protocols::rotamer_sampler::rigid_body Namespace Reference

Classes
class	EulerAngles
class	RigidBodyRotamer
class	RigidBodyRotamerValueRange
class	RigidBodyRotamerWithResidueAlternatives
class	RigidBodyRotamerWithResidueList

Typedefs
typedef utility::pointer::owning_ptr < EulerAngles >	EulerAnglesOP
typedef utility::pointer::owning_ptr < EulerAngles const >	EulerAnglesCOP
typedef utility::pointer::owning_ptr < RigidBodyRotamer >	RigidBodyRotamerOP
typedef utility::pointer::owning_ptr < RigidBodyRotamer const >	RigidBodyRotamerCOP
typedef utility::pointer::owning_ptr < RigidBodyRotamerValueRange >	RigidBodyRotamerValueRangeOP
typedef utility::pointer::owning_ptr < RigidBodyRotamerValueRange const >	RigidBodyRotamerValueRangeCOP
typedef utility::pointer::owning_ptr < RigidBodyRotamerWithResidueAlternatives >	RigidBodyRotamerWithResidueAlternativesOP
typedef utility::pointer::owning_ptr < RigidBodyRotamerWithResidueAlternatives const >	RigidBodyRotamerWithResidueAlternativesCOP
typedef utility::pointer::owning_ptr < RigidBodyRotamerWithResidueList >	RigidBodyRotamerWithResidueListOP
typedef utility::pointer::owning_ptr < RigidBodyRotamerWithResidueList const >	RigidBodyRotamerWithResidueListCOP

Functions
void	get_atom_coordinates (utility::vector1< std::pair< id::AtomID, numeric::xyzVector< Real > > > &xyz_list, Size const &seq_num, conformation::Residue const &rsd_at_origin, kinematics::Stub const &moving_res_base_stub)
void	get_specific_atom_coordinate (Size const atom_index, Vector &atom_pos, conformation::Residue const &rsd_at_origin, kinematics::Stub const &moving_res_base_stub)
void	get_specific_atom_coordinate (Vector &atom_pos, kinematics::Stub const &moving_res_base_stub)
void	get_specific_atom_coordinate (std::string const &atom_name, Vector &atom_pos, conformation::Residue const &rsd_at_origin, kinematics::Stub const &moving_res_base_stub)
Size	figure_out_reference_res_for_jump (pose::Pose const &pose, Size const moving_res)
utility::vector1< Size >	figure_out_moving_partition_res (pose::Pose const &pose, Size const moving_res, Size const reference_res)
void	set_to_origin (pose::Pose &pose, Size const seq_num, utility::vector1< Size > const &move_res_list, bool verbose=false)
void	set_to_origin (pose::Pose &pose, Size const seq_num, bool verbose)
kinematics::Stub	initialize_stub (conformation::Residue const &rsd)
PoseCOP	transform_moving_partition_to_origin (pose::Pose const &pose_start, Size const moving_res, utility::vector1< Size > const &moving_partition_res)

Typedef Documentation

typedef utility::pointer::owning_ptr< EulerAngles const > protocols::rotamer_sampler::rigid_body::EulerAnglesCOP

typedef utility::pointer::owning_ptr< EulerAngles > protocols::rotamer_sampler::rigid_body::EulerAnglesOP

typedef utility::pointer::owning_ptr< RigidBodyRotamer const > protocols::rotamer_sampler::rigid_body::RigidBodyRotamerCOP

typedef utility::pointer::owning_ptr< RigidBodyRotamer > protocols::rotamer_sampler::rigid_body::RigidBodyRotamerOP

typedef utility::pointer::owning_ptr< RigidBodyRotamerValueRange const > protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRangeCOP

typedef utility::pointer::owning_ptr< RigidBodyRotamerValueRange > protocols::rotamer_sampler::rigid_body::RigidBodyRotamerValueRangeOP

typedef utility::pointer::owning_ptr< RigidBodyRotamerWithResidueAlternatives const > protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternativesCOP

typedef utility::pointer::owning_ptr< RigidBodyRotamerWithResidueAlternatives > protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueAlternativesOP

typedef utility::pointer::owning_ptr< RigidBodyRotamerWithResidueList const > protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueListCOP

typedef utility::pointer::owning_ptr< RigidBodyRotamerWithResidueList > protocols::rotamer_sampler::rigid_body::RigidBodyRotamerWithResidueListOP

Function Documentation

utility::vector1< Size > protocols::rotamer_sampler::rigid_body::figure_out_moving_partition_res	(	pose::Pose const &	pose,
		Size const	moving_res,
		Size const	reference_res
	)

References core::kinematics::FoldTree::downstream_jump_residue(), fold_tree, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::num_jump(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::total_residue(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::RigidBodyRotamer().

