Bola Struct Reference

Public Member Functions
	Bola (vector1< PoseOP > const &p, vector1< string > const &l, vector1< core::Size > const &target_residues, core::scoring::RamachandranCOP _rama)
X	get_target_xform ()
core::Real	get_target_distance ()
void	random_close_phipsi_from_rama (Real sd, core::chemical::AA const aa, Real const phi0, Real const psi0, Real &phi, Real &psi)
void	random_move (core::chemical::AA &moved_aa, Real &moved_phi, Real &moved_psi)
void	random_nonclashing_move (core::chemical::AA &moved_aa, Real &moved_phi, Real &moved_psi)
void	undo_most_recent_move ()
void	refold ()
void	dump_pdb (std::string const &fn)
bool	clashes ()
bool	is_connected ()

Public Attributes
vector1< Rose >	roses
vector1< Link >	links
vector1< Link >::iterator	last_moved_link
X	target
X	target_stub1
X	target_stub2
core::Size	target_rose1
core::Size	target_rose2
core::Size	ntrials
core::Size	nclashes
core::Size	naccepts
V	T11
V	T12
V	T13
V	T21
V	T22
V	T23
core::scoring::RamachandranCOP	rama
utility::vector1< Size >	clash_intralink_
utility::vector1< Size >	clash_crosslink_
utility::vector1< Size >	clash_roselink_
utility::vector1< Size >	clash_roserose_
Real	move_sd_
bool	started_
vector1< xyzVector< Real > >	tgtatoms_

Constructor & Destructor Documentation

Bola()

Bola::Bola ( vector1< PoseOP > const &  p, vector1< string > const &  l, vector1< core::Size > const &  target_residues, core::scoring::RamachandranCOP  _rama  )

inline

References create_a3b_hbs::i, extract_by_sidechain_sasa_score::l, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, res, residue, basic::options::OptionKeys::hotspot::target, basic::options::OptionKeys::in::target_residues, utility_exit_with_message, and basic::options::OptionKeys::in::file::xyz.

Member Function Documentation

clashes()

bool Bola::clashes ( )

inline

References clash(), create_a3b_hbs::i, create_a3b_hbs::ii, and create_a3b_hbs::j.

dump_pdb()

void Bola::dump_pdb ( std::string const &  fn )

inline

References ObjexxFCL::format::F(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, create_a3b_hbs::i, test.T110_numeric::I, erraser_single_res_analysis::out, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::v.

Referenced by main().

get_target_distance()

core::Real Bola::get_target_distance ( )

inline

References numeric::distance_squared().

Referenced by main().

get_target_xform()

X Bola::get_target_xform ( )

inline

References x.

is_connected()

bool Bola::is_connected ( )

inline

References create_a3b_hbs::i.

random_close_phipsi_from_rama()

void Bola::random_close_phipsi_from_rama ( Real  sd, core::chemical::AA const  aa, Real const  phi0, Real const  psi0, Real &  phi, Real &  psi  )

inline

References aa, utility::io::oc::cout, fastexp(), create_a3b_hbs::i, numeric::min(), P, oop_conformations::phi, oop_conformations::psi, basic::options::OptionKeys::remodel::rama, sd(), and numeric::random::uniform().

random_move()

void Bola::random_move ( core::chemical::AA &  moved_aa, Real &  moved_phi, Real &  moved_psi  )

inline

References run_backbone::choices, create_a3b_hbs::i, subloop_histogram::iterator, create_a3b_hbs::j, basic::options::OptionKeys::backrub::ntrials, random_element(), and numeric::random::uniform().

random_nonclashing_move()

void Bola::random_nonclashing_move ( core::chemical::AA &  moved_aa, Real &  moved_phi, Real &  moved_psi  )

inline

References basic::options::OptionKeys::matdes::dock::dump_pdb, create_a3b_hbs::i, out::file::o(), option, test.Workshop4test::random_move(), and utility_exit_with_message.

Referenced by main().

refold()

void Bola::refold ( )

inline

References create_a3b_hbs::i.

undo_most_recent_move()

void Bola::undo_most_recent_move ( )

inline

References utility_exit_with_message.

Referenced by main().

Member Data Documentation

clash_crosslink_

utility::vector1<Size> Bola::clash_crosslink_

clash_intralink_

utility::vector1<Size> Bola::clash_intralink_

clash_roselink_

utility::vector1<Size> Bola::clash_roselink_

clash_roserose_

utility::vector1<Size> Bola::clash_roserose_

last_moved_link

vector1<Link>::iterator Bola::last_moved_link

links

vector1<Link> Bola::links

move_sd_

Real Bola::move_sd_

Referenced by main().

naccepts

core::Size Bola::naccepts

Referenced by main().

nclashes

core::Size Bola::nclashes

Referenced by main().

ntrials

core::Size Bola::ntrials

Referenced by main().

rama

core::scoring::RamachandranCOP Bola::rama

roses

vector1<Rose> Bola::roses

started_

bool Bola::started_

T11

V Bola::T11

T12

V Bola::T12

T13

V Bola::T13

T21

V Bola::T21

T22

V Bola::T22

T23

V Bola::T23

target

X Bola::target

target_rose1

core::Size Bola::target_rose1

target_rose2

core::Size Bola::target_rose2

target_stub1

X Bola::target_stub1

target_stub2

X Bola::target_stub2

tgtatoms_

vector1<xyzVector<Real> > Bola::tgtatoms_

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The documentation for this struct was generated from the following file:

• src/apps/pilot/will/old/flail.cc