pack_missing_sidechains.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/pack_missing_sidechains.cc
/// @brief  function to fix missing sidechains in input PDBs (especially those surface lysines that get sidechain-backbone clashes!)
/// @author Steven Lewis smlewi@gmail.com

// Unit headers
#include <core/pack/pack_missing_sidechains.hh>

// Package headers
#include <core/pack/pack_rotamers.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>

// Project headers
#include <core/chemical/AtomType.hh>
#include <core/chemical/ResidueType.hh>

// AUTO-REMOVED #include <core/id/AtomID_Mask.hh>

#include <core/pose/Pose.hh>

#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>

#include <basic/Tracer.hh>

#include <core/id/AtomID_Map.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>


// ObjexxFCL headers


static basic::Tracer TR("core.pack.pack_missing_sidechains");

namespace core {
namespace pack {

///@details this function will run rotamer trials on sidechains with missing density.  It first sets up a PackerTask with repacking freedom for residues with sidechain missing atoms in the missing AtomID_Mask, then runs rotamer_trials.  This function is smart enough to ignore missing virtual atoms
void
pack_missing_sidechains(
  core::pose::Pose & pose,
  core::id::AtomID_Mask const & missing
)
{
  //build a PackerTask to control rotamer_trials
  core::pack::task::PackerTaskOP task = core::pack::task::TaskFactory::create_packer_task( pose );
  task->initialize_from_command_line();
  task->restrict_to_repacking();

  utility::vector1_bool repackable;
  bool something_to_pack = figure_out_repackable_residues( pose, missing, repackable );
  if (!something_to_pack) return;

  //task is set up
  task->restrict_to_residues(repackable);

  core::scoring::ScoreFunctionOP sfxn = scoring::ScoreFunctionFactory::create_score_function( "standard", "score12" );
  (*sfxn)(pose); // structure must be scored before rotamer_trials can be called (?)
  //chu change from rotamer_trials to pack_rotamers
  core::pack::pack_rotamers( pose, *sfxn, task );
}//pack_missing_sidechains


bool figure_out_repackable_residues( core::pose::Pose & pose,
  core::id::AtomID_Mask const & to_repack,
  utility::vector1_bool& repackable
) {
  repackable.resize( pose.total_residue() );
  bool any_to_repack(false);

  //set up the PackerTask
  //iterate over all sidechain atoms, and compare to the state of the input missing map.
  for ( core::Size resid(1); resid <= pose.total_residue(); ++resid ) {

    //iterate over all heavy sidechain atoms
    core::chemical::ResidueType const & restype(pose.residue_type(resid));

    for( core::Size atomno=restype.first_sidechain_atom(); atomno <= restype.nheavyatoms(); ++atomno) {
      core::id::AtomID atomid(atomno, resid);
      //if the atom is to_repack and not a virtual atom...
      if ( to_repack.get(atomid) &&
        ! restype.is_virtual(atomno) &&
        restype.atom_type(atomno).name() != "ORBS"  &&
        restype.atom_type(atomno).name() != "LPbb"
      ) {
        TR << "packing residue number " << resid << " because of missing atom number " << atomno << " atom name "
           << restype.atom_name(atomno) << std::endl;
        repackable[resid] = true;
        any_to_repack = true;
        break; //we can stop now
      }
    }//for all sidechain heavyatoms
  }//all residues
  return any_to_repack; //return early - prevents weird "0 residues at 0 positions" packer calls
}

} //namespace pack
} //namespace core