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Public Member Functions | Static Public Member Functions | Private Types | Private Attributes | List of all members
ThisApplication Class Reference

Public Member Functions

 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()=default
 
 ThisApplication ()
 
 ThisApplication ()=default
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()=default
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
void setup ()
 
void run ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 
void run ()
 
void analyze_tree (kinematics::FoldTree f, SecondaryStructureOP)
 
void show_jumps (std::ostream &)
 
void show_cuts (std::ostream &)
 
void pick_frags ()
 
 ThisApplication ()
 
 ThisApplication ()
 
 ThisApplication ()
 

Static Public Member Functions

static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 
static void register_options ()
 

Private Types

typedef std::pair< Size, Size > Pairing
 
typedef std::map< Pairing, Size > Jumps
 
typedef std::map< Size, Size > Cuts
 

Private Attributes

fragment::FragSetOP fragset_
 
Pose aligned_
 
std::string aligned_seq_
 
std::string target_seq_
 
Size frag_length_
 
core::id::SequenceMapping mapping_
 
Jumps jumps_
 
Cuts cuts_
 

Detailed Description

Author
TJ Brunette

Member Typedef Documentation

◆ Cuts

typedef std::map< Size, Size > ThisApplication::Cuts
private

◆ Jumps

typedef std::map< Pairing, Size > ThisApplication::Jumps
private

◆ Pairing

typedef std::pair< Size, Size > ThisApplication::Pairing
private

Constructor & Destructor Documentation

◆ ThisApplication() [1/27]

ThisApplication::ThisApplication ( )
default

◆ ThisApplication() [2/27]

ThisApplication::ThisApplication ( )

◆ ThisApplication() [3/27]

ThisApplication::ThisApplication ( )

◆ ThisApplication() [4/27]

ThisApplication::ThisApplication ( )

◆ ThisApplication() [5/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [6/27]

ThisApplication::ThisApplication ( )

◆ ThisApplication() [7/27]

ThisApplication::ThisApplication ( )

◆ ThisApplication() [8/27]

ThisApplication::ThisApplication ( )

◆ ThisApplication() [9/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [10/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [11/27]

ThisApplication::ThisApplication ( )
default

◆ ThisApplication() [12/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [13/27]

ThisApplication::ThisApplication ( )
default

◆ ThisApplication() [14/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [15/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [16/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [17/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [18/27]

ThisApplication::ThisApplication ( )
default

◆ ThisApplication() [19/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [20/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [21/27]

ThisApplication::ThisApplication ( )

◆ ThisApplication() [22/27]

ThisApplication::ThisApplication ( )

◆ ThisApplication() [23/27]

ThisApplication::ThisApplication ( )

◆ ThisApplication() [24/27]

ThisApplication::ThisApplication ( )

◆ ThisApplication() [25/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [26/27]

ThisApplication::ThisApplication ( )
inline

◆ ThisApplication() [27/27]

ThisApplication::ThisApplication ( )

Member Function Documentation

◆ analyze_tree()

void ThisApplication::analyze_tree ( kinematics::FoldTree  f,
SecondaryStructureOP  ss_def 
)

References utility::io::oc::cout, basic::Tracer::Debug, create_a3b_hbs::f, create_a3b_hbs::i, docking::jumps, option, tr, and basic::options::OptionKeys::inout::dbms::user.

◆ pick_frags()

void ThisApplication::pick_frags ( )

why was this function duplicated here? another copy lives in core/chemical/util.cc/hh, which seems like a better place for it.

References begin, basic::options::OptionKeys::frags::frags, subloop_histogram::iterator, option, beta_nonlocal::pose, sfd, basic::options::OptionKeys::in::file::silent, in::file::silent(), subloop_histogram::size, and tag.

◆ register_options() [1/28]

void ThisApplication::register_options ( )
static

References NEW_OPT.

Referenced by main().

◆ register_options() [2/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [3/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [4/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [5/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [6/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [7/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [8/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [9/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [10/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [11/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [12/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [13/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [14/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [15/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [16/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [17/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [18/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [19/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [20/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [21/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [22/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [23/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [24/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [25/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [26/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [27/28]

static void ThisApplication::register_options ( )
static

◆ register_options() [28/28]

static void ThisApplication::register_options ( )
static

◆ run() [1/2]

void ThisApplication::run ( )

References dump_movemap(), basic::Tracer::Error, numeric::kinematic_closure::frame(), basic::Tracer::Info, beta_nonlocal::mm, basic::options::OptionKeys::out::file::o, option, make_symmdef_file_denovo::pos, loops_kic::success, tr, and basic::Tracer::Trace.

◆ run() [2/2]

void ThisApplication::run ( )

◆ setup()

void ThisApplication::setup ( )

References a, utility::io::oc::cerr, create_a3b_hbs::f, basic::Tracer::Info, option, pyrosetta.distributed.io::pose_from_file, subloop_histogram::size, and tr.

Referenced by pyrosetta.distributed.tasks.taskbase.TaskBase::maybe_setup().

◆ show_cuts()

void ThisApplication::show_cuts ( std::ostream &  os)

References subloop_histogram::iterator, and ObjexxFCL::format::RJ().

◆ show_jumps()

void ThisApplication::show_jumps ( std::ostream &  os)

References subloop_histogram::iterator, and ObjexxFCL::format::RJ().

Member Data Documentation

◆ aligned_

Pose ThisApplication::aligned_
private

◆ aligned_seq_

std::string ThisApplication::aligned_seq_
private

◆ cuts_

Cuts ThisApplication::cuts_
private

◆ frag_length_

Size ThisApplication::frag_length_
private

◆ fragset_

fragment::FragSetOP ThisApplication::fragset_
private

◆ jumps_

Jumps ThisApplication::jumps_
private

◆ mapping_

core::id::SequenceMapping ThisApplication::mapping_
private

◆ target_seq_

std::string ThisApplication::target_seq_
private
The documentation for this class was generated from the following files:
Generated on Mon Sep 4 2023 13:55:01 for Rosetta by doxygen 1.9.1