protocols::stepwise::monte_carlo Namespace Reference

Namespaces
	mover
	options
	rna
	submotif

Classes
class	StepWiseMonteCarlo

Typedefs
typedef utility::pointer::shared_ptr < StepWiseMonteCarlo >	StepWiseMonteCarloOP
typedef utility::pointer::shared_ptr < StepWiseMonteCarlo const >	StepWiseMonteCarloCOP

Functions
void	output_to_silent_file (std::string const &out_tag, std::string const &silent_file, pose::Pose &pose, pose::PoseCOP native_pose, bool const superimpose_over_all_instantiated, bool const do_rms_fill_calculation)
core::io::silent::SilentStructOP	prepare_silent_struct (std::string const &out_tag, pose::Pose &pose, pose::PoseCOP native_pose, bool const superimpose_over_all_instantiated, bool const do_rms_fill_calculation, core::pose::PoseOP full_model_pose)
void	output_to_silent_file (std::string const &out_tag, std::string const &silent_file, pose::Pose const &pose)
void	output_to_silent_file (std::string const &silent_file, utility::vector1< pose::PoseOP > &pose_list, pose::PoseCOP native_pose)
void	build_full_model (pose::Pose const &start_pose, pose::Pose &full_model_pose, bool const &enumerate, Real const &skip_bulge_freq)
core::pose::PoseOP	build_full_model (pose::Pose const &start_pose)
std::string	get_move_type_string (mover::StepWiseMove const &swa_move)
std::string	get_all_res_list (pose::Pose &pose)
void	output_to_silent_file (std::string const &silent_file, utility::vector1< core::pose::PoseOP > &pose_list, core::pose::PoseCOP native_pose)

Typedef Documentation

typedef utility::pointer::shared_ptr< StepWiseMonteCarlo const > protocols::stepwise::monte_carlo::StepWiseMonteCarloCOP

typedef utility::pointer::shared_ptr< StepWiseMonteCarlo > protocols::stepwise::monte_carlo::StepWiseMonteCarloOP

Function Documentation

void protocols::stepwise::monte_carlo::build_full_model	(	pose::Pose const &	start_pose,
		pose::Pose &	full_model_pose,
		bool const &	enumerate,
		Real const &	skip_bulge_freq
	)

References protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::build_full_model().

Referenced by protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), and protocols::rna::setup::RNA_CSA_JobDistributor::update_bank().

core::pose::PoseOP protocols::stepwise::monte_carlo::build_full_model

(

pose::Pose const &

start_pose

)

Referenced by prepare_silent_struct().

std::string protocols::stepwise::monte_carlo::get_all_res_list

(

pose::Pose &

pose

)

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::get_res_list_from_full_model_info_const(), and core::pose::full_model_info::FullModelInfo::other_pose_list().

Referenced by protocols::stepwise::monte_carlo::StepWiseMonteCarlo::display_progress(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::do_main_loop(), and protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::test_all_moves_recursively().

std::string protocols::stepwise::monte_carlo::get_move_type_string

(

mover::StepWiseMove const &

swa_move

)

References protocols::stepwise::monte_carlo::mover::StepWiseMove::move_type(), and core::id::to_string().

Referenced by protocols::stepwise::monte_carlo::mover::AddOrDeleteMover::apply(), and protocols::stepwise::monte_carlo::mover::StepWiseMasterMover::apply().

void protocols::stepwise::monte_carlo::output_to_silent_file	(	std::string const &	silent_file,
		utility::vector1< core::pose::PoseOP > &	pose_list,
		core::pose::PoseCOP	native_pose
	)

References output_to_silent_file(), and core::pose::tag_from_pose().

Referenced by output_to_silent_file().

void protocols::stepwise::monte_carlo::output_to_silent_file	(	std::string const &	out_tag,
		std::string const &	silent_file,
		pose::Pose &	pose,
		pose::PoseCOP	native_pose,
		bool const	superimpose_over_all_instantiated,
		bool const	do_rms_fill_calculation
	)

References prepare_silent_struct(), and core::io::silent::SilentFileData::write_silent_struct().

Referenced by protocols::rna::setup::RNA_MonteCarloJobDistributor::apply(), protocols::stepwise::modeler::align::StepWiseClusterer::apply(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::output_checkpoint_file(), protocols::stepwise::modeler::StepWiseMinimizer::output_minimized_pose_list(), protocols::stepwise::monte_carlo::StepWiseMonteCarlo::output_movie(), and protocols::rna::movers::write_checkpoint().

void protocols::stepwise::monte_carlo::output_to_silent_file	(	std::string const &	out_tag,
		std::string const &	silent_file,
		pose::Pose const &	pose
	)

References output_to_silent_file().

void protocols::stepwise::monte_carlo::output_to_silent_file	(	std::string const &	silent_file,
		utility::vector1< pose::PoseOP > &	pose_list,
		pose::PoseCOP	native_pose
	)

References output_to_silent_file(), and core::pose::tag_from_pose().

Referenced by output_to_silent_file().

core::io::silent::SilentStructOP protocols::stepwise::monte_carlo::prepare_silent_struct	(	std::string const &	out_tag,
		pose::Pose &	pose,
		pose::PoseCOP	native_pose,
		bool const	superimpose_over_all_instantiated,
		bool const	do_rms_fill_calculation,
		core::pose::PoseOP	full_model_pose
	)

References core::pose::rna::add_number_base_pairs(), core::pose::rna::add_number_native_base_pairs(), build_full_model(), core::pose::full_model_info::check_all_residues_sampled(), core::pose::full_model_info::get_number_missing_residues_and_connections(), core::scoring::rms, protocols::stepwise::modeler::align::superimpose_with_stepwise_aligner(), and core::pose::TR().

Referenced by output_to_silent_file(), and protocols::rna::setup::RNA_CSA_JobDistributor::update_bank().