C++ AtomMask::None方法代码示例

/** Print atoms for which the cumulative energy satisfies the given
  * cutoffs. Also create MOL2 files containing those atoms.
  */
int Action_Pairwise::PrintCutAtoms(Frame const& frame, int frameNum, EoutType ctype,
                                   Darray const& Earray, double cutIn)
{
  AtomMask CutMask;  // Hold atoms that satisfy the cutoff
  Darray CutCharges; // Hold evdw/eelec corresponding to CutMask atoms.

  if (Eout_ != 0) {
    if (nb_calcType_==COMPARE_REF)
      Eout_->Printf("\tPAIRWISE: Cumulative d%s:", CalcString[ctype]);
    else
      Eout_->Printf("\tPAIRWISE: Cumulative %s:", CalcString[ctype]);
    Eout_->Printf(" %s < %.4f, %s > %.4f\n", CalcString[ctype], -cutIn,
                 CalcString[ctype], cutIn);
  }
  for (AtomMask::const_iterator atom = Mask0_.begin(); atom != Mask0_.end(); ++atom)
  {
    if (fabs(Earray[*atom]) > cutIn)
    {
      if (Eout_ != 0) 
        Eout_->Printf("\t\t%[email protected]%s: %12.4f\n", *atom+1,
                    (*CurrentParm_)[*atom].c_str(), Earray[*atom]);
      CutMask.AddAtom(*atom);
      CutCharges.push_back(Earray[*atom]);
    }
  }
  // Write mol2 with atoms satisfying cutoff
  if (!mol2Prefix_.empty() && !CutMask.None()) {
    if (WriteCutFrame(frameNum, *CurrentParm_, CutMask, CutCharges, 
                      frame, mol2Prefix_ + CutName[ctype])) 
      return 1;
  }

  return 0;
}

/** Check that all atoms in mask belong to same residue. */
int Action_NMRrst::CheckSameResidue(Topology const& top, AtomMask const& mask) const {
  if (mask.None()) return -1;
  int resnum = top[mask[0]].ResNum();
  for (AtomMask::const_iterator at = mask.begin(); at != mask.end(); ++at) {
    int r = top[*at].ResNum();
    if (r != resnum) {
      mprintf("Warning: Mask atom %i %s not in same residue as %i %s\n",
              *at + 1, top.AtomMaskName(*at).c_str(),
              mask[0] + 1, top.AtomMaskName(mask[0]).c_str());
    }
  }
  return resnum;
}

/** Set up masks. */
int Cpptraj::MaskArray::SetupMasks(AtomMask const& maskIn, Topology const& topIn)
{
  if (type_ == BY_MOLECULE && topIn.Nmol() < 1) {
    mprintf("Warning: '%s' has no molecule information, cannot setup by molecule.\n",
             topIn.c_str());
    return 1;
  }
  masks_.clear();
  if ( maskIn.None() ) {
    mprintf("Warning: Nothing selected by mask '%s'\n", maskIn.MaskString());
    return 0;
  }
  int last = -1;
  int current = 0;
  maxAtomsPerMask_ = 0;
  sameNumAtomsPerMask_ = true;
  for (AtomMask::const_iterator atm = maskIn.begin(); atm != maskIn.end(); ++atm)
  {
    switch (type_) {
      case BY_ATOM     : current = *atm; break;
      case BY_RESIDUE  : current = topIn[*atm].ResNum(); break;
      case BY_MOLECULE : current = topIn[*atm].MolNum(); break;
    }
    if (current != last) {
      if (!masks_.empty())
        checkAtomsPerMask( masks_.back().Nselected() );
      masks_.push_back( AtomMask() );
      masks_.back().SetNatoms( topIn.Natom() );
    }
    masks_.back().AddSelectedAtom( *atm );
    last = current;
  }
  if (!masks_.empty())
    checkAtomsPerMask( masks_.back().Nselected() );

