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

Classes
class	CcdLoopClosureMover
class	CcdMover
class	FASelectSlidingWindowLoopClosure
class	LoopClosure
class	ShortLoopClosure
class	SlidingWindowLoopClosure
class	WidthFirstSlidingWindowLoopClosure

Typedