C++ Topology::SetupCharMask方法代码示例

/** Based on the given atom mask expression determine what molecules are
  * selected by the mask.
  * \return A list of atom pairs that mark the beginning and end of each
  *         selected molecule.
  */
Action_AutoImage::pairList
  Action_AutoImage::SetupAtomRanges( Topology const& currentParm, std::string const& maskexpr )
{
  pairList imageList;
  CharMask Mask1( maskexpr.c_str() );

  if (currentParm.SetupCharMask( Mask1 )) return imageList;
  if (Mask1.None()) return imageList;
  for (Topology::mol_iterator mol = currentParm.MolStart(); mol != currentParm.MolEnd(); mol++)
  {
    int firstAtom = mol->BeginAtom();
    int lastAtom = mol->EndAtom();
    // Check that each atom in the range is in Mask1
    bool rangeIsValid = true;
    for (int atom = firstAtom; atom < lastAtom; ++atom) {
      if (!Mask1.AtomInCharMask(atom)) {
        rangeIsValid = false;
        break;
      }
    }
    if (rangeIsValid) {
      imageList.push_back( firstAtom );
      imageList.push_back( lastAtom );
    }
  }
  mprintf("\tMask [%s] corresponds to %zu molecules\n", Mask1.MaskString(), imageList.size()/2);
  return imageList;
}

/** An atom pair list consists of 2 values for each entry, a beginning
  * index and ending index. For molecules and residues this is the first
  * and just beyond the last atom; for atoms it is just the atom itself
  * twice.
  */
Image::PairType Image::CreatePairList(Topology const& Parm, Mode modeIn,
                                       std::string const& maskExpression)
{
  PairType atomPairs;
  // Set up mask based on desired imaging mode.
  if ( modeIn == BYMOL || modeIn == BYRES ) {
    CharMask cmask( maskExpression );
    if ( Parm.SetupCharMask( cmask ) ) return atomPairs;
    cmask.MaskInfo();
    if (cmask.None()) return atomPairs;
    // Set up atom range for each entity to be imaged.
    if (modeIn == BYMOL) {
      atomPairs.reserve( Parm.Nmol()*2 );
      for (Topology::mol_iterator mol = Parm.MolStart();
                                  mol != Parm.MolEnd(); ++mol)
        CheckRange( atomPairs, cmask, mol->BeginAtom(), mol->EndAtom());
    } else { // BYRES
      atomPairs.reserve( Parm.Nres()*2 );
      for (Topology::res_iterator residue = Parm.ResStart();
                                  residue != Parm.ResEnd(); ++residue)
        CheckRange( atomPairs, cmask, residue->FirstAtom(), residue->LastAtom() );
    }
  } else { // BYATOM
    AtomMask imask( maskExpression );
    if ( Parm.SetupIntegerMask( imask ) ) return atomPairs;
    imask.MaskInfo();
    if (imask.None()) return atomPairs;
    atomPairs.reserve( Parm.Natom()*2 );
    for (AtomMask::const_iterator atom = imask.begin(); atom != imask.end(); ++atom) {
      atomPairs.push_back(  *atom    );
      atomPairs.push_back( (*atom)+1 );
    }
  }
//  mprintf("\tNumber of %ss to be imaged is %zu based on mask '%s'\n",
//           ModeString[modeIn], atomPairs.size()/2, maskIn.MaskString());
  return atomPairs;
}