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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  LoopClosure
 
class  RamaCheckBase
 
class  RamaCheck1B
 
class  RamaCheck2B
 
class  ShortLoopClosure
 
class  SlidingWindowLoopClosure
 
class  WidthFirstSlidingWindowLoopClosure
 @detail More...
 
class  FASelectSlidingWindowLoopClosure
 

Typedefs

using Matrix = numeric::xyzMatrix< Real >
 
typedef utility::pointer::shared_ptr< CCDLoopClosureMoverCCDLoopClosureMoverOP
 
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< LoopClosureLoopClosureOP
 
typedef utility::pointer::shared_ptr< LoopClosure const > LoopClosureCOP
 
typedef utility::pointer::shared_ptr< RamaCheckBaseRamaCheckBaseOP
 
typedef utility::pointer::shared_ptr< RamaCheckBase const > RamaCheckBaseCOP
 
typedef utility::pointer::shared_ptr< RamaCheck1BRamaCheck1BOP
 
typedef utility::pointer::shared_ptr< RamaCheck1B const > RamaCheck1BCOP
 
typedef utility::pointer::shared_ptr< RamaCheck2BRamaCheck2BOP
 
typedef utility::pointer::shared_ptr< RamaCheck2B const > RamaCheck2BCOP
 
typedef utility::pointer::shared_ptr< ShortLoopClosureShortLoopClosureOP
 
typedef utility::pointer::shared_ptr< ShortLoopClosure const > ShortLoopClosureCOP
 
typedef utility::pointer::shared_ptr< SlidingWindowLoopClosureSlidingWindowLoopClosureOP
 
typedef utility::pointer::shared_ptr< SlidingWindowLoopClosure const > SlidingWindowLoopClosureCOP
 
typedef utility::pointer::shared_ptr< FASelectSlidingWindowLoopClosureFASelectSlidingWindowLoopClosureOP
 
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

◆ CCDLoopClosureMoverCOP

◆ CCDLoopClosureMoverOP

◆ CcdMoverCOP

typedef utility::pointer::shared_ptr< CcdMover const > protocols::loops::loop_closure::ccd::CcdMoverCOP

◆ CcdMoverOP

typedef utility::pointer::shared_ptr< CcdMover > protocols::loops::loop_closure::ccd::CcdMoverOP

◆ FASelectSlidingWindowLoopClosureCOP

◆ FASelectSlidingWindowLoopClosureOP

◆ LoopClosureCOP

typedef utility::pointer::shared_ptr< LoopClosure const > protocols::loops::loop_closure::ccd::LoopClosureCOP

◆ LoopClosureOP

typedef utility::pointer::shared_ptr< LoopClosure > protocols::loops::loop_closure::ccd::LoopClosureOP

◆ Matrix

using protocols::loops::loop_closure::ccd::Matrix = typedef numeric::xyzMatrix<Real>

◆ RamaCheck1BCOP

typedef utility::pointer::shared_ptr< RamaCheck1B const > protocols::loops::loop_closure::ccd::RamaCheck1BCOP

◆ RamaCheck1BOP

typedef utility::pointer::shared_ptr< RamaCheck1B > protocols::loops::loop_closure::ccd::RamaCheck1BOP

◆ RamaCheck2BCOP

typedef utility::pointer::shared_ptr< RamaCheck2B const > protocols::loops::loop_closure::ccd::RamaCheck2BCOP

◆ RamaCheck2BOP

typedef utility::pointer::shared_ptr< RamaCheck2B > protocols::loops::loop_closure::ccd::RamaCheck2BOP

◆ RamaCheckBaseCOP

typedef utility::pointer::shared_ptr< RamaCheckBase const > protocols::loops::loop_closure::ccd::RamaCheckBaseCOP

◆ RamaCheckBaseOP

◆ ShortLoopClosureCOP

typedef utility::pointer::shared_ptr< ShortLoopClosure const > protocols::loops::loop_closure::ccd::ShortLoopClosureCOP

◆ ShortLoopClosureOP

◆ SlidingWindowLoopClosureCOP

◆ SlidingWindowLoopClosureOP

Enumeration Type Documentation

◆ ChainDirection

Enumerator
forward 
backward 
n_chain_directions 

◆ SecondaryStructureType

Enumerator
helix 
strand 
coil 
n_secondary_structure_types 

Function Documentation

◆ compute_single_direction_deviation()

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 
)

◆ get_deviation()

std::pair< core::Real, core::Real > protocols::loops::loop_closure::ccd::get_deviation ( core::pose::Pose const &  pose,
core::uint const  cutpoint 
)

◆ get_overlap_pos()

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 
)

◆ load_coords_and_torsions()

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 core::conformation::Residue::atom(), protocols::simple_filters::coords(), core::conformation::Residue::mainchain_atoms(), core::conformation::Residue::mainchain_torsion(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Atom::xyz().

Referenced by get_deviation().

◆ operator<<() [1/2]

std::ostream & protocols::loops::loop_closure::ccd::operator<< ( std::ostream &  os,
CCDLoopClosureMover const &  mover 
)

◆ operator<<() [2/2]

std::ostream & protocols::loops::loop_closure::ccd::operator<< ( std::ostream &  os,
RamaCheckBase const &  rama_check 
)

◆ REALLY_BAD_SCORE()

const Real protocols::loops::loop_closure::ccd::REALLY_BAD_SCORE ( 1000000000.  0)

◆ RMSD_FRAG_STORE()

std::string const protocols::loops::loop_closure::ccd::RMSD_FRAG_STORE ( "closure_loop_rmsd"  )

◆ SCORE_FRAG_STORE()

std::string const protocols::loops::loop_closure::ccd::SCORE_FRAG_STORE ( "closure_loop_score"  )

◆ TR() [1/2]

static basic::Tracer protocols::loops::loop_closure::ccd::TR ( "protocols.loops.loop_closure.ccd.ccd_closure"  )
static

◆ tr() [1/4]

static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure"  )
static

◆ tr() [2/4]

static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.LoopClosure"  )
static

◆ TR() [2/2]

static basic::Tracer protocols::loops::loop_closure::ccd::TR ( "protocols.loops.loop_closure.ccd.RamaCheck"  )
static

◆ tr() [3/4]

static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.ShortLoopClosure"  )
static

◆ tr() [4/4]

static basic::Tracer protocols::loops::loop_closure::ccd::tr ( "protocols.loops.loop_closure.ccd.SlidingWindowLoopClosure"  )
static

◆ VDW_FRAG_STORE()

std::string const protocols::loops::loop_closure::ccd::VDW_FRAG_STORE ( "closure_loop_vdw"  )

Variable Documentation

◆ RMSD_FRAG_STORE

std::string const protocols::loops::loop_closure::ccd::RMSD_FRAG_STORE
extern

◆ SCORE_FRAG_STORE

std::string const protocols::loops::loop_closure::ccd::SCORE_FRAG_STORE
extern

◆ VDW_FRAG_STORE

std::string const protocols::loops::loop_closure::ccd::VDW_FRAG_STORE
extern