#include <FullModelParameters.hh>

Inheritance diagram for core::pose::full_model_info::FullModelParameters:

Public Member Functions
	FullModelParameters ()

	FullModelParameters (std::string const &full_sequence)

	FullModelParameters (std::string const &full_sequence, utility::vector1< Size > const &cutpoint_open_in_full_model, utility::vector1< Size > const &res_numbers_in_pose)

	FullModelParameters (pose::Pose const &pose, utility::vector1< Size > &res_list)

	FullModelParameters (FullModelParameters const &src)

	~FullModelParameters () override

FullModelParametersOP	clone () const

FullModelParametersOP	slice (utility::vector1< Size > const &slice_res) const

std::string const &	full_sequence () const

std::string const &	global_sequence () const

utility::vector1< Size > const &	global_mapping () const

std::map< Size, std::string > const &	non_standard_residue_map () const

std::map< Size, std::string > &	non_standard_residue_map_nonconst ()

std::string	full_annotated_sequence () const

utility::vector1< int > const &	conventional_numbering () const

utility::vector1< char > const &	conventional_chains () const

utility::vector1< std::string > const &	conventional_segids () const

void	set_conventional_numbering (utility::vector1< int > const &setting)

void	set_conventional_chains (utility::vector1< char > const &setting)

void	set_conventional_segids (utility::vector1< std::string > const &setting)

void	set_non_standard_residue_map (std::map< Size, std::string > const &setting)

void	set_parameter (FullModelParameterType const type, utility::vector1< Size > const &setting)

void	set_parameter_as_res_list (FullModelParameterType const type, utility::vector1< Size > const &setting)

void	set_parameter_as_res_lists (FullModelParameterType const type, std::map< Size, utility::vector1< Size > > const &setting)

void	set_parameter_as_res_list_in_pairs (FullModelParameterType const type, utility::vector1< Size > const &setting)

utility::vector1< Size > const &	get_res_list (FullModelParameterType const type, Size const value) const

utility::vector1< Size > const &	get_res_list (FullModelParameterType const type) const

utility::vector1< std::pair < Size, Size > >	get_res_list_as_pairs (FullModelParameterType const type) const

utility::vector1< Size > const &	get_parameter (FullModelParameterType const type) const

std::map< Size, utility::vector1< Size > > const &	get_parameter_as_res_lists (FullModelParameterType const type) const

utility::vector1< Size >	conventional_to_full (utility::vector1< int > const &res_list) const

utility::vector1< Size >	conventional_to_full (std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &resnum_and_chain_and_segid) const

bool	has_conventional_residue (int const res_num) const

bool	has_conventional_residue (int const res_num, char const chain, std::string const &segid=" ") const

Size	conventional_to_full (int const res_num) const

Size	conventional_to_full (int const res_num, char const chain, std::string const &segid=" ") const

utility::vector1< int >	full_to_conventional (utility::vector1< Size > const &res_list) const

int	full_to_conventional (Size const res_num) const

std::tuple< utility::vector1 < int >, utility::vector1 < char >, utility::vector1 < std::string > >	full_to_conventional_resnum_and_chain_and_segid (utility::vector1< Size > const &res_list) const

std::tuple< int, char, std::string >	full_to_conventional_resnum_and_chain_and_segid (Size const res_num) const

utility::vector1< Size >	chains_in_full_model () const

Size	size () const

void	read_cst_file (std::string const &cst_file)

scoring::constraints::ConstraintSetCOP	cst_set () const

void	update_pose_and_cst_set_from_cst_string (chemical::ResidueTypeSet const &rsd_type_set) const

Pose const &	full_model_pose_for_constraints () const

void	set_cst_string (std::string const &setting)

std::string	cst_string () const

void	set_slice_res_list (utility::vector1< Size > const &setting)

utility::vector1< Size > const &	slice_res_list () const

void	set_parent_full_model_parameters (FullModelParametersCOP setting)

FullModelParametersCOP	parent_full_model_parameters () const

void	read_global_seq_info (std::string const &global_seq_file)

void	read_disulfides (std::string const &disulfide_file)