Size protocols::rotamer_sampler::rigid_body::figure_out_reference_res_for_jump	(	pose::Pose const &	pose,
		Size const	moving_res
	)

References core::kinematics::FoldTree::downstream_jump_residue(), fold_tree, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::num_jump(), and core::kinematics::FoldTree::upstream_jump_residue().

Referenced by protocols::stepwise::sampling::rna::connection::StepWiseRNA_ConnectionSampler::figure_out_reference_res().

void protocols::rotamer_sampler::rigid_body::get_atom_coordinates	(	utility::vector1< std::pair< id::AtomID, numeric::xyzVector< Real > > > &	xyz_list,
		Size const &	seq_num,
		conformation::Residue const &	rsd_at_origin,
		kinematics::Stub const &	moving_res_base_stub
	)

References at(), get_specific_atom_coordinate(), and core::conformation::Residue::natoms().

Referenced by protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::apply(), protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::transform_single_residue(), and protocols::stepwise::sampling::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen().

void protocols::rotamer_sampler::rigid_body::get_specific_atom_coordinate	(	Size const	atom_index,
		Vector &	atom_pos,
		conformation::Residue const &	rsd_at_origin,
		kinematics::Stub const &	moving_res_base_stub
	)

References get_specific_atom_coordinate(), and core::conformation::Residue::xyz().

Referenced by protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::apply(), protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::calculate_jump(), and protocols::stepwise::sampling::rna::checker::ChainClosableGeometryChecker::check_chain_closable_geometry().

void protocols::rotamer_sampler::rigid_body::get_specific_atom_coordinate	(	Vector &	atom_pos,
		kinematics::Stub const &	moving_res_base_stub
	)

References core::kinematics::Stub::M, and core::kinematics::Stub::v.

void protocols::rotamer_sampler::rigid_body::get_specific_atom_coordinate	(	std::string const &	atom_name,
		Vector &	atom_pos,
		conformation::Residue const &	rsd_at_origin,
		kinematics::Stub const &	moving_res_base_stub
	)

References core::conformation::Residue::atom_index().

Referenced by get_atom_coordinates(), and get_specific_atom_coordinate().

kinematics::Stub protocols::rotamer_sampler::rigid_body::initialize_stub

(

conformation::Residue const &

rsd

)

References core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system(), core::conformation::Residue::is_RNA(), and runtime_assert.

Referenced by protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::RigidBodyRotamer().

void protocols::rotamer_sampler::rigid_body::set_to_origin	(	pose::Pose &	pose,
		Size const	seq_num,
		utility::vector1< Size > const &	move_res_list,
		bool	verbose = false
	)

References at(), centroid, chemical, core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), inverse(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), scoring, core::pose::Pose::set_xyz(), verbose, and core::pose::Pose::xyz().

Referenced by protocols::stepwise::sampling::rna::rigid_body::setup_pose_at_origin_list().

void protocols::rotamer_sampler::rigid_body::set_to_origin	(	pose::Pose &	pose,
		Size const	seq_num,
		bool	verbose
	)

References utility::tools::make_vector1().

Referenced by transform_moving_partition_to_origin().

PoseCOP protocols::rotamer_sampler::rigid_body::transform_moving_partition_to_origin	(	pose::Pose const &	pose_start,
		Size const	moving_res,
		utility::vector1< Size > const &	moving_partition_res
	)

References core::pose::Pose::clone(), and set_to_origin().

Referenced by protocols::rotamer_sampler::rigid_body::RigidBodyRotamer::RigidBodyRotamer().