MolAtomPtr MolCoord::getAtom(const LString &chain, ResidIndex resid,
const LString &aname, char cConfID /*='\0'*/) const
{
MolResiduePtr pResid = getResidue(chain, resid);
if (pResid.isnull())
return MolAtomPtr();
int id = pResid->getAtomID(aname, cConfID);
if (id<0) return MolAtomPtr();
return getAtom(id);
/*
if (cConfID=='\0') {
int id = pResid->getAtomID(aname);
if (id<0) return MolAtomPtr();
return getAtom(id);
}
else {
LString key = aname + ":" + cConfID;
int id = pResid->getAtomID(key);
if (id<0) return MolAtomPtr();
return getAtom(id);
}
*/
}
int MolCoord::appendAtomScrHelper(MolAtomPtr pAtom, const LString &ch,
ResidIndex resid, const LString &resn)
{
qlib::uid_t nuid = pAtom->getParentUID();
if (nuid!=qlib::invalid_uid) {
// pAtom has been already belonged to other mol
// --> ERROR!!
MB_DPRINTLN("MolCoord.appendAtom> ERROR, pAtom already belongs to mol %d ().", nuid);
return -1;
}
pAtom->setParentUID(getUID());
pAtom->setChainName(ch);
pAtom->setResIndex(resid);
if (resn.isEmpty()) {
// res name is determined by chain name and resindex
MolResiduePtr pRes = getResidue(ch, resid);
if (pRes.isnull()) {
// ERROR!! cannot determine the residue to append to
return -1;
}
pAtom->setResName(pRes->getName());
}
else {
pAtom->setResName(resn);
}
return appendAtom(pAtom);
}
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;
}
/// read one MOL entry from stream
bool MOL2MolReader::readMol(qlib::LineStream &lin, bool bskip)
{
LString sline;
std::vector<LString> slist;
for (;;) {
sline = lin.readLine().chomp();
if (sline.isEmpty() && !lin.ready())
return false; // EOF
if (sline.equals("@<TRIPOS>MOLECULE")) {
break;
}
}
// mol_name
LString cmpd_name = lin.readLine().trim(" \t\r\n");
if (cmpd_name.isEmpty())
cmpd_name = "_"; // XXX
// molecule info
sline = lin.readLine().chomp();
split(sline, ' ', std::back_inserter(slist));
if (slist.size()<1) {
MB_THROW(MOL2FormatException, "Invalid atom info record");
}
int natoms;
if (!slist[0].toInt(&natoms)) {
MB_THROW(MOL2FormatException, "Invalid atom info record");
}
int nbonds=0;
if (slist.size()>1) {
if (!slist[1].toInt(&nbonds)) {
MB_THROW(MOL2FormatException, "Invalid atom info record");
}
}
// mol_type
LString mol_type = lin.readLine().chomp();
bool bApplyTopo = false;
if (mol_type.equals("PROTEIN") ||
mol_type.equals("NUCLEIC_ACID"))
bApplyTopo = true;
// Ignore charge_type
// Ignore mol_comment
// Search ATOM record
for (;;) {
sline = lin.readLine().chomp();
if (sline.isEmpty() && !lin.ready())
return false; // EOF
if (sline.equals("@<TRIPOS>ATOM")) {
break;
}
}
int i, idot, iresid, naid, ind, prev_resid;
ElemID eleid;
double xx, yy, zz;
LString aname, atype, satom, res_name;
std::map<int,int> atommap;
std::map<LString, int> aname_counts;
std::map<LString, int>::iterator an_iter;
// XXXX
prev_resid = -999999;
for (i=0; i<natoms; ++i) {
//LOG_DPRINTLN("i=%d, natoms=%d", i, natoms);
sline = lin.readLine().chomp();
slist.clear();
split(sline, ' ', std::back_inserter(slist));
if (slist.size()<8) {
MB_THROW(MOL2FormatException, "Invalid atom record");
}
if (!slist[0].toInt(&ind)) {
MB_THROW(MOL2FormatException, "Invalid atom ID record");
}
aname = slist[1];
an_iter = aname_counts.find(aname);
if (an_iter==aname_counts.end()) {
aname_counts.insert(std::pair<LString, int>(aname, 1));
}
else {
an_iter->second = an_iter->second + 1;
aname = LString::format("%d%s", an_iter->second, aname.c_str());
}
if (!slist[2].toRealNum(&xx)) {
MB_THROW(MOL2FormatException, "Invalid atom coord record");
}
if (!slist[3].toRealNum(&yy)) {
MB_THROW(MOL2FormatException, "Invalid atom coord record");
}
if (!slist[4].toRealNum(&zz)) {
MB_THROW(MOL2FormatException, "Invalid atom coord record");
}
atype = slist[5];
satom = "";
idot = atype.indexOf('.');
if (idot<0) {
satom = atype;
}
else if (idot>0) {
satom = atype.substr(0, idot);
}
else {
MB_THROW(MOL2FormatException, "Invalid SYBYL atom type");
}
iresid = 0;
if (!slist[6].toInt(&iresid)) {
MB_THROW(MOL2FormatException, "Invalid atom resid record");
}
res_name = slist[7];
if (res_name.equals("<0>"))
res_name = cmpd_name;
if (bApplyTopo) {
// protein or nucleic acid
// strip residue number from res_name
int ntmp;
if (res_name.substr(3).toInt(&ntmp)) {
res_name = res_name.substr(0, 3);
iresid = ntmp;
}
if (iresid!=prev_resid)
// residue is changed --> clear atom name count
aname_counts.clear();
}
eleid = ElemSym::str2SymID(satom);
// LOG_DPRINTLN("Atom: %f, %f, %f, <%s> %d", xx, yy, zz, aname.c_str(), eleid);
if (!bskip) {
MolAtomPtr pAtom = MolAtomPtr(MB_NEW MolAtom());
pAtom->setParentUID(m_pMol->getUID());
pAtom->setName(aname);
pAtom->setElement(eleid);
pAtom->setChainName(m_sCurrChName);
pAtom->setResIndex(iresid);
pAtom->setResName(res_name);
pAtom->setPos(Vector4D(xx,yy,zz));
pAtom->setBfac(0.0);
pAtom->setOcc(1.0);
naid = m_pMol->appendAtom(pAtom);
if (naid<0)
MB_THROW(MOL2FormatException, "appendAtom() failed");
atommap.insert(std::pair<int,int>(ind, naid));
m_nReadAtoms++;
}
prev_resid = iresid;
}
// Search BOND record
for (;;) {
sline = lin.readLine().chomp();
if (sline.isEmpty() && !lin.ready())
return false; // EOF
if (sline.equals("@<TRIPOS>BOND")) {
break;
}
}
int natm1, natm2;
int natm_id1, natm_id2;
std::map<int,int>::const_iterator iter;
for (i=0; i<nbonds; ++i) {
sline = lin.readLine().chomp();
slist.clear();
split(sline, ' ', std::back_inserter(slist));
if (slist.size()<4) {
MB_THROW(MOL2FormatException, "Invalid bond record");
}
if (!slist[1].toInt(&natm1)) {
MB_THROW(MOL2FormatException, "Invalid bond line (atom1)");
}
if (!slist[2].toInt(&natm2)) {
MB_THROW(MOL2FormatException, "Invalid bond line (atom2)");
}
LString sbont = slist[3];
if (!bskip) {
iter = atommap.find(natm1);
if (iter==atommap.end())
MB_THROW(MOL2FormatException, "Invalid bond line (bond atom1 not found)");
natm_id1 = iter->second;
iter = atommap.find(natm2);
if (iter==atommap.end())
MB_THROW(MOL2FormatException, "Invalid bond line (bond atom2 not found)");
natm_id2 = iter->second;
MolBond *pB = m_pMol->makeBond(natm_id1, natm_id2, true);
if (pB==NULL)
MB_THROW(MOL2FormatException, "makeBond failed");
if (sbont.equals("1"))
pB->setType(MolBond::SINGLE);
else if (sbont.equals("2"))
pB->setType(MolBond::DOUBLE);
else if (sbont.equals("3"))
pB->setType(MolBond::TRIPLE);
else if (sbont.equals("ar")||sbont.equals("am"))
pB->setType(MolBond::DELOC);
m_nReadBonds++;
}
//LOG_DPRINTLN("bond %d<-->%d: %d", natm_id1, natm_id2, nbont);
}
if (bApplyTopo) {
m_pMol->applyTopology();
if (mol_type.equals("PROTEIN"))
m_pMol->calcProt2ndry(-500.0);
if (mol_type.equals("NUCLEIC_ACID"))
m_pMol->calcBasePair(3.7, 30);
}
else {
// Set noautogen prop to this residue,
// to avoid topology autogen, when saved to and loaded from the qdf stream.
if (!bskip) {
iter = atommap.begin();
if (iter!=atommap.end()) {
int aid0 = iter->second;
MolAtomPtr pA = m_pMol->getAtom(aid0);
if (!pA.isnull()) {
MolResiduePtr pRes = pA->getParentResidue();
if (!pRes.isnull()) {
pRes->setPropStr("noautogen", "true");
}
}
}
}
}
/*
*/
return true;
}
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;
}
