core::pose::full_model_info::FullModelParameters Class Reference

#include <FullModelParameters.hh>

Public Member Functions
	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 ()
FullModelParametersOP	clone () const
std::string const &	full_sequence () const
utility::vector1< int > const &	conventional_numbering () const
utility::vector1< char > const &	conventional_chains () const
void	set_conventional_numbering (utility::vector1< int > const &setting)
void	set_conventional_chains (utility::vector1< char > 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)
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< Size > const &	get_parameter (FullModelParameterType const type) const
utility::vector1< Size >	conventional_to_full (utility::vector1< int > const &res_list) const
utility::vector1< Size >	conventional_to_full (std::pair< utility::vector1< int >, utility::vector1< char > > const &resnum_and_chain) const
bool	has_conventional_residue (int const res_num) const
bool	has_conventional_residue (int const res_num, char const chain) const
Size	conventional_to_full (int const res_num) const
Size	conventional_to_full (int const res_num, char const chain) const
utility::vector1< int >	full_to_conventional (utility::vector1< Size > const &res_list) const
int	full_to_conventional (Size const res_num) const
Size	size () const

Private Member Functions
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)
void	get_sequence_with_gaps_filled_with_n (pose::Pose const &pose, std::string &sequence, utility::vector1< int > &conventional_numbering, utility::vector1< Size > &res_list) const
utility::vector1< Size >	get_cutpoint_open_from_pdb_info (pose::Pose const &pose) const
utility::vector1< Size >	chains_in_full_model () const
void	keep_chain_and_cutpoint_open_matched (FullModelParameterType const &type)

Private Attributes
std::map < FullModelParameterType, utility::vector1< Size > >	parameter_values_at_res_
std::map < FullModelParameterType, std::map< Size, utility::vector1< Size > > >	parameter_values_as_res_lists_
std::string	full_sequence_
utility::vector1< int >	conventional_numbering_
utility::vector1< char >	conventional_chains_

Constructor & Destructor Documentation

core::pose::full_model_info::FullModelParameters::FullModelParameters

(

std::string const

full_sequence

)

References conventional_numbering_, and core::pose::full_model_info::initialize_parameters().

Referenced by clone().

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_numbering_, 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(), and set_parameter().

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

References conventional_numbering_, 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(), and set_parameter().

core::pose::full_model_info::FullModelParameters::FullModelParameters

(

FullModelParameters const &

src

)

core::pose::full_model_info::FullModelParameters::~FullModelParameters

(

)

Member Function Documentation

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

private

References core::pose::full_model_info::CUTPOINT_OPEN, full_sequence_, get_parameter(), and utility::vector1< T, class >::has_value().

Referenced by keep_chain_and_cutpoint_open_matched().

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

inline

References FullModelParameters().

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

inline

References conventional_chains_.

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

inline

References conventional_numbering_.

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

(

utility::vector1< int > const &

res_list

)

const

Referenced by conventional_to_full().

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

(

std::pair< utility::vector1< int >, utility::vector1< char > > const &

resnum_and_chain

)

const

References chain, conventional_to_full(), and runtime_assert.

Size core::pose::full_model_info::FullModelParameters::conventional_to_full

(

int const

res_num

)

const

References conventional_numbering_, runtime_assert, and utility_exit_with_message.

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

References conventional_chains_, conventional_numbering_, runtime_assert, and utility_exit_with_message.

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

private

References runtime_assert, and size().

Referenced by FullModelParameters(), and set_parameter_as_res_list().

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 runtime_assert, and size().

Referenced by set_parameter().

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().

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_, and runtime_assert.

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

private

References cutpoint_open, core::chemical::ResidueType::is_protein(), core::chemical::ResidueType::is_RNA(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by FullModelParameters().

utility::vector1< Size > const & core::pose::full_model_info::FullModelParameters::get_parameter

(

FullModelParameterType const

type

)

const

References parameter_values_at_res_, and runtime_assert.

Referenced by chains_in_full_model(), and keep_chain_and_cutpoint_open_matched().

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_, and runtime_assert.

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().

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< Size > &  res_list  ) const

private

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

Referenced by FullModelParameters().

bool core::pose::full_model_info::FullModelParameters::has_conventional_residue

(

int const

res_num

)

const

References conventional_numbering_.

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

References conventional_chains_, and conventional_numbering_.

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

private

References core::pose::full_model_info::CHAIN, chains_in_full_model(), core::pose::full_model_info::CUTPOINT_OPEN, get_parameter(), runtime_assert, and set_parameter().

Referenced by set_parameter().

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

References convert_to_res_lists_by_value(), keep_chain_and_cutpoint_open_matched(), parameter_values_as_res_lists_, and parameter_values_at_res_.

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

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().

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

inline

References full_sequence_.

Referenced by convert_to_parameter_values_at_res(), and convert_to_res_lists_by_value().

Member Data Documentation

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

private

Referenced by conventional_chains(), conventional_to_full(), has_conventional_residue(), and set_conventional_chains().

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

private

Referenced by conventional_numbering(), conventional_to_full(), full_to_conventional(), FullModelParameters(), has_conventional_residue(), and set_conventional_numbering().

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

private

Referenced by chains_in_full_model(), full_sequence(), FullModelParameters(), and size().

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

private

Referenced by get_res_list(), and set_parameter().

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

private

Referenced by get_parameter(), and set_parameter().

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The documentation for this class was generated from the following files:

• src/core/pose/full_model_info/FullModelParameters.hh
• src/core/pose/full_model_info/FullModelParameters.cc