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C++ MolAtomPtr类代码示例

本文整理汇总了C++中MolAtomPtr类的典型用法代码示例。如果您正苦于以下问题：C++ MolAtomPtr类的具体用法？C++ MolAtomPtr怎么用？C++ MolAtomPtr使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。


在下文中一共展示了MolAtomPtr类的15个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的C++代码示例。

示例1: aiter

bool MolSurfBuilder::init(MolCoordPtr pmol)
{
  AtomIterator aiter(pmol);
  int i, natoms=0;

  // count atom number
  for (aiter.first(); aiter.hasMore(); aiter.next()) {
    MolAtomPtr pAtom = aiter.get();
    MB_ASSERT(!pAtom.isnull());
    ++natoms;
  }

  // copy to the m_data
  m_data.resize(natoms);
  m_tree.alloc(natoms);
  for (i=0,aiter.first(); aiter.hasMore()&&i<natoms; aiter.next(),++i) {
    MolAtomPtr pAtom = aiter.get();
    m_data[i].pos = pAtom->getPos();
    m_data[i].rad = 1.5;
    m_data[i].aid = pAtom->getID();

    m_tree.setAt(i, m_data[i].pos, i);
  }

  // build BSP tree
  m_tree.build();

  m_rmax = 1.5;
  m_rprobe = 1.2;
  return true;
}
开发者ID:biochem-fan，项目名称:cuemol2，代码行数:31，代码来源:MolSurfBuilder.cpp

示例2: getVdwRadius

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;
}
开发者ID:biochem-fan，项目名称:cuemol2，代码行数:32，代码来源:TopparManager.cpp

示例3: drawSelInterAtomLine

static void drawSelInterAtomLine(MolAtomPtr pAtom1, MolAtomPtr pAtom2,
                                 DisplayContext *pdl)
{
  if (pAtom1.isnull() || pAtom2.isnull()) return;

  pdl->vertex(pAtom1->getPos());
  pdl->vertex(pAtom2->getPos());
}
开发者ID:biochem-fan，项目名称:cuemol2，代码行数:8，代码来源:SelectionRenderer.cpp

示例4: rendAtom

void BallStickRenderer::rendAtom(DisplayContext *pdl, MolAtomPtr pAtom, bool)
{
  if (m_sphr>0.0) {
    pdl->color(ColSchmHolder::getColor(pAtom));
    pdl->sphere(m_sphr, pAtom->getPos());
  }
  
  checkRing(pAtom->getID());
}
开发者ID:biochem-fan，项目名称:cuemol2，代码行数:9，代码来源:BallStickRenderer.cpp

示例5: getCharge

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;
*/
}
开发者ID:biochem-fan，项目名称:cuemol2，代码行数:47，代码来源:TopparManager.cpp

示例6: drawAtom

void SimpleRenderer::drawAtom(MolAtomPtr pAtom, DisplayContext *pdl)
{
  pdl->color(ColSchmHolder::getColor(pAtom));
  const Vector4D pos = pAtom->getPos();
  const double rad = 0.25;
  pdl->drawAster(pos, rad);
  ++m_nAtomDrawn;
}
开发者ID:CueMol，项目名称:cuemol2，代码行数:8，代码来源:SimpleRenderer.cpp

示例7: LOG_DPRINTLN

/// Convert from (persistent) string representation to aid
int MolCoord::fromStrAID(const LString &strid) const
{
  if (!m_reAid.match(strid)) {
    LOG_DPRINTLN("MolCoord> Invalid aid strid=%s (re match failed)", strid.c_str());
    return -1;
  }

  // text type aid
  int nsc = m_reAid.getSubstrCount();
  if (nsc<4) {
    LOG_DPRINTLN("MolCoord> Invalid aid strid=%s", strid.c_str());
    return -1;
  }
  //elem.setAtomID(-1);
  LString sChainName = m_reAid.getSubstr(1);
  LString sResInd = m_reAid.getSubstr(2);
  ResidIndex nResInd;
  if (!sResInd.toInt(&nResInd.first)) {
    LOG_DPRINTLN("MolCoord> Invalid aid resid value=%s", sResInd.c_str());
    return -1;
  }
  LString sInsCode = m_reAid.getSubstr(3);
  if (sInsCode.isEmpty())
    nResInd.second = '\0';
  else
    nResInd.second = sInsCode.getAt(0);
  LString sAtomName = m_reAid.getSubstr(4);
  char cAltLoc = '\0';
  if (nsc>6) {
    LString sAltLoc = m_reAid.getSubstr(6);
    if (!sAltLoc.isEmpty())
      cAltLoc = sAltLoc.getAt(0);
  }

