DesignAroundOperation.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   protocols/toolbox/task_operations/DesignAroundOperation.cc
/// @brief
/// @author Sarelf Fleishman sarelf@uw.edu

// Unit Headers
#include <protocols/toolbox/task_operations/DesignAroundOperation.hh>
#include <protocols/toolbox/task_operations/DesignAroundOperationCreator.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/pose/selection.hh>

// Project Headers
#include <core/pose/Pose.hh>

// AUTO-REMOVED #include <core/pack/task/PackerTask.hh>
// AUTO-REMOVED #include <core/pack/task/operation/TaskOperations.hh>

// Utility Headers
#include <core/types.hh>
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <utility/vector1.hh>
#include <core/conformation/Conformation.hh>
#include <utility/tag/Tag.hh>
#include <core/pack/task/operation/ResLvlTaskOperations.hh>
// AUTO-REMOVED #include <basic/options/keys/pose_metrics.OptionKeys.gen.hh>
// AUTO-REMOVED #include <basic/options/option.hh>
#include <core/pack/task/operation/OperateOnCertainResidues.hh>
// AUTO-REMOVED #include <core/pack/task/operation/NoRepackDisulfides.hh>
// AUTO-REMOVED #include <protocols/toolbox/task_operations/RestrictToInterface.hh>
// AUTO-REMOVED #include <protocols/toolbox/task_operations/RestrictChainToRepackingOperation.hh>
// AUTO-REMOVED #include <protocols/toolbox/task_operations/PreventChainFromRepackingOperation.hh>
// Auto-header: duplicate removed #include <core/pack/task/operation/TaskOperations.hh>

#include <boost/foreach.hpp>
#define foreach BOOST_FOREACH

// C++ Headers
#include <set>

#include <utility/vector0.hh>


using basic::Error;
using basic::Warning;
static basic::Tracer TR( "protocols.toolbox.TaskOperations.DesignAroundOperation" );

namespace protocols {
namespace toolbox {
namespace task_operations {

using namespace core::pack::task::operation;
using namespace std;

DesignAroundOperation::DesignAroundOperation() :
  design_shell_( 8.0 ),
  repack_shell_( 8.0 ),
  allow_design_( true ),
  string_resnums_( "" )
{
  resid_.clear();
}

DesignAroundOperation::~DesignAroundOperation() {}

core::pack::task::operation::TaskOperationOP
DesignAroundOperationCreator::create_task_operation() const
{
  return new DesignAroundOperation;
}

core::pack::task::operation::TaskOperationOP DesignAroundOperation::clone() const
{
  return new DesignAroundOperation( *this );
}

///@brief restricts to repacking all residues outside of design_shell_ around each residue
void
DesignAroundOperation::apply( core::pose::Pose const & pose, core::pack::task::PackerTask & task ) const
{
  using namespace core::pack::task::operation;


  runtime_assert( repack_shell() >= design_shell() );
  set< core::Size > focus_residues;// all of the residues that were input (notice that the method is const, so I can't change resid_)
  focus_residues.clear();
  focus_residues.insert( resid_.begin(), resid_.end() );
  set< core::Size > const res_vec( core::pose::get_resnum_list( string_resnums_, pose ) );
  focus_residues.insert( res_vec.begin(), res_vec.end() );

    utility::vector1< core::Size > packing_residues, prevent_repacking_residues;
  packing_residues.clear(); prevent_repacking_residues.clear();
  for( core::Size i=1; i<=pose.total_residue(); ++i ){
    bool allow_design_res( false );
    bool allow_packing( false );
    foreach( core::Size const res, focus_residues ){ // don't change anything for focus residues
      if( i == res ){
        allow_design_res = true;
        break;
      }
    }
    if( allow_design() && !allow_design_res ){
      foreach( core::Size const res, focus_residues ){
        core::Real const distance( pose.residue( i ).xyz( pose.residue( i ).nbr_atom() ).distance( pose.residue( res ).xyz( pose.residue( res ).nbr_atom() )) );
        if( distance <= design_shell() || distance <= 0.0001 /*if design_shell is specified as 0 ensure that focus residues are allowed to design*/){
          allow_design_res = true;
          break;
        }// fi distance
      } //foreach res
    }
    if( allow_design_res ) continue;
    foreach( core::Size const res, focus_residues ){
      core::Real const distance( pose.residue( i ).xyz( pose.residue( i ).nbr_atom() ).distance( pose.residue( res ).xyz( pose.residue( res ).nbr_atom() )) );
      if( distance <= repack_shell() ){
        allow_packing = true;
        break;
      }// fi distance
    } //foreach res
    if( allow_packing ) packing_residues.push_back( i );
    else prevent_repacking_residues.push_back( i );
  }//for i
///for some unfathomable reason OperateOnCertainResidues defaults to applying to all residues if none are defined, so you have to be careful here...
  OperateOnCertainResidues oocr_repacking, oocr_prevent_repacking;
  if( packing_residues.size() ){
    oocr_repacking.op( new RestrictToRepackingRLT );
    oocr_repacking.residue_indices( packing_residues );
    oocr_repacking.apply( pose, task );
  }
  if( prevent_repacking_residues.size() ){
    oocr_prevent_repacking.op( new PreventRepackingRLT );
    oocr_prevent_repacking.residue_indices( prevent_repacking_residues );
    oocr_prevent_repacking.apply( pose, task );
  }
}

void
DesignAroundOperation::design_shell( core::Real const radius )
{
  design_shell_ = radius;
  if( radius >= repack_shell() )
    repack_shell_ = radius;
}

void
DesignAroundOperation::include_residue( core::Size const resid )
{
  resid_.insert( resid );
}

void
DesignAroundOperation::parse_tag( TagPtr tag )
{
  string_resnums_ = tag->getOption< std::string >( "resnums" );// these are kept in memory until the pose is available (at apply time)
  design_shell( tag->getOption< core::Real >( "design_shell", 8.0 ) );
  allow_design( tag->getOption< bool >( "allow_design", 1 ) );
  repack_shell( tag->getOption< core::Real >( "repack_shell", 8.0 ));
  runtime_assert( design_shell() <= repack_shell() );
  TR<<"repack_shell = "<<repack_shell()<<" design shell = "<<design_shell()<<std::endl;
}
void DesignAroundOperation::parse_def( utility::lua::LuaObject const & def ) {
  if( def["resnums"] ) {
    ostringstream oss("");
    utility::lua::LuaIterator beg = def["resnums"].begin();
    for (utility::lua::LuaIterator i=beg, end; i != end; ++i) {
      if( i != beg )
        oss << ",";
      oss << (*i).to<core::Size>();
    }
    string_resnums_ = oss.str();
  }
  design_shell( def["design_shell"] ? def["design_shell"].to<core::Real>() : 8.0 );
  allow_design( def["allow_design"] ? def["allow_design"].to<bool>() : true );
  repack_shell( def["repack_shell"] ? def["repack_shell"].to<core::Real>() : 8.0 );
  runtime_assert( design_shell() <= repack_shell() );
  TR<<"repack_shell = "<<repack_shell()<<" design shell = "<<design_shell()<<std::endl;
}
} //namespace protocols
} //namespace toolbox
} //namespace task_operations