protocols::stepwise::modeler::rna::phosphate Namespace Reference

Classes
class	MultiPhosphateSampler
class	PhosphateMove
class	PhosphateMover

Typedefs
typedef utility::pointer::owning_ptr < MultiPhosphateSampler >	MultiPhosphateSamplerOP
typedef utility::pointer::owning_ptr < MultiPhosphateSampler const >	MultiPhosphateSamplerCOP
typedef utility::pointer::owning_ptr < PhosphateMove >	PhosphateMoveOP
typedef utility::pointer::owning_ptr < PhosphateMove const >	PhosphateMoveCOP
typedef utility::pointer::owning_ptr < PhosphateMover >	PhosphateMoverOP
typedef utility::pointer::owning_ptr < PhosphateMover const >	PhosphateMoverCOP

Enumerations
enum	PhosphateTerminus { NONE, FIVE_PRIME_PHOSPHATE, THREE_PRIME_PHOSPHATE }

Functions
std::string	to_string (PhosphateTerminus const &phosphate_terminus)
std::ostream &	operator<< (std::ostream &os, PhosphateMove const &phosphate_move)
void	remove_terminal_phosphates (pose::Pose &pose)
void	remove_terminal_phosphates (pose::Pose &pose, utility::vector1< Size > const &res_list)
void	correctly_position_five_prime_phosphate_SLOW (pose::Pose &pose, Size const res)
void	correctly_position_five_prime_phosphate (pose::Pose &pose, Size const res)
void	copy_over_phosphate_variants (pose::Pose &pose_input, pose::Pose const &reference_pose, utility::vector1< PhosphateMove > const &phosphate_move_list)
void	copy_over_phosphate_variants (pose::Pose &pose_input, pose::Pose const &reference_pose, utility::vector1< Size > const &res_list)
core::scoring::ScoreFunctionCOP	get_phosphate_scorefxn ()
core::scoring::ScoreFunctionCOP	get_phosphate_scorefxn (core::scoring::ScoreFunctionCOP)

Typedef Documentation

typedef utility::pointer::owning_ptr< MultiPhosphateSampler const > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSamplerCOP

typedef utility::pointer::owning_ptr< MultiPhosphateSampler > protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSamplerOP

typedef utility::pointer::owning_ptr< PhosphateMove const > protocols::stepwise::modeler::rna::phosphate::PhosphateMoveCOP

typedef utility::pointer::owning_ptr< PhosphateMove > protocols::stepwise::modeler::rna::phosphate::PhosphateMoveOP

typedef utility::pointer::owning_ptr< PhosphateMover const > protocols::stepwise::modeler::rna::phosphate::PhosphateMoverCOP

typedef utility::pointer::owning_ptr< PhosphateMover > protocols::stepwise::modeler::rna::phosphate::PhosphateMoverOP

Enumeration Type Documentation

enum protocols::stepwise::modeler::rna::phosphate::PhosphateTerminus

Enumerator
NONE
FIVE_PRIME_PHOSPHATE
THREE_PRIME_PHOSPHATE

Function Documentation

void protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants	(	pose::Pose &	pose_input,
		pose::Pose const &	reference_pose,
		utility::vector1< PhosphateMove > const &	phosphate_move_list
	)

References ALPHA, core::id::BB, BETA, correctly_position_five_prime_phosphate(), EPSILON, FIVE_PRIME_PHOSPHATE, GAMMA, LOWER_TERMINUS_VARIANT, protocols::stepwise::modeler::make_variants_match(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), runtime_assert, protocols::stepwise::modeler::rna::phosphate::PhosphateMove::terminus(), THREE_PRIME_PHOSPHATE, core::pose::Pose::torsion(), core::pose::Pose::total_residue(), UPPER_TERMINUS_VARIANT, and ZETA.

Referenced by protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::copy_phosphates(), protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::do_prepack(), protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler::reinstantiate_distal_partition(), and protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::sample_phosphates().

void protocols::stepwise::modeler::rna::phosphate::copy_over_phosphate_variants	(	pose::Pose &	pose_input,
		pose::Pose const &	reference_pose,
		utility::vector1< Size > const &	res_list
	)

References FIVE_PRIME_PHOSPHATE, and THREE_PRIME_PHOSPHATE.

void protocols::stepwise::modeler::rna::phosphate::correctly_position_five_prime_phosphate	(	pose::Pose &	pose,
		Size const	res
	)

References dihedral_degrees(), core::pose::Pose::dof(), PHI, numeric::conversions::radians(), core::pose::Pose::residue(), and core::pose::Pose::set_dof().

Referenced by copy_over_phosphate_variants(), and protocols::stepwise::modeler::rna::phosphate::PhosphateMover::setup_variants_and_free_pose_for_five_prime_phosphate().

void protocols::stepwise::modeler::rna::phosphate::correctly_position_five_prime_phosphate_SLOW	(	pose::Pose &	pose,
		Size const	res
	)

References aa_from_name(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::delete_polymer_residue(), core::pose::Pose::prepend_polymer_residue_before_seqpos(), core::pose::Pose::residue(), and core::conformation::Residue::residue_type_set().

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::phosphate::get_phosphate_scorefxn

(

)

References get_phosphate_scorefxn().

Referenced by protocols::stepwise::modeler::packer::StepWiseMasterPacker::initialize(), and protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::initialize_parameters().

core::scoring::ScoreFunctionCOP protocols::stepwise::modeler::rna::phosphate::get_phosphate_scorefxn

(

core::scoring::ScoreFunctionCOP

)

References core::scoring::fa_atr, core::scoring::fa_rep, core::scoring::free_suite, core::scoring::hbond_lr_bb_sc, core::scoring::hbond_sr_bb_sc, core::scoring::rna_torsion, and scoring.

Referenced by get_phosphate_scorefxn().

std::ostream & protocols::stepwise::modeler::rna::phosphate::operator<<	(	std::ostream &	os,
		PhosphateMove const &	phosphate_move
	)

References protocols::stepwise::modeler::rna::phosphate::PhosphateMove::rsd(), protocols::stepwise::modeler::rna::phosphate::PhosphateMove::terminus(), and to_string().

void protocols::stepwise::modeler::rna::phosphate::remove_terminal_phosphates

(

pose::Pose &

pose

)

References remove_terminal_phosphates(), and core::pose::Pose::total_residue().

Referenced by protocols::stepwise::legacy::modeler::rna::connection::StepWiseRNA_ConnectionSampler::initialize_poses_and_checkers(), and protocols::stepwise::modeler::rna::sugar::StepWiseRNA_VirtualSugarSampler::virtualize_distal_partition().

void protocols::stepwise::modeler::rna::phosphate::remove_terminal_phosphates	(	pose::Pose &	pose,
		utility::vector1< Size > const &	res_list
	)

References add_variant_type_to_pose_residue(), core::conformation::Residue::has_variant_type(), remove_variant_type_from_pose_residue(), and core::pose::Pose::residue().

Referenced by remove_terminal_phosphates().

std::string protocols::stepwise::modeler::rna::phosphate::to_string

(

PhosphateTerminus const &

phosphate_terminus

)

References FIVE_PRIME_PHOSPHATE, protocols::init::init(), NONE, and THREE_PRIME_PHOSPHATE.

Referenced by operator<<().