OperateOnCertainResidues.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   core/pack/task/operation/OperateOnCertainResidues.cc
/// @brief  class to support the general case of configuring PackerTask at the ResidueLevelTask level in some way, with an optional filter to limit the effects to certain residues
/// @author ashworth

// Unit Headers
#include <core/pack/task/operation/OperateOnCertainResidues.hh>
#include <core/pack/task/operation/OperateOnCertainResiduesCreator.hh>


#include <core/pose/Pose.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/operation/ResLvlTaskOperation.hh>
#include <core/pack/task/operation/ResLvlTaskOperationFactory.hh>
#include <core/pack/task/operation/ResFilter.hh>
#include <core/pack/task/operation/ResFilterFactory.hh>

#include <basic/Tracer.hh>

// Utility Headers
#include <utility/tag/Tag.hh>

#include <utility/vector0.hh>
#include <utility/vector1.hh>


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

using basic::t_info;
using basic::t_debug;
static basic::Tracer TR("core.pack.task.operation.OperateOnCertainResidues",t_info);

OperateOnCertainResidues::OperateOnCertainResidues()
  : parent(),
    op_(0),
    filter_(0)
{}

OperateOnCertainResidues::OperateOnCertainResidues(
  ResLvlTaskOperationOP rlto,
  ResFilterOP filter
)
  : parent(),
    op_( rlto ),
    filter_( filter )
{}

OperateOnCertainResidues::OperateOnCertainResidues( OperateOnCertainResidues const & src )
  : TaskOperation( src )
{
  *this = src;
}

OperateOnCertainResidues &
OperateOnCertainResidues::operator = ( OperateOnCertainResidues const & src )
{
  residue_indices_ = src.residue_indices();
  if ( src.op_ ) op_ = src.op_->clone();
  else op_ = 0;
  if ( src.filter_ ) filter_ = src.filter_->clone();
  else filter_ = 0;
  return *this;
}

OperateOnCertainResidues::~OperateOnCertainResidues() {}

TaskOperationOP OperateOnCertainResiduesCreator::create_task_operation() const
{
  return new OperateOnCertainResidues;
}

TaskOperationOP OperateOnCertainResidues::clone() const
{
  return new OperateOnCertainResidues( *this );
}

void
OperateOnCertainResidues::apply( Pose const & pose, PackerTask & ptask ) const
{
  Size const nres( pose.total_residue() );
  runtime_assert( nres == ptask.total_residue() );
  // local nonconst version of residue indices container allows default applicability over
  // all residues in input pose (while avoiding code duplication or extra function call)
  ResidueIndices residue_indices_local;
  if ( residue_indices_.empty() ) {
    for ( Size i(1); i <= nres; ++i ) residue_indices_local.push_back(i);
  } else {
    residue_indices_local = residue_indices_;
  }
  for ( ResidueIndices::const_iterator index( residue_indices_local.begin() ),
    end( residue_indices_local.end() ); index != end; ++index ) {
    runtime_assert( *index > 0 && *index <= nres );
    // skip this residue if there is a filter and it returns false
    if ( filter_ && ! (*filter_)( pose, *index ) ) continue;
    op_->apply( ptask.nonconst_residue_task( *index ) );
  }
}

void OperateOnCertainResidues::residue_indices( utility::vector1< Size > const & indices )
{
  residue_indices_ = indices;
}

void OperateOnCertainResidues::op( ResLvlTaskOperationCOP op_in )
{
  runtime_assert( op_in );
  op_ = op_in->clone();
}

void OperateOnCertainResidues::filter( ResFilterCOP filter_in )
{
  runtime_assert( filter_in );
  filter_ = filter_in->clone();
}


///@brief tag parsing for factory construction of this class and its children
/*!
Example Tag syntax for parser as of Summer 2009

<OperateOnCertainResidues name=PROTEINnopack>
  <PreventRepackingRLT/>
  <ResidueHasProperty property=PROTEIN/>
</OperateOnCertainResidues>

*/
void OperateOnCertainResidues::parse_tag( TagPtr tag )
{
  utility::vector0< TagPtr > const subtags( tag->getTags() );
  for ( utility::vector0< TagPtr >::const_iterator subtag( subtags.begin() ), end( subtags.end() );
    subtag != end; ++subtag ) {
    std::string const type( (*subtag)->getName() );
    ResLvlTaskOperationFactory * rltof = ResLvlTaskOperationFactory::get_instance();
    if ( rltof && rltof->has_type( type ) ) {
      op_ = rltof->newRLTO( type );
      op_->parse_tag( *subtag );
      TR(t_debug) << "using ResLvlTaskOperation of type " << type << std::endl;
      continue;
    }
    ResFilterFactory * res_filter_factory = ResFilterFactory::get_instance();
    if ( res_filter_factory && res_filter_factory->has_type( type ) ) {
      filter_ = res_filter_factory->newResFilter( type );
      filter_->parse_tag( *subtag );
      TR(t_debug) << "using ResFilter of type " << type << std::endl;
      continue;
    }
    utility_exit_with_message( type + " is not known to the factories passed to OperateOnCertainResidues." );
  }
}

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