CrystDesign Class Reference

Inheritance diagram for CrystDesign:

Public Member Functions
	CrystDesign (bool revertonly)
std::string	get_name () const override
void	filter_and_report (core::pose::Pose &pose, core::scoring::ScoreFunctionOP sf, bool &pass, bool &need_greedy, bool runfilter, bool report)
void	design_cycle (Pose &pose, core::scoring::ScoreFunctionOP sf, core::scoring::ScoreFunctionOP sfsoft, utility::vector1< bool > interface)
void	get_interface_residues (Pose &pose, core::scoring::ScoreFunctionOP sf, utility::vector1< bool > &interface)
void	get_neighbor_residues (Pose &pose, core::Size res_i, utility::vector1< bool > &neighbor)
void	do_reversion (Pose &pose, core::scoring::ScoreFunctionOP sf, core::scoring::ScoreFunctionOP sfsoft)
void	greedy_revert_unsats (Pose &pose, core::scoring::ScoreFunctionOP sf, core::scoring::ScoreFunctionOP sfsoft)
void	apply (Pose &pose) override

Private Attributes
protocols::cryst::MakeLatticeMover	setup_
core::Real	DDG_CUT_
core::Real	WEAKE_CUT_
core::Real	UNSATS_SOFT_CUT_
core::Real	UNSATS_CUT_
core::Real	SC_CUT_
core::Size	WFY_MUT_CUT_
core::Size	M_MUT_CUT_
core::Size	MUT_CUT_
core::Real	K_
core::Size	NCYC_
bool	NOFILT_
core::pose::Pose	native_
bool	revertonly_

Constructor & Destructor Documentation

CrystDesign()

CrystDesign::CrystDesign ( bool  revertonly )

inline

References PREcst::K, and option.

Member Function Documentation

apply()

void CrystDesign::apply ( Pose &  pose )

inlineoverride

References adjust_ref_weights(), basic::options::OptionKeys::chemical::chemical, get_interface_residues(), create_a3b_hbs::i, enumerate_junctions::int, interface, in::file::native(), option, beta_nonlocal::pose, pyrosetta.distributed.io::pose_from_file, runtime_assert, basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, basic::TR, and basic::options::OptionKeys::inout::dbms::user.

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

design_cycle()

void CrystDesign::design_cycle ( Pose &  pose, core::scoring::ScoreFunctionOP  sf, core::scoring::ScoreFunctionOP  sfsoft, utility::vector1< bool >  interface  )

inline

References basic::options::OptionKeys::chemical::chemical, create_a3b_hbs::i, enumerate_junctions::int, interface, beta_nonlocal::mm, option, options, parse_resfile(), beta_nonlocal::pose, packing::resfile(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, and basic::options::OptionKeys::inout::dbms::user.

do_reversion()

void CrystDesign::do_reversion ( Pose &  pose, core::scoring::ScoreFunctionOP  sf, core::scoring::ScoreFunctionOP  sfsoft  )

inline

References basic::options::OptionKeys::ddg::ddg, get_interface_energies(), get_neighbor_residues(), get_sasa(), get_sc(), create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, beta_nonlocal::mm, option, options, beta_nonlocal::pose, numeric::random::random_permutation(), basic::options::OptionKeys::casp::repack, numeric::random::rg(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, erraser_analysis::temp, basic::TR, and unsatisfied_buried_polars().

filter_and_report()

void CrystDesign::filter_and_report ( core::pose::Pose &  pose, core::scoring::ScoreFunctionOP  sf, bool &  pass, bool &  need_greedy, bool  runfilter, bool  report  )

inline

References basic::options::OptionKeys::chemical::chemical, basic::options::OptionKeys::ddg::ddg, filter, get_interface_energies(), get_sasa(), get_sc(), create_a3b_hbs::i, beta_nonlocal::pose, report(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, erraser_analysis::temp, utility::to_string(), basic::TR, and unsatisfied_buried_polars().

get_interface_residues()

void CrystDesign::get_interface_residues ( Pose &  pose, core::scoring::ScoreFunctionOP  sf, utility::vector1< bool > &  interface  )

inline

References erraser_analysis::angle1, erraser_analysis::angle2, numeric::angle_degrees(), compute_difference::b, dist(), utility::graph::Node::edge_list_end(), detail::find(), utility::graph::Edge::get_node(), create_a3b_hbs::i, interface, create_a3b_hbs::j, PREcst::K, oop_conformations::length, option, beta_nonlocal::pose, mutant_modeler::protein_residues, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::symmetry::symmetry.

get_name()

std::string CrystDesign::get_name ( ) const

inlineoverride

get_neighbor_residues()

void CrystDesign::get_neighbor_residues ( Pose &  pose, core::Size  res_i, utility::vector1< bool > &  neighbor  )

inline

References erraser_analysis::angle1, erraser_analysis::angle2, numeric::angle_degrees(), compute_difference::b, dist(), create_a3b_hbs::i, create_a3b_hbs::j, PREcst::K, oop_conformations::length, option, beta_nonlocal::pose, mutant_modeler::protein_residues, test.T200_Scoring::rsd1, test.T200_Scoring::rsd2, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::symmetry::symmetry.

greedy_revert_unsats()

void CrystDesign::greedy_revert_unsats ( Pose &  pose, core::scoring::ScoreFunctionOP  sf, core::scoring::ScoreFunctionOP  sfsoft  )

inline

References get_interface_energies(), get_neighbor_residues(), create_a3b_hbs::i, enumerate_junctions::int, create_a3b_hbs::j, create_a3b_hbs::k, beta_nonlocal::mm, options, beta_nonlocal::pose, numeric::random::random_permutation(), basic::options::OptionKeys::casp::repack, build_restypes::restype, numeric::random::rg(), basic::options::OptionKeys::frags::scoring::scoring, basic::options::OptionKeys::out::sf, basic::options::OptionKeys::symmetry::symmetry, basic::TR, and unsatisfied_buried_polars().

Member Data Documentation

DDG_CUT_

core::Real CrystDesign::DDG_CUT_

private

K_

core::Real CrystDesign::K_

private

M_MUT_CUT_

core::Size CrystDesign::M_MUT_CUT_

private

MUT_CUT_

core::Size CrystDesign::MUT_CUT_

private

native_

core::pose::Pose CrystDesign::native_

private

NCYC_

core::Size CrystDesign::NCYC_

private

NOFILT_

bool CrystDesign::NOFILT_

private

revertonly_

bool CrystDesign::revertonly_

private

SC_CUT_

core::Real CrystDesign::SC_CUT_

private

setup_

protocols::cryst::MakeLatticeMover CrystDesign::setup_

private

UNSATS_CUT_

core::Real CrystDesign::UNSATS_CUT_

private

UNSATS_SOFT_CUT_

core::Real CrystDesign::UNSATS_SOFT_CUT_

private

WEAKE_CUT_

core::Real CrystDesign::WEAKE_CUT_

private

WFY_MUT_CUT_

core::Size CrystDesign::WFY_MUT_CUT_

private

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

• src/apps/pilot/frank/cryst_design.cc