Private Member Functions
void	fill_parameter_values (utility::vector1< Size > &parameter_values_at_res, Size const idx, utility::vector1< Size > const &res_list) const

std::map< Size, utility::vector1< Size > >	convert_to_res_lists_by_value (utility::vector1< Size > const &parameter_values_at_res)

utility::vector1< Size >	convert_to_parameter_values_at_res (utility::vector1< Size > const &res_list)

utility::vector1< Size >	convert_to_parameter_values_at_res (std::map< Size, utility::vector1< Size > > const &res_lists)

void	get_sequence_with_gaps_filled_with_n (pose::Pose const &pose, std::string &sequence, utility::vector1< int > &conventional_numbering, utility::vector1< char > &conventional_chains, utility::vector1< std::string > &conventional_segids, utility::vector1< Size > &res_list) const

utility::vector1< Size >	get_cutpoint_open_from_pdb_info (pose::Pose const &pose, utility::vector1< Size > const &res_list) const

void	keep_chain_and_cutpoint_open_matched (FullModelParameterType const &type)

Private Attributes
std::string	full_sequence_

std::string	global_sequence_

utility::vector1< Size >	global_mapping_

utility::vector1< int >	conventional_numbering_

utility::vector1< char >	conventional_chains_

utility::vector1< std::string >	conventional_segids_

std::map< Size, std::string >	non_standard_residue_map_

std::string	cst_string_

core::scoring::constraints::ConstraintSetCOP	cst_set_

pose::PoseCOP	full_model_pose_for_constraints_

std::map < FullModelParameterType, utility::vector1< Size > >	parameter_values_at_res_

std::map < FullModelParameterType, std::map< Size, utility::vector1< Size > > >	parameter_values_as_res_lists_

utility::vector1< Size >	slice_res_list_

FullModelParametersCOP	parent_full_model_parameters_

Friends
std::istream &	operator>> (std::istream &is, FullModelParameters &t)
	input operator More...

std::ostream &	operator<< (std::ostream &os, FullModelParameters const &t)
	output operator More...

bool	operator== (FullModelParameters const &a, FullModelParameters const &b)
	equal to operator More...

bool	operator!= (FullModelParameters const &a, FullModelParameters const &b)
	not equal to operator More...

Constructor & Destructor Documentation

core::pose::full_model_info::FullModelParameters::FullModelParameters ( )

References core::pose::full_model_info::initialize_parameters().

Referenced by slice().

core::pose::full_model_info::FullModelParameters::FullModelParameters ( std::string const & full_sequence )

References conventional_chains_, conventional_numbering_, conventional_segids_, core::pose::full_model_info::initialize_parameters(), and core::pose::rna::remove_bracketed().

core::pose::full_model_info::FullModelParameters::FullModelParameters	(	std::string const &	full_sequence,
		utility::vector1< Size > const &	cutpoint_open_in_full_model,
		utility::vector1< Size > const &	res_numbers_in_pose
	)

References conventional_chains_, conventional_numbering_, conventional_segids_, convert_to_parameter_values_at_res(), core::pose::full_model_info::CUTPOINT_OPEN, core::pose::full_model_info::FIXED_DOMAIN, core::pose::full_model_info::initialize_parameters(), core::pose::full_model_info::INPUT_DOMAIN, core::pose::rna::remove_bracketed(), set_parameter(), and core::pose::full_model_info::WORKING.

core::pose::full_model_info::FullModelParameters::FullModelParameters	(	pose::Pose const &	pose,
		utility::vector1< Size > &	res_list
	)

References conventional_chains_, conventional_numbering_, conventional_segids_, convert_to_parameter_values_at_res(), core::pose::full_model_info::CUTPOINT_OPEN, core::pose::full_model_info::FIXED_DOMAIN, full_sequence_, get_cutpoint_open_from_pdb_info(), get_sequence_with_gaps_filled_with_n(), core::pose::full_model_info::initialize_parameters(), core::pose::full_model_info::INPUT_DOMAIN, set_parameter(), and core::pose::full_model_info::WORKING.

core::pose::full_model_info::FullModelParameters::FullModelParameters ( FullModelParameters const & src )

default

core::pose::full_model_info::FullModelParameters::~FullModelParameters ( )

overridedefault

Member Function Documentation

utility::vector1< Size > core::pose::full_model_info::FullModelParameters::chains_in_full_model ( ) const

References core::pose::full_model_info::CUTPOINT_OPEN, core::pose::full_model_info::get_chains_from_cutpoint_open(), get_parameter(), and size().