  MolAtomPtr pAtom = getAtom(sChainName, nResInd, sAtomName, cAltLoc);
  if (pAtom.isnull()) {
    LOG_DPRINTLN("MolCoord> fromStrAID/ atom <%s %s %s %c> not found in %s",
		 sChainName.c_str(), nResInd.toString().c_str(), sAtomName.c_str(),
		 cAltLoc=='\0'?' ':cAltLoc,
		 getName().c_str());
    return -1;
  }

  return pAtom->getID();
}
开发者ID:CueMol，项目名称:cuemol2，代码行数:46，代码来源:MolCoord.cpp

示例8: getClientMol

void TubeRenderer::beginRend(DisplayContext *pdl)
{
  if (!m_pts->isValid())
    m_pts->setupSectionTable();

  super_t::beginRend(pdl);

  if (m_nPuttyMode==TBR_PUTTY_OFF) {
    return;
  }

  // calc max bfac/occ in the putty mode

  SelectionPtr pSel;
  MolCoordPtr pMol = getClientMol();
  //MolRenderer *pMolRend = dynamic_cast<MolRenderer *>(pRend);
  //if (pMolRend!=NULL && m_nAuto==BFA_REND)
  pSel = getSelection();

  double dmin = 1.0e100, dmax = -1.0e100, val, dsum = 0.0;
  int nadd=0;
  ResidIterator iter(pMol, pSel);
  for (iter.first(); iter.hasMore(); iter.next()) {
    MolResiduePtr pRes = iter.get();
    MolAtomPtr pAtom = getPivotAtom(pRes);

    if (pAtom.isnull()) continue;
    
    if (m_nPuttyMode==TBR_PUTTY_OCC)
      val = pAtom->getOcc();
    else
      val = pAtom->getBfac();
    
    dsum += val;
    dmin = qlib::min(dmin, val);
    dmax = qlib::max(dmax, val);
    ++nadd;
  }
  
  m_dParHi = dmax;
  m_dParLo = dmin;
  m_dParAver = dsum/double(nadd);

  MB_DPRINTLN("Tube> init high=%f, low=%f, aver=%f OK.", dmax, dmin, m_dParAver);
}
开发者ID:biochem-fan，项目名称:cuemol2，代码行数:45，代码来源:TubeRenderer.cpp

示例9: iter

void MolArrayMap::setup(MolCoordPtr pRefMol)
{
  m_data.erase(m_data.begin(), m_data.end());
  int i = 0;
  AtomIterator iter(pRefMol);
  for (iter.first(); iter.hasMore(); iter.next(), ++i) {
    MolAtomPtr pa = iter.get();
    MolArrayMapElem a;
    a.chain = pa->getChainName().c_str();
    a.resid = pa->getResIndex().toInt();
    a.atom = pa->getName().c_str();
    a.pA = pa;
    m_data.insert(data_t::value_type(a, -1));
    //MB_DPRINTLN("fitref %s %d %s", a.chain.c_str(), a.resid, a.atom.c_str());
  }

  setupIndex();
}
开发者ID:CueMol，项目名称:cuemol2，代码行数:18，代码来源:MolArrayMap.cpp

示例10: iter

bool BfacColoring::init(MolCoordPtr pMol, Renderer *pRend)
{
  if (m_nMode!=BFC_CENTER && !isAutoMode()) return true;

  m_parAutoLo = m_parAutoHi = 0.0;
  // MolCoordPtr pMol(pRend->getClientObj(), qlib::no_throw_tag());
  if (pMol.isnull()) {
    return false;
  }
  
  if (m_nMode==BFC_CENTER) {
    m_vCenter = pMol->getCenterPos(false);
    if (!isAutoMode())
      return true;
  }

  SelectionPtr pSel;
  MolRenderer *pMolRend = dynamic_cast<MolRenderer *>(pRend);
  if (pMolRend!=NULL && m_nAuto==BFA_REND)
    pSel = pMolRend->getSelection();

