OptCysHG.cc

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// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
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/// @file   core/pack/task/operation/OptCysHG.cc
/// @brief  run optH on non-disulfided bonded CYS only; meant to relieve
///         any clashes caused by swapping of CYD->CYS after calling
///         Conformation::detect_disulfides()
/// @author Yih-En Andrew Ban (yab@u.washington.edu)

// unit headers
#include <core/pack/task/operation/OptCysHG.hh>
#include <core/pack/task/operation/OptCysHGCreator.hh>

// package headers
#include <core/pack/task/operation/OptH.hh>

// package headers
#include <core/chemical/AA.hh>
#include <core/chemical/VariantType.hh>
#include <core/conformation/Residue.hh>
// AUTO-REMOVED #include <core/pack/task/PackerTask.hh>
#include <core/pose/Pose.hh>

#include <utility/vector1.hh>



namespace core {
namespace pack {
namespace task {
namespace operation {


/// @brief default constructor
OptCysHG::OptCysHG() :
  Super()
{}


/// @brief copy constructor
OptCysHG::OptCysHG( OptCysHG const & rval ) :
  Super( rval )
{}


/// @brief default destructor
OptCysHG::~OptCysHG() {}

TaskOperationOP OptCysHGCreator::create_task_operation() const
{
  return new OptCysHG;
}

/// @brief clone this object
OptCysHG::TaskOperationOP OptCysHG::clone() const {
  return new OptCysHG( *this );
}


/// @brief apply operations to PackerTask
void OptCysHG::apply( Pose const & pose, PackerTask & task ) const {
  using core::chemical::aa_cys;
  using core::chemical::DISULFIDE;

  OptH optH;

  // restrict to only non-disulfide bonded CYS
  for ( Size i = 1, ie = pose.n_residue(); i <= ie; ++i ) {
    if ( !strncmp(pose.residue_type(i).name3().c_str(), "CYS", 3) || pose.residue( i ).aa() != aa_cys || pose.residue( i ).has_variant_type( DISULFIDE ) ) { //check both names to be double sure; used in fake Cys catalytic residues
      optH.disallow_resid( i );
    }
  }

  optH.apply( pose, task );
}


} // namespace operation
} // namespace task
} // namespace pack
} // namespace core