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::Real >	get_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< CCDLoopClosureMover const > protocols::loops::loop_closure::ccd::CCDLoopClosureMoverCOP

typedef utility::pointer::shared_ptr< CCDLoopClosureMover > protocols::loops::loop_closure::ccd::CCDLoopClosureMoverOP

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< FASelectSlidingWindowLoopClosure const > protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosureCOP

typedef utility::pointer::shared_ptr< FASelectSlidingWindowLoopClosure > protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosureOP

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< RamaCheckBase > protocols::loops::loop_closure::ccd::RamaCheckBaseOP

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

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

typedef utility::pointer::shared_ptr< SlidingWindowLoopClosure const > protocols::loops::loop_closure::ccd::SlidingWindowLoopClosureCOP

typedef utility::pointer::shared_ptr< SlidingWindowLoopClosure > protocols::loops::loop_closure::ccd::SlidingWindowLoopClosureOP

Enumeration Type Documentation

enum protocols::loops::loop_closure::ccd::ChainDirection

Enumerator
forward
backward
n_chain_directions

enum protocols::loops::loop_closure::ccd::SecondaryStructureType

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
	)

References protocols::simple_filters::coords(), core::chemical::element::F, get_overlap_pos(), and core::scoring::electron_density::square().

Referenced by get_deviation().

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

References compute_single_direction_deviation(), protocols::simple_filters::coords(), core::chemical::AtomICoor::d(), core::chemical::element::F, core::chemical::ResidueConnection::icoor(), load_coords_and_torsions(), core::conformation::Residue::lower_connect(), core::conformation::Residue::mainchain_atoms(), core::pose::Pose::residue(), core::chemical::AtomICoor::theta(), and core::conformation::Residue::upper_connect().

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
	)

References core::scoring::packstat::old::angles, protocols::simple_filters::coords(), and core::kinematics::distance().

Referenced by compute_single_direction_deviation().

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
	)

References protocols::loops::loop_closure::ccd::RamaCheckBase::show().

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

References protocols::loops::loop_closure::ccd::CCDLoopClosureMover::show().

const Real protocols::loops::loop_closure::ccd::REALLY_BAD_SCORE

(

1000000000.

0

)

Referenced by protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), and protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop().

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

Referenced by protocols::loops::loop_closure::ccd::RamaCheckBase::accept_new_conformation(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::adjust_residue_to_minimize_deviation(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::apply(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::calculate_ccd_angle(), protocols::loops::loop_closure::ccd::CCDLoopClosureMover::close_loop_in_single_direction(), protocols::loops::loop_closure::ccd::RamaCheckBase::initialize_starting_rama_scores(), and protocols::loops::loop_closure::ccd::RamaCheckBase::total_net_change_in_rama_score_over_range().

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

static

Referenced by protocols::loops::loop_closure::ccd::ShortLoopClosure::apply(), protocols::loops::loop_closure::ccd::LoopClosure::apply(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::apply(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::determine_loop(), protocols::loops::loop_closure::ccd::LoopClosure::do_frag_cycles(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::generate_window_list(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::sample_loops(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::select_final_loop(), protocols::loops::loop_closure::ccd::WidthFirstSlidingWindowLoopClosure::set_defaults(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::set_defaults(), protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::setup_frag_scorefxn(), and protocols::loops::loop_closure::ccd::ShortLoopClosure::ShortLoopClosure().

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

Referenced by protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments().

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

Referenced by protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), and protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::select_final_loop().

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

Referenced by protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::process_fragments(), protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosure::select_final_loop(), and protocols::loops::loop_closure::ccd::SlidingWindowLoopClosure::select_final_loop().