AssembleLinkerMover.cc

Go to the documentation of this file.

/// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
// :noTabs=false:tabSize=4:indentSize=4:
//
// (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/domain_assembly/AssembleLinkerMover.cc
/// @brief  A mover for assembling domains
/// @author James Thompson

#include <protocols/domain_assembly/AssembleLinkerMover.hh>

#include <protocols/comparative_modeling/util.hh>
// AUTO-REMOVED #include <protocols/docking/stateless/SaneDockingProtocol.hh>
// AUTO-REMOVED #include <protocols/jd2/JobDistributor.hh>
#include <protocols/loops/LoopMoverFactory.hh>
#include <protocols/loops/loop_mover/LoopMover.hh>
#include <protocols/loops/Loop.hh>
#include <protocols/loops/Loops.hh>

// AUTO-REMOVED #include <protocols/loops/loops_main.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/FragSet.fwd.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/Conformation.hh>
#include <core/pose/Pose.hh>
#include <core/pose/PDBInfo.hh>
// AUTO-REMOVED #include <core/pose/util.hh>
// AUTO-REMOVED #include <core/io/pdb/pose_io.hh>
// AUTO-REMOVED #include <core/scoring/constraints/util.hh>
// AUTO-REMOVED #include <core/scoring/ScoreFunctionFactory.hh>


#include <core/chemical/ChemicalManager.fwd.hh>

// AUTO-REMOVED #include <core/scoring/constraints/Func.hh>
// AUTO-REMOVED #include <core/scoring/constraints/Constraint.hh>
// AUTO-REMOVED #include <core/scoring/constraints/ConstraintSet.hh>
// AUTO-REMOVED #include <core/scoring/constraints/LinearPenaltyFunction.hh>
// AUTO-REMOVED #include <core/scoring/constraints/AtomPairConstraint.hh>


#include <protocols/moves/Mover.hh>
// AUTO-REMOVED #include <protocols/simple_moves/ScoreMover.hh>
// AUTO-REMOVED #include <protocols/moves/CompositionMover.hh>
// AUTO-REMOVED #include <protocols/simple_moves/ConstraintSetMover.hh>

//#include <devel/init.hh>

// C++ headers
#include <iostream>
#include <string>

// AUTO-REMOVED #include <basic/Tracer.hh>
#include <core/types.hh>
#include <utility/vector1.hh>

// option key includes

// AUTO-REMOVED #include <basic/options/keys/cm.OptionKeys.gen.hh>
// AUTO-REMOVED #include <basic/options/keys/loops.OptionKeys.gen.hh>
// AUTO-REMOVED #include <basic/options/keys/constraints.OptionKeys.gen.hh>

#include <core/util/SwitchResidueTypeSet.hh>


namespace protocols {
namespace domain_assembly {

void AssembleLinkerMover::apply( core::pose::Pose & pose ) {
    using core::Real;
    using std::string;

    char const first_chain( pose.pdb_info()->chain(1) );
    // rename second chain
    Size breakpoint(0);
    for ( Size ii = 1; ii <= pose.total_residue(); ++ii ) {
      char const chain_ii( pose.pdb_info()->chain(ii) );
      if ( !breakpoint && chain_ii != first_chain ) {
        breakpoint = ii;
      }
      pose.pdb_info()->number(ii,ii);
    }
    // make a single-chain pdb
    pose.pdb_info()->set_chains(first_chain);
    pose.conformation().reset_chain_endings();

    // new fold tree
    using core::kinematics::FoldTree;
    FoldTree new_fold_tree(pose.total_residue());
    pose.fold_tree(new_fold_tree);

    // remodel loops
    using namespace protocols::loops;
    using namespace protocols::comparative_modeling;
    Size const loop_start( breakpoint - min_loop_size_ );
    Size const loop_stop ( breakpoint + min_loop_size_ );

    core::util::switch_to_residue_type_set(
      pose, core::chemical::CENTROID
    );

    Loop loop( loop_start, loop_stop, 0, 0, false );
    LoopsOP loops = new Loops();
    loops->add_loop(loop);
    loop_mover::LoopMoverOP loop_mover = LoopMoverFactory::get_instance()->create_loop_mover(
      loop_mover_name_, loops
    );
    for ( Size ii = 1; ii <= frag_libs_.size(); ++ii ) {
      loop_mover->add_fragments( frag_libs_[ii] );
    }
    loop_mover->apply(pose);
    Size const max_tries( 10 ); // make this an option?
    bool loops_closed( false );
    for ( Size ii = 1; (ii <= max_tries) && !loops_closed; ++ii ) {
      LoopsOP loops = pick_loops_chainbreak( pose, min_loop_size_ );
      loops_closed = ( loops->size() == 0 );
      if ( loops_closed ) {
        loop_mover = LoopMoverFactory::get_instance()->create_loop_mover( loop_mover_name_, loops );
        loop_mover->apply( pose );
      }
    }

    core::util::switch_to_residue_type_set(
      pose, core::chemical::FA_STANDARD
    );
} // apply


}//namespace domain_assembly
}//namespace protocols