protocols::toolbox::rigid_body Namespace Reference

Typedefs
typedef numeric::xyzMatrix< core::Real >	Matrix

Functions
void	get_atom_coordinates (utility::vector1< std::pair< id::AtomID, numeric::xyzVector< Real > > > &xyz_list, core::Size const &seq_num, conformation::Residue const &rsd_at_origin, kinematics::Stub const &moving_res_base_stub)
void	get_specific_atom_coordinate (core::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, core::Size const moving_res)
utility::vector1< core::Size >	figure_out_moving_partition_res (pose::Pose const &pose, core::Size const moving_res, core::Size const reference_res)
void	set_to_origin (pose::Pose &pose, core::Size const seq_num, utility::vector1< core::Size > const &move_res_list, bool verbose=false)
void	set_to_origin (pose::Pose &pose, core::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, core::Size const moving_res, utility::vector1< core::Size > const &moving_partition_res)
void	create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma, Vector const &, Vector const &axis2, Vector const &axis3)
void	create_euler_rotation (Matrix &M, Real const &alpha, Real const &beta, Real const &gamma)
void	get_euler_angles (Real &alpha, Real &beta, Real &gamma, Matrix M1, Matrix M2, bool const verbose)
void	translate (pose::Pose &pose, Vector const &shift, pose::Pose const &ref_pose, utility::vector1< core::Size > const &moving_res)
void	rotate (pose::Pose &pose, Matrix const &M, pose::Pose const &ref_pose, utility::vector1< core::Size > const &moving_res, Vector const &centroid)
void	rotate (pose::Pose &pose, Matrix const &M, pose::Pose const &ref_pose, utility::vector1< core::Size > const &moving_res)
void	get_base_centroid_and_rotation_matrix (pose::Pose const &pose, core::Size const i, Vector &centroid, Matrix &M)
void	translate_and_rotate_residue_to_origin (pose::Pose &pose, core::Size const i, utility::vector1< core::Size > const &moving_res, bool const do_not_rotate)
void	translate_and_rotate_residue_to_origin (pose::Pose &pose, core::Size const i)
void	get_atom_coordinates (utility::vector1< std::pair< core::id::AtomID, numeric::xyzVector< core::Real > > > &xyz_list, core::Size const &seq_num, core::conformation::Residue const &rsd_at_origin, core::kinematics::Stub const &moving_res_base_stub)

Typedef Documentation

Matrix

typedef numeric::xyzMatrix< core::Real > protocols::toolbox::rigid_body::Matrix

Function Documentation

create_euler_rotation() [1/2]

void protocols::toolbox::rigid_body::create_euler_rotation	(	Matrix &	M,
		Real const &	alpha,
		Real const &	beta,
		Real const &	gamma
	)

Referenced by get_euler_angles().

create_euler_rotation() [2/2]

void protocols::toolbox::rigid_body::create_euler_rotation	(	Matrix &	M,
		Real const &	alpha,
		Real const &	beta,
		Real const &	gamma,
		Vector const &	,
		Vector const &	axis2,
		Vector const &	axis3
	)

Referenced by protocols::toolbox::sample_around::sample_all_rotations_at_jump().

figure_out_moving_partition_res()

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

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

Referenced by protocols::stepwise::modeler::figure_out_moving_cutpoints_closed_from_moving_res(), protocols::stepwise::modeler::figure_out_moving_partition_res(), protocols::stepwise::modeler::figure_out_root_partition_res(), protocols::stepwise::modeler::packer::figure_out_working_interface_res(), and protocols::stepwise::modeler::working_parameters::setup_working_parameters_for_swa().

figure_out_reference_res_for_jump()

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

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

Referenced by protocols::stepwise::modeler::StepWiseConnectionSampler::initialize_useful_info().

get_atom_coordinates() [1/2]

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

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

Referenced by protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::transform_single_residue(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen().

get_atom_coordinates() [2/2]

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

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

Referenced by protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::apply(), protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::transform_single_residue(), and protocols::stepwise::modeler::rna::checker::RNA_VDW_BinChecker::VDW_rep_screen().

get_base_centroid_and_rotation_matrix()

void protocols::toolbox::rigid_body::get_base_centroid_and_rotation_matrix	(	pose::Pose const &	pose,
		core::Size const	i,
		Vector &	centroid,
		Matrix &	M
	)

References core::kinematics::Stub::M, and core::pose::Pose::residue().

