C++ (Cpp) SetupImaging Examples

Example #1

File: Action_DNAionTracker.cpp Project: jonathandgough/cpptraj

Action::RetType Action_DNAionTracker::Setup(Topology* currentParm, Topology** parmAddress) {
  // Setup masks
  if (currentParm->SetupIntegerMask( p1_ )) return Action::ERR; 
  if ( p1_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask1\n");
    return Action::ERR;
  }
  if (currentParm->SetupIntegerMask( p2_ )) return Action::ERR;  
  if ( p2_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask2\n");
    return Action::ERR;
  }
  if (currentParm->SetupIntegerMask( base_ )) return Action::ERR;  
  if ( base_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask3\n");
    return Action::ERR;
  }
  if (currentParm->SetupIntegerMask( ions_ )) return Action::ERR;  
  if ( ions_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask4\n");
    return Action::ERR;
  }
  SetupImaging( currentParm->BoxType() );
  mprintf("\tPhosphate1 Mask [%s] %i atoms.\n", p1_.MaskString(), p1_.Nselected());
  mprintf("\tPhosphate2 Mask [%s] %i atoms.\n", p2_.MaskString(), p2_.Nselected());
  mprintf("\t      Base Mask [%s] %i atoms.\n", base_.MaskString(), base_.Nselected());
  mprintf("\t      Ions Mask [%s] %i atoms.\n", ions_.MaskString(), ions_.Nselected());

  return Action::OK;
}

Example #2

File: Action_DNAionTracker.cpp Project: jcr13/cpptraj

Action::RetType Action_DNAionTracker::Setup(ActionSetup& setup) {
  // Setup masks
  if (setup.Top().SetupIntegerMask( p1_ )) return Action::ERR; 
  if ( p1_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask1\n");
    return Action::ERR;
  }
  if (setup.Top().SetupIntegerMask( p2_ )) return Action::ERR;  
  if ( p2_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask2\n");
    return Action::ERR;
  }
  if (setup.Top().SetupIntegerMask( base_ )) return Action::ERR;  
  if ( base_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask3\n");
    return Action::ERR;
  }
  if (setup.Top().SetupIntegerMask( ions_ )) return Action::ERR;  
  if ( ions_.None() ) {
    mprinterr("Error: dnaiontracker: No atoms in mask4\n");
    return Action::ERR;
  }
  SetupImaging( setup.CoordInfo().TrajBox().Type() );
  mprintf("\tPhosphate1 Mask [%s] %i atoms.\n", p1_.MaskString(), p1_.Nselected());
  mprintf("\tPhosphate2 Mask [%s] %i atoms.\n", p2_.MaskString(), p2_.Nselected());
  mprintf("\t      Base Mask [%s] %i atoms.\n", base_.MaskString(), base_.Nselected());
  mprintf("\t      Ions Mask [%s] %i atoms.\n", ions_.MaskString(), ions_.Nselected());

  return Action::OK;
}

Example #3

File: Action_Watershell.cpp Project: jcr13/cpptraj

/** Set up solute and solvent masks. If no solvent mask was specified use 
  * solvent information in the current topology.
  */
Action::RetType Action_Watershell::Setup(ActionSetup& setup) {
  // Set up solute mask
  if (setup.Top().SetupIntegerMask( soluteMask_ )) return Action::ERR;
  if ( soluteMask_.None() ) {
    mprintf("Warning: No atoms in solute mask [%s].\n",soluteMask_.MaskString());
    return Action::SKIP;
  }
  // Set up solvent mask
  if (!solventmaskexpr_.empty()) {
    if (setup.Top().SetupIntegerMask( solventMask_ )) return Action::ERR;
  } else {
    solventMask_.ResetMask();
    for (Topology::mol_iterator mol = setup.Top().MolStart();
                                mol != setup.Top().MolEnd(); ++mol)
    {
      if ( mol->IsSolvent() )
        solventMask_.AddAtomRange( mol->BeginAtom(), mol->EndAtom() );
    }
  }
  if ( solventMask_.None() ) {
    if (!solventmaskexpr_.empty())
      mprintf("Warning: No solvent atoms selected by mask [%s]\n",
                solventmaskexpr_.c_str());
    else
      mprintf("Warning: No solvent atoms in topology %s\n",setup.Top().c_str());
    return Action::SKIP;
  }
  SetupImaging( setup.CoordInfo().TrajBox().Type() );
  // Create space for residues
# ifdef _OPENMP
  // Only re-allocate for larger # of residues
  if ( setup.Top().Nres() > NactiveResidues_ ) {
    if (activeResidues_thread_ != 0) {
      // Deallocate each thread
      for (int i = 0; i < NactiveResidues_; ++i)
        delete[] activeResidues_thread_[i];
    } else {
      // Initial thread allocation needed
      activeResidues_thread_ = new int*[ numthreads_ ];
    }
    // Allocate each thread
    for (int i = 0; i < numthreads_; ++i) {
      activeResidues_thread_[i] = new int[ setup.Top().Nres() ];
      std::fill( activeResidues_thread_[i], activeResidues_thread_[i] + setup.Top().Nres(), 0 );
    }
  }
  NactiveResidues_ = setup.Top().Nres();
# else
  activeResidues_.resize( setup.Top().Nres(), 0 );
# endif
  // Store current Parm
  CurrentParm_ = setup.TopAddress();
  return Action::OK;    
}

Example #4

File: Action_Distance.cpp Project: zhangxiaoyu11/mAMBER

/** Determine what atoms each mask pertains to for the current parm file.
  * Imaging is checked for in Action::Setup. 
  */
Action::RetType Action_Distance::Setup(Topology* currentParm, Topology** parmAddress) {
  if (currentParm->SetupIntegerMask( Mask1_ )) return Action::ERR;
  if (currentParm->SetupIntegerMask( Mask2_ )) return Action::ERR;
  mprintf("\t%s (%i atoms) to %s (%i atoms)",Mask1_.MaskString(), Mask1_.Nselected(),
          Mask2_.MaskString(),Mask2_.Nselected());
  if (Mask1_.None() || Mask2_.None()) {
    mprintf("\nWarning: distance: One or both masks have no atoms.\n");
    return Action::ERR;
  }
  // Set up imaging info for this parm
  SetupImaging( currentParm->BoxType() );
  if (ImagingEnabled())
    mprintf(", imaged");
  else
    mprintf(", imaging off");
  mprintf(".\n");

  return Action::OK;  
}