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

Classes
class	MultiPhosphateSampler
class	PhosphateMove
class	PhosphateMover

Typedefs
typedef utility::pointer::shared_ptr< MultiPhosphateSampler >	MultiPhosphateSamplerOP
typedef utility::pointer::shared_ptr< MultiPhosphateSampler const >	MultiPhosphateSamplerCOP
typedef utility::pointer::shared_ptr< PhosphateMove >	PhosphateMoveOP
typedef utility::pointer::shared_ptr< PhosphateMove const >	PhosphateMoveCOP
typedef utility::pointer::shared_ptr< PhosphateMover >	PhosphateMoverOP
typedef utility::pointer::shared_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< core::Size > const &res_list)
void	position_five_prime_phosphate_SLOW (pose::Pose &pose, core::Size const res)
void	position_five_prime_phosphate (pose::Pose &pose, core::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< core::Size > const &res_list)
core::scoring::ScoreFunctionCOP	get_phosphate_scorefxn ()
core::scoring::ScoreFunctionCOP	get_phosphate_scorefxn (core::scoring::methods::EnergyMethodOptions const &options)

Typedef Documentation

MultiPhosphateSamplerCOP

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

MultiPhosphateSamplerOP

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

PhosphateMoveCOP

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

PhosphateMoveOP

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

PhosphateMoverCOP

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

PhosphateMoverOP

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

Enumeration Type Documentation

PhosphateTerminus

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

Enumerator
NONE
FIVE_PRIME_PHOSPHATE
THREE_PRIME_PHOSPHATE

Function Documentation

copy_over_phosphate_variants() [1/2]

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

References core::chemical::FIVE_PRIME_PHOSPHATE, and core::chemical::THREE_PRIME_PHOSPHATE.

copy_over_phosphate_variants() [2/2]

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 core::chemical::rna::ALPHA, core::id::BB, core::chemical::rna::BETA, core::chemical::rna::EPSILON, core::chemical::FIVE_PRIME_PHOSPHATE, core::pose::Pose::fold_tree(), core::chemical::rna::GAMMA, core::conformation::Residue::has_variant_type(), core::kinematics::FoldTree::is_cutpoint(), core::chemical::LOWER_TERMINUS_VARIANT, protocols::stepwise::modeler::make_variants_match(), core::scoring::constraints::map_constraints_from_original_pose(), position_five_prime_phosphate(), core::pose::Pose::residue(), core::pose::Pose::set_torsion(), core::pose::Pose::size(), core::chemical::THREE_PRIME_PHOSPHATE, core::pose::Pose::torsion(), core::chemical::UPPER_TERMINUS_VARIANT, core::chemical::VIRTUAL_PHOSPHATE, core::chemical::VIRTUAL_RIBOSE, and core::chemical::rna::ZETA.

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

get_phosphate_scorefxn() [1/2]

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

(

)

References get_phosphate_scorefxn().

Referenced by protocols::stepwise::modeler::packer::StepWiseMasterPacker::initialize(), protocols::stepwise::monte_carlo::mover::DeleteMover::minimize_after_delete(), and protocols::stepwise::modeler::rna::phosphate::MultiPhosphateSampler::sample_phosphates().

get_phosphate_scorefxn() [2/2]

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

(

core::scoring::methods::EnergyMethodOptions const &

options

)

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, and core::scoring::rna_torsion.

Referenced by get_phosphate_scorefxn().

operator<<()

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().

position_five_prime_phosphate()

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

References core::conformation::Residue::atom_index(), core::pose::Pose::dof(), core::chemical::rings::PHI, core::pose::Pose::residue(), core::pose::Pose::set_dof(), and core::conformation::Residue::xyz().

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

position_five_prime_phosphate_SLOW()

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

References core::chemical::aa_from_name(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::delete_polymer_residue(), core::chemical::ResidueTypeBase::mode(), core::pose::Pose::prepend_polymer_residue_before_seqpos(), core::pose::Pose::residue_type(), and core::pose::Pose::residue_type_set_for_pose().

remove_terminal_phosphates() [1/2]

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

(

pose::Pose &

pose

)

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

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_checkers(), and protocols::stepwise::modeler::rna::sugar::VirtualSugarSampler::virtualize_distal_partition().

remove_terminal_phosphates() [2/2]

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

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

Referenced by remove_terminal_phosphates().

to_string()

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

(

PhosphateTerminus const &

phosphate_terminus

)

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

Referenced by operator<<().