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

#include <FullModelParameters.hh>

Inheritance diagram for core::pose::full_model_info::FullModelParameters:
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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< Sizeconventional_to_full (utility::vector1< int > const &res_list) const
 
utility::vector1< Sizeconventional_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< Sizechains_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< Sizeconvert_to_parameter_values_at_res (utility::vector1< Size > const &res_list)
 
utility::vector1< Sizeconvert_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< Sizeget_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< Sizeglobal_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< Sizeslice_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 ( )
core::pose::full_model_info::FullModelParameters::FullModelParameters ( std::string const &  full_sequence)
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 
)
core::pose::full_model_info::FullModelParameters::FullModelParameters ( pose::Pose const &  pose,
utility::vector1< Size > &  res_list 
)
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
FullModelParametersOP core::pose::full_model_info::FullModelParameters::clone ( ) const
inline
utility::vector1< char > const& core::pose::full_model_info::FullModelParameters::conventional_chains ( ) const
inline
utility::vector1< int > const& core::pose::full_model_info::FullModelParameters::conventional_numbering ( ) const
inline
utility::vector1< std::string > const& core::pose::full_model_info::FullModelParameters::conventional_segids ( ) const
inline
utility::vector1< Size > core::pose::full_model_info::FullModelParameters::conventional_to_full ( utility::vector1< int > const &  res_list) const
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
Size core::pose::full_model_info::FullModelParameters::conventional_to_full ( int const  res_num) const
Size core::pose::full_model_info::FullModelParameters::conventional_to_full ( int const  res_num,
char const  chain,
std::string const &  segid = "    " 
) const
utility::vector1< Size > core::pose::full_model_info::FullModelParameters::convert_to_parameter_values_at_res ( utility::vector1< Size > const &  res_list)
private
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
Pose const & core::pose::full_model_info::FullModelParameters::full_model_pose_for_constraints ( ) const
std::string const& core::pose::full_model_info::FullModelParameters::full_sequence ( ) const
inline
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
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
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
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
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
utility::vector1< Size > const & core::pose::full_model_info::FullModelParameters::get_res_list ( FullModelParameterType const  type,
Size const  value 
) const
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
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
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
bool core::pose::full_model_info::FullModelParameters::has_conventional_residue ( int const  res_num) const
bool core::pose::full_model_info::FullModelParameters::has_conventional_residue ( int const  res_num,
char const  chain,
std::string const &  segid = "    " 
) const
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
std::map< Size, std::string >& core::pose::full_model_info::FullModelParameters::non_standard_residue_map_nonconst ( )
inline
FullModelParametersCOP core::pose::full_model_info::FullModelParameters::parent_full_model_parameters ( ) const
inline
void core::pose::full_model_info::FullModelParameters::read_cst_file ( std::string const &  cst_file)
void core::pose::full_model_info::FullModelParameters::read_disulfides ( std::string const &  disulfide_file)
void core::pose::full_model_info::FullModelParameters::read_global_seq_info ( std::string const &  global_seq_file)
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
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
void core::pose::full_model_info::FullModelParameters::set_parameter ( FullModelParameterType const  type,
utility::vector1< Size > const &  setting 
)
void core::pose::full_model_info::FullModelParameters::set_parameter_as_res_list ( FullModelParameterType const  type,
utility::vector1< Size > const &  setting 
)
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 
)
void core::pose::full_model_info::FullModelParameters::set_parent_full_model_parameters ( FullModelParametersCOP  setting)
inline
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
FullModelParametersOP core::pose::full_model_info::FullModelParameters::slice ( utility::vector1< Size > const &  slice_res) const
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

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
utility::vector1< int > core::pose::full_model_info::FullModelParameters::conventional_numbering_
private
utility::vector1< std::string > core::pose::full_model_info::FullModelParameters::conventional_segids_
private
core::scoring::constraints::ConstraintSetCOP core::pose::full_model_info::FullModelParameters::cst_set_
mutableprivate
std::string core::pose::full_model_info::FullModelParameters::cst_string_
private
pose::PoseCOP core::pose::full_model_info::FullModelParameters::full_model_pose_for_constraints_
mutableprivate
std::string core::pose::full_model_info::FullModelParameters::full_sequence_
private
utility::vector1< Size > core::pose::full_model_info::FullModelParameters::global_mapping_
private
std::string core::pose::full_model_info::FullModelParameters::global_sequence_
private
std::map< Size, std::string > core::pose::full_model_info::FullModelParameters::non_standard_residue_map_
private
std::map< FullModelParameterType, std::map< Size, utility::vector1< Size > > > core::pose::full_model_info::FullModelParameters::parameter_values_as_res_lists_
private
std::map< FullModelParameterType, utility::vector1< Size > > core::pose::full_model_info::FullModelParameters::parameter_values_at_res_
private

Referenced by get_parameter(), and set_parameter().

FullModelParametersCOP core::pose::full_model_info::FullModelParameters::parent_full_model_parameters_
private
utility::vector1< Size > core::pose::full_model_info::FullModelParameters::slice_res_list_
private

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