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core::pack::task::ResfileContents Class Reference

#include <ResfileReader.hh>

Inheritance diagram for core::pack::task::ResfileContents:
Inheritance graph
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Public Member Functions

 ResfileContents (pose::Pose const &pose, std::string const &fname, std::istream &istream)
 
 ~ResfileContents () override
 
std::list< ResfileCommandCOP >
const & 
default_commands () const
 
bool specialized_commands_exist_for_residue (Size resid) const
 
std::list< ResfileCommandCOP >
const & 
commands_for_residue (Size resid) const
 
std::string const & fname_initialized_from () const
 

Private Types

enum  residue_identifier_type { SINGLE_RESID =1, RANGE_RESID, CHAIN_RESID }
 

Private Member Functions

void check_for_deprecated_commands (utility::vector1< std::string > const &tokens) const
 Given a vector of strings corresponding to the words in a whitespace-separated line, look for deprecated commands and issue a suitable warning. More...
 
void parse_header_line (utility::vector1< std::string > const &tokens, std::map< std::string, ResfileCommandOP > const &command_map, Size const lineno, bool &have_read_start_token)
 
void parse_body_line (pose::Pose const &pose, utility::vector1< std::string > const &tokens, std::map< std::string, ResfileCommandOP > const &command_map, Size const lineno, utility::vector1< std::list< ResfileCommandOP > > &residue_range_commands, utility::vector1< std::list< ResfileCommandOP > > &residue_chain_commands)
 
void parse_resid (Size &which_token, utility::vector1< std::string > const &tokens, Size const lineno, int &PDBnum, int &PDBnum_end, char &icode, char &icode_end, char &chain, residue_identifier_type &id_type) const
 
void parse_PDBnum_icode (std::string const &token, Size const lineno, int &PDBnum, char &icode) const
 
Size locate_resid (core::pose::Pose const &pose, char const chain, Size const PDBnum, char const icode, Size const lineno) const
 
ResfileCommandOP locate_command (Size const which_token, utility::vector1< std::string > const &tokens, std::map< std::string, ResfileCommandOP > const &command_map, Size const lineno) const
 

Private Attributes

std::string fname_initialized_from_
 
std::list< ResfileCommandCOPdefault_commands_
 
utility::vector1< std::list
< ResfileCommandCOP > > 
commands_
 

Member Enumeration Documentation

Enumerator
SINGLE_RESID 
RANGE_RESID 
CHAIN_RESID 

Constructor & Destructor Documentation

core::pack::task::ResfileContents::ResfileContents ( pose::Pose const &  pose,
std::string const &  fname,
std::istream &  istream 
)
core::pack::task::ResfileContents::~ResfileContents ( )
overridedefault

Member Function Documentation

void core::pack::task::ResfileContents::check_for_deprecated_commands ( utility::vector1< std::string > const &  tokens) const
private

Given a vector of strings corresponding to the words in a whitespace-separated line, look for deprecated commands and issue a suitable warning.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org).

Referenced by ResfileContents().

std::list< ResfileCommandCOP > const & core::pack::task::ResfileContents::commands_for_residue ( Size  resid) const
std::list< ResfileCommandCOP > const & core::pack::task::ResfileContents::default_commands ( ) const
std::string const & core::pack::task::ResfileContents::fname_initialized_from ( ) const
ResfileCommandOP core::pack::task::ResfileContents::locate_command ( Size const  which_token,
utility::vector1< std::string > const &  tokens,
std::map< std::string, ResfileCommandOP > const &  command_map,
Size const  lineno 
) const
private
Size core::pack::task::ResfileContents::locate_resid ( core::pose::Pose const &  pose,
char const  chain,
Size const  PDBnum,
char const  icode,
Size const  lineno 
) const
private
void core::pack::task::ResfileContents::parse_body_line ( pose::Pose const &  pose,
utility::vector1< std::string > const &  tokens,
std::map< std::string, ResfileCommandOP > const &  command_map,
Size const  lineno,
utility::vector1< std::list< ResfileCommandOP > > &  residue_range_commands,
utility::vector1< std::list< ResfileCommandOP > > &  residue_chain_commands 
)
private

@ details Parse body line in resfile expected formats: <residue identifier>=""> <chain identifier>=""> <commands*> <residue identifier>=""> - <residue identifier>=""> <chain identifier>=""> <commands*>

  • <chain identifer>=""> <commands*>

The here is how a residue specification is resolved if it is specified multiple times:

1) If a residue is specified by multiple commands of the same level (SINGLE, RANGE, or CHAIN), then this is an error 2) If a residue is specified by multiple commands of different levels then the more restricted level takes precidence, SINGLE over RANGE and CHAIN, and RANGE over CHAIN

References CHAIN_RESID, commands_, core::pack::task::comment_begin(), locate_command(), locate_resid(), core::pack::task::onError(), parse_resid(), core::pose::Pose::pdb_info(), RANGE_RESID, SINGLE_RESID, and core::pose::Pose::size().

Referenced by ResfileContents().

void core::pack::task::ResfileContents::parse_header_line ( utility::vector1< std::string > const &  tokens,
std::map< std::string, ResfileCommandOP > const &  command_map,
Size const  lineno,
bool have_read_start_token 
)
private
void core::pack::task::ResfileContents::parse_PDBnum_icode ( std::string const &  token,
Size const  lineno,
int &  PDBnum,
char &  icode 
) const
private
void core::pack::task::ResfileContents::parse_resid ( Size which_token,
utility::vector1< std::string > const &  tokens,
Size const  lineno,
int &  PDBnum,
int &  PDBnum_end,
char &  icode,
char &  icode_end,
char &  chain,
residue_identifier_type id_type 
) const
private
bool core::pack::task::ResfileContents::specialized_commands_exist_for_residue ( Size  resid) const

Member Data Documentation

utility::vector1< std::list< ResfileCommandCOP > > core::pack::task::ResfileContents::commands_
private
std::list< ResfileCommandCOP > core::pack::task::ResfileContents::default_commands_
private
std::string core::pack::task::ResfileContents::fname_initialized_from_
private

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