C++ AtomMask::MaskString方法代码示例

// Action_Matrix::MaskToMatResArray()
Action_Matrix::MatResArray Action_Matrix::MaskToMatResArray(Topology const& currentParm,
                                                            AtomMask const& mask) const
{
  MatResArray residues;
  int currentResNum = -1;
  matrix_res blank_res;
  for (int idx = 0; idx != mask.Nselected(); idx++)
  {
    int atom1 = mask[idx];
    int resNum = currentParm[atom1].ResNum();
    if (resNum != currentResNum) {
      residues.push_back( blank_res );
      residues.back().resnum_ = resNum;
      currentResNum = resNum;
    }
    residues.back().maskIdxs_.push_back( idx );
  }
  if (debug_ > 0) {
    mprintf("DEBUG: BYRES: MASK '%s'\n", mask.MaskString());
    for (MatResArray::const_iterator res = residues.begin(); res != residues.end(); ++res) {
      mprintf("\tRes %i:", res->resnum_+1);
      for (Iarray::const_iterator it = res->maskIdxs_.begin(); it != res->maskIdxs_.end(); ++it)
        mprintf(" %i (%i)", mask[*it] + 1, *it);
      mprintf("\n");
    }
  }
  return residues;
}

// Action_Center::Init()
Action::RetType Action_Center::Init(ArgList& actionArgs, ActionInit& init, int debugIn)
{
  // Get keywords
  useMass_ = actionArgs.hasKey("mass");
  ReferenceFrame refFrm = init.DSL().GetReferenceFrame( actionArgs );
  if (refFrm.error()) return Action::ERR;
  // Determine center mode.
  if (!refFrm.empty())
    centerMode_ = REF;
  else if (actionArgs.hasKey("origin"))
    centerMode_ = ORIGIN;
  else if (actionArgs.hasKey("point")) {
    centerMode_ = POINT;
    refCenter_[0] = actionArgs.getNextDouble(0.0);
    refCenter_[1] = actionArgs.getNextDouble(0.0);
    refCenter_[2] = actionArgs.getNextDouble(0.0);
  } else
    centerMode_ = BOXCTR;

  // Get Masks
  Mask_.SetMaskString( actionArgs.GetMaskNext() );
  // Get reference mask if reference specified.
  AtomMask refMask;
  if (centerMode_ == REF) {
    std::string rMaskExpr = actionArgs.GetMaskNext();
    if (rMaskExpr.empty())
      rMaskExpr = Mask_.MaskExpression();
    refMask.SetMaskString( rMaskExpr );
    if (refFrm.Parm().SetupIntegerMask( refMask, refFrm.Coord() ))
      return Action::ERR;
    // Get center of mask in reference
    if (useMass_)
      refCenter_ = refFrm.Coord().VCenterOfMass( refMask );
    else
      refCenter_ = refFrm.Coord().VGeometricCenter( refMask );
  }

  mprintf("    CENTER: Centering coordinates using");
  if (useMass_)
    mprintf(" center of mass");
  else
    mprintf(" geometric center");
  mprintf(" of atoms in mask (%s) to\n", Mask_.MaskString());
  switch (centerMode_) {
    case ORIGIN: mprintf("\tcoordinate origin.\n"); break;
    case BOXCTR: mprintf("\tbox center.\n"); break;
    case REF:
      mprintf("\tcenter of mask (%s) in reference '%s'.\n", refMask.MaskString(),
              refFrm.refName());
      break;
    case POINT:  mprintf("\tpoint (%g, %g, %g).\n",
                         refCenter_[0], refCenter_[1], refCenter_[2]);
      break;
  }
  return Action::OK;
}

// Action_Center::Init()
Action::RetType Action_Center::Init(ArgList& actionArgs, TopologyList* PFL, DataSetList* DSL, DataFileList* DFL, int debugIn)
{
  // Get keywords
  if (actionArgs.hasKey("origin"))
    centerMode_ = ORIGIN;
  else
    centerMode_ = BOXCTR;
  useMass_ = actionArgs.hasKey("mass");
  ReferenceFrame refFrm = DSL->GetReferenceFrame( actionArgs );
  if (refFrm.error()) return Action::ERR;

  // Get Masks
  Mask_.SetMaskString( actionArgs.GetMaskNext() );
  // Get reference mask if reference specified.
  AtomMask refMask;
  if (!refFrm.empty()) {
    std::string rMaskExpr = actionArgs.GetMaskNext();
    if (rMaskExpr.empty())
      rMaskExpr = Mask_.MaskExpression();
    refMask.SetMaskString( rMaskExpr );
    if (refFrm.Parm().SetupIntegerMask( refMask, refFrm.Coord() ))
      return Action::ERR;
    // Get center of mask in reference
    if (useMass_)
      refCenter_ = refFrm.Coord().VCenterOfMass( refMask );
    else
      refCenter_ = refFrm.Coord().VGeometricCenter( refMask );
    centerMode_ = POINT; 
  }

  mprintf("    CENTER: Centering coordinates using");
  if (useMass_)
    mprintf(" center of mass");
  else
    mprintf(" geometric center");
  mprintf(" of atoms in mask (%s) to\n", Mask_.MaskString());
  if (centerMode_ == POINT)
    mprintf("\tcenter of mask (%s) in reference '%s'.\n", refMask.MaskString(),
            refFrm.refName());
  else if (centerMode_ == ORIGIN)
    mprintf("\tcoordinate origin.\n");
  else
    mprintf("\tbox center.\n");

  return Action::OK;
}

/** 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;
}

static inline Exec::RetType MaskError(AtomMask const& mask) {
  mprinterr("Error: Mask '%s' selects %i atoms, expected 1.\n",
            mask.MaskString(), mask.Nselected());
  return CpptrajState::ERR;
}