protocols::geometry Namespace Reference

Functions
numeric::xyzMatrix_double	random_reorientation_matrix (const double phi_range, const double psi_range)
void	centroids_by_jump (core::pose::Pose const &pose, core::Size const jump_id, core::Vector &upstream_ctrd, core::Vector &downstream_ctrd)
	Unweighted centroids of all atoms upstream of the jump vs. all atoms downstream of the jump. More...
void	centroids_by_jump (core::pose::Pose const &pose, core::Size const jump_id, core::Vector &upstream_ctrd, core::Vector &downstream_ctrd, utility::vector1< bool > ok_for_centroid_calculation)
	Unweighted centroids of all atoms upstream of the jump vs. all atoms downstream of the jump. More...
std::pair< core::Vector, core::Vector >	centroid_pair_by_jump (core::pose::Pose const &pose, core::Size jump_id)
core::Vector	upstream_centroid_by_jump (core::pose::Pose const &pose, core::Size jump_id)
core::Vector	downstream_centroid_by_jump (core::pose::Pose const &pose, core::Size jump_id)
void	centroids_by_jump_int (core::pose::Pose const &pose, core::Size jump_id, core::Vector &upstream_ctrd, core::Vector &downstream_ctrd)
	Unweighted centroids of all atoms upstream of the jump vs. all atoms downstream of the jump for interface residues only. needed to calculate rb_centers for fullatom docking - Sid C. More...
numeric::xyzVector< core::Real >	center_of_mass (pose::Pose const &pose, int const start, int const stop)
	calculates the center of mass of a pose More...
int	residue_center_of_mass (pose::Pose const &pose, int const start, int const stop)
	calculates the center of mass of a pose More...
int	return_nearest_residue (pose::Pose const &pose, int const begin, int const end, Vector center)
	finds the residue nearest some position passed in (normally a center of mass) More...

Function Documentation

numeric::xyzVector< core::Real > protocols::geometry::center_of_mass	(	pose::Pose const &	pose,
		int const	start,
		int const	stop
	)

calculates the center of mass of a pose

center_of_mass

Detailed:

the start and stop positions (or residues) within the pose are used to find the starting and finishing locations

Authors

Monica Berrondo June 14 2007

Last Modified: Javier Castellanos June 4 2012

References core::conformation::Residue::atom(), center(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), protocols::loops::stop, and core::conformation::Atom::xyz().

Referenced by protocols::simple_moves::symmetry::DetectSymmetry::apply(), protocols::sic_dock::get_rg(), protocols::match::NumNeighborsMPM::modified_match_positions(), protocols::rigid::RollMover::parse_my_tag(), protocols::features::SmotifFeatures::report_features(), and residue_center_of_mass().

std::pair< core::Vector, core::Vector > protocols::geometry::centroid_pair_by_jump	(	core::pose::Pose const &	pose,
		core::Size	jump_id
	)

References centroids_by_jump().

Referenced by downstream_centroid_by_jump(), and upstream_centroid_by_jump().

void protocols::geometry::centroids_by_jump	(	core::pose::Pose const &	pose,
		core::Size const	jump_id,
		core::Vector &	upstream_ctrd,
		core::Vector &	downstream_ctrd
	)

Unweighted centroids of all atoms upstream of the jump vs. all atoms downstream of the jump.

Deliberately includes H – is this OK?

References centroids_by_jump().

Referenced by protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::surface_docking::SurfaceOrientMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTransMover::centroid_axis(), protocols::ligand_docking::LigandBaseProtocol::choose_desired_centroid(), protocols::surface_docking::FullatomRelaxMover::reposition_above_surface(), protocols::rigid::RigidBodyRandomizeMover::RigidBodyRandomizeMover(), and protocols::surface_docking::SurfaceDockingProtocol::setup_slide_movers().

void protocols::geometry::centroids_by_jump	(	core::pose::Pose const &	pose,
		core::Size const	jump_id,
		core::Vector &	upstream_ctrd,
		core::Vector &	downstream_ctrd,
		utility::vector1< bool >	ok_for_centroid_calculation
	)

Unweighted centroids of all atoms upstream of the jump vs. all atoms downstream of the jump.

Deliberately includes H – is this OK?

References core::pose::Pose::fold_tree(), core::conformation::Residue::natoms(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by centroid_pair_by_jump(), centroids_by_jump(), and centroids_by_jump_int().

void protocols::geometry::centroids_by_jump_int	(	core::pose::Pose const &	pose,
		core::Size	jump_id,
		core::Vector &	upstream_ctrd,
		core::Vector &	downstream_ctrd
	)

Unweighted centroids of all atoms upstream of the jump vs. all atoms downstream of the jump for interface residues only. needed to calculate rb_centers for fullatom docking - Sid C.

