dsRNA_grow Class Reference

Inheritance diagram for dsRNA_grow:

Public Member Functions
	dsRNA_grow ()
virtual std::string	get_name () const
void	constrain_and_minimize (pose::Pose &pose, utility::vector1< std::pair< Size, Size > > const &pairings) const
void	minimize (pose::Pose &pose) const
void	set_Aform_torsions (pose::Pose &pose, Size const &n) const
void	append_Aform_residue (pose::Pose &pose, Size const &n, std::string const &nt) const
void	prepend_Aform_residue (pose::Pose &pose, Size const &n, std::string const &nt) const
void	apply (core::pose::Pose &pose)

Private Attributes
core::chemical::rna::RNA_FittedTorsionInfo const	torsion_info_
core::chemical::ResidueTypeSetCOP	rsd_set_
core::scoring::ScoreFunctionOP	scorefxn_
core::optimization::AtomTreeMinimizerOP	minimizer_
core::optimization::MinimizerOptionsOP	minimizer_options_

Constructor & Destructor Documentation

dsRNA_grow()

dsRNA_grow::dsRNA_grow ( )

inline

References basic::options::OptionKeys::optimization::optimization.

Member Function Documentation

append_Aform_residue()

void dsRNA_grow::append_Aform_residue ( pose::Pose &  pose, Size const &  n, std::string const &  nt  ) const

inline

References basic::options::OptionKeys::chemical::chemical, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, residue_types_from_sequence(), test.T200_Scoring::rsd1, and runtime_assert.

apply()

void dsRNA_grow::apply ( core::pose::Pose &  pose )

inline

References create_a3b_hbs::f, create_a3b_hbs::i, basic::init(), create_a3b_hbs::j, basic::Tracer::Magenta, edensity::mapfile(), basic::options::OptionKeys::dna::design::minimize, N, option, basic::options::OptionKeys::templates::pairings, beta_nonlocal::pose, basic::Tracer::Reset, utility::to_string(), basic::TR, and basic::options::OptionKeys::inout::dbms::user.

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

constrain_and_minimize()

void dsRNA_grow::constrain_and_minimize ( pose::Pose &  pose, utility::vector1< std::pair< Size, Size > > const &  pairings  ) const

inline

References basic::options::OptionKeys::constraints::cst_weight, create_a3b_hbs::first, create_a3b_hbs::i, beta_nonlocal::mm, basic::options::OptionKeys::optimization::optimization, basic::options::OptionKeys::templates::pairings, beta_nonlocal::pose, basic::options::OptionKeys::frags::scoring::scoring, and basic::options::OptionKeys::recces::thermal_sampling::setup_base_pair_constraints.

get_name()

virtual std::string dsRNA_grow::get_name ( ) const

inlinevirtual

minimize()

void dsRNA_grow::minimize ( pose::Pose &  pose ) const

inline

References beta_nonlocal::mm, basic::options::OptionKeys::optimization::optimization, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

prepend_Aform_residue()

void dsRNA_grow::prepend_Aform_residue ( pose::Pose &  pose, Size const &  n, std::string const &  nt  ) const

inline

References basic::options::OptionKeys::chemical::chemical, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, residue_types_from_sequence(), test.T200_Scoring::rsd2, and runtime_assert.

set_Aform_torsions()

void dsRNA_grow::set_Aform_torsions ( pose::Pose &  pose, Size const &  n  ) const

inline

References kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, beta_nonlocal::pose, and basic::options::OptionKeys::full_model::rna::rna.

Member Data Documentation

minimizer_

core::optimization::AtomTreeMinimizerOP dsRNA_grow::minimizer_

private

minimizer_options_

core::optimization::MinimizerOptionsOP dsRNA_grow::minimizer_options_

private

rsd_set_

core::chemical::ResidueTypeSetCOP dsRNA_grow::rsd_set_

private

scorefxn_

core::scoring::ScoreFunctionOP dsRNA_grow::scorefxn_

private

torsion_info_

core::chemical::rna::RNA_FittedTorsionInfo const dsRNA_grow::torsion_info_

private

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

• src/apps/pilot/frank/dsrna_grow.cc