C++ MolAtomPtr::setChainName方法代码示例

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);
}

//.........这里部分代码省略.........
    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;

//.........这里部分代码省略.........
  
  for (i=0; i<ncomment; ++i) {
    readLine();
    m_line = m_line.trim("\r\n ");
    LOG_DPRINTLN("%s", m_line.c_str());
  }
  readLine();

  ///////////////////
  // read atoms
  readLine();
  removeComment();

  if (!m_line.toInt(&m_natom)) {
    MB_THROW(qlib::FileFormatException, "Cannot read natom line");
    return;
  }
  MB_DPRINTLN("natoms=%d", m_natom);
  
  LString stmp;

  for (i=0; i<m_natom; ++i) {
    readLine();
    // LOG_DPRINTLN("%s", m_line.c_str());

    // chain name
    stmp = m_line.substr(9, 3);
    stmp = stmp.trim(" ");
    // stmp = stmp.toLowerCase();
    LString chain(stmp.c_str());

    // residue number
    stmp = m_line.substr(14, 4);
    int nresi;
    if (!stmp.toInt(&nresi)) {
      LString msg = LString::format("cannot convert resid number: %s", stmp.c_str());
      MB_THROW(qlib::FileFormatException, msg);
      return;
    }
    ResidIndex residx(nresi);

    //  residue name
    stmp = m_line.substr(19, 4);
    stmp = stmp.trim(" ");
    // stmp = stmp.toLowerCase();
    LString resn(stmp.c_str());

    // atom name
    stmp = m_line.substr(24, 4);
    stmp = stmp.trim(" ");
    // stmp = stmp.toLowerCase();
    LString name(stmp.c_str());
    
    // charge
    stmp = m_line.substr(34, 10);
    double charge;
    if (!stmp.toDouble(&charge)) {
      LString msg = LString::format("cannot convert charge %s", stmp.c_str());
      MB_THROW(qlib::FileFormatException, msg);
      return;
    }

    // mass
    stmp = m_line.substr(50, 8);
    double mass;
    if (!stmp.toDouble(&mass)) {
      LString msg = LString::format("cannot convert mass <%s>", stmp.c_str());
      MB_THROW(qlib::FileFormatException, msg);
      return;
    }

    ElemID eleid = convMassElem(mass);

    //LOG_DPRINTLN("ATOM %s %s %d %s",
    //(*pAtoms)[i].name.c_str(),
    //(*pAtoms)[i].resn.c_str(),
    //(*pAtoms)[i].resid,
    //(*pAtoms)[i].chain.c_str());

    MolAtomPtr pAtom = MolAtomPtr(MB_NEW MolAtom());
    pAtom->setParentUID(m_pMol->getUID());
    pAtom->setName(name);
    pAtom->setElement(eleid);
    pAtom->setChainName(chain);
    pAtom->setResIndex(residx);
    pAtom->setResName(resn);
    
    if (m_pMol->appendAtom(pAtom)<0) {
      LString stmp = m_line;
      stmp = stmp.chomp();
      // stmp = stmp.toUpperCase();
      // m_nErrCount ++;
      // if (m_nErrCount<m_nErrMax)
      LOG_DPRINTLN("PsfReader> read ATOM line failed: %s", stmp.c_str());
    }
    
  }
  readLine();

}