int SelCommand::isSelectedResid(MolResiduePtr pRes) { if (m_pSelRoot==NULL) return true; MolCoordPtr pmol = pRes->getParent(); if (pmol.isnull()) { LOG_DPRINTLN("isSelectedResid: parent mol is NULL!!"); return SEL_NONE; } MolResidue::AtomCursor iter = pRes->atomBegin(); int nsel=0, natoms=0; // m_pCurClient = pRes->getParent(); for ( ; iter!=pRes->atomEnd(); iter++) { MolAtomPtr pAtom = pmol->getAtom(iter->second); if (m_pSelRoot->isSelected(pAtom)) nsel++; natoms++; } // m_pCurClient = NULL; if (nsel==natoms) 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; }