protocols::stepwise::modeler::rna::rigid_body Namespace Reference

Classes
struct	BaseBin
struct	compare_base_bin
struct	compare_int_pair

Typedefs
typedef std::map< BaseBin, int, compare_base_bin >	BaseBinMap

Functions
core::Real	get_max_centroid_to_atom_distance (utility::vector1< core::conformation::ResidueOP > const &rsd_at_origin_list, std::string const &atom_name)
void	initialize_xyz_parameters (Distance &max_distance, Distance &max_distance_squared, int &centroid_bin_min, int &centroid_bin_max, utility::vector1< core::conformation::ResidueOP > const &moving_rsd_at_origin_list, core::Size const gap_size_to_anchor)
utility::vector1< core::pose::PoseOP >	setup_pose_with_moving_residue_alternative_list (pose::Pose const &pose, core::Size const &moving_res, bool const extra_chi, bool const use_phenix_geo)
int	DOF_bin_value (BaseBin const &base_bin, std::string const &DOF)
Real	DOF_bin_size (std::string const &DOF)
void	analyze_base_bin_map (std::map< BaseBin, int, compare_base_bin > const &base_bin_map, std::string const &DOF_one, std::string const &DOF_two, std::string const &foldername)
void	analyze_base_bin_map (std::map< BaseBin, int, compare_base_bin > const &base_bin_map, std::string const &foldername)

Typedef Documentation

BaseBinMap

typedef std::map< BaseBin, int, compare_base_bin > protocols::stepwise::modeler::rna::rigid_body::BaseBinMap

Function Documentation

analyze_base_bin_map() [1/2]

void protocols::stepwise::modeler::rna::rigid_body::analyze_base_bin_map	(	std::map< BaseBin, int, compare_base_bin > const &	base_bin_map,
		std::string const &	DOF_one,
		std::string const &	DOF_two,
		std::string const &	foldername
	)

References DOF_bin_size(), DOF_bin_value(), protocols::abinitio::filename(), core::sequence::left, and core::chemical::rna::TR().

analyze_base_bin_map() [2/2]

void protocols::stepwise::modeler::rna::rigid_body::analyze_base_bin_map	(	std::map< BaseBin, int, compare_base_bin > const &	base_bin_map,
		std::string const &	foldername
	)

References STANDARD_CENTROID_BIN_SIZE, STANDARD_EULER_ANGLE_BIN_SIZE, STANDARD_EULER_Z_BIN_SIZE, and core::chemical::rna::TR().

DOF_bin_size()

core::Real protocols::stepwise::modeler::rna::rigid_body::DOF_bin_size

(

std::string const &

DOF

)

References STANDARD_CENTROID_BIN_SIZE, STANDARD_EULER_ANGLE_BIN_SIZE, and STANDARD_EULER_Z_BIN_SIZE.

Referenced by analyze_base_bin_map().

DOF_bin_value()

int protocols::stepwise::modeler::rna::rigid_body::DOF_bin_value	(	BaseBin const &	base_bin,
		std::string const &	DOF
	)

References protocols::stepwise::modeler::rna::rigid_body::BaseBin::centroid_x, protocols::stepwise::modeler::rna::rigid_body::BaseBin::centroid_y, protocols::stepwise::modeler::rna::rigid_body::BaseBin::centroid_z, protocols::stepwise::modeler::rna::rigid_body::BaseBin::euler_alpha, protocols::stepwise::modeler::rna::rigid_body::BaseBin::euler_gamma, and protocols::stepwise::modeler::rna::rigid_body::BaseBin::euler_z.

Referenced by analyze_base_bin_map().

get_max_centroid_to_atom_distance()

core::Real protocols::stepwise::modeler::rna::rigid_body::get_max_centroid_to_atom_distance	(	utility::vector1< core::conformation::ResidueOP > const &	rsd_at_origin_list,
		std::string const &	atom_name
	)

References protocols::cluster::calibur::aa, protocols::mpi_refinement::distance(), core::chemical::rna::get_rna_base_centroid(), core::chemical::name_from_aa(), and core::chemical::rna::TR().

Referenced by initialize_xyz_parameters().

initialize_xyz_parameters()

void protocols::stepwise::modeler::rna::rigid_body::initialize_xyz_parameters	(	Distance &	max_distance,
		Distance &	max_distance_squared,
		int &	centroid_bin_min,
		int &	centroid_bin_max,
		utility::vector1< core::conformation::ResidueOP > const &	moving_rsd_at_origin_list,
		core::Size const	gap_size_to_anchor
	)

References get_max_centroid_to_atom_distance(), O3I_C5I_PLUS_ONE_MAX_DIST, O3I_C5I_PLUS_TWO_MAX_DIST, STANDARD_CENTROID_BIN_SIZE, and core::chemical::rna::TR().

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

setup_pose_with_moving_residue_alternative_list()

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::rna::rigid_body::setup_pose_with_moving_residue_alternative_list	(	pose::Pose const &	pose,
		core::Size const &	moving_res,
		bool const	extra_chi,
		bool const	use_phenix_geo
	)

References core::chemical::rna::ANTI, core::chemical::rna::ANY_CHI, core::chemical::rna::ANY_PUCKER, core::pose::Pose::clone(), core::chemical::ResidueType::is_purine(), and core::pose::Pose::residue_type().

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