  {
    double dmin = 1.0e100, dmax = -1.0e100, val;
    AtomIterator iter(pMol, pSel);
    for (iter.first(); iter.hasMore(); iter.next()) {
      MolAtomPtr pAtom = iter.get();
      if (m_nMode==BFC_OCC)
        val = pAtom->getOcc();
      else if (m_nMode==BFC_CENTER)
        val = (pAtom->getPos()-m_vCenter).length();
      else
        val = pAtom->getBfac();
      
      dmin = qlib::min(dmin, val);
      dmax = qlib::max(dmax, val);
    }

    MB_DPRINTLN("BfaxColoring> init high=%f, low=%f, OK.", dmax, dmin);
    m_parAutoHi = dmax;
    m_parAutoLo = dmin;
  }

  return true;
}
开发者ID:biochem-fan，项目名称:cuemol2，代码行数:44，代码来源:BfacColoring.cpp

示例11: rendAtom

void SelectionRenderer::rendAtom(DisplayContext *pdl, MolAtomPtr pAtom, bool fbonded)
{
  if (m_nMode==0) {
    if (!fbonded)
      drawSelAtom(pAtom, pdl);
  }
  else {
    pdl->vertex(pAtom->getPos());
    //Vector4D pos = pAtom->getPos();
    //pdl->drawPixels(pos, m_boximg, *(m_color.get()));
  }
}
开发者ID:biochem-fan，项目名称:cuemol2，代码行数:12，代码来源:SelectionRenderer.cpp

示例12: appendAtomScrHelper

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);
}
开发者ID:CueMol，项目名称:cuemol2，代码行数:30，代码来源:MolCoord.cpp

示例13: formatAtomName

LString PDBFileWriter::formatAtomName(MolAtomPtr pAtom)
{
  LString atomnam = pAtom->getName();
  char cConfID = pAtom->getConfID();
  int elem = pAtom->getElement();
  
  if (cConfID=='\0')
    cConfID = ' ';

  // invalid name case
  if (atomnam.length()>=4||
      elem==ElemSym::XX) {
    return LString::format("%4s%c", atomnam.c_str(), cConfID);
  }

  LString elenam = ElemSym::symID2Str(elem);
  elenam = elenam.toUpperCase();
  int elepos = atomnam.indexOf(elenam);
  if (elepos<0) {
    return LString::format("%4s%c", atomnam.c_str(), cConfID);
  }
  
  LString atommod;
  // if (atomnam.equals(elenam)) {
  // // atom name==elem name
  // shead += LString::format(" %2s  ", elenam.c_str());
  // break;
  // }
  
  elepos += elenam.length();
  atommod = atomnam.substr(elepos);
  elenam = atomnam.substr(0, elepos);
  
  if (atommod.length()<=2) {
    return LString::format("%2s%-2s%c",
                           elenam.c_str(), atommod.c_str(), cConfID);
  }
  
  return LString::format("%4s%c", atomnam.c_str(), cConfID);
}
开发者ID:CueMol，项目名称:cuemol2，代码行数:40，代码来源:PDBFileWriter.cpp

示例14: getAtomColor

bool AtomPropColoring::getAtomColor(MolAtomPtr pAtom, gfx::ColorPtr &col)
{
  MB_DPRINTLN("***** AtomPropCol getAtomColor called");
  try {
    int ccode = pAtom->getAtomPropInt(m_propname);
    col = gfx::SolidColorPtr(new gfx::SolidColor(ccode)); 
  }
  catch (...) {
    col = SolidColor::createRGB(0.5,0.5,0.5);
    //return false;
  }
  return true;
}
开发者ID:biochem-fan，项目名称:cuemol2，代码行数:13，代码来源:AtomPropColoring.cpp

示例15: drawInterAtomLine

void BallStickRenderer::drawInterAtomLine(MolAtomPtr pAtom1, MolAtomPtr pAtom2,
                                          DisplayContext *pdl)
{
  if (pAtom1.isnull() || pAtom2.isnull()) return;

  const Vector4D pos1 = pAtom1->getPos();
  const Vector4D pos2 = pAtom2->getPos();

  ColorPtr pcol1 = ColSchmHolder::getColor(pAtom1);
  ColorPtr pcol2 = ColSchmHolder::getColor(pAtom2);

  if ( pcol1->equals(*pcol2.get()) ) {
    pdl->color(pcol1);
    pdl->cylinder(m_bondw, pos1, pos2);
  }
  else {
    const Vector4D mpos = (pos1 + pos2).divide(2.0);
    pdl->color(pcol1);
    pdl->cylinder(m_bondw, pos1, mpos);
    pdl->color(pcol2);
    pdl->cylinder(m_bondw, pos2, mpos);
  }
}
开发者ID:biochem-fan，项目名称:cuemol2，代码行数:23，代码来源:BallStickRenderer.cpp


注：本文中的MolAtomPtr类示例由纯净天空整理自Github/MSDocs等开源代码及文档管理平台，相关代码片段筛选自各路编程大神贡献的开源项目，源码版权归原作者所有，传播和使用请参考对应项目的License；未经允许，请勿转载。