HubDenovo Struct Reference

Public Member Functions
virtual	~HubDenovo ()
	HubDenovo (std::string cstcfgfile)
Pose	make_start_pose ()
void	reset_hub (Pose &p)
bool	cen_fold (Pose &p)
void	min_as_poly_ala (Pose &p, ScoreFunctionOP sf)
void	design (Pose &p, bool hydrophobic_only=false)
Real	stupid_ddg (Pose const &pose_in)
void	run (Size NITER=999999999)

Public Attributes
Pose	hub_
Pose	target_
ConstraintConfig	cfg
ScoreFunctionOP	sf3
ScoreFunctionOP	sfsym
ScoreFunctionOP	sfasym
ScoreFunctionOP	sfsymnocst
protocols::moves::MoverOP	rlxcst
protocols::moves::MoverOP	rlxnocst
protocols::moves::MoverOP	des
protocols::moves::MoverOP	fragins3
protocols::moves::MoverOP	fraginsL
protocols::moves::MoverOP	fragins
protocols::moves::MoverOP	cenmin
protocols::moves::MoverOP	famin

Constructor & Destructor Documentation

~HubDenovo()

virtual HubDenovo::~HubDenovo ( )

inlinevirtual

HubDenovo()

HubDenovo::HubDenovo ( std::string  cstcfgfile )

inline

References pyrosetta::create_score_function, ConstraintConfig::cst_bb, test.T009_Exceptions::e, ERROR_UINT, get_frags_map(), create_a3b_hbs::i, ObjexxFCL::format::I(), create_a3b_hbs::j, ObjexxFCL::format::LJ(), make_frag_set(), basic::options::OptionKeys::in::file::movemap, ConstraintConfig::nres, basic::options::option, pyrosetta.distributed.io::pose_from_file, basic::options::OptionKeys::in::file::residue_type_set, basic::options::OptionKeys::frags::scoring::scoring, ConstraintConfig::ss, ConstraintConfig::ssmap, ConstraintConfig::ssstr(), basic::options::OptionKeys::hotspot::target, basic::options::TR, basic::options::OptionKeys::inout::dbms::user, and basic::options::OptionKeys::remodel::vdw.

Member Function Documentation

cen_fold()

bool HubDenovo::cen_fold ( Pose &  p )

inline

References ConstraintConfig::apply_csts(), test.T009_Exceptions::e, numeric::random::gaussian(), ConstraintConfig::get_highest_intrahub_seqsep(), create_a3b_hbs::i, create_a3b_hbs::j, mc, basic::options::OptionKeys::MonteCarlo::MonteCarlo, basic::options::OptionKeys::in::file::movemap, ConstraintConfig::nres, ConstraintConfig::nsub, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, numeric::rotation_matrix(), numeric::sign(), erraser_analysis::temp, basic::options::TR, numeric::random::uniform(), and predPRE::z.

design()

void HubDenovo::design ( Pose &  p, bool  hydrophobic_only = false  )

inline

References detail::find(), create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, ConstraintConfig::nres, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, basic::options::OptionKeys::casp::repack, ConstraintConfig::seq, basic::options::OptionKeys::out::sf, vancomycin::task, basic::options::TR, and utility_exit_with_message.

make_start_pose()

Pose HubDenovo::make_start_pose ( )

inline

References ConstraintConfig::frs, test.T020_Pose_Bindings::ft, create_a3b_hbs::i, enumerate_junctions::int, ConstraintConfig::nhub, ConstraintConfig::nres, basic::options::option, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, ConstraintConfig::pick_sequence(), ConstraintConfig::template_seq_bb, ConstraintConfig::template_seq_sc, and basic::options::TR.

min_as_poly_ala()

void HubDenovo::min_as_poly_ala ( Pose &  p, ScoreFunctionOP  sf  )

inline

References ConstraintConfig::apply_csts(), test.T009_Exceptions::e, create_a3b_hbs::i, basic::options::OptionKeys::in::file::movemap, ConstraintConfig::nres, kmeans_adaptive_kernel_density_bb_dependent_rotlib::p, and basic::options::OptionKeys::out::sf.

reset_hub()

void HubDenovo::reset_hub ( Pose &  p )

inline

References create_a3b_hbs::i, basic::options::option, and kmeans_adaptive_kernel_density_bb_dependent_rotlib::p.

run()

void HubDenovo::run ( Size  NITER = 999999999 )

inline

References ConstraintConfig::apply_csts(), cen_fold(), utility::io::oc::cout, revert_app::design, utility::file_basename(), kmeans_adaptive_kernel_density_bb_dependent_rotlib::fn, ConstraintConfig::fname, enumerate_junctions::int, basic::options::OptionKeys::out::file::o, basic::options::option, ConstraintConfig::reset_csts(), basic::options::OptionKeys::remodel::rg, loops_kic::rms, basic::options::OptionKeys::frags::scoring::scoring, sfd, basic::options::OptionKeys::out::file::silent, str(), basic::options::OptionKeys::hotspot::target, basic::options::TR, numeric::random::uniform(), and basic::options::OptionKeys::inout::dbms::user.

stupid_ddg()

Real HubDenovo::stupid_ddg ( Pose const &  pose_in )

inline

References create_a3b_hbs::i, enumerate_junctions::int, ConstraintConfig::nhub, basic::options::OptionKeys::mh::filter::nodisulf, numeric::xyzVector< T >::normalized(), ConstraintConfig::nres, ConstraintConfig::nsub, vancomycin::pack, beta_nonlocal::pose, basic::options::TR, trans_pose(), utility_exit_with_message, and basic::Tracer::Warning.

Member Data Documentation

cenmin

protocols::moves::MoverOP HubDenovo::cenmin

cfg

ConstraintConfig HubDenovo::cfg

des

protocols::moves::MoverOP HubDenovo::des

famin

protocols::moves::MoverOP HubDenovo::famin

fragins

protocols::moves::MoverOP HubDenovo::fragins

fragins3

protocols::moves::MoverOP HubDenovo::fragins3

fraginsL

protocols::moves::MoverOP HubDenovo::fraginsL

hub_

Pose HubDenovo::hub_

rlxcst

protocols::moves::MoverOP HubDenovo::rlxcst

rlxnocst

protocols::moves::MoverOP HubDenovo::rlxnocst

sf3

ScoreFunctionOP HubDenovo::sf3

sfasym

ScoreFunctionOP HubDenovo::sfasym

sfsym

ScoreFunctionOP HubDenovo::sfsym

sfsymnocst

ScoreFunctionOP HubDenovo::sfsymnocst

target_

Pose HubDenovo::target_

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

• src/apps/pilot/will/old/hubdenovo.cc