util.hh File Reference

Utility methods for working with proteins in the membrane Several groups of utilities for working in the memrbane environment. More...

#include <core/conformation/membrane/MembraneInfo.fwd.hh>
#include <core/conformation/membrane/SpanningTopology.hh>
#include <protocols/membrane/geometry/EmbeddingDef.fwd.hh>
#include <protocols/membrane/geometry/Embedding.fwd.hh>
#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/kinematics/FoldTree.fwd.hh>
#include <core/pose/Pose.hh>
#include <core/types.hh>
#include <utility/tag/Tag.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

Functions
core::Real	protocols::membrane::mem_bb_rmsd_no_super (core::pose::Pose &native_pose, core::pose::Pose &pose)
	Compute backbone RMSD between TM regions - don't superimpose. More...
core::Real	protocols::membrane::mem_all_atom_rmsd_no_super (core::pose::Pose &native_pose, core::pose::Pose &pose)
	Compute all-atom RMSD between TM regions - don't superimpose. More...
core::Real	protocols::membrane::mem_bb_rmsd_with_super (core::pose::Pose &native_pose, core::pose::Pose &pose)
	Compute backbone RMSD between TM regions - do superimpose. More...
core::Real	protocols::membrane::mem_all_atom_rmsd_with_super (core::pose::Pose &native_pose, core::pose::Pose &pose)
	Compute all-atom RMSD between TM regions - do superimpose. More...
core::Real	protocols::membrane::calc_helix_tilt_angle (core::pose::Pose &pose, core::Size span_no)
	Calculate tilt of a TM span relative to the membrane normal. More...
core::Vector	protocols::membrane::calc_helix_axis (core::pose::Pose &pose, core::Size span_no)
	Determine the axis used to define a single TM Helix. More...
core::Vector	protocols::membrane::com (core::Vector a, core::Vector b, core::Vector c)
	Calculate center of mass between 3 xyz coords. More...
core::Real	protocols::membrane::calc_angle_rmsd (core::Real measured_angle, core::Real ref_angle)
	Calculate the RMSD between a helix tilt angle & reference. More...
utility::vector1< core::Real >	protocols::membrane::pose_tilt_angle_and_center_distance (core::pose::Pose &pose)
	Calculate tilt angle and distance from membrane center. More...
bool	protocols::membrane::is_membrane_fixed (core::pose::Pose &pose)
	Determine whether the membrane is modeled as fixed. More...
bool	protocols::membrane::is_membrane_moveable_by_itself (core::pose::Pose &pose)
	Determine whether membrane can move on its own. More...
void	protocols::membrane::reorder_membrane_foldtree (core::pose::Pose &pose)
	Set membrane residue to root of foldtree. More...
core::Size	protocols::membrane::create_membrane_docking_foldtree_from_partners (core::pose::Pose &pose, std::string const partners)
	Create a membrane foldtree with an interface. More...
core::Size	protocols::membrane::create_membrane_foldtree_anchor_com (core::pose::Pose &pose)
	Create membrane foldtree from scratch. More...
core::Size	protocols::membrane::create_membrane_foldtree_anchor_tmcom (core::pose::Pose &pose)
	Create membrane foldtree from scratch. More...
core::Size	protocols::membrane::create_membrane_foldtree_anchor_pose_tmcom (core::pose::Pose &pose)
	Create membrane foldtree from scratch. More...
utility::vector1< core::Size >	protocols::membrane::create_membrane_multi_partner_foldtree_anchor_tmcom (core::pose::Pose &pose, std::string partner)
	Create foldtree for multiple docking partners. More...
void	protocols::membrane::create_membrane_foldtree_from_anchors (core::pose::Pose &pose, utility::vector1< core::Size > anchors)
	Helper function to create membrane foldtrees. More...
core::Size	protocols::membrane::create_specific_membrane_foldtree (core::pose::Pose &pose, utility::vector1< core::Vector > anchors)
	Helper function to create a specific membrane foldtree. More...
utility::vector1< core::Size >	protocols::membrane::get_anchor_points_for_tmcom (core::pose::Pose &pose)
	Helper function to create membrane foldtrees. More...
core::Size	protocols::membrane::setup_foldtree_pose_com (core::pose::Pose &pose)
	Setup foldtree from scratch. More...
void	protocols::membrane::setup_foldtree_from_anchors (core::pose::Pose &pose, utility::vector1< core::Size > anchors)
	Helper function to setup foldtrees. More...
std::pair< utility::vector1 < core::Real > , utility::vector1< core::Real > >	protocols::membrane::get_chain_and_z (core::pose::Pose const &pose)
	Grab the z-coordinates and chainIDs from the entire pose. More...
utility::vector1< char >	protocols::membrane::get_secstruct (core::pose::Pose &pose)
	Get dssp defined secondary structure from the pose. More...
void	protocols::membrane::compute_structure_based_embedding (core::pose::Pose const &pose, core::conformation::membrane::SpanningTopology const &topology, core::Vector &center, core::Vector &normal)
	Compute Membrane Center/Normal from Membrane Spanning topology. More...
void	protocols::membrane::compute_structure_based_embedding (core::pose::Pose const &pose, core::Vector &center, core::Vector &normal)
	Compute Membrane Center/Normal from Membrane Spanning topology, uses topology from MembraneInfo. More...
