util.hh File Reference

Utility methods for membrane framework. More...

#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <core/chemical/ChemicalManager.fwd.hh>
#include <core/conformation/Residue.fwd.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/Conformation.fwd.hh>
#include <core/conformation/membrane/MembraneInfo.fwd.hh>
#include <core/conformation/membrane/SpanningTopology.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <protocols/membrane/geometry/EmbeddingDef.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/types.hh>
#include <utility/vector1.hh>
#include <numeric/conversions.hh>
#include <numeric/xyzVector.hh>
#include <numeric/xyz.functions.hh>
#include <cstdlib>
#include <cmath>

Namespaces
	protocols
	The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.
	protocols::membrane
	protocols::membrane::geometry

Functions
numeric::xyzVector< core::Real >	protocols::membrane::geometry::center_of_mass (pose::Pose const &pose, core::SSize const start, core::SSize const stop)
	Center of Mass. More...
core::SSize	protocols::membrane::geometry::residue_center_of_mass (pose::Pose const &pose, core::SSize const start, core::SSize const stop)
	Residue Center of Mass. More...
core::SSize	protocols::membrane::geometry::return_nearest_residue (pose::Pose const &pose, core::SSize const begin, core::SSize const end, Vector center)
	Return nearest residue. More...
std::pair< utility::vector1 < Real >, utility::vector1 < Real > >	protocols::membrane::geometry::get_chain_and_z (pose::Pose const &pose)
	Get z-coord and chainID. More...
void	protocols::membrane::geometry::compute_structure_based_embedding (pose::Pose const &pose, SpanningTopology const &topology, Vector &center, Vector &normal)
	Compute Membrane Center/Normal from Membrane Spanning topology. More...
void	protocols::membrane::geometry::compute_structure_based_embedding (pose::Pose const &pose, Vector &center, Vector &normal)
	Compute Membrane Center/Normal from Membrane Spanning topology, uses topology from MembraneInfo. More...
EmbeddingDefOP	protocols::membrane::geometry::compute_structure_based_embedding (pose::Pose const &pose, SpanningTopology const &topo)
	Compute Membrane Center/Normal from Membrane Spanning topology. More...
EmbeddingDefOP	protocols::membrane::geometry::compute_structure_based_embedding (pose::Pose const &pose)
	Compute Membrane Center/Normal from Membrane Spanning topology, uses topology from MembraneInfo. More...
void	protocols::membrane::geometry::check_vector (core::Vector const vector)
	Check reasonable range of vector. More...
EmbeddingDefOP	protocols::membrane::geometry::average_embeddings (utility::vector1< EmbeddingDefOP > const parts)
	Average EmbeddingDefs as they are without vector inversion accounting for topology. More...
EmbeddingDefOP	protocols::membrane::geometry::average_antiparallel_embeddings (utility::vector1< EmbeddingDefOP > const parts)
	Average EmbeddingDefs after first inverting some vectors accounting for topology. More...
void	protocols::membrane::geometry::membrane_normal_to_length_15 (pose::Pose &pose)
	Normalize normal vector to length 15 for visualization. More...
void	protocols::membrane::geometry::reorder_membrane_foldtree (pose::Pose &pose)
	Set membrane residue to root of foldtree. More...
core::Vector const	protocols::membrane::geometry::membrane_axis (core::pose::Pose &pose, int jumpnum)
	Calculates translation axis lying in the membrane (= projection of COM axis into the membrane plane) More...
void	protocols::membrane::geometry::split_topology_by_jump (Pose const &pose, Size const jumpnum, SpanningTopology const &topo, Pose &pose_up, Pose &pose_down, SpanningTopology &topo_up, SpanningTopology &topo_down)
	Splits the SpanningTopology object into two objects, depending on given jump number. More...

Detailed Description

Utility methods for membrane framework.

Utility methods include determining center of mass (moved down in the tree) and adjusting normal parameters for visualization.

Author

Rebecca Alford (rfalf.nosp@m.ord1.nosp@m.2@gma.nosp@m.il.c.nosp@m.om)