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)
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	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, vector1< Size > const &root_res)
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< vector1< bool > > &chain_connected, 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 (vector1< Size > &jump_partners1, vector1< Size > &jump_partners2, vector1< vector1< bool > > &chain_connected, vector1< vector1< Size > > const &all_res_in_chain)
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	reroot (FoldTree &f, vector1< Size > const &res_list, vector1< Size > const &root_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 &domain_map, utility::vector1< Size > const &sample_res)
utility::vector1< Size >	figure_out_sample_res (utility::vector1< Size > const &domain_map, utility::vector1< Size > const &working_res)
void	check_working_res (utility::vector1< Size > const &working_res, utility::vector1< Size > const &domain_map, utility::vector1< Size > const &sample_res)
void	filter_out_bulge_res (utility::vector1< Size > &sample_res, utility::vector1< Size > const &bulge_res)

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 fill_full_model_info_from_command_line().

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 fill_full_model_info_from_command_line().

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

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

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_sample_res	(	utility::vector1< Size > const &	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 &	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 add_cutpoint_closed(), add_virtual_sugar_res(), core::pose::full_model_info::CALC_RMS, check_working_res(), core::pose::full_model_info::CUTPOINT_OPEN, core::pose::Pose::data(), core::pose::full_model_info::EXTRA_MINIMIZE, figure_out_sample_res(), figure_out_working_res(), filter_out_bulge_res(), core::pose::full_model_info::FIXED_DOMAIN, core::pose::Pose::fold_tree(), 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::chemical::ResidueType::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_RNA(), core::pose::full_model_info::make_sure_full_model_info_is_setup(), option, parse_out_non_standard_residues(), put_in_cutpoint(), core::sequence::read_fasta_file(), core::pose::Pose::residue_type(), core::pose::full_model_info::RNA_BULGE, core::pose::full_model_info::RNA_SYN_CHI, core::pose::full_model_info::RNA_TERMINAL, runtime_assert, core::pose::full_model_info::SAMPLE, basic::datacache::BasicDataCache::set(), core::pose::Pose::total_residue(), core::pose::TR(), update_pose_fold_tree(), core::pose::full_model_info::update_pose_objects_from_full_model_info(), user, utility_exit_with_message, 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().

void protocols::stepwise::setup::filter_out_bulge_res	(	utility::vector1< Size > &	sample_res,
		utility::vector1< Size > const &	bulge_res
	)

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

Referenced by fill_full_model_info_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

)

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.

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(), 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 fill_full_model_info_from_command_line().

void protocols::stepwise::setup::reroot	(	FoldTree &	f,
		vector1< Size > const &	res_list,
		vector1< Size > const &	root_res
	)

References utility::vector1< T, class >::has_value(), utility::vector1< T, class >::index(), core::kinematics::FoldTree::possible_root(), core::kinematics::FoldTree::reorder(), and runtime_assert.

Referenced by update_pose_fold_tree().

void protocols::stepwise::setup::setup_jumps	(	vector1< Size > &	jump_partners1,
		vector1< Size > &	jump_partners2,
		vector1< vector1< bool > > &	chain_connected,
		vector1< vector1< Size > > const &	all_res_in_chain
	)

Referenced by update_pose_fold_tree().

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

References get_chain(), 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_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,
		vector1< Size > const &	root_res
	)

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

Referenced by fill_full_model_info_from_command_line().