fold_from_loops.cc File Reference

#include <core/types.hh>
#include <core/conformation/Conformation.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueTypeSelector.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/fragment/FragmentIO.hh>
#include <protocols/abinitio/AbrelaxApplication.hh>
#include <protocols/abinitio/ClassicAbinitio.hh>
#include <protocols/abinitio/FoldConstraints.hh>
#include <protocols/checkpoint/CheckPointer.hh>
#include <protocols/loops/SlidingWindowLoopClosure.hh>
#include <protocols/loops/SlidingWindowLoopClosure.fwd.hh>
#include <protocols/loops/Loops.hh>
#include <protocols/loops/loops_main.hh>
#include <protocols/loops/Exceptions.hh>
#include <protocols/jumping/util.hh>
#include <protocols/Protocol.hh>
#include <protocols/evaluation/PoseEvaluator.hh>
#include <core/scoring/rms_util.hh>
#include <core/scoring/rms_util.tmpl.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/ScoreFunctionFactory.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/func/Func.hh>
#include <core/pose/Pose.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/pose/util.hh>
#include <devel/init.hh>
#include <basic/options/util.hh>
#include <basic/options/option.hh>
#include <basic/Tracer.hh>
#include <core/io/pdb/pdb_writer.hh>
#include <core/io/silent/silent.fwd.hh>
#include <core/io/silent/ProteinSilentStruct.hh>
#include <core/io/silent/SilentFileData.hh>
#include <core/io/silent/SilentFileData.fwd.hh>
#include <core/io/silent/BinarySilentStruct.hh>
#include <utility/vector1.hh>
#include <utility/io/ozstream.hh>
#include <utility/string_util.hh>
#include <apps/pilot/bcorreia/fold_from_loops.hh>
#include <vector>
#include <fstream>
#include <iostream>
#include <string>
#include <basic/options/keys/out.OptionKeys.gen.hh>
#include <basic/options/keys/abinitio.OptionKeys.gen.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>
#include <basic/options/keys/loops.OptionKeys.gen.hh>
#include <basic/options/keys/fold_from_loops.OptionKeys.gen.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/TaskFactory.hh>
#include <core/pack/pack_rotamers.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/chemical/VariantType.hh>
#include <core/import_pose/import_pose.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/Energies.hh>
#include <protocols/relax/ClassicRelax.hh>
#include <core/util/SwitchResidueTypeSet.hh>

Functions
std::vector< Size >	define_cut_points (protocols::loops::Loops &loops, core::pose::Pose &nat_pose)
bool	is_loop (protocols::loops::Loops &loops, Size &residue)
bool	is_loop_neighbor (protocols::loops::Loops &loops, Size &residue, Size &range)
void	fold_tree_generator (protocols::loops::Loops &loops, std::vector< Size > &cutpoints, core::pose::Pose &pose, kinematics::FoldTree &f)
void	define_movemap_extending_chain (core::kinematics::MoveMapOP &movemap, core::pose::Pose &pose, utility::vector1< protocols::loops::Loop > &loops)
void	get_fragments (core::fragment::FragSetOP &fragset_large_, core::fragment::FragSetOP &fragset_small_)
void	extending_chain (core::kinematics::MoveMapOP &movemap, core::pose::Pose &pose)
void	copying_side_chains (core::pose::Pose &nat_pose, core::pose::Pose &fold_pose, protocols::loops::Loops &loops, core::kinematics::MoveMapOP &movemap)
void	exclude_loop_residues (core::pose::Pose &pose, utility::vector1< bool > &residues_to_mutate, utility::vector1< bool > &allowed_aas, core::pack::task::PackerTaskOP &task, protocols::loops::Loops &loops)
void	refresh_cutpoints (core::pose::Pose &pose, std::vector< Size > &cut_points)
void	CA_cst_generator (core::pose::Pose &pose, scoring::constraints::ConstraintSetOP &cst, protocols::loops::Loops &loops, std::vector< Size > &cut_points)
void	CA_cst_generator (core::pose::Pose &pose, scoring::constraints::ConstraintSetOP &cst, protocols::loops::Loops &loops)
void	new_pose_generator (core::pose::Pose &target_loops, core::pose::Pose &nat_prot, protocols::loops::Loops &loops)
void	copying_side_chains_swap_loop (core::pose::Pose &swap_loops, core::pose::Pose &fold_pose, protocols::loops::Loops &loops, core::kinematics::MoveMapOP &movemap)
void	define_movemap_extending_chain (core::kinematics::MoveMapOP &movemap, core::pose::Pose &pose, protocols::loops::Loops &loops)
bool	is_cut (std::vector< Size > &cut_points, Size &residue)
int	main (int argc, char *argv[])