Referenced by slice().

FullModelParametersOP core::pose::full_model_info::FullModelParameters::clone ( ) const

inline

utility::vector1< char > const& core::pose::full_model_info::FullModelParameters::conventional_chains ( ) const

inline

References conventional_chains_.

Referenced by core::pose::full_model_info::operator<<().

utility::vector1< int > const& core::pose::full_model_info::FullModelParameters::conventional_numbering ( ) const

inline

References conventional_numbering_.

Referenced by core::pose::full_model_info::operator<<().

utility::vector1< std::string > const& core::pose::full_model_info::FullModelParameters::conventional_segids ( ) const

inline

References conventional_segids_.

Referenced by core::pose::full_model_info::operator<<().

utility::vector1< Size > core::pose::full_model_info::FullModelParameters::conventional_to_full ( utility::vector1< int > const & res_list ) const

Referenced by conventional_to_full(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_res_list_in_reference(), and read_disulfides().

utility::vector1< Size > core::pose::full_model_info::FullModelParameters::conventional_to_full ( std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const & resnum_and_chain_and_segid ) const

References conventional_to_full().

Size core::pose::full_model_info::FullModelParameters::conventional_to_full ( int const res_num ) const

References conventional_numbering_.

Size core::pose::full_model_info::FullModelParameters::conventional_to_full	(	int const	res_num,
		char const	chain,
		std::string const &	segid = `" "`
	)		const

References conventional_chains_, conventional_numbering_, conventional_segids_, and core::pose::TR().

utility::vector1< Size > core::pose::full_model_info::FullModelParameters::convert_to_parameter_values_at_res ( utility::vector1< Size > const & res_list )

private

References fill_parameter_values(), and size().

Referenced by FullModelParameters(), set_parameter_as_res_list(), and set_parameter_as_res_lists().

utility::vector1< Size > core::pose::full_model_info::FullModelParameters::convert_to_parameter_values_at_res ( std::map< Size, utility::vector1< Size > > const & res_lists )

private

References fill_parameter_values(), and size().

std::map< Size, utility::vector1< Size > > core::pose::full_model_info::FullModelParameters::convert_to_res_lists_by_value ( utility::vector1< Size > const & parameter_values_at_res )

private

References size().

Referenced by set_parameter().

scoring::constraints::ConstraintSetCOP core::pose::full_model_info::FullModelParameters::cst_set ( ) const

References cst_set_.

std::string core::pose::full_model_info::FullModelParameters::cst_string ( ) const

inline

References cst_string_.

void core::pose::full_model_info::FullModelParameters::fill_parameter_values	(	utility::vector1< Size > &	parameter_values_at_res,
		Size const	idx,
		utility::vector1< Size > const &	res_list
	)		const

private

References size().

Referenced by convert_to_parameter_values_at_res().

std::string core::pose::full_model_info::FullModelParameters::full_annotated_sequence ( ) const

References full_sequence_, and non_standard_residue_map_.

Pose const & core::pose::full_model_info::FullModelParameters::full_model_pose_for_constraints ( ) const

References full_model_pose_for_constraints_.

std::string const& core::pose::full_model_info::FullModelParameters::full_sequence ( ) const

inline

References full_sequence_.

Referenced by core::pose::full_model_info::initialize_parameters(), and core::pose::full_model_info::operator<<().

utility::vector1< int > core::pose::full_model_info::FullModelParameters::full_to_conventional ( utility::vector1< Size > const & res_list ) const

int core::pose::full_model_info::FullModelParameters::full_to_conventional ( Size const res_num ) const

References conventional_numbering_.

std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > core::pose::full_model_info::FullModelParameters::full_to_conventional_resnum_and_chain_and_segid ( utility::vector1< Size > const & res_list ) const

References conventional_chains_, conventional_numbering_, and conventional_segids_.

Referenced by core::import_pose::dump_stems(), protocols::stepwise::modeler::align::StepWisePoseAligner::get_res_list_in_reference(), and core::import_pose::update_pose_fold_tree().

std::tuple< int, char, std::string > core::pose::full_model_info::FullModelParameters::full_to_conventional_resnum_and_chain_and_segid ( Size const res_num ) const

References conventional_chains_, conventional_numbering_, and conventional_segids_.

utility::vector1< Size > core::pose::full_model_info::FullModelParameters::get_cutpoint_open_from_pdb_info	(	pose::Pose const &	pose,
		utility::vector1< Size > const &	res_list
	)		const

private

References core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by FullModelParameters().

utility::vector1< Size > const & core::pose::full_model_info::FullModelParameters::get_parameter ( FullModelParameterType const type ) const

References parameter_values_at_res_.

Referenced by chains_in_full_model(), and slice().

std::map< Size, utility::vector1< Size > > const & core::pose::full_model_info::FullModelParameters::get_parameter_as_res_lists ( FullModelParameterType const type ) const

References parameter_values_as_res_lists_.

Referenced by get_res_list_as_pairs(), and core::pose::full_model_info::operator<<().

utility::vector1< Size > const & core::pose::full_model_info::FullModelParameters::get_res_list	(	FullModelParameterType const	type,
		Size const	value
	)		const

References parameter_values_as_res_lists_.

utility::vector1< Size > const& core::pose::full_model_info::FullModelParameters::get_res_list ( FullModelParameterType const type ) const

inline

References get_res_list().

Referenced by get_res_list().

utility::vector1< std::pair< Size, Size > > core::pose::full_model_info::FullModelParameters::get_res_list_as_pairs ( FullModelParameterType const type ) const

References get_parameter_as_res_lists().

void core::pose::full_model_info::FullModelParameters::get_sequence_with_gaps_filled_with_n	(	pose::Pose const &	pose,
		std::string &	sequence,
		utility::vector1< int > &	conventional_numbering,
		utility::vector1< char > &	conventional_chains,
		utility::vector1< std::string > &	conventional_segids,
		utility::vector1< Size > &	res_list
	)		const

private

References core::pose::Pose::chain(), core::pose::full_model_info::get_res_num_from_pdb_info(), core::pose::Pose::pdb_info(), core::pose::Pose::sequence(), and core::pose::Pose::size().

Referenced by FullModelParameters().

utility::vector1< Size > const& core::pose::full_model_info::FullModelParameters::global_mapping ( ) const

inline

References global_mapping_.

std::string const& core::pose::full_model_info::FullModelParameters::global_sequence ( ) const

inline

References global_sequence_.

Referenced by core::pose::full_model_info::operator<<().

bool core::pose::full_model_info::FullModelParameters::has_conventional_residue ( int const res_num ) const

References conventional_numbering_.

Referenced by protocols::stepwise::modeler::align::StepWisePoseAligner::get_res_list_in_reference().

bool core::pose::full_model_info::FullModelParameters::has_conventional_residue	(	int const	res_num,
		char const	chain,
		std::string const &	segid = `" "`
	)		const

References conventional_chains_, conventional_numbering_, and conventional_segids_.

void core::pose::full_model_info::FullModelParameters::keep_chain_and_cutpoint_open_matched ( FullModelParameterType const & type )

private

std::map< Size, std::string > const& core::pose::full_model_info::FullModelParameters::non_standard_residue_map ( ) const

inline

References non_standard_residue_map_.

Referenced by core::pose::full_model_info::operator<<().

std::map< Size, std::string >& core::pose::full_model_info::FullModelParameters::non_standard_residue_map_nonconst ( )

inline

References non_standard_residue_map_.

Referenced by core::pose::full_model_info::operator>>().

