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protocols::backrub::BackrubSegment Class Reference

a class for holind information about individual backrub segments More...

#include <BackrubSegment.hh>

Public Types

typedef
utility::keys::Key3Vector
< core::id::AtomID
BondAngleKey
 

Public Member Functions

 BackrubSegment (core::id::AtomID start_atomid, core::id::AtomID start_atomid1, core::id::AtomID start_atomid2, core::id::AtomID end_atomid, core::Size size, core::Real max_angle_disp)
 
core::id::AtomID start_atomid () const
 get AtomID of starting atom More...
 
core::id::AtomID start_atomid1 () const
 get AtomID of first atom along the path from start to end More...
 
core::id::AtomID start_atomid2 () const
 get AtomID of second atom along the path from start to end More...
 
core::id::AtomID end_atomid () const
 get AtomID of starting atom More...
 
core::Size size () const
 get the segment size More...
 
void start_atoms1 (core::pose::Pose const &pose, core::kinematics::tree::AtomCOP &start_atom_m1, core::kinematics::tree::AtomCOP &start_atom, core::kinematics::tree::AtomCOP &start_atom_p1) const
 get mainchain atom tree atoms 1 bond away from the start pivot More...
 
void start_atoms2 (core::pose::Pose const &pose, core::kinematics::tree::AtomCOP &start_atom_m2, core::kinematics::tree::AtomCOP &start_atom_m1, core::kinematics::tree::AtomCOP &start_atom, core::kinematics::tree::AtomCOP &start_atom_p1, core::kinematics::tree::AtomCOP &start_atom_p2) const
 get mainchain atom tree atoms 2 bonds away from the start pivot More...
 
BondAngleKey start_bond_angle_key (core::pose::Pose const &pose)
 get a key representing the starting mainchain bond angle atoms More...
 
void end_atoms1 (core::pose::Pose const &pose, core::kinematics::tree::AtomCOP &end_atom_m1, core::kinematics::tree::AtomCOP &end_atom, core::kinematics::tree::AtomCOP &end_atom_p1) const
 get mainchain atom tree atoms 1 bond away from the end pivot More...
 
void end_atoms2 (core::pose::Pose const &pose, core::kinematics::tree::AtomCOP &end_atom_m2, core::kinematics::tree::AtomCOP &end_atom_m1, core::kinematics::tree::AtomCOP &end_atom, core::kinematics::tree::AtomCOP &end_atom_p1, core::kinematics::tree::AtomCOP &end_atom_p2) const
 get mainchain atom tree atoms 2 bonds away from the end pivot More...
 
BondAngleKey end_bond_angle_key (core::pose::Pose const &pose)
 get a key representing the ending mainchain bond angle atoms More...
 
core::Real max_angle_disp () const
 get maximum angular displacement More...
 
core::Real angle_disp () const
 get overall angular displacement More...
 

Static Public Member Functions

static void bond_angle_atoms (core::pose::Pose const &pose, BackrubSegment::BondAngleKey bond_angle_key, core::kinematics::tree::AtomCOP &atom_m1, core::kinematics::tree::AtomCOP &atom, core::kinematics::tree::AtomCOP &atom_p1)
 get the current bond angle atoms referred to by a key More...
 

Private Attributes

core::id::AtomID start_atomid_
 
core::id::AtomID start_atomid1_
 
core::id::AtomID start_atomid2_
 
core::id::AtomID end_atomid_
 
core::Size size_
 
core::Real max_angle_disp_
 
core::Real angle_disp_
 

Detailed Description

a class for holind information about individual backrub segments

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::backrub::BackrubSegment::BackrubSegment ( core::id::AtomID  start_atomid,
core::id::AtomID  start_atomid1,
core::id::AtomID  start_atomid2,
core::id::AtomID  end_atomid,
core::Size  size,
core::Real  max_angle_disp 
)
inline

Member Function Documentation

core::Real protocols::backrub::BackrubSegment::angle_disp ( ) const
inline

get overall angular displacement

References angle_disp_.

void protocols::backrub::BackrubSegment::bond_angle_atoms ( core::pose::Pose const &  pose,
BackrubSegment::BondAngleKey  bond_angle_key,
core::kinematics::tree::AtomCOP atom_m1,
core::kinematics::tree::AtomCOP atom,
core::kinematics::tree::AtomCOP atom_p1 
)
static

get the current bond angle atoms referred to by a key

References core::kinematics::AtomTree::atom(), and core::pose::Pose::atom_tree().

core::id::AtomID protocols::backrub::BackrubSegment::end_atomid ( ) const
inline
void protocols::backrub::BackrubSegment::end_atoms1 ( core::pose::Pose const &  pose,
core::kinematics::tree::AtomCOP end_atom_m1,
core::kinematics::tree::AtomCOP end_atom,
core::kinematics::tree::AtomCOP end_atom_p1 
) const

get mainchain atom tree atoms 1 bond away from the end pivot

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), and core::kinematics::tree::Atom::get_self_ptr().

void protocols::backrub::BackrubSegment::end_atoms2 ( core::pose::Pose const &  pose,
core::kinematics::tree::AtomCOP end_atom_m2,
core::kinematics::tree::AtomCOP end_atom_m1,
core::kinematics::tree::AtomCOP end_atom,
core::kinematics::tree::AtomCOP end_atom_p1,
core::kinematics::tree::AtomCOP end_atom_p2 
) const

get mainchain atom tree atoms 2 bonds away from the end pivot

protocols::backrub::BackrubSegment::BondAngleKey protocols::backrub::BackrubSegment::end_bond_angle_key ( core::pose::Pose const &  pose)

get a key representing the ending mainchain bond angle atoms

References core::id::GLOBAL_BOGUS_ATOM_ID.

core::Real protocols::backrub::BackrubSegment::max_angle_disp ( ) const
inline

get maximum angular displacement

References max_angle_disp_.

core::Size protocols::backrub::BackrubSegment::size ( ) const
inline

get the segment size

References size_.

core::id::AtomID protocols::backrub::BackrubSegment::start_atomid ( ) const
inline
core::id::AtomID protocols::backrub::BackrubSegment::start_atomid1 ( ) const
inline
core::id::AtomID protocols::backrub::BackrubSegment::start_atomid2 ( ) const
inline
void protocols::backrub::BackrubSegment::start_atoms1 ( core::pose::Pose const &  pose,
core::kinematics::tree::AtomCOP start_atom_m1,
core::kinematics::tree::AtomCOP start_atom,
core::kinematics::tree::AtomCOP start_atom_p1 
) const

get mainchain atom tree atoms 1 bond away from the start pivot

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), and core::kinematics::tree::Atom::get_self_ptr().

void protocols::backrub::BackrubSegment::start_atoms2 ( core::pose::Pose const &  pose,
core::kinematics::tree::AtomCOP start_atom_m2,
core::kinematics::tree::AtomCOP start_atom_m1,
core::kinematics::tree::AtomCOP start_atom,
core::kinematics::tree::AtomCOP start_atom_p1,
core::kinematics::tree::AtomCOP start_atom_p2 
) const

get mainchain atom tree atoms 2 bonds away from the start pivot

References core::kinematics::AtomTree::atom(), core::pose::Pose::atom_tree(), and core::kinematics::tree::Atom::get_self_ptr().

protocols::backrub::BackrubSegment::BondAngleKey protocols::backrub::BackrubSegment::start_bond_angle_key ( core::pose::Pose const &  pose)

get a key representing the starting mainchain bond angle atoms

Member Data Documentation

core::Real protocols::backrub::BackrubSegment::angle_disp_
private

Referenced by angle_disp().

core::id::AtomID protocols::backrub::BackrubSegment::end_atomid_
private

Referenced by end_atomid().

core::Real protocols::backrub::BackrubSegment::max_angle_disp_
private

Referenced by max_angle_disp().

core::Size protocols::backrub::BackrubSegment::size_
private

Referenced by size().

core::id::AtomID protocols::backrub::BackrubSegment::start_atomid1_
private

Referenced by start_atomid1().

core::id::AtomID protocols::backrub::BackrubSegment::start_atomid2_
private

Referenced by start_atomid2().

core::id::AtomID protocols::backrub::BackrubSegment::start_atomid_
private

Referenced by start_atomid().


The documentation for this class was generated from the following files: