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

#include <ResfileReader.hh>

Inheritance diagram for core::pack::task::ResfileContents:

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< ResfileCommandCOP >	default_commands_
utility::vector1< std::list< ResfileCommandCOP > >	commands_

Member Enumeration Documentation

residue_identifier_type

enum core::pack::task::ResfileContents::residue_identifier_type

private

Enumerator
SINGLE_RESID
RANGE_RESID
CHAIN_RESID

Constructor & Destructor Documentation

ResfileContents()

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

References check_for_deprecated_commands(), commands_, core::pack::task::comment_begin(), core::pack::task::create_command_map(), default_commands(), core::sequence::end, parse_body_line(), parse_header_line(), core::pose::Pose::size(), core::pack::task::tokenize_line(), and core::pack::task::TR().

~ResfileContents()

core::pack::task::ResfileContents::~ResfileContents ( )

overridedefault

Member Function Documentation

check_for_deprecated_commands()

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().

commands_for_residue()

std::list< ResfileCommandCOP > const & core::pack::task::ResfileContents::commands_for_residue

(

Size

resid

)

const

References commands_, and core::id::to_string().

Referenced by protocols::pack_daemon::initialize_task_from_entity_resfile_and_secondary_resfile(), core::pack::task::parse_resfile_string(), and core::pack::task::operation::ReadResfileAndObeyLengthEvents::resfile_commands().

default_commands()

std::list< ResfileCommandCOP > const & core::pack::task::ResfileContents::default_commands

(

)

const

References default_commands_.

Referenced by protocols::pack_daemon::initialize_task_from_entity_resfile_and_secondary_resfile(), core::pack::task::parse_resfile_string(), core::pack::task::operation::ReadResfileAndObeyLengthEvents::resfile_commands(), and ResfileContents().

fname_initialized_from()

std::string const & core::pack::task::ResfileContents::fname_initialized_from

(

)

const

References fname_initialized_from_.

locate_command()

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

References core::pack::task::get_token(), and core::pack::task::onError().

Referenced by parse_body_line(), and parse_header_line().

locate_resid()

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

References core::pack::task::onError(), core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by parse_body_line().

parse_body_line()

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().

parse_header_line()

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

References core::pack::task::comment_begin(), default_commands_, core::pack::task::get_token(), and locate_command().

Referenced by ResfileContents().

parse_PDBnum_icode()

void core::pack::task::ResfileContents::parse_PDBnum_icode ( std::string const &  token, Size const  lineno, int &  PDBnum, char &  icode  ) const

private

parse_resid()

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

References CHAIN_RESID, core::chemical::chr_chains(), fname_initialized_from_, core::pack::task::get_token(), core::pack::task::onError(), core::pose::parse_PDBnum_icode(), RANGE_RESID, and SINGLE_RESID.

Referenced by parse_body_line().

specialized_commands_exist_for_residue()

bool core::pack::task::ResfileContents::specialized_commands_exist_for_residue

(

Size

resid

)

const

References commands_, and core::id::to_string().

Referenced by protocols::pack_daemon::initialize_task_from_entity_resfile_and_secondary_resfile(), core::pack::task::parse_resfile_string(), and core::pack::task::operation::ReadResfileAndObeyLengthEvents::resfile_commands().

Member Data Documentation

commands_

utility::vector1< std::list< ResfileCommandCOP > > core::pack::task::ResfileContents::commands_

private

Referenced by commands_for_residue(), parse_body_line(), ResfileContents(), and specialized_commands_exist_for_residue().

default_commands_

std::list< ResfileCommandCOP > core::pack::task::ResfileContents::default_commands_

private

Referenced by default_commands(), and parse_header_line().

fname_initialized_from_

std::string core::pack::task::ResfileContents::fname_initialized_from_

private

Referenced by fname_initialized_from(), and parse_resid().

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

• src/core/pack/task/ResfileReader.hh
• src/core/pack/task/ResfileReader.cc