FullModelParametersCOP core::pose::full_model_info::FullModelParameters::parent_full_model_parameters ( ) const

inline

References parent_full_model_parameters_.

void core::pose::full_model_info::FullModelParameters::read_cst_file ( std::string const & cst_file )

References cst_set_, cst_string_, and full_model_pose_for_constraints_.

void core::pose::full_model_info::FullModelParameters::read_disulfides ( std::string const & disulfide_file )

References conventional_to_full(), core::pose::full_model_info::DISULFIDE, full_sequence_, set_parameter_as_res_list_in_pairs(), and size().

void core::pose::full_model_info::FullModelParameters::read_global_seq_info ( std::string const & global_seq_file )

References conventional_chains_, conventional_numbering_, core::sequence::get_conventional_chains_and_numbering(), global_mapping_, global_sequence_, core::sequence::read_fasta_file(), and core::pose::TR().

void core::pose::full_model_info::FullModelParameters::set_conventional_chains ( utility::vector1< char > const & setting )

inline

References conventional_chains_.

void core::pose::full_model_info::FullModelParameters::set_conventional_numbering ( utility::vector1< int > const & setting )

inline

References conventional_numbering_.

void core::pose::full_model_info::FullModelParameters::set_conventional_segids ( utility::vector1< std::string > const & setting )

inline

References conventional_segids_.

void core::pose::full_model_info::FullModelParameters::set_cst_string ( std::string const & setting )

inline

References cst_string_.

void core::pose::full_model_info::FullModelParameters::set_non_standard_residue_map ( std::map< Size, std::string > const & setting )

inline

References non_standard_residue_map_.

void core::pose::full_model_info::FullModelParameters::set_parameter	(	FullModelParameterType const	type,
		utility::vector1< Size > const &	setting
	)

References convert_to_res_lists_by_value(), parameter_values_as_res_lists_, and parameter_values_at_res_.

Referenced by FullModelParameters(), core::pose::full_model_info::operator>>(), set_parameter_as_res_list(), set_parameter_as_res_list_in_pairs(), and set_parameter_as_res_lists().

void core::pose::full_model_info::FullModelParameters::set_parameter_as_res_list	(	FullModelParameterType const	type,
		utility::vector1< Size > const &	setting
	)

References convert_to_parameter_values_at_res(), and set_parameter().

Referenced by core::pose::full_model_info::initialize_parameters().

void core::pose::full_model_info::FullModelParameters::set_parameter_as_res_list_in_pairs	(	FullModelParameterType const	type,
		utility::vector1< Size > const &	setting
	)

References set_parameter(), and size().

Referenced by read_disulfides().

void core::pose::full_model_info::FullModelParameters::set_parameter_as_res_lists	(	FullModelParameterType const	type,
		std::map< Size, utility::vector1< Size > > const &	setting
	)

References convert_to_parameter_values_at_res(), and set_parameter().

void core::pose::full_model_info::FullModelParameters::set_parent_full_model_parameters ( FullModelParametersCOP setting )

inline

References parent_full_model_parameters_.

void core::pose::full_model_info::FullModelParameters::set_slice_res_list ( utility::vector1< Size > const & setting )

inline

References slice_res_list_.

Size core::pose::full_model_info::FullModelParameters::size ( ) const

References full_sequence_, and core::pose::rna::remove_bracketed().

Referenced by chains_in_full_model(), convert_to_parameter_values_at_res(), convert_to_res_lists_by_value(), fill_parameter_values(), core::pose::full_model_info::operator>>(), read_disulfides(), and set_parameter_as_res_list_in_pairs().

FullModelParametersOP core::pose::full_model_info::FullModelParameters::slice ( utility::vector1< Size > const & slice_res ) const

References chains_in_full_model(), conventional_chains_, conventional_numbering_, conventional_segids_, cst_string_, core::pose::full_model_info::CUTPOINT_OPEN, full_sequence_, FullModelParameters(), core::pose::full_model_info::get_cutpoint_open_from_chains(), get_parameter(), core::pose::full_model_info::LAST_TYPE, non_standard_residue_map_, parent_full_model_parameters_, core::chemical::rings::q, and slice_res_list_.

utility::vector1< Size > const& core::pose::full_model_info::FullModelParameters::slice_res_list ( ) const

inline

References slice_res_list_.

void core::pose::full_model_info::FullModelParameters::update_pose_and_cst_set_from_cst_string ( chemical::ResidueTypeSet const & rsd_type_set ) const

References conventional_chains_, conventional_numbering_, cst_set_, cst_string_, full_model_pose_for_constraints_, full_sequence_, and core::pose::make_pose_from_sequence().