Referenced by translate_and_rotate_residue_to_origin().

get_euler_angles()

void protocols::toolbox::rigid_body::get_euler_angles	(	Real &	alpha,
		Real &	beta,
		Real &	gamma,
		Matrix	M1,
		Matrix	M2,
		bool const	verbose
	)

References create_euler_rotation().

get_specific_atom_coordinate() [1/3]

void protocols::toolbox::rigid_body::get_specific_atom_coordinate	(	core::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::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::calculate_jump(), and protocols::stepwise::modeler::rna::checker::RNA_ChainClosableGeometryChecker::check_chain_closable_geometry().

get_specific_atom_coordinate() [2/3]

void protocols::toolbox::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().

get_specific_atom_coordinate() [3/3]

void protocols::toolbox::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.

initialize_stub()

core::kinematics::Stub protocols::toolbox::rigid_body::initialize_stub

(

conformation::Residue const &

rsd

)

References core::scoring::rna::RNA_CentroidInfo::get_base_coordinate_system(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueTypeBase::is_protein(), core::conformation::Residue::is_RNA(), and core::conformation::Residue::type().

Referenced by protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::RigidBodyStepWiseSampler().

rotate() [1/2]

void protocols::toolbox::rigid_body::rotate	(	pose::Pose &	pose,
		Matrix const &	M,
		pose::Pose const &	ref_pose,
		utility::vector1< core::Size > const &	moving_res
	)

Referenced by translate_and_rotate_residue_to_origin().

rotate() [2/2]

void protocols::toolbox::rigid_body::rotate	(	pose::Pose &	pose,
		Matrix const &	M,
		pose::Pose const &	ref_pose,
		utility::vector1< core::Size > const &	moving_res,
		Vector const &	centroid
	)

References core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

set_to_origin() [1/2]

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

Referenced by transform_moving_partition_to_origin().

set_to_origin() [2/2]

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

References core::chemical::rna::get_rna_base_centroid(), core::chemical::rna::get_rna_base_coordinate_system(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

transform_moving_partition_to_origin()

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

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

Referenced by protocols::stepwise::sampler::rigid_body::RigidBodyStepWiseSampler::RigidBodyStepWiseSampler().

translate()

void protocols::toolbox::rigid_body::translate	(	pose::Pose &	pose,
		Vector const &	shift,
		pose::Pose const &	ref_pose,
		utility::vector1< core::Size > const &	moving_res
	)

References core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().

Referenced by protocols::ligand_docking::CompoundTranslate::apply(), protocols::membrane::RandomPositionTranslationMover::apply(), protocols::membrane::TranslationRotationMover::apply(), protocols::protein_interface_design::movers::PrepackMover::apply(), protocols::task_operations::SelectBySASAOperation::apply(), protocols::ncbb::calculate_statistics(), protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute(), protocols::protein_interface_design::filters::InterfaceHolesFilter::compute(), protocols::simple_ddg::DdgFilter::compute(), protocols::simple_filters::InterfaceSasaFilter::compute(), protocols::simple_filters::TaskAwareScoreTypeFilter::compute(), protocols::simple_filters::TaskAwareSASAFilter::compute(), protocols::analysis::InterfaceAnalyzerMover::make_separated_pose(), protocols::protein_interface_design::movers::part_complex(), protocols::mean_field::GenMeanFieldMover::prepare_task_poses(), protocols::toolbox::pose_manipulation::rigid_body_move(), protocols::hybridization::DomainAssembly::run(), translate_and_rotate_residue_to_origin(), protocols::features::InterfaceDdGMover::unbind(), and protocols::simple_ddg::ddG::unbind().

translate_and_rotate_residue_to_origin() [1/2]

void protocols::toolbox::rigid_body::translate_and_rotate_residue_to_origin	(	pose::Pose &	pose,
		core::Size const	i
	)

translate_and_rotate_residue_to_origin() [2/2]

void protocols::toolbox::rigid_body::translate_and_rotate_residue_to_origin	(	pose::Pose &	pose,
		core::Size const	i,
		utility::vector1< core::Size > const &	moving_res,
		bool const	do_not_rotate
	)

References get_base_centroid_and_rotation_matrix(), rotate(), and translate().