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protocols::loops::loop_closure::ccd Namespace Reference

Classes

class  CCDLoopClosureMover
 Close a loop (protein or otherwise) using bi-directional Cyclic Coordinate Descent. More...
 
class  CCDLoopClosureMoverCreator
 CCDLoopClosureMoverCreator allows the MoverFactory to create a CCDLoopClosureMover instance. More...
 
class  FASelectSlidingWindowLoopClosure
 
class  LoopClosure
 
class  RamaCheck1B
 
class  RamaCheck2B
 
class  RamaCheckBase
 
class  ShortLoopClosure
 
class  SlidingWindowLoopClosure
 
class  WidthFirstSlidingWindowLoopClosure
 

Typedefs

using Matrix = numeric::xyzMatrix< Real >
 
typedef
utility::pointer::shared_ptr
< CCDLoopClosureMover
CCDLoopClosureMoverOP
 
typedef
utility::pointer::shared_ptr
< CCDLoopClosureMover const > 
CCDLoopClosureMoverCOP
 
typedef
utility::pointer::shared_ptr
< CcdMover > 
CcdMoverOP
 
typedef
utility::pointer::shared_ptr
< CcdMover const > 
CcdMoverCOP
 
typedef
utility::pointer::shared_ptr
< LoopClosure
LoopClosureOP
 
typedef
utility::pointer::shared_ptr
< LoopClosure const > 
LoopClosureCOP
 
typedef
utility::pointer::shared_ptr
< RamaCheckBase
RamaCheckBaseOP
 
typedef
utility::pointer::shared_ptr
< RamaCheckBase const > 
RamaCheckBaseCOP
 
typedef
utility::pointer::shared_ptr
< RamaCheck1B
RamaCheck1BOP
 
typedef
utility::pointer::shared_ptr
< RamaCheck1B const > 
RamaCheck1BCOP
 
typedef
utility::pointer::shared_ptr
< RamaCheck2B
RamaCheck2BOP
 
typedef
utility::pointer::shared_ptr
< RamaCheck2B const > 
RamaCheck2BCOP
 
typedef
utility::pointer::shared_ptr
< ShortLoopClosure
ShortLoopClosureOP
 
typedef
utility::pointer::shared_ptr
< ShortLoopClosure const > 
ShortLoopClosureCOP
 
typedef
utility::pointer::shared_ptr
< SlidingWindowLoopClosure
SlidingWindowLoopClosureOP
 
typedef
utility::pointer::shared_ptr
< SlidingWindowLoopClosure
const > 
SlidingWindowLoopClosureCOP
 
typedef
utility::pointer::shared_ptr
< FASelectSlidingWindowLoopClosure
FASelectSlidingWindowLoopClosureOP
 
typedef
utility::pointer::shared_ptr
< FASelectSlidingWindowLoopClosure
const > 
FASelectSlidingWindowLoopClosureCOP
 

Enumerations

enum  ChainDirection { forward = 1, backward, n_chain_directions = backward }
 
enum  SecondaryStructureType { helix = 1, strand, coil, n_secondary_structure_types = coil }
 

Functions

static basic::Tracer TR ("protocols.loops.loop_closure.ccd.ccd_closure")
 
void load_coords_and_torsions (pose::Pose const &pose, utility::vector1< utility::vector1< core::Vector > > &coords, utility::vector1< utility::vector1< core::Angle > > &torsions)
 
void get_overlap_pos (utility::vector1< utility::vector1< core::Vector > > const &coords, utility::vector1< utility::vector1< core::Angle > > const &torsions, core::uint const cutpoint, core::uint const direction, core::Angle const bond_angle1, core::Length const bond_length, core::Angle const bond_angle2, Matrix &M)
 
Distance compute_single_direction_deviation (vector1< vector1< Vector > > const &coords, vector1< vector1< Angle > > const &torsions, int const cutpoint, core::uint const direction, Angle const ideal_theta_lower, Length const bond_length, Angle const bond_angle2, Matrix const &F)
 
std::pair< core::Real, core::Realget_deviation (core::pose::Pose const &pose, core::uint const cutpoint)
 
std::ostream & operator<< (std::ostream &os, CCDLoopClosureMover const &mover)
 
static basic::Tracer tr ("protocols.loops.loop_closure.ccd.LoopClosure")
 
static basic::Tracer TR ("protocols.loops.loop_closure.ccd.RamaCheck")
 
std::ostream & operator<< (std::ostream &os, RamaCheckBase const &rama_check)
 
static basic::Tracer tr ("protocols.loops.loop_closure.ccd.ShortLoopClosure")
 
static basic::Tracer tr ("protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure")
 
std::string const VDW_FRAG_STORE ("closure_loop_vdw")
 
std::string const SCORE_FRAG_STORE ("closure_loop_score")
 
std::string const RMSD_FRAG_STORE ("closure_loop_rmsd")
 
const Real REALLY_BAD_SCORE (1000000000.0)
 
static basic::Tracer tr ("protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure")
 

