protocols::stepwise::setup Namespace Reference

Classes
class	StepWiseCSA_JobDistributor
class	StepWiseJobDistributor
class	StepWiseMonteCarloJobDistributor

Typedefs
typedef utility::pointer::shared_ptr < FullModelInfoSetupFromCommandLine >	FullModelInfoSetupFromCommandLineOP
typedef utility::pointer::shared_ptr < FullModelInfoSetupFromCommandLine const >	FullModelInfoSetupFromCommandLineCOP
typedef utility::pointer::shared_ptr < StepWiseCSA_JobDistributor >	StepWiseCSA_JobDistributorOP
typedef utility::pointer::shared_ptr < StepWiseCSA_JobDistributor const >	StepWiseCSA_JobDistributorCOP
typedef utility::pointer::shared_ptr < StepWiseJobDistributor >	StepWiseJobDistributorOP
typedef utility::pointer::shared_ptr < StepWiseJobDistributor const >	StepWiseJobDistributorCOP
typedef utility::pointer::shared_ptr < StepWiseMonteCarloJobDistributor >	StepWiseMonteCarloJobDistributorOP
typedef utility::pointer::shared_ptr < StepWiseMonteCarloJobDistributor const >	StepWiseMonteCarloJobDistributorCOP

Functions
core::pose::PoseOP	get_pdb_with_full_model_info (std::string const input_file, core::chemical::ResidueTypeSetCAP rsd_set)
core::pose::PoseOP	get_pdb_and_cleanup (std::string const input_file, core::chemical::ResidueTypeSetCAP rsd_set)
void	cleanup (pose::Pose &pose)
void	initialize_native_and_align_pose (PoseOP &native_pose, PoseOP &align_pose, core::chemical::ResidueTypeSetCAP rsd_set)
pose::PoseOP	initialize_pose_and_other_poses_from_command_line (core::chemical::ResidueTypeSetCAP rsd_set)
void	get_other_poses (utility::vector1< pose::PoseOP > &other_poses, utility::vector1< std::string > const &other_files, core::chemical::ResidueTypeSetCAP rsd_set)
void	fill_full_model_info_from_command_line (pose::Pose &pose)
void	fill_full_model_info_from_command_line (vector1< PoseOP > &pose_ops)
void	fill_full_model_info_from_command_line (pose::Pose &pose, vector1< PoseOP > &other_pose_ops)
std::string	get_concatenated_sequence (vector1< core::sequence::SequenceCOP > const &fasta_sequences)
vector1< Size >	get_cutpoints (vector1< core::sequence::SequenceCOP > const &fasta_sequences, vector1< char > const &conventional_chains, vector1< int > const &conventional_numbering)
void	get_conventional_chains_and_numbering (vector1< core::sequence::SequenceCOP > const &fasta_sequences, vector1< char > &conventional_chains, vector1< int > &conventional_numbering)
std::map< Size, std::string >	parse_out_non_standard_residues (vector1< core::sequence::SequenceOP > &fasta_sequences)
std::map< Size, std::string >	parse_out_non_standard_residues (std::string &sequence)
void	fill_full_model_info_from_command_line (vector1< Pose * > &pose_pointers)
void	setup_fold_trees (vector1< Pose * > &pose_pointers, vector1< Size > &cutpoint_open_in_full_model, vector1< Size > &fixed_domain_map, vector1< Size > const &cutpoint_closed, vector1< Size > const &extra_minimize_res, vector1< Size > const &extra_minimize_jump_res, vector1< Size > const &sample_res, vector1< Size > const &working_res, vector1< Size > const &jump_res, vector1< Size > const &preferred_root_res, vector1< Size > const &virtual_sugar_res, FullModelParameters const &full_model_parameters, vector1< vector1< Size > > const &pose_res_lists)
void	update_pose_fold_tree (pose::Pose &pose, vector1< Size > const &res_list, vector1< Size > const &extra_min_res, vector1< Size > const &sample_res, vector1< Size > const &jump_res, core::pose::full_model_info::FullModelParameters const &full_model_parameters)
void	define_chains (pose::Pose const &pose, vector1< vector1< Size > > &all_res_in_chain, vector1< vector1< Size > > &all_fixed_res_in_chain, vector1< Size > const &res_list, vector1< Size > const &moveable_res)
void	setup_user_defined_jumps (vector1< Size > const &jump_res, vector1< Size > &jump_partners1, vector1< Size > &jump_partners2, vector1< std::pair< Size, Size > > &chain_connections, vector1< Size > const &res_list, vector1< vector1< Size > > const &all_res_in_chain)
Size	get_chain (Size const i, vector1< vector1< Size > > const &all_res_in_chain)
void	setup_jumps (core::pose::Pose const &pose, vector1< Size > &jump_partners1, vector1< Size > &jump_partners2, vector1< std::pair< Size, Size > > &chain_connections, vector1< vector1< Size > > const &all_res_in_chain, std::pair< vector1< int >, vector1< char > > const &resnum_and_chain_in_pose)