Friends And Related Function Documentation

bool operator!=	(	FullModelParameters const &	a,
		FullModelParameters const &	b
	)

friend

not equal to operator

std::ostream& operator<<	(	std::ostream &	os,
		FullModelParameters const &	t
	)

friend

output operator

Nice one-line format summarizing everything in FullModelParameters.

bool operator==	(	FullModelParameters const &	a,
		FullModelParameters const &	b
	)

friend

equal to operator

std::istream& operator>>	(	std::istream &	is,
		FullModelParameters &	t
	)

friend

input operator

Read in of one-line format for FullModelParameters – better be exact reverse of <<

Member Data Documentation

utility::vector1< char > core::pose::full_model_info::FullModelParameters::conventional_chains_

private

Referenced by conventional_chains(), conventional_to_full(), full_to_conventional_resnum_and_chain_and_segid(), FullModelParameters(), has_conventional_residue(), core::pose::full_model_info::operator>>(), read_global_seq_info(), set_conventional_chains(), slice(), and update_pose_and_cst_set_from_cst_string().

utility::vector1< int > core::pose::full_model_info::FullModelParameters::conventional_numbering_

private

Referenced by conventional_numbering(), conventional_to_full(), full_to_conventional(), full_to_conventional_resnum_and_chain_and_segid(), FullModelParameters(), has_conventional_residue(), core::pose::full_model_info::operator>>(), read_global_seq_info(), set_conventional_numbering(), slice(), and update_pose_and_cst_set_from_cst_string().

utility::vector1< std::string > core::pose::full_model_info::FullModelParameters::conventional_segids_

private

Referenced by conventional_segids(), conventional_to_full(), full_to_conventional_resnum_and_chain_and_segid(), FullModelParameters(), has_conventional_residue(), core::pose::full_model_info::operator>>(), set_conventional_segids(), and slice().

core::scoring::constraints::ConstraintSetCOP core::pose::full_model_info::FullModelParameters::cst_set_

mutableprivate

Referenced by cst_set(), read_cst_file(), and update_pose_and_cst_set_from_cst_string().

std::string core::pose::full_model_info::FullModelParameters::cst_string_

private

Referenced by cst_string(), core::pose::full_model_info::operator<<(), core::pose::full_model_info::operator>>(), read_cst_file(), set_cst_string(), slice(), and update_pose_and_cst_set_from_cst_string().

pose::PoseCOP core::pose::full_model_info::FullModelParameters::full_model_pose_for_constraints_

mutableprivate

Referenced by full_model_pose_for_constraints(), read_cst_file(), and update_pose_and_cst_set_from_cst_string().

std::string core::pose::full_model_info::FullModelParameters::full_sequence_

private

Referenced by full_annotated_sequence(), full_sequence(), FullModelParameters(), core::pose::full_model_info::operator>>(), read_disulfides(), size(), slice(), and update_pose_and_cst_set_from_cst_string().

utility::vector1< Size > core::pose::full_model_info::FullModelParameters::global_mapping_

private

Referenced by global_mapping(), core::pose::full_model_info::operator<<(), core::pose::full_model_info::operator>>(), and read_global_seq_info().

std::string core::pose::full_model_info::FullModelParameters::global_sequence_

private

Referenced by global_sequence(), core::pose::full_model_info::operator>>(), and read_global_seq_info().

std::map< Size, std::string > core::pose::full_model_info::FullModelParameters::non_standard_residue_map_

private

Referenced by full_annotated_sequence(), non_standard_residue_map(), non_standard_residue_map_nonconst(), set_non_standard_residue_map(), and slice().

std::map< FullModelParameterType, std::map< Size, utility::vector1< Size > > > core::pose::full_model_info::FullModelParameters::parameter_values_as_res_lists_

private

Referenced by get_parameter_as_res_lists(), get_res_list(), and set_parameter().