Variables
static basic::Tracer	TR ("bcorreia_fold_from_loops")

Function Documentation

CA_cst_generator() [1/2]

void CA_cst_generator	(	core::pose::Pose &	pose,
		scoring::constraints::ConstraintSetOP &	cst,
		protocols::loops::Loops &	loops
	)

References basic::options::OptionKeys::fold_from_loops::ca_csts_dev, basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::templates::cst::cst, is_loop(), is_loop_neighbor(), offset, option, make_symmdef_file_denovo::pos, beta_nonlocal::pose, sd(), and TR.

CA_cst_generator() [2/2]

void CA_cst_generator	(	core::pose::Pose &	pose,
		scoring::constraints::ConstraintSetOP &	cst,
		protocols::loops::Loops &	loops,
		std::vector< Size > &	cut_points
	)

References basic::options::OptionKeys::fold_from_loops::ca_csts_dev, basic::options::OptionKeys::constraints::constraints, basic::options::OptionKeys::templates::cst::cst, is_cut(), is_loop(), option, make_symmdef_file_denovo::pos, beta_nonlocal::pose, sd(), and TR.

Referenced by main().

copying_side_chains()

void copying_side_chains	(	core::pose::Pose &	nat_pose,
		core::pose::Pose &	fold_pose,
		protocols::loops::Loops &	loops,
		core::kinematics::MoveMapOP &	movemap
	)

References is_loop(), basic::options::OptionKeys::in::file::movemap, and make_symmdef_file_denovo::pos.

Referenced by main().

copying_side_chains_swap_loop()

void copying_side_chains_swap_loop	(	core::pose::Pose &	swap_loops,
		core::pose::Pose &	fold_pose,
		protocols::loops::Loops &	loops,
		core::kinematics::MoveMapOP &	movemap
	)

References is_loop(), basic::options::OptionKeys::in::file::movemap, make_symmdef_file_denovo::pos, basic::options::OptionKeys::fold_from_loops::swap_loops, and TR.

Referenced by main().

define_cut_points()

std::vector< Size > define_cut_points	(	protocols::loops::Loops &	loops,
		core::pose::Pose &	nat_pose
	)

References loops::cutpoint, create_a3b_hbs::i, is_loop(), create_a3b_hbs::j, challenge::ss, basic::options::OptionKeys::cutoutdomain::start, and TR.

Referenced by main().

define_movemap_extending_chain() [1/2]

void define_movemap_extending_chain	(	core::kinematics::MoveMapOP &	movemap,
		core::pose::Pose &	pose,
		protocols::loops::Loops &	loops
	)

References create_a3b_hbs::i, is_loop_neighbor(), basic::options::OptionKeys::fold_from_loops::loop_mov_cterm, basic::options::OptionKeys::fold_from_loops::loop_mov_nterm, basic::options::OptionKeys::in::file::movemap, option, make_symmdef_file_denovo::pos, beta_nonlocal::pose, TR, and basic::options::OptionKeys::inout::dbms::user.

define_movemap_extending_chain() [2/2]

void define_movemap_extending_chain	(	core::kinematics::MoveMapOP &	movemap,
		core::pose::Pose &	pose,
		utility::vector1< protocols::loops::Loop > &	loops
	)

Referenced by main().

exclude_loop_residues()

void exclude_loop_residues	(	core::pose::Pose &	pose,
		utility::vector1< bool > &	residues_to_mutate,
		utility::vector1< bool > &	allowed_aas,
		core::pack::task::PackerTaskOP &	task,
		protocols::loops::Loops &	loops
	)

References is_loop(), make_symmdef_file_denovo::pos, beta_nonlocal::pose, and vancomycin::task.

Referenced by main().

extending_chain()

void extending_chain	(	core::kinematics::MoveMapOP &	movemap,
		core::pose::Pose &	pose
	)

References basic::options::OptionKeys::in::file::movemap, make_symmdef_file_denovo::pos, and beta_nonlocal::pose.