protocols::membrane::geometry::EmbeddingDefOP	protocols::membrane::compute_structure_based_embedding (core::pose::Pose const &pose, core::conformation::membrane::SpanningTopology const &topo)
	Compute Membrane Center/Normal from Membrane Spanning topology. More...
protocols::membrane::geometry::EmbeddingDefOP	protocols::membrane::compute_structure_based_embedding (core::pose::Pose const &pose)
	Compute Membrane Center/Normal from Membrane Spanning topology, uses topology from MembraneInfo. More...
protocols::membrane::geometry::EmbeddingOP	protocols::membrane::compute_embeddings_by_chain (core::pose::Pose const &pose)
	Compute embedding by chain. More...
protocols::membrane::geometry::EmbeddingDefOP	protocols::membrane::average_embeddings (utility::vector1< protocols::membrane::geometry::EmbeddingDefOP > const parts)
	Average EmbeddingDefs as they are without vector inversion accounting for topology. More...
protocols::membrane::geometry::EmbeddingDefOP	protocols::membrane::average_antiparallel_embeddings (utility::vector1< protocols::membrane::geometry::EmbeddingDefOP > const parts)
	Average EmbeddingDefs after first inverting some vectors accounting for topology. More...
void	protocols::membrane::update_partner_embeddings (core::pose::Pose const &pose, core::Size const jumpnum, protocols::membrane::geometry::EmbeddingDef &emb_up, protocols::membrane::geometry::EmbeddingDef &emb_down)
	Update embedding of the partners after a move. More...
core::Vector	protocols::membrane::pose_tm_com (core::pose::Pose const &pose)
	Pose transmembrane center-of-mass. More...
core::Vector	protocols::membrane::chain_com (core::pose::Pose const &pose, int chainid)
	Chain center-of-mass. More...
core::Vector	protocols::membrane::chain_tm_com (core::pose::Pose const &pose, int chain)
	Chain center-of-mass of TM regions. More...
core::Size	protocols::membrane::rsd_closest_to_pose_tm_com (core::pose::Pose const &pose)
	Residue closest to pose transmembrane center-of-mass. More...
core::Size	protocols::membrane::rsd_closest_to_chain_com (core::pose::Pose const &pose, int chainid)
	Residue closest to chain center-of-mass. More...
core::Size	protocols::membrane::rsd_closest_to_chain_tm_com (core::pose::Pose const &pose, int chainid)
	Residue closest to chain TM center-of-mass. More...
void	protocols::membrane::check_vector (core::Vector const vector)
	Check reasonable range of vector. More...
void	protocols::membrane::membrane_normal_to_length_15 (core::pose::Pose &pose)
	Normalize normal vector to length 15 for visualization. More...
core::Vector const	protocols::membrane::membrane_axis (core::pose::Pose &pose, int jumpnum)
	Calculates translation axis lying in the membrane (= projection axis between embedding centers) More...
void	protocols::membrane::split_topology_by_jump (core::pose::Pose const &pose, core::Size const jumpnum, core::conformation::membrane::SpanningTopology const &topo, core::pose::Pose &pose_up, core::pose::Pose &pose_down, core::conformation::membrane::SpanningTopology &topo_up, core::conformation::membrane::SpanningTopology &topo_down)
	Splits the SpanningTopology object into two objects, depending on given jump number. More...
void	protocols::membrane::split_topology_by_jump_noshift (core::pose::Pose const &pose, core::Size const jumpnum, core::conformation::membrane::SpanningTopologyOP topo, core::conformation::membrane::SpanningTopologyOP topo_up, core::conformation::membrane::SpanningTopologyOP topo_down)
	Splits the SpanningTopology object into two objects, depending on given jump number. More...
utility::vector1 < core::conformation::membrane::SpanningTopologyOP >	protocols::membrane::split_topology_by_chain_noshift (core::pose::Pose const &pose, core::conformation::membrane::SpanningTopologyOP const topo)
	Split topology by chain. More...
void	protocols::membrane::read_center_normal_from_tag (core::Vector &center, core::Vector &normal, utility::tag::TagCOP tag)
	Read in a user provided center/normal pair from RosettaScripts. More...
void	protocols::membrane::read_center_normal_from_cmd (core::Vector &center, core::Vector &normal)
	Read in a user provided center/normal pair from the commandline, safetly. More...

Detailed Description

Utility methods for working with proteins in the membrane Several groups of utilities for working in the memrbane environment.

• Calculate RMSD between the transmembrane domains of two poses (with or without superimposition)
• Calculate the tilt of the protien relative to the membrane normal
• Safety checks and convenience methods for working with membrane foldtrees
• Utility for accessing DSSP secstruc and z coordinates
• Calculate protein embedding based on the structure
• Split topology by jump, and other multi-chain (or partner) functions
• Methods for reducing the amount of code duplication in RosettaScripts and init_from_cmd functions in the membrane framework

NOTE: All of these methods require a RosettaMP framework pose or eventually may require this. Use pose.conformation().is_membrane() for safety checks!

Last Modified: 7/9/15

Author

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

JKLeman (julia.nosp@m..koe.nosp@m.hler1.nosp@m.982@.nosp@m.gmail.nosp@m..com)