void ResidIterator::first()
{
m_citer = m_pTarg->begin();
if (m_citer==m_pTarg->end())
return; // no chains in mol (error)
MolChainPtr pchain = m_citer->second;
m_riter = m_citer->second->begin();
if (m_riter==pchain->end()) {
// pchain is empty (no residue)
// --> try the next chain
next();
return;
}
if (m_pSel.isnull()) return;
//
if (m_pSel->isSelectedResid(*m_riter)!=Selection::SEL_NONE)
return; // OK
// proceed to the next selected residue
next();
}
void ResidIterator::next()
{
while (m_citer != m_pTarg->end()) {
MolChainPtr pchain = m_citer->second;
MB_ASSERT(!pchain.isnull());
if (m_riter != pchain->end()) {
++m_riter;
}
else {
// the m_riter reached to the end of the chain
++m_citer;
if (m_citer == m_pTarg->end())
break; // end of chain --> no more resid!!
pchain = m_citer->second;
m_riter = pchain->begin();
}
if (m_riter == pchain->end()) {
// the m_riter reached to the end of the chain
// --> check the next residue
continue;
}
if (m_pSel.isnull()) return;
if (m_pSel->isSelectedResid(*m_riter)!=Selection::SEL_NONE)
return; // OK
// check the next residue
}
return;
}
MolResiduePtr MolCoord::getResidue(const LString &chain, ResidIndex resid) const
{
MolChainPtr pChain = getChain(chain);
if (pChain.isnull())
return MolResiduePtr();
return pChain->getResidue(resid);
}
bool MolCoord::removeAtom(int atomid)
{
MolAtomPtr pAtom = getAtom(atomid);
if (pAtom.isnull() || pAtom->getParentUID()!=getUID())
return false;
m_atomPool.remove(atomid);
// invalidate ID
pAtom->setID(-1);
const LString &aname = pAtom->getName();
char cConfID = pAtom->getConfID();
ResidIndex nresid = pAtom->getResIndex();
const LString &cname = pAtom->getChainName();
MolChainPtr pCh = getChain(cname);
if (pCh.isnull())
return false;
MolResiduePtr pRes = getResidue(cname, nresid);
if (pRes.isnull())
return false;
// remove atom
if (!pRes->removeAtom(aname, cConfID))
return false;
if (pRes->getAtomSize()>0)
return true;
// purge the empty residue
if (!pCh->removeResidue(nresid))
return false;
// delete pRes;
if (pCh->getSize()>0)
return true;
// purge the empty chain
if (!removeChain(cname))
return false;
// delete pCh;
return true;
}
int SelCommand::isSelectedChain(MolChainPtr pCh)
{
if (m_pSelRoot==NULL)
return true;
MolChain::ResidCursor riter = pCh->begin();
int nsel=0, nresid=0;
for ( ; riter!=pCh->end(); riter++) {
MolResiduePtr pRes = *riter;
if (pRes.isnull())
continue;
if (isSelectedResid(pRes))
nsel++;
nresid++;
}
if (nsel==nresid)
return SEL_ALL;
else if (nsel==0)
return SEL_NONE;
else
return SEL_PART;
}
// 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;
}
bool MolCoord::appendChain(MolChainPtr pChain)
{
return m_chains.insert(ChainPool::value_type(pChain->getName(), pChain)).second;
}
int MolCoord::appendAtom(MolAtomPtr pAtom)
{
pAtom->setParentUID(getUID());
const LString &cname = pAtom->getChainName();
const LString &rname = pAtom->getResName();
const LString &aname = pAtom->getName();
ResidIndex nresid = pAtom->getResIndex();
if (cname.length()<=0 ||
aname.length()<=0) {
LString msg =
LString::format("MolCoord> ERROR: appending atom with invalid properties"
" (c:'%s' rn:'%s' ri:'%s' an:'%s')",
cname.c_str(), rname.c_str(), nresid.toString().c_str(),
aname.c_str());
MB_DPRINTLN(msg);
MB_THROW(qlib::IllegalArgumentException, msg);
return -1;
}
MolChainPtr pCh = getChain(cname);
if (pCh.isnull()) {
pCh = MolChainPtr(MB_NEW MolChain());
pCh->setParentUID(getUID());
pCh->setName(cname);
appendChain(pCh);
}
MolResiduePtr pRes = pCh->getResidue(nresid);
if (pRes.isnull()) {
pRes = MolResiduePtr(MB_NEW MolResidue());
pRes->setParentUID(getUID());
pRes->setIndex(nresid);
pRes->setName(rname);
// pRes->setChainName(cname);
pCh->appendResidue(pRes);
}
else {
const LString &pre_rname = pRes->getName();
if (!pre_rname.equals(rname)) {
MB_DPRINTLN("MolCoord> ERROR: appending an atom (%s %s%s %s) with inconsistent residue (%s)",
cname.c_str(), rname.c_str(),
nresid.toString().c_str(), aname.c_str(),
pre_rname.c_str());
// TO DO: throw exception (???)
// This is often the case, so is not an exception.
// return -1;
}
}
//
// Append to the atompool --> assign the atom ID
//
int atomid = m_atomPool.put(pAtom);
if (atomid<0) {
// This isn't fail in normal situation.
MB_THROW(qlib::RuntimeException, "append to the atompool failed");
return -1;
}
pAtom->setID(atomid);
// MolResidue::appendAtom() must be called after setID(),
// because MolResidue makes map from name to AID, which requires "AID".
if (!pRes->appendAtom(pAtom)) {
// This is often the case with malformed PDB files, so is not an exception.
MB_DPRINTLN("MolCoord> ERROR: appending duplicated atom (%s %s%s %s)",
cname.c_str(), rname.c_str(), nresid.toString().c_str(),
aname.c_str());
// Remove the mis-appended atom from the pool.
m_atomPool.remove(atomid);
return -1;
}
// Update the cached xform matrix if required
pAtom->resetXformMatrix();
if (!getXformMatrix().isIdent())
pAtom->setXformMatrix(getXformMatrix());
return atomid;
}
