C++ MolAtomPtr::getResName方法代码示例

double TopparManager::getVdwRadius(MolAtomPtr pAtom, bool bExplH)
{
  LString resn = pAtom->getResName();
  
  TopoDB *pDB = getTopoDB();

  // Resolve alias name
  ResiToppar *pTop = pDB->get(resn);
  if (pTop==NULL)
    return elemBasedVdw(pAtom->getElement());

  LString aname = pAtom->getName();
  
  TopAtom *pTA = pTop->getAtom(aname);
  if (pTA==NULL)
    return elemBasedVdw(pAtom->getElement());

  LString atype = pTA->type;

  ParamDB *pPDB = getParamDB();
  param::AtomVal *pPA = pPDB->getAtom(atype);
  if (pPA==NULL)
    return elemBasedVdw(pAtom->getElement());

  if (bExplH)
    return pPA->vdwr;

  if (pPA->vdwhr > 0.0)
    return pPA->vdwhr;

  return pPA->vdwr;
}

bool TopparManager::getCharge(MolAtomPtr pAtom, bool bExplH,
                              const LString &ns, double &rval)
{
  LString resn = pAtom->getResName();
  
  TopoDB *pDB = getTopoDB();

  // Resolve alias name
  ResiToppar *pTop = pDB->get(resn);
  if (pTop==NULL)
    return false;

  LString aname = pAtom->getName();
  return getChargeImpl(pTop, aname, ns, bExplH, rval);
  
/*
  LString ns_aname = aname;
  if (!ns.isEmpty())
    ns_aname = ns + ":" + aname;

  TopAtom *pTA = pTop->getAtom(ns_aname);
  if (pTA==NULL)
    return false;
  
  if (bExplH) {
    rval = pTA->charge;
    return true;
  }

  double prot_chg = 0.0;
  ResiToppar::BondList *pBL= pTop->getBondList();
  BOOST_FOREACH (const TopBond *pBond,
                 *pBL) {
    if (pBond->a1==pTA) {
      if (pBond->a2->elem.equals("H"))
        prot_chg += pBond->a2->charge;
    }
    else if (pBond->a2==pTA) {
      if (pBond->a1->elem.equals("H"))
        prot_chg += pBond->a1->charge;
    }
  }

  rval = pTA->charge + prot_chg;
  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;
}