RestrictIdentitiesAtAlignedPositions.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/RestrictIdentitiesAtAlignedPositionsOperation.cc
/// @brief
/// @author Sarelf Fleishman sarelf@uw.edu

// Unit Headers
#include <protocols/toolbox/task_operations/RestrictIdentitiesAtAlignedPositions.hh>
#include <protocols/toolbox/task_operations/RestrictIdentitiesAtAlignedPositionsCreator.hh>
#include <protocols/rosetta_scripts/util.hh>
#include <core/pose/selection.hh>
#include <core/import_pose/import_pose.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Conformation.hh>
#include <protocols/toolbox/task_operations/DesignAroundOperation.hh>
#include <core/pack/task/TaskFactory.hh>
// Project Headers
#include <core/pose/Pose.hh>
#include <utility/string_util.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 <utility/tag/Tag.hh>
#include <core/pack/task/operation/ResLvlTaskOperations.hh>
#include <core/pack/task/operation/OperateOnCertainResidues.hh>

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

// C++ Headers

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

namespace protocols {
namespace toolbox {
namespace task_operations {

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

RestrictIdentitiesAtAlignedPositionsOperation::RestrictIdentitiesAtAlignedPositionsOperation() :
  RestrictOperationsBase(),
  chain_( 1 ),
  design_only_target_residues_( false ),
  prevent_repacking_( false ),
  keep_aas_( "ACDEFGHIKLMNPQRSTVWY" ),
  restrict_identities_( false )
{
  source_pose_ = new core::pose::Pose;
  res_ids_.clear();
}

RestrictIdentitiesAtAlignedPositionsOperation::~RestrictIdentitiesAtAlignedPositionsOperation() {}

core::pack::task::operation::TaskOperationOP
RestrictIdentitiesAtAlignedPositionsOperationCreator::create_task_operation() const
{
  return new RestrictIdentitiesAtAlignedPositionsOperation;
}

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

void
RestrictIdentitiesAtAlignedPositionsOperation::apply( core::pose::Pose const & pose, core::pack::task::PackerTask & task ) const
{
  using namespace protocols::rosetta_scripts;
  using namespace core::pack::task::operation;

  DesignAroundOperation dao;
  dao.design_shell( 0.01 );
  dao.repack_shell( 6.0 );
  foreach( core::Size const resid, res_ids_ ){
    core::Size const nearest_to_res = find_nearest_res( pose, *source_pose_, resid, chain() );
    if( nearest_to_res == 0 ){
      TR<<"WARNING: could not find a residue near to "<<resid<<std::endl;
      continue;
    }//fi
    RestrictAbsentCanonicalAASRLTOP racaas1 = new RestrictAbsentCanonicalAASRLT; /// used to determine the single residue identity taken from the source pose
    RestrictAbsentCanonicalAASRLTOP racaas2 = new RestrictAbsentCanonicalAASRLT; /// used to limit identities to those specified by the user
    PreventRepackingRLTOP pr = new PreventRepackingRLT;
    char const residue_id( source_pose_->residue( resid ).name1() );
    std::string residues_to_keep("");
    residues_to_keep += residue_id;
    racaas1->aas_to_keep( residues_to_keep );
    racaas2->aas_to_keep( keep_aas_ );
    OperateOnCertainResidues oocr;
    if( prevent_repacking() && source_pose_->residue( resid ).name1() == pose.residue( nearest_to_res ).name1() ) /// if the source and designed pose have the same residue identity we can additionally prevent repacking at this position
      oocr.op( pr );
    else if( restrict_identities() )
      oocr.op( racaas2 );
    else
      oocr.op( racaas1 );
    utility::vector1< core::Size > temp_vec;
    temp_vec.clear();
    temp_vec.push_back( nearest_to_res );
    oocr.residue_indices( temp_vec );
    oocr.apply( pose, task );
    dao.include_residue( nearest_to_res );
  }//foreach resid
  if( design_only_target_residues() )
    dao.apply( pose, task );
}

void
RestrictIdentitiesAtAlignedPositionsOperation::source_pose( std::string const s ) {
  core::import_pose::pose_from_pdb( *source_pose_, s );
}

void
RestrictIdentitiesAtAlignedPositionsOperation::parse_tag( TagPtr tag )
{
  using namespace protocols::rosetta_scripts;
  utility::vector1< std::string > pdb_names, start_res, stop_res;
  source_pose( tag->getOption< std::string >( "source_pdb" ) );
  std::string const res_list( tag->getOption< std::string >( "resnums" ) );
  utility::vector1< std::string > const split_reslist( utility::string_split( res_list,',' ) );
  chain( tag->getOption< core::Size >( "chain", 1 ) );
  TR<<"source_pdb: "<<tag->getOption< std::string >( "source_pdb" )<<" restricting residues: ";
  foreach( std::string const res_str, split_reslist ){
    res_ids_.push_back( core::pose::parse_resnum( res_str, *source_pose_ ) );
    TR<<res_str<<",";
  }
  design_only_target_residues( tag->getOption< bool >( "design_only_target_residues", false ) );
  prevent_repacking( tag->getOption< bool >( "prevent_repacking", false ) );
  keep_aas_ = tag->getOption< std::string >( "keep_aas", "ACDEFGHIKLMNPQRSTVWY" );
  restrict_identities( tag->hasOption( "keep_aas" ) );
  TR<<std::endl;
}

} //namespace protocols
} //namespace toolbox
} //namespace task_operations