Rosetta 3.4
Functions
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.
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.
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.
int residue_center_of_mass (pose::Pose const &pose, int const start, int const stop)
 calculates the center of mass of a pose
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)

Function Documentation

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::total_residue(), and core::conformation::Residue::xyz().

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 
)
numeric::xyzMatrix_double protocols::geometry::random_reorientation_matrix ( const double  phi_range,
const double  psi_range 
)
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: June 29 2007

References core::conformation::Residue::atom(), core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), core::conformation::symmetry::return_nearest_residue(), and core::conformation::Atom::xyz().

Referenced by protocols::antibody2::Ab_ModelCDRH3::all_cdr_VL_VH_fold_tree(), protocols::antibody::AntibodyModeler::all_cdr_VL_VH_fold_tree(), and protocols::docking::setup_foldtree().

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::sequence::end, core::conformation::Residue::is_protein(), core::conformation::Residue::nbr_atom_xyz(), core::pose::Pose::residue(), and core::conformation::Atom::xyz().

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