#include <ResfileReader.hh>

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

Collaboration diagram for core::pack::task::ResfileContents:

Public Member Functions
	ResfileContents (pose::Pose const &pose, std::istream &istream)

virtual	~ResfileContents ()

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

Private Types
enum	residue_identifier_type { SINGLE_RESID =1, RANGE_RESID, CHAIN_RESID }

Private Member Functions
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::list< ResfileCommandCOP >	default_commands_

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

Detailed Description

Definition at line 66 of file ResfileReader.hh.

Member Enumeration Documentation

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

private

Enumerator
SINGLE_RESID
RANGE_RESID
CHAIN_RESID

Definition at line 83 of file ResfileReader.hh.

Constructor & Destructor Documentation

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

Definition at line 82 of file ResfileReader.cc.

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

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

virtual

Definition at line 134 of file ResfileReader.cc.

Member Function Documentation

std::list< ResfileCommandCOP > const & core::pack::task::ResfileContents::commands_for_residue ( Size resid) const

Definition at line 155 of file ResfileReader.cc.

References commands_.

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

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

Definition at line 137 of file ResfileReader.cc.

References default_commands_.

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

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

Definition at line 473 of file ResfileReader.cc.

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

Referenced by parse_body_line(), and parse_header_line().

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

Definition at line 441 of file ResfileReader.cc.

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

Referenced by 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

Definition at line 201 of file ResfileReader.cc.

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::total_residue().

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

Definition at line 166 of file ResfileReader.cc.

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

Referenced by ResfileContents().

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

private

Definition at line 413 of file ResfileReader.cc.

References core::pack::task::onError().

Referenced by 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