FoldTree	get_tree (pose::Pose const &pose, vector1< Size > const &cuts, vector1< Size > const &jump_partners1, vector1< Size > const &jump_partners2)
FoldTree	get_tree (Size const nres, vector1< Size > const &cuts, vector1< Size > const &jump_partners1, vector1< Size > const &jump_partners2, vector1< std::string > const &jump_atoms1, vector1< std::string > const &jump_atoms2)
void	update_fixed_domain_from_extra_minimize_jump_pairs (utility::vector1< Size > &fixed_domain, pose::Pose const &pose, utility::vector1< Size > const &res_list, utility::vector1< std::pair< Size, Size > > const &extra_minimize_jump_pairs)
void	update_fixed_domain_from_extra_minimize_jump_res (vector1< Size > &fixed_domain, pose::Pose const &pose, vector1< Size > const &res_list, vector1< Size > const &extra_minimize_jump_res)
void	add_cutpoint_closed (pose::Pose &pose, vector1< Size > const &res_list, vector1< Size > const &cutpoint_closed)
void	put_in_cutpoint (pose::Pose &pose, Size const i)
void	add_virtual_sugar_res (pose::Pose &pose, vector1< Size > const &res_list, vector1< Size > const &virtual_sugar_res)
utility::vector1< Size >	figure_out_working_res (utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &sample_res)
utility::vector1< Size >	figure_out_sample_res (utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &working_res)
void	check_working_res (utility::vector1< Size > const &working_res, utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &sample_res)
void	figure_out_motif_mode (utility::vector1< Size > &extra_min_res, utility::vector1< Size > &terminal_res, utility::vector1< Size > const &working_res, utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &cutpoint_open_in_full_model)
bool	looks_like_reference_pose (utility::vector1< Size > const &input_domain_map)
void	update_jump_res (utility::vector1< Size > &jump_res, utility::vector1< Size > const &extra_minimize_jump_res)
void	check_extra_minimize_res_are_input (utility::vector1< core::Size > const &extra_minimize_res, utility::vector1< core::Size > const &input_domain_map)
utility::vector1< Size >	figure_out_fixed_domain_map (utility::vector1< Size > const &input_domain_map, utility::vector1< Size > const &extra_minimize_res)
utility::vector1< Size >	figure_out_dock_domain_map (utility::vector1< Size > &cutpoint_open_in_full_model, utility::vector1< utility::vector1< Size > > const &pose_res_lists, utility::vector1< Size > const &working_res, utility::vector1< Size > const &sample_res, Size const nres)
bool	just_modeling_RNA (utility::vector1< std::string > const &fasta_files)
void	setup_user_defined_jumps (vector1< core::Size > const &jump_res, vector1< core::Size > &jump_partners1, vector1< core::Size > &jump_partners2, vector1< std::pair< core::Size, core::Size > > &chain_connections, vector1< core::Size > const &res_list, vector1< vector1< core::Size > > const &all_res_in_chain)
void	setup_jumps (core::pose::Pose const &pose, vector1< core::Size > &jump_partners1, vector1< core::Size > &jump_partners2, vector1< std::pair< core::Size, core::Size > > &chain_connections, vector1< vector1< core::Size > > const &all_res_in_chain, std::pair< vector1< int >, vector1< char > > const &resnum_and_chain_in_pose)

Typedef Documentation

typedef utility::pointer::shared_ptr< FullModelInfoSetupFromCommandLine const > protocols::stepwise::setup::FullModelInfoSetupFromCommandLineCOP

typedef utility::pointer::shared_ptr< FullModelInfoSetupFromCommandLine > protocols::stepwise::setup::FullModelInfoSetupFromCommandLineOP

typedef utility::pointer::shared_ptr< StepWiseCSA_JobDistributor const > protocols::stepwise::setup::StepWiseCSA_JobDistributorCOP

typedef utility::pointer::shared_ptr< StepWiseCSA_JobDistributor > protocols::stepwise::setup::StepWiseCSA_JobDistributorOP

typedef utility::pointer::shared_ptr< StepWiseJobDistributor const > protocols::stepwise::setup::StepWiseJobDistributorCOP

typedef utility::pointer::shared_ptr< StepWiseJobDistributor > protocols::stepwise::setup::StepWiseJobDistributorOP

typedef utility::pointer::shared_ptr< StepWiseMonteCarloJobDistributor const > protocols::stepwise::setup::StepWiseMonteCarloJobDistributorCOP

typedef utility::pointer::shared_ptr< StepWiseMonteCarloJobDistributor > protocols::stepwise::setup::StepWiseMonteCarloJobDistributorOP

Function Documentation

void protocols::stepwise::setup::add_cutpoint_closed	(	pose::Pose &	pose,
		vector1< Size > const &	res_list,
		vector1< Size > const &	cutpoint_closed
	)

References core::pose::correctly_add_cutpoint_variants(), utility::vector1< T, class >::has_value(), utility::vector1< T, class >::index(), and put_in_cutpoint().

Referenced by setup_fold_trees().

void protocols::stepwise::setup::add_virtual_sugar_res	(	pose::Pose &	pose,
		vector1< Size > const &	res_list,
		vector1< Size > const &	virtual_sugar_res
	)

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::fold_tree(), utility::vector1< T, class >::has_value(), utility::vector1< T, class >::index(), core::kinematics::FoldTree::is_cutpoint(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by setup_fold_trees().

void protocols::stepwise::setup::check_extra_minimize_res_are_input	(	utility::vector1< core::Size > const &	extra_minimize_res,
		utility::vector1< core::Size > const &	input_domain_map
	)

References runtime_assert.

Referenced by fill_full_model_info_from_command_line().

void protocols::stepwise::setup::check_working_res	(	utility::vector1< Size > const &	working_res,
		utility::vector1< Size > const &	input_domain_map,
		utility::vector1< Size > const &	sample_res
	)

References utility::vector1< T, class >::has_value(), looks_like_reference_pose(), runtime_assert, and utility_exit_with_message.

Referenced by fill_full_model_info_from_command_line().

void protocols::stepwise::setup::cleanup

(

pose::Pose &

pose

)

References core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), core::pose::rna::figure_out_reasonable_rna_fold_tree(), and core::pose::rna::virtualize_5prime_phosphates().

Referenced by get_pdb_and_cleanup().

void protocols::stepwise::setup::define_chains	(	pose::Pose const &	pose,
		vector1< vector1< Size > > &	all_res_in_chain,
		vector1< vector1< Size > > &	all_fixed_res_in_chain,
		vector1< Size > const &	res_list,
		vector1< Size > const &	moveable_res
	)

References core::pose::Pose::fold_tree(), utility::vector1< T, class >::has_value(), core::kinematics::FoldTree::is_cutpoint(), and core::pose::Pose::total_residue().

Referenced by update_pose_fold_tree().

utility::vector1< core::Size > protocols::stepwise::setup::figure_out_dock_domain_map	(	utility::vector1< Size > &	cutpoint_open_in_full_model,
		utility::vector1< utility::vector1< Size > > const &	pose_res_lists,
		utility::vector1< Size > const &	working_res,
		utility::vector1< Size > const &	sample_res,
		Size const	nres
	)

References core::pose::full_model_info::get_connection_domains(), utility::vector1< T, class >::has_value(), max(), and core::pose::TR().

Referenced by fill_full_model_info_from_command_line().

utility::vector1< core::Size > protocols::stepwise::setup::figure_out_fixed_domain_map	(	utility::vector1< Size > const &	input_domain_map,
		utility::vector1< Size > const &	extra_minimize_res
	)

Referenced by fill_full_model_info_from_command_line().

void protocols::stepwise::setup::figure_out_motif_mode	(	utility::vector1< Size > &	extra_min_res,
		utility::vector1< Size > &	terminal_res,
		utility::vector1< Size > const &	working_res,
		utility::vector1< Size > const &	input_domain_map,
		utility::vector1< Size > const &	cutpoint_open_in_full_model
	)

References utility::vector1< T, class >::has_value(), looks_like_reference_pose(), and runtime_assert.

Referenced by fill_full_model_info_from_command_line().

utility::vector1< core::Size > protocols::stepwise::setup::figure_out_sample_res	(	utility::vector1< Size > const &	input_domain_map,
		utility::vector1< Size > const &	working_res
	)

References utility::vector1< T, class >::has_value().

Referenced by fill_full_model_info_from_command_line().

utility::vector1< core::Size > protocols::stepwise::setup::figure_out_working_res	(	utility::vector1< Size > const &	input_domain_map,
		utility::vector1< Size > const &	sample_res
	)

References utility::vector1< T, class >::has_value().

Referenced by fill_full_model_info_from_command_line().

void protocols::stepwise::setup::fill_full_model_info_from_command_line

(

pose::Pose &

pose

)

References fill_full_model_info_from_command_line().

void protocols::stepwise::setup::fill_full_model_info_from_command_line

(

vector1< PoseOP > &

pose_ops

)

References fill_full_model_info_from_command_line(), and runtime_assert.

void protocols::stepwise::setup::fill_full_model_info_from_command_line	(	pose::Pose &	pose,
		vector1< PoseOP > &	other_pose_ops
	)

References fill_full_model_info_from_command_line(), core::pose::full_model_info::nonconst_full_model_info(), and core::pose::full_model_info::FullModelInfo::set_other_pose_list().

void protocols::stepwise::setup::fill_full_model_info_from_command_line

(

vector1< Pose * > &

pose_pointers

)

References core::pose::full_model_info::CALC_RMS, check_extra_minimize_res_are_input(), check_working_res(), core::pose::full_model_info::CUTPOINT_OPEN, core::pose::Pose::data(), core::pose::full_model_info::DOCK_DOMAIN, core::pose::full_model_info::EXTRA_MINIMIZE, core::pose::full_model_info::EXTRA_MINIMIZE_JUMP, figure_out_dock_domain_map(), figure_out_fixed_domain_map(), figure_out_motif_mode(), figure_out_sample_res(), figure_out_working_res(), core::pose::full_model_info::FIXED_DOMAIN, core::pose::datacache::CacheableDataType::FULL_MODEL_INFO, core::pose::full_model_info::get_chains_from_pdb_info(), get_concatenated_sequence(), get_conventional_chains_and_numbering(), get_cutpoints(), core::pose::full_model_info::get_res_num_from_pdb_info(), core::pose::full_model_info::INPUT_DOMAIN, core::pose::full_model_info::JUMP, core::pose::full_model_info::make_sure_full_model_info_is_setup(), option, parse_out_non_standard_residues(), core::pose::full_model_info::PREFERRED_ROOT, core::sequence::read_fasta_file(), core::pose::full_model_info::RNA_BULGE, core::pose::full_model_info::RNA_SYN_CHI, core::pose::full_model_info::RNA_TERMINAL, core::pose::full_model_info::SAMPLE, basic::datacache::BasicDataCache::set(), setup_fold_trees(), core::pose::Pose::total_residue(), update_jump_res(), core::pose::full_model_info::update_pose_objects_from_full_model_info(), user, and core::pose::full_model_info::WORKING.

Referenced by fill_full_model_info_from_command_line(), get_pdb_with_full_model_info(), and initialize_pose_and_other_poses_from_command_line().

core::Size protocols::stepwise::setup::get_chain	(	Size const	i,
		vector1< vector1< Size > > const &	all_res_in_chain
	)

References has_value().

Referenced by setup_user_defined_jumps().

std::string protocols::stepwise::setup::get_concatenated_sequence

(

vector1< core::sequence::SequenceCOP > const &

fasta_sequences

)

Referenced by fill_full_model_info_from_command_line().

void protocols::stepwise::setup::get_conventional_chains_and_numbering	(	vector1< core::sequence::SequenceCOP > const &	fasta_sequences,
		vector1< char > &	conventional_chains,
		vector1< int > &	conventional_numbering
	)

References utility::get_resnum_and_chain(), q, runtime_assert, size(), and utility::string_split().

Referenced by fill_full_model_info_from_command_line().

vector1< Size > protocols::stepwise::setup::get_cutpoints	(	vector1< core::sequence::SequenceCOP > const &	fasta_sequences,
		vector1< char > const &	conventional_chains,
		vector1< int > const &	conventional_numbering
	)

References utility::vector1< T, class >::has_value(), and runtime_assert.

Referenced by fill_full_model_info_from_command_line().

void protocols::stepwise::setup::get_other_poses	(	utility::vector1< pose::PoseOP > &	other_poses,
		utility::vector1< std::string > const &	other_files,
		core::chemical::ResidueTypeSetCAP	rsd_set
	)

References get_pdb_and_cleanup().

Referenced by initialize_pose_and_other_poses_from_command_line().

core::pose::PoseOP protocols::stepwise::setup::get_pdb_and_cleanup	(	std::string const	input_file,
		core::chemical::ResidueTypeSetCAP	rsd_set
	)

References cleanup(), core::pose::full_model_info::make_sure_full_model_info_is_setup(), and core::import_pose::pose_from_pdb().

Referenced by get_other_poses(), get_pdb_with_full_model_info(), and initialize_pose_and_other_poses_from_command_line().

core::pose::PoseOP protocols::stepwise::setup::get_pdb_with_full_model_info	(	std::string const	input_file,
		core::chemical::ResidueTypeSetCAP	rsd_set
	)

References fill_full_model_info_from_command_line(), and get_pdb_and_cleanup().

Referenced by initialize_native_and_align_pose().

FoldTree protocols::stepwise::setup::get_tree	(	pose::Pose const &	pose,
		vector1< Size > const &	cuts,
		vector1< Size > const &	jump_partners1,
		vector1< Size > const &	jump_partners2
	)

References core::chemical::rna::default_jump_atom(), get_tree(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::modeler::merge_two_poses().

FoldTree protocols::stepwise::setup::get_tree	(	Size const	nres,
		vector1< Size > const &	cuts,
		vector1< Size > const &	jump_partners1,
		vector1< Size > const &	jump_partners2,
		vector1< std::string > const &	jump_atoms1,
		vector1< std::string > const &	jump_atoms2
	)

References core::kinematics::FoldTree::jump_nr(), core::kinematics::FoldTree::reassign_atoms_for_intra_residue_stubs(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

Referenced by get_tree(), and update_pose_fold_tree().

void protocols::stepwise::setup::initialize_native_and_align_pose	(	PoseOP &	native_pose,
		PoseOP &	align_pose,
		core::chemical::ResidueTypeSetCAP	rsd_set
	)

References get_pdb_with_full_model_info(), option, user, and protocols::stepwise::modeler::rna::virtualize_free_rna_moieties().

core::pose::PoseOP protocols::stepwise::setup::initialize_pose_and_other_poses_from_command_line

(

core::chemical::ResidueTypeSetCAP

rsd_set

)

References core::io::silent::SilentFileData::begin(), fill_full_model_info_from_command_line(), get_other_poses(), get_pdb_and_cleanup(), option, core::pose::Pose::pdb_info(), core::io::silent::SilentFileData::read_file(), runtime_assert, core::pose::Pose::total_residue(), and user.

bool protocols::stepwise::setup::just_modeling_RNA

(

utility::vector1< std::string > const &

fasta_files

)

References parse_out_non_standard_residues(), and core::sequence::read_fasta_file().

bool protocols::stepwise::setup::looks_like_reference_pose

(

utility::vector1< Size > const &

input_domain_map

)

Referenced by check_working_res(), and figure_out_motif_mode().

std::map< Size, std::string > protocols::stepwise::setup::parse_out_non_standard_residues

(

vector1< core::sequence::SequenceOP > &

fasta_sequences

)

References parse_out_non_standard_residues().

Referenced by protocols::stepwise::modeler::rna::helix::RNA_HelixAssembler::apply().

std::map< core::Size, std::string > protocols::stepwise::setup::parse_out_non_standard_residues

(

std::string &

sequence

)

References core::pose::parse_sequence().

Referenced by fill_full_model_info_from_command_line(), just_modeling_RNA(), and parse_out_non_standard_residues().

void protocols::stepwise::setup::put_in_cutpoint	(	pose::Pose &	pose,
		Size const	i
	)

References core::chemical::rna::default_jump_atom(), core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), core::chemical::ResidueType::is_RNA(), core::kinematics::FoldTree::new_jump(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::set_jump_atoms(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by add_cutpoint_closed(), and setup_fold_trees().

void protocols::stepwise::setup::setup_fold_trees	(	vector1< Pose * > &	pose_pointers,
		vector1< Size > &	cutpoint_open_in_full_model,
		vector1< Size > &	fixed_domain_map,
		vector1< Size > const &	cutpoint_closed,
		vector1< Size > const &	extra_minimize_res,
		vector1< Size > const &	extra_minimize_jump_res,
		vector1< Size > const &	sample_res,
		vector1< Size > const &	working_res,
		vector1< Size > const &	jump_res,
		vector1< Size > const &	preferred_root_res,
		vector1< Size > const &	virtual_sugar_res,
		FullModelParameters const &	full_model_parameters,
		vector1< vector1< Size > > const &	pose_res_lists
	)

References add_cutpoint_closed(), add_virtual_sugar_res(), core::pose::Pose::fold_tree(), utility::vector1< T, class >::has_value(), core::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_RNA(), put_in_cutpoint(), protocols::stepwise::modeler::reroot(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), core::pose::TR(), update_fixed_domain_from_extra_minimize_jump_res(), and update_pose_fold_tree().

Referenced by fill_full_model_info_from_command_line().

void protocols::stepwise::setup::setup_jumps	(	core::pose::Pose const &	pose,
		vector1< core::Size > &	jump_partners1,
		vector1< core::Size > &	jump_partners2,
		vector1< std::pair< core::Size, core::Size > > &	chain_connections,
		vector1< vector1< core::Size > > const &	all_res_in_chain,
		std::pair< vector1< int >, vector1< char > > const &	resnum_and_chain_in_pose
	)

void protocols::stepwise::setup::setup_jumps	(	core::pose::Pose const &	pose,
		vector1< Size > &	jump_partners1,
		vector1< Size > &	jump_partners2,
		vector1< std::pair< Size, Size > > &	chain_connections,
		vector1< vector1< Size > > const &	all_res_in_chain,
		std::pair< vector1< int >, vector1< char > > const &	resnum_and_chain_in_pose
	)

References core::pose::full_model_info::get_connection_domains(), max(), min(), core::conformation::Residue::nheavyatoms(), q, core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by update_pose_fold_tree().

void protocols::stepwise::setup::setup_user_defined_jumps	(	vector1< core::Size > const &	jump_res,
		vector1< core::Size > &	jump_partners1,
		vector1< core::Size > &	jump_partners2,
		vector1< std::pair< core::Size, core::Size > > &	chain_connections,
		vector1< core::Size > const &	res_list,
		vector1< vector1< core::Size > > const &	all_res_in_chain
	)

void protocols::stepwise::setup::setup_user_defined_jumps	(	vector1< Size > const &	jump_res,
		vector1< Size > &	jump_partners1,
		vector1< Size > &	jump_partners2,
		vector1< std::pair< Size, Size > > &	chain_connections,
		vector1< Size > const &	res_list,
		vector1< vector1< Size > > const &	all_res_in_chain
	)

References get_chain(), core::pose::full_model_info::get_connection_domains(), utility::vector1< T, class >::has_value(), utility::vector1< T, class >::index(), and runtime_assert.

Referenced by update_pose_fold_tree().

void protocols::stepwise::setup::update_fixed_domain_from_extra_minimize_jump_pairs	(	utility::vector1< Size > &	fixed_domain,
		pose::Pose const &	pose,
		utility::vector1< Size > const &	res_list,
		utility::vector1< std::pair< Size, Size > > const &	extra_minimize_jump_pairs
	)

References core::kinematics::FoldTree::downstream_jump_residue(), core::pose::Pose::fold_tree(), utility::vector1< T, class >::has_value(), utility::vector1< T, class >::index(), core::kinematics::FoldTree::jump_exists(), core::kinematics::FoldTree::jump_nr(), max(), core::kinematics::FoldTree::partition_by_jump(), runtime_assert, and core::pose::Pose::total_residue().

Referenced by update_fixed_domain_from_extra_minimize_jump_res().

void protocols::stepwise::setup::update_fixed_domain_from_extra_minimize_jump_res	(	vector1< Size > &	fixed_domain,
		pose::Pose const &	pose,
		vector1< Size > const &	res_list,
		vector1< Size > const &	extra_minimize_jump_res
	)

References update_fixed_domain_from_extra_minimize_jump_pairs().

Referenced by setup_fold_trees().

void protocols::stepwise::setup::update_jump_res	(	utility::vector1< Size > &	jump_res,
		utility::vector1< Size > const &	extra_minimize_jump_res
	)

References q, and runtime_assert.

Referenced by fill_full_model_info_from_command_line().

void protocols::stepwise::setup::update_pose_fold_tree	(	pose::Pose &	pose,
		vector1< Size > const &	res_list,
		vector1< Size > const &	extra_min_res,
		vector1< Size > const &	sample_res,
		vector1< Size > const &	jump_res,
		core::pose::full_model_info::FullModelParameters const &	full_model_parameters
	)

References define_chains(), core::pose::Pose::fold_tree(), core::pose::full_model_info::FullModelParameters::full_to_conventional_resnum_and_chain(), get_tree(), runtime_assert, setup_jumps(), setup_user_defined_jumps(), and core::pose::Pose::total_residue().

Referenced by setup_fold_trees().