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...
utility::vector1< char >	protocols::membrane::geometry::get_secstruct (pose::Pose &pose)
	Get secondary structure of the pose. 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 (pose::Pose &pose, int jumpnum)
	Calculates translation axis lying in the membrane (= projection axis between embedding centers) 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...
void	protocols::membrane::geometry::split_topology_by_jump_noshift (pose::Pose const &pose, Size const jumpnum, SpanningTopologyOP topo, SpanningTopologyOP topo_up, SpanningTopologyOP topo_down)
	Splits the SpanningTopology object into two objects, depending on given jump number. More...
void	protocols::membrane::geometry::update_partner_embeddings (pose::Pose const &pose, Size const jumpnum, EmbeddingDef &emb_up, EmbeddingDef &emb_down)
	Update embedding of the partners after a move. 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)