  return 0;
}

/** Set up each mask/integer loop. */
int ControlBlock_For::SetupBlock(CpptrajState& State, ArgList& argIn) {
  mprintf("    Setting up 'for' loop.\n");
  Vars_.clear();
  Topology* currentTop = 0;
  static const char* TypeStr[] = { "ATOMS ", "RESIDUES ", "MOLECULES ",
                                   "MOL_FIRST_RES ", "MOL_LAST_RES " };
  static const char* OpStr[] = {"+=", "-=", "<", ">"};
  description_.assign("for (");
  int MaxIterations = -1;
  int iarg = 0;
  while (iarg < argIn.Nargs())
  {
    // Advance to next unmarked argument.
    while (iarg < argIn.Nargs() && argIn.Marked(iarg)) iarg++;
    if (iarg == argIn.Nargs()) break;
    // Determine 'for' type
    ForType ftype = UNKNOWN;
    bool isMaskFor = true;
    int argToMark = iarg;
    if      ( argIn[iarg] == "atoms"       ) ftype = ATOMS;
    else if ( argIn[iarg] == "residues"    ) ftype = RESIDUES;
    else if ( argIn[iarg] == "molecules"   ) ftype = MOLECULES;
    else if ( argIn[iarg] == "molfirstres" ) ftype = MOLFIRSTRES;
    else if ( argIn[iarg] == "mollastres"  ) ftype = MOLLASTRES;
    else if ( argIn[iarg].find(";") != std::string::npos ) {
      isMaskFor = false;
      ftype = INTEGER;
    }
    // If type is still unknown, check for list.
    if (ftype == UNKNOWN) {
      if (iarg+1 < argIn.Nargs() && argIn[iarg+1] == "in") {
        ftype = LIST;
        isMaskFor = false;
        argToMark = iarg+1;
      }
    }
    // Exit if type could not be determined.
    if (ftype == UNKNOWN) {
      mprinterr("Error: for loop type not specfied.\n");
      return 1;
    }
    argIn.MarkArg(argToMark);
    Vars_.push_back( LoopVar() );
    LoopVar& MH = Vars_.back();
    int Niterations = -1;
    // Set up for specific type
    if (description_ != "for (") description_.append(", ");
    // -------------------------------------------
    if (isMaskFor)
    {
      // {atoms|residues|molecules} <var> inmask <mask> [TOP KEYWORDS]
      if (argIn[iarg+2] != "inmask") {
        mprinterr("Error: Expected 'inmask', got %s\n", argIn[iarg+2].c_str());
        return 1;
      }
      AtomMask currentMask;
      if (currentMask.SetMaskString( argIn.GetStringKey("inmask") )) return 1;
      MH.varType_ = ftype;
      Topology* top = State.DSL().GetTopByIndex( argIn );
      if (top != 0) currentTop = top;
      if (currentTop == 0) return 1;
      MH.varname_ = argIn.GetStringNext();
      if (MH.varname_.empty()) {
        mprinterr("Error: 'for inmask': missing variable name.\n");
        return 1;
      }
      MH.varname_ = "$" + MH.varname_;
      // Set up mask
      if (currentTop->SetupIntegerMask( currentMask )) return 1;
      currentMask.MaskInfo();
      if (currentMask.None()) return 1;
      // Set up indices
      if (MH.varType_ == ATOMS)
        MH.Idxs_ = currentMask.Selected();
      else if (MH.varType_ == RESIDUES) {
        int curRes = -1;
        for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
          int res = (*currentTop)[*at].ResNum();
          if (res != curRes) {
            MH.Idxs_.push_back( res );
            curRes = res;
          }
        }
      } else if (MH.varType_ == MOLECULES ||
                 MH.varType_ == MOLFIRSTRES ||
                 MH.varType_ == MOLLASTRES)
      {
        int curMol = -1;
        for (AtomMask::const_iterator at = currentMask.begin(); at != currentMask.end(); ++at) {
          int mol = (*currentTop)[*at].MolNum();
          if (mol != curMol) {
            if (MH.varType_ == MOLECULES)
              MH.Idxs_.push_back( mol );
            else {
              int res;
              if (MH.varType_ == MOLFIRSTRES)
                res = (*currentTop)[ currentTop->Mol( mol ).BeginAtom() ].ResNum();
              else // MOLLASTRES
                res = (*currentTop)[ currentTop->Mol( mol ).EndAtom()-1 ].ResNum();
//.........这里部分代码省略.........