasMore(); riter.next()) {
LString sec;
LString pfx;
MolResiduePtr pRes = riter.get();
pRes->getPropStr("secondary2", sec);
// MB_DPRINTLN("%s%d => %s", pRes->getChainName().c_str(), pRes->getIndex().first, sec.c_str());
if (sec.length()>=2)
pfx= sec.substr(1,1);
if (!(sec.startsWith("H")||sec.startsWith("G")||sec.startsWith("I")))
continue;
if (pfx.equals("s"))
pRes1 = pRes;
else if (pfx.equals("e")) {
LString resn1 = pRes1->getName().substr(0,3);
LString chn1 = pRes1->getChainName().substr(0,1);
ResidIndex resix1 = pRes1->getIndex();
char ins1 = resix1.second;
if (ins1=='\0') ins1 = ' ';
LString resn2 = pRes->getName().substr(0,3);
LString chn2 = pRes->getChainName().substr(0,1);
ResidIndex resix2 = pRes->getIndex();
char ins2 = resix2.second;
if (ins2=='\0') ins2 = ' ';
prs.print("HELIX ");
// helix seqno
prs.format(" %3d", nhx);
// helix ID
prs.format(" %3d", nhx);
// start resname
prs.format(" %3s", resn1.c_str());
prs.format(" %1s", chn1.c_str());
prs.format(" %4d", resix1.first);
prs.format("%c", ins1);
// end resname
prs.format(" %3s", resn2.c_str());
prs.format(" %1s", chn2.c_str());
prs.format(" %4d", resix2.first);
prs.format("%c", ins2);
// typeof helix
int ntype = 1;
if (sec.startsWith("G"))
ntype = 5;
else if (sec.startsWith("I"))
ntype = 3;
prs.format("%2d", ntype);
prs.println("");
++nhx;
}
}
// Write SHEET records
int nsh = 1;
for (riter.first(); riter.hasMore(); riter.next()) {
LString sec;
LString pfx;
MolResiduePtr pRes = riter.get();
pRes->getPropStr("secondary2", sec);
// MB_DPRINTLN("%s%d => %s", pRes->getChainName().c_str(), pRes->getIndex().first, sec.c_str());
if (sec.length()>=2)
pfx= sec.substr(1,1);
if (!(sec.startsWith("E")))
continue;
if (pfx.equals("s"))
pRes1 = pRes;
else if (pfx.equals("e")) {
LString resn1 = pRes1->getName().substr(0,3);
LString chn1 = pRes1->getChainName().substr(0,1);
ResidIndex resix1 = pRes1->getIndex();
char ins1 = resix1.second;
if (ins1=='\0') ins1 = ' ';
LString resn2 = pRes->getName().substr(0,3);
LString chn2 = pRes->getChainName().substr(0,1);
ResidIndex resix2 = pRes->getIndex();
char ins2 = resix2.second;
if (ins2=='\0') ins2 = ' ';
prs.print("SHEET ");
// helix seqno
prs.format(" %3d", nsh);
// helix ID
prs.format(" %3d", nsh);
// num of strands
prs.print(" 1");
// start resname
prs.format(" %3s", resn1.c_str());
prs.format(" %1s", chn1.c_str());
prs.format("%4d", resix1.first);
prs.format("%c", ins1);
// end resname
prs.format(" %3s", resn2.c_str());
prs.format(" %1s", chn2.c_str());
prs.format("%4d", resix2.first);
prs.format("%c", ins2);
// direction
prs.print(" 0");
prs.println("");
++nsh;
}
} // for
}
