#include <FragsToAtomDist.hh>

Inheritance diagram for protocols::noesy_assign::FragsToAtomDist:

Collaboration diagram for protocols::noesy_assign::FragsToAtomDist:

Classes
class	DistanceRecord

Public Types
typedef std::map < core::id::NamedAtomID, DistanceRecord >	NamedInnerMap

typedef std::map < core::id::NamedAtomID, NamedInnerMap >	NamedDistanceMap

Public Member Functions
	FragsToAtomDist ()

	FragsToAtomDist (std::string const &filename)

void	read_from_stream (std::istream &)

void	write_to_stream (std::ostream &) const

void	read_from_file (std::string const &filename)

void	write_to_file (std::string const &filename) const

void	generate_from_fragments (core::fragment::FragSetOP fragments, std::string const &sequence, core::Size cycles, core::Size dump_freq)

void	generate_from_frag_file (std::string const &filename, std::string const &sequence, core::Size cycles, core::Size dump_freq)

FragsToAtomDist::DistanceRecord const &	distance_record (core::id::NamedAtomID atom1, core::id::NamedAtomID atom2) const

core::Real	distance (core::id::NamedAtomID atom1, core::id::NamedAtomID atom2, bool r6_averaged=true) const

bool	check_sequence (std::string const &other_sequence) const

std::string const &	sequence () const

Static Public Attributes
static DistanceRecord	NO_CONTACT

Private Member Functions
void	swap_atoms (core::id::NamedAtomID &atom1, core::id::NamedAtomID &atom2) const

void	set_sequence (std::string const &sequence)

void	compute_average_distances (core::Size, core::Size)

Private Attributes
std::string	sequence_

core::fragment::FragSetOP	frags_

NamedDistanceMap	named_distmap_

Detailed Description

Definition at line 42 of file FragsToAtomDist.hh.

Member Typedef Documentation

typedef std::map< core::id::NamedAtomID, NamedInnerMap > protocols::noesy_assign::FragsToAtomDist::NamedDistanceMap

Definition at line 70 of file FragsToAtomDist.hh.

typedef std::map< core::id::NamedAtomID, DistanceRecord > protocols::noesy_assign::FragsToAtomDist::NamedInnerMap

Definition at line 69 of file FragsToAtomDist.hh.

Constructor & Destructor Documentation

protocols::noesy_assign::FragsToAtomDist::FragsToAtomDist ( )

inline

Definition at line 75 of file FragsToAtomDist.hh.

protocols::noesy_assign::FragsToAtomDist::FragsToAtomDist ( std::string const & filename)

inline

Definition at line 76 of file FragsToAtomDist.hh.

References read_from_file().

Member Function Documentation

bool protocols::noesy_assign::FragsToAtomDist::check_sequence ( std::string const & other_sequence) const

Definition at line 175 of file FragsToAtomDist.cc.

void protocols::noesy_assign::FragsToAtomDist::compute_average_distances	(	core::Size	cycles,
		core::Size	dump_freq
	)

private

Definition at line 367 of file FragsToAtomDist.cc.

References core::scoring::fa_dun, core::scoring::getScoreFunction(), protocols::noesy_assign::initialize_group_list(), core::pose::make_pose_from_sequence(), core::pose::Pose::residue(), core::conformation::symmetry::RG(), core::pose::Pose::sequence(), core::pose::Pose::set_chi(), protocols::noesy_assign::store_distance_snapshot(), protocols::noesy_assign::store_distmap_with_namedatoms(), and tr().

core::Real protocols::noesy_assign::FragsToAtomDist::distance	(	core::id::NamedAtomID	atom1,
		core::id::NamedAtomID	atom2,
		bool	r6_averaged = `true`
	)		const

inline

Definition at line 107 of file FragsToAtomDist.hh.

References protocols::noesy_assign::FragsToAtomDist::DistanceRecord::average_dist(), protocols::noesy_assign::FragsToAtomDist::DistanceRecord::average_dist6(), and distance_record().

FragsToAtomDist::DistanceRecord const & protocols::noesy_assign::FragsToAtomDist::distance_record	(	core::id::NamedAtomID	atom1,
		core::id::NamedAtomID	atom2
	)		const

Definition at line 183 of file FragsToAtomDist.cc.

Referenced by distance().

void protocols::noesy_assign::FragsToAtomDist::generate_from_frag_file	(	std::string const &	filename,
		std::string const &	sequence,
		core::Size	cycles,
		core::Size	dump_freq
	)

Definition at line 285 of file FragsToAtomDist.cc.

void protocols::noesy_assign::FragsToAtomDist::generate_from_fragments	(	core::fragment::FragSetOP	fragments,
		std::string const &	sequence,
		core::Size	cycles,
		core::Size	dump_freq
	)

Definition at line 278 of file FragsToAtomDist.cc.

void protocols::noesy_assign::FragsToAtomDist::read_from_file ( std::string const & filename)

Definition at line 271 of file FragsToAtomDist.cc.

Referenced by FragsToAtomDist().

void protocols::noesy_assign::FragsToAtomDist::read_from_stream ( std::istream & input)

Definition at line 238 of file FragsToAtomDist.cc.

std::string const& protocols::noesy_assign::FragsToAtomDist::sequence ( ) const

inline

Definition at line 121 of file FragsToAtomDist.hh.

References sequence_.

Referenced by set_sequence().

void protocols::noesy_assign::FragsToAtomDist::set_sequence ( std::string const & sequence)

inlineprivate

Definition at line 131 of file FragsToAtomDist.hh.

References sequence(), and sequence_.

void protocols::noesy_assign::FragsToAtomDist::swap_atoms	(	core::id::NamedAtomID &	atom1,
		core::id::NamedAtomID &	atom2
	)		const

private

Definition at line 290 of file FragsToAtomDist.cc.

References core::chemical::aa_from_oneletter_code(), core::id::NamedAtomID::atom(), core::id::NamedAtomID::rsd(), and core::id::swap().

void protocols::noesy_assign::FragsToAtomDist::write_to_file ( std::string const & filename) const

Definition at line 233 of file FragsToAtomDist.cc.

void protocols::noesy_assign::FragsToAtomDist::write_to_stream ( std::ostream & output) const

Definition at line 195 of file FragsToAtomDist.cc.

Member Data Documentation

core::fragment::FragSetOP protocols::noesy_assign::FragsToAtomDist::frags_

private

Definition at line 150 of file FragsToAtomDist.hh.

NamedDistanceMap protocols::noesy_assign::FragsToAtomDist::named_distmap_

private

Definition at line 151 of file FragsToAtomDist.hh.

FragsToAtomDist::DistanceRecord protocols::noesy_assign::FragsToAtomDist::NO_CONTACT

static

Definition at line 72 of file FragsToAtomDist.hh.

std::string protocols::noesy_assign::FragsToAtomDist::sequence_

private

Definition at line 148 of file FragsToAtomDist.hh.

Referenced by sequence(), and set_sequence().

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

src/protocols/noesy_assign/FragsToAtomDist.hh
src/protocols/noesy_assign/FragsToAtomDist.cc

Classes

Public Types

Public Member Functions

Static Public Attributes

Private Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation