protocols::noesy_assign::FragsToAtomDist Class Reference

#include <FragsToAtomDist.hh>

Inheritance 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	write_hist_to_stream (std::ostream &) const
void	read_from_file (std::string const &filename)
void	write_to_file (std::string const &filename) const
void	write_hist_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_

Member Typedef Documentation

NamedDistanceMap

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

NamedInnerMap

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

Constructor & Destructor Documentation

FragsToAtomDist() [1/2]

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

inline

FragsToAtomDist() [2/2]

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

inline

References protocols::abinitio::filename(), and read_from_file().

Member Function Documentation

check_sequence()

bool protocols::noesy_assign::FragsToAtomDist::check_sequence

(

std::string const &

other_sequence

)

const

compute_average_distances()

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

private

References core::conformation::Residue::chi(), core::scoring::fa_dun, core::chemical::FA_STANDARD, core::scoring::get_score_function(), protocols::noesy_assign::initialize_group_list(), protocols::simple_moves::sidechain_moves::JumpRotamerSidechainMover::make_chi_move(), core::pose::make_pose_from_sequence(), core::conformation::Residue::nchi(), core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::set_chi(), protocols::noesy_assign::store_distance_snapshot(), protocols::noesy_assign::store_distmap_with_namedatoms(), and tr().

distance()

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

inline

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

distance_record()

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

Referenced by distance().

generate_from_frag_file()

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

References protocols::abinitio::filename().

generate_from_fragments()

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

read_from_file()

void protocols::noesy_assign::FragsToAtomDist::read_from_file

(

std::string const &

filename

)

References protocols::abinitio::filename().

Referenced by FragsToAtomDist().

read_from_stream()

void protocols::noesy_assign::FragsToAtomDist::read_from_stream

(

std::istream &

input

)

sequence()

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

inline

References sequence_.

Referenced by set_sequence().

set_sequence()

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

inlineprivate

References sequence(), and sequence_.

swap_atoms()

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

private

References protocols::cluster::calibur::aa, core::chemical::aa_from_oneletter_code(), core::id::NamedAtomID::atom(), core::id::NamedAtomID::rsd(), and core::id::swap().

write_hist_to_file()

void protocols::noesy_assign::FragsToAtomDist::write_hist_to_file

(

std::string const &

filename

)

const

References protocols::abinitio::filename().

write_hist_to_stream()

void protocols::noesy_assign::FragsToAtomDist::write_hist_to_stream

(

std::ostream &

output

)

const

References core::sequence::end, and simple_histogram().

write_to_file()

void protocols::noesy_assign::FragsToAtomDist::write_to_file

(

std::string const &

filename

)

const

References protocols::abinitio::filename().

write_to_stream()

void protocols::noesy_assign::FragsToAtomDist::write_to_stream

(

std::ostream &

output

)

const

Member Data Documentation

frags_

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

private

named_distmap_

NamedDistanceMap protocols::noesy_assign::FragsToAtomDist::named_distmap_

private

NO_CONTACT

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

static

sequence_

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

private

Referenced by sequence(), and set_sequence().

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

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