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); }
// 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 }
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; }