C++ MolAtomPtr::getBfac方法代码示例

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);
}

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;
}

bool BfacColoring::getAtomColor(MolAtomPtr pAtom, gfx::ColorPtr &col)
{
  double par;
  
  if (m_nMode==BFC_OCC)
    par = pAtom->getOcc();
  else if (m_nMode==BFC_CENTER)
    par = (pAtom->getPos()-m_vCenter).length();
  else
    par = pAtom->getBfac();

  col = m_colLow;
  
  double parLo = m_parLow;
  double parHi = m_parHigh;

  if (isAutoMode()) {
    parLo = m_parAutoLo;
    parHi = m_parAutoHi;
  }

  if (par<parLo)
    col = m_colLow;
  else if (par>parHi)
    col = m_colHigh;
  else {
    double ratio;
    if (qlib::isNear4(parHi, parLo))
      ratio = 1.0;
    else
      ratio = (par-parLo)/(parHi-parLo);

    col = ColorPtr(MB_NEW gfx::GradientColor(m_colHigh, m_colLow, ratio));
  }

  return true;
}

bool PDBFileWriter::writeAtomLine(int nserial, const ResidIndex &rindex,
                                  const char *resnam, char chainch,
                                  MolAtomPtr pa, qlib::PrintStream &prs)
{
  int resind = rindex.first;
  char inscode = rindex.second;
  LString atomnam = pa->getName().c_str();
  // atomnam = atomnam.toUpperCase();

  // conv ILE's CD name
  // (CD is converted to CD1 in PDBFileReader, so this should not occur)
  if (LChar::equals(resnam, "ILE") && atomnam.equals("CD"))
    atomnam = "CD1";

#ifdef QTL_CONV
  // conv nucl's prime to aster
  atomnam.replace('\'', '*');

  // convert THY's C5A to C5M
  if (LChar::equals(resnam, "THY") &&
      atomnam.equals("C5A")) {
    atomnam = "C5M";
  }

  // conv nucl name
  if (LChar::equals(resnam, "ADE")) {
    resnam = "  A";
  }
  else if (LChar::equals(resnam, "THY")) {
    resnam = "  T";
  }
  else if (LChar::equals(resnam, "GUA")) {
    resnam = "  G";
  }
  else if (LChar::equals(resnam, "CYT")) {
    resnam = "  C";
  }
  else if (LChar::equals(resnam, "URI")) {
    resnam = "  U";
  }
#endif

  LString shead;

  shead = LString::format("%5d ", nserial);

  // format atom name
  shead += formatAtomName(pa);

  shead += LString::format("%3s "
                           "%c"
                           "%4d"
                           "%c",
                           resnam,
                           chainch,
                           resind,
                           (inscode=='\0') ? ' ' : inscode);
                           
  //////////
  // output to the stream

  prs.print("ATOM  ");
  prs.print(shead);

  // Get atom position before applying xformMat, if xformMat is set
  Vector4D pos = pa->getRawPos();

  prs.formatln("   "
               "%8.3f"
               "%8.3f"
               "%8.3f"
               "%6.2f"
               "%6.2f"
               "          "
               "    ",
               pos.x(),
               pos.y(),
               pos.z(),
               pa->getOcc(),
               pa->getBfac());

  if (pa->hasAnIsoU()) {
    prs.print("ANISOU");
    prs.print(shead);

    int u11 = int(pa->getU(0,0) * 1.0e4);
    int u22 = int(pa->getU(1,1) * 1.0e4);
    int u33 = int(pa->getU(2,2) * 1.0e4);
    int u12 = int(pa->getU(0,1) * 1.0e4);
    int u13 = int(pa->getU(0,2) * 1.0e4);
    int u23 = int(pa->getU(1,2) * 1.0e4);

    prs.formatln(" "
                 " %6d"
                 " %6d"
                 " %6d"
                 " %6d"
                 " %6d"
                 " %6d"
                 "          ",
//.........这里部分代码省略.........