Referenced by main().

fold_tree_generator()

void fold_tree_generator	(	protocols::loops::Loops &	loops,
		std::vector< Size > &	cutpoints,
		core::pose::Pose &	pose,
		kinematics::FoldTree &	f
	)

References loops::cutpoint, create_a3b_hbs::f, create_a3b_hbs::i, beta_nonlocal::pose, and TR.

Referenced by main().

get_fragments()

void get_fragments	(	core::fragment::FragSetOP &	fragset_large_,
		core::fragment::FragSetOP &	fragset_small_
	)

References in::file::frag3(), in::file::frag9(), in::file::fragA(), in::file::fragB(), basic::options::OptionKeys::abinitio::number_3mer_frags, basic::options::OptionKeys::abinitio::number_9mer_frags, option, and basic::options::OptionKeys::inout::dbms::user.

Referenced by main().

is_cut()

bool is_cut	(	std::vector< Size > &	cut_points,
		Size &	residue
	)

References subloop_histogram::iterator, and residue.

Referenced by CA_cst_generator().

is_loop()

bool is_loop	(	protocols::loops::Loops &	loops,
		Size &	residue
	)

References create_a3b_hbs::i, residue, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by CA_cst_generator(), copying_side_chains(), copying_side_chains_swap_loop(), define_cut_points(), and exclude_loop_residues().

is_loop_neighbor()

bool is_loop_neighbor	(	protocols::loops::Loops &	loops,
		Size &	residue,
		Size &	range
	)

References create_a3b_hbs::i, range, residue, and basic::options::OptionKeys::cutoutdomain::start.

Referenced by CA_cst_generator(), and define_movemap_extending_chain().

main()

int main	(	int	argc,
		char *	argv[]
	)

References basic::options::OptionKeys::fold_from_loops::add_relax_cycles, argv, CA_cst_generator(), basic::options::OptionKeys::loops::ccd_closure, copying_side_chains(), copying_side_chains_swap_loop(), pyrosetta::create_score_function, define_cut_points(), define_movemap_extending_chain(), basic::options::OptionKeys::matdes::dock::dump_pdb, test.T009_Exceptions::e, exclude_loop_residues(), basic::options::OptionKeys::in::file::extended_pose, extending_chain(), create_a3b_hbs::f, lactamize::filename, basic::Tracer::flush(), fold_tree_generator(), get_fragments(), create_a3b_hbs::i, basic::init(), load_checkpoint(), kic_runner::loop_file, basic::options::OptionKeys::in::file::movemap, basic::options::OptionKeys::fold_from_loops::native_ca_cst, new_pose_generator(), local::nstruct, out::nstruct(), option, lactamize::outfile, basic::options::OptionKeys::jumps::overlap_chainbreak, out::pdb(), pyrosetta.distributed.io::pose_from_file, out::prefix(), basic::options::OptionKeys::in::file::psipred_ss2, refresh_cutpoints(), register_options(), ObjexxFCL::right_string_of(), oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, set_secstruct_from_psipred_ss2(), out::file::silent(), basic::options::start_file(), basic::options::OptionKeys::fold_from_loops::swap_loops, vancomycin::task, TR, basic::options::OptionKeys::inout::dbms::user, and write_checkpoint().

new_pose_generator()

void new_pose_generator	(	core::pose::Pose &	target_loops,
		core::pose::Pose &	nat_prot,
		protocols::loops::Loops &	loops
	)

References aa, create_a3b_hbs::j, create_a3b_hbs::k, residue, and TR.

Referenced by main().

refresh_cutpoints()

void refresh_cutpoints	(	core::pose::Pose &	pose,
		std::vector< Size > &	cut_points
	)

References subloop_histogram::iterator, beta_nonlocal::pose, residue, and TR.

Referenced by main().

Variable Documentation

TR

basic::Tracer TR("bcorreia_fold_from_loops") ( "bcorreia_fold_from_loops"  )

static

Referenced by CA_cst_generator(), copying_side_chains_swap_loop(), define_cut_points(), define_movemap_extending_chain(), fold_tree_generator(), main(), new_pose_generator(), and refresh_cutpoints().