Deliberately includes H – is this OK?

References protocols::scoring::Interface::calculate(), centroids_by_jump(), protocols::scoring::Interface::distance(), core::pose::Pose::fold_tree(), protocols::scoring::Interface::is_interface(), core::conformation::Residue::natoms(), core::kinematics::FoldTree::partition_by_jump(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), TR, and core::conformation::Residue::xyz().

Referenced by protocols::rigid::RigidBodyPerturbMover::apply().

core::Vector protocols::geometry::downstream_centroid_by_jump	(	core::pose::Pose const &	pose,
		core::Size	jump_id
	)

References centroid_pair_by_jump().

Referenced by protocols::ligand_docking::append_ligand_grid_scores(), protocols::ligand_docking::append_ligand_travel(), protocols::ligand_docking::append_radius_of_gyration(), protocols::qsar::qsarMover::apply(), protocols::qsar::scoring_grid::GridInitMover::apply(), protocols::ligand_docking::Translate::apply(), protocols::ligand_docking::Rotate::apply(), protocols::ligand_docking::Transform::apply(), protocols::ligand_docking::Rotate::create_random_rotations(), protocols::ligand_docking::Translate::gaussian_translate_ligand(), protocols::ligand_docking::LigandBaseProtocol::move_ligand_to_desired_centroid(), protocols::ligand_docking::move_ligand_to_desired_centroid(), protocols::features::ResidueGridScoresFeatures::report_features(), and protocols::ligand_docking::Translate::uniform_translate_ligand().

numeric::xyzMatrix_double protocols::geometry::random_reorientation_matrix	(	const double	phi_range,
		const double	psi_range
	)

References numeric::conversions::degrees(), protocols::stepwise::sampling::protein::phi(), protocols::stepwise::sampling::protein::psi(), RG, numeric::sin_cos_range(), TR, numeric::random::RandomGenerator::uniform(), numeric::y_rotation_matrix_degrees(), and numeric::z_rotation_matrix_degrees().

Referenced by protocols::toolbox::pose_metric_calculators::append_rsd_by_jump_near_atom(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodyDofRandomizeMover::apply(), protocols::electron_density::dockPoseIntoMap(), and protocols::ligand_docking::LigandDockProtocol::optimize_orientation3().

int protocols::geometry::residue_center_of_mass	(	pose::Pose const &	pose,
		int const	start,
		int const	stop
	)

calculates the center of mass of a pose

residue_center_of_mass

Detailed:

the start and stop positions (or residues) within the pose are used to find the starting and finishing locations

Authors

Monica Berrondo June 14 2007

Last Modified: Javier Castellanos June 4 2012

References center(), center_of_mass(), and return_nearest_residue().

Referenced by protocols::antibody_legacy::AntibodyModeler::all_cdr_VL_VH_fold_tree(), protocols::protein_interface_design::movers::SetAtomTree::apply(), protocols::antibody::AntibodyInfo::get_FoldTree_AllCDRs_LHDock(), protocols::antibody::AntibodyInfo::get_FoldTree_L_HA(), protocols::antibody::AntibodyInfo::get_FoldTree_LA_H(), protocols::antibody::AntibodyInfo::get_FoldTree_LH_A(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::ub_e2c::ubi_e2c_modeler::monoub_setup_key_residues(), protocols::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree(), protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors(), protocols::docking::setup_foldtree(), protocols::hotspot_hashing::HotspotStubSet::setup_hotspot_foldtree_(), protocols::ub_e2c::ubi_e2c_modeler::setup_key_residues(), protocols::ncbb::NcbbDockDesignProtocol::setup_pert_foldtree(), protocols::ncbb::oop::OopDockDesignProtocol::setup_pert_foldtree(), and protocols::hotspot_hashing::stub_tgt_angle().

int protocols::geometry::return_nearest_residue	(	pose::Pose const &	pose,
		int const	begin,
		int const	end,
		Vector	center
	)

finds the residue nearest some position passed in (normally a center of mass)

return_nearest_residue

Detailed:

the start and stop positions (or residues) within the pose are used to find the starting and finishing locations

Authors

Monica Berrondo June 14 2007

Last Modified: June 29 2007

References core::conformation::Residue::atom(), core::conformation::Residue::is_protein(), numeric::xyzVector< class >::length_squared(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

Referenced by residue_center_of_mass(), and protocols::flexpep_docking::FlexPepDockingFlags::setDefaultAnchors().

core::Vector protocols::geometry::upstream_centroid_by_jump	(	core::pose::Pose const &	pose,
		core::Size	jump_id
	)

References centroid_pair_by_jump().