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Functions
protocols::geometry Namespace Reference

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

Function Documentation

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::stop, and core::conformation::Atom::xyz().

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

core::Vector protocols::geometry::centroid_by_chain ( core::pose::Pose const &  pose,
core::Size const  chain_id 
)
core::Vector protocols::geometry::centroid_by_chains ( core::pose::Pose const &  pose,
utility::vector1< core::Size chain_ids 
)
core::Vector protocols::geometry::centroid_by_residues ( core::conformation::ResidueCOPs  residue_c_pointers)
std::pair< core::Vector, core::Vector > protocols::geometry::centroid_pair_by_jump ( core::pose::Pose const &  pose,
core::Size  jump_id 
)
void protocols::geometry::centroids_by_jump ( core::pose::Pose const &  pose,
core::Size const  jump_id,
core::Vector upstream_ctrd,
core::Vector downstream_ctrd 
)
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().

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().

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

core::Vector protocols::geometry::downstream_centroid_by_jump ( core::pose::Pose const &  pose,
core::Size  jump_id 
)
numeric::xyzMatrix_real protocols::geometry::random_reorientation_matrix ( const core::Real  phi_range,
const core::Real  psi_range 
)
core::Vector protocols::geometry::upstream_centroid_by_jump ( core::pose::Pose const &  pose,
core::Size  jump_id 
)