Variables

std::string const VDW_FRAG_STORE
 
std::string const SCORE_FRAG_STORE
 
std::string const RMSD_FRAG_STORE
 

Typedef Documentation

typedef utility::pointer::shared_ptr< CcdMover const > protocols::loops::loop_closure::ccd::CcdMoverCOP
typedef utility::pointer::shared_ptr< CcdMover > protocols::loops::loop_closure::ccd::CcdMoverOP
typedef utility::pointer::shared_ptr< LoopClosure const > protocols::loops::loop_closure::ccd::LoopClosureCOP
typedef utility::pointer::shared_ptr< LoopClosure > protocols::loops::loop_closure::ccd::LoopClosureOP
using protocols::loops::loop_closure::ccd::Matrix = typedef numeric::xyzMatrix<Real>
typedef utility::pointer::shared_ptr< RamaCheck1B const > protocols::loops::loop_closure::ccd::RamaCheck1BCOP
typedef utility::pointer::shared_ptr< RamaCheck1B > protocols::loops::loop_closure::ccd::RamaCheck1BOP
typedef utility::pointer::shared_ptr< RamaCheck2B const > protocols::loops::loop_closure::ccd::RamaCheck2BCOP
typedef utility::pointer::shared_ptr< RamaCheck2B > protocols::loops::loop_closure::ccd::RamaCheck2BOP
typedef utility::pointer::shared_ptr< RamaCheckBase const > protocols::loops::loop_closure::ccd::RamaCheckBaseCOP
typedef utility::pointer::shared_ptr< ShortLoopClosure const > protocols::loops::loop_closure::ccd::ShortLoopClosureCOP

Enumeration Type Documentation

Enumerator
forward 
backward 
n_chain_directions 
Enumerator
helix 
strand 
coil 
n_secondary_structure_types 

Function Documentation

Distance protocols::loops::loop_closure::ccd::compute_single_direction_deviation ( vector1< vector1< Vector > > const &  coords,
vector1< vector1< Angle > > const &  torsions,
int const  cutpoint,
core::uint const  direction,
Angle const  ideal_theta_lower,
Length const  bond_length,
Angle const  bond_angle2,
Matrix const &  F 
)
std::pair< core::Real, core::Real > protocols::loops::loop_closure::ccd::get_deviation ( core::pose::Pose const &  pose,
core::uint const  cutpoint 
)
void protocols::loops::loop_closure::ccd::get_overlap_pos ( utility::vector1< utility::vector1< core::Vector > > const &  coords,
utility::vector1< utility::vector1< core::Angle > > const &  torsions,
core::uint const  cutpoint,
core::uint const  direction,
core::Angle const  bond_angle1,
core::Length const  bond_length,
core::Angle const  bond_angle2,
Matrix M 
)
void protocols::loops::loop_closure::ccd::load_coords_and_torsions ( pose::Pose const &  pose,
utility::vector1< utility::vector1< core::Vector > > &  coords,
utility::vector1< utility::vector1< core::Angle > > &  torsions 
)
Parameters
<coords>an array of coordinates of the main-chain atoms for every residue in the Pose
<torsions>an array of values for the main-chain torsion angles for every residue in the Pose

References protocols::simple_filters::coords(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::kinmatch::xyz().

Referenced by get_deviation().

std::ostream & protocols::loops::loop_closure::ccd::operator<< ( std::ostream &  os,
RamaCheckBase const &  rama_check 
)
std::ostream & protocols::loops::loop_closure::ccd::operator<< ( std::ostream &  os,
CCDLoopClosureMover const &  mover 
)
const Real protocols::loops::loop_closure::ccd::REALLY_BAD_SCORE ( 1000000000.  0)
std::string const protocols::loops::loop_closure::ccd::RMSD_FRAG_STORE ( "closure_loop_rmsd"  )
std::string const protocols::loops::loop_closure::ccd::SCORE_FRAG_STORE ( "closure_loop_score"  )
static basic::Tracer protocols::loops::loop_closure::ccd::TR ( "protocols.loops.loop_closure.ccd.RamaCheck"  )
static
static basic::Tracer protocols::loops::loop_closure::ccd::TR ( "protocols.loops.loop_closure.ccd.ccd_closure"  )
static
static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.LoopClosure"  )
static
static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.ShortLoopClosure"  )
static
static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure"  )
static
static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure"  )
static
std::string const protocols::loops::loop_closure::ccd::VDW_FRAG_STORE ( "closure_loop_vdw"  )

Variable Documentation

std::string const protocols::loops::loop_closure::ccd::RMSD_FRAG_STORE
std::string const protocols::loops::loop_closure::ccd::SCORE_FRAG_STORE
std::string const protocols::loops::loop_closure::ccd::VDW_FRAG_STORE