protocols::toolbox::sample_around Namespace Reference

Functions
void	add_virtual_res (core::pose::Pose &pose, bool set_res_as_root)
void	add_another_virtual_res (core::pose::Pose &pose)
void	rotate_into_nucleobase_frame (core::pose::Pose &pose)
void	rotate_into_phosphate_frame (core::pose::Pose &pose, core::Size const n, bool const center_on_OP2)
Real	centroid_dist (core::pose::Pose &pose, bool const sample_another_adenosine_)
Real	sample_all_rotations_at_jump (pose::Pose &pose, core::Size const num_jump, scoring::ScoreFunctionOP scorefxn)
Real	do_scoring (pose::Pose &pose, scoring::ScoreFunctionOP scorefxn, bool const &sample_rotations, core::Size const probe_jump_num)
void	do_xy_scan (pose::Pose &pose, scoring::ScoreFunctionOP scorefxn, std::string const &outfile, Real const z, core::Size const probe_jump_num, Real const box_bins, Real const translation_increment, bool const sample_rotations)

Function Documentation

void protocols::toolbox::sample_around::add_another_virtual_res

(

core::pose::Pose &

pose

)

References core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::size(), and core::pose::virtual_type_for_pose().

void protocols::toolbox::sample_around::add_virtual_res	(	core::pose::Pose &	pose,
		bool	set_res_as_root
	)

References protocols::cluster::calibur::aa, core::chemical::aa_vrt, core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), and core::pose::virtual_type_for_pose().

core::Real protocols::toolbox::sample_around::centroid_dist	(	core::pose::Pose &	pose,
		bool const	sample_another_adenosine_
	)

References core::chemical::rna::get_rna_base_centroid(), and core::pose::Pose::residue().

core::Real protocols::toolbox::sample_around::do_scoring	(	pose::Pose &	pose,
		scoring::ScoreFunctionOP	scorefxn,
		bool const &	sample_rotations,
		core::Size const	probe_jump_num
	)

References sample_all_rotations_at_jump().

Referenced by do_xy_scan().

void protocols::toolbox::sample_around::do_xy_scan	(	pose::Pose &	pose,
		scoring::ScoreFunctionOP	scorefxn,
		std::string const &	outfile,
		Real const	z,
		core::Size const	probe_jump_num,
		Real const	box_bins,
		Real const	translation_increment,
		bool const	sample_rotations
	)

References do_scoring(), core::pose::Pose::jump(), core::conformation::membrane::out, protocols::hybridization::score, core::pose::Pose::set_jump(), and core::kinematics::Jump::set_translation().

void protocols::toolbox::sample_around::rotate_into_nucleobase_frame

(

core::pose::Pose &

pose

)

References core::chemical::rna::get_rna_base_coordinate_system_stub(), core::kinematics::Stub::global2local(), core::conformation::Residue::natoms(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

void protocols::toolbox::sample_around::rotate_into_phosphate_frame	(	core::pose::Pose &	pose,
		core::Size const	n,
		bool const	center_on_OP2
	)

References core::kinematics::Stub::global2local(), core::pose::Pose::residue(), core::pose::Pose::set_xyz(), and core::conformation::Residue::xyz().

core::Real protocols::toolbox::sample_around::sample_all_rotations_at_jump	(	pose::Pose &	pose,
		core::Size const	num_jump,
		scoring::ScoreFunctionOP	scorefxn
	)

References protocols::toolbox::rigid_body::create_euler_rotation(), core::pose::Pose::dump_pdb(), core::pose::Pose::jump(), protocols::hybridization::score, core::pose::Pose::set_jump(), and core::kinematics::Jump::set_rotation().

Referenced by do_scoring().