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protocols::noesy_assign::FragsToAtomDist Class Reference

#include <FragsToAtomDist.hh>

Inheritance diagram for protocols::noesy_assign::FragsToAtomDist:
Inheritance graph
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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

Constructor & Destructor Documentation

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

References read_from_file().

Member Function Documentation

bool protocols::noesy_assign::FragsToAtomDist::check_sequence ( std::string const &  other_sequence) const
void protocols::noesy_assign::FragsToAtomDist::compute_average_distances ( core::Size  cycles,
core::Size  dump_freq 
)
private
core::Real protocols::noesy_assign::FragsToAtomDist::distance ( core::id::NamedAtomID  atom1,
core::id::NamedAtomID  atom2,
bool  r6_averaged = true 
) const
inline
FragsToAtomDist::DistanceRecord const & protocols::noesy_assign::FragsToAtomDist::distance_record ( core::id::NamedAtomID  atom1,
core::id::NamedAtomID  atom2 
) const

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

Referenced by FragsToAtomDist().

void protocols::noesy_assign::FragsToAtomDist::read_from_stream ( std::istream &  input)
std::string const& protocols::noesy_assign::FragsToAtomDist::sequence ( ) const
inline

References sequence_.

Referenced by set_sequence().

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

References sequence(), and sequence_.

void protocols::noesy_assign::FragsToAtomDist::swap_atoms ( core::id::NamedAtomID atom1,
core::id::NamedAtomID atom2 
) const
private
void protocols::noesy_assign::FragsToAtomDist::write_hist_to_file ( std::string const &  filename) const
void protocols::noesy_assign::FragsToAtomDist::write_hist_to_stream ( std::ostream &  output) const
void protocols::noesy_assign::FragsToAtomDist::write_to_file ( std::string const &  filename) const
void protocols::noesy_assign::FragsToAtomDist::write_to_stream ( std::ostream &  output) const

Member Data Documentation

core::fragment::FragSetOP protocols::noesy_assign::FragsToAtomDist::frags_
private
NamedDistanceMap protocols::noesy_assign::FragsToAtomDist::named_distmap_
private
FragsToAtomDist::DistanceRecord protocols::noesy_assign::FragsToAtomDist::NO_CONTACT
static
std::string protocols::noesy_assign::FragsToAtomDist::sequence_
private

Referenced by sequence(), and set_sequence().


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