Functions
numeric::xyzMatrix_real	random_reorientation_matrix (const core::Real phi_range, const core::Real psi_range)

core::Vector	centroid_by_residues (core::conformation::ResidueCOPs residue_c_pointers)

core::Vector	centroid_by_chains (core::pose::Pose const &pose, utility::vector1< core::Size > chain_ids)

core::Vector	centroid_by_chain (core::pose::Pose const &pose, core::Size const chain_id)

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 (core::pose::Pose const &pose, int const start, int const stop)
	calculates the center of mass of a pose More...

Function Documentation

◆ center_of_mass()

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

calculates the center of mass of a pose

center_of_mass

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

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

◆ centroid_by_chain()

core::Vector protocols::geometry::centroid_by_chain	(	core::pose::Pose const &	pose,
		core::Size const	chain_id
	)

References centroid_by_residues(), and core::pose::get_chain_residues().

◆ centroid_by_chains()

core::Vector protocols::geometry::centroid_by_chains	(	core::pose::Pose const &	pose,
		utility::vector1< core::Size >	chain_ids
	)

References centroid_by_residues(), and core::pose::get_residues_from_chains().

Referenced by protocols::ligand_docking::TransformEnsemble::apply(), and protocols::ligand_docking::move_ligand_to_desired_centroid().

◆ centroid_by_residues()

core::Vector protocols::geometry::centroid_by_residues ( core::conformation::ResidueCOPs residue_c_pointers )

References core::sequence::end.

Referenced by centroid_by_chain(), and centroid_by_chains().

◆ centroid_pair_by_jump()

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().

◆ centroids_by_jump() [1/2]

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::surface_docking::SurfaceOrientMover::apply(), protocols::ligand_docking::RigidSearchMover::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodyRandomizeMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), protocols::rigid::RigidBodyDeterministicSpinMover::apply(), protocols::rigid::RigidBodyTiltMover::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().

◆ centroids_by_jump() [2/2]

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::size(), TR(), and core::conformation::Residue::xyz().

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

◆ 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::size(), TR(), and core::conformation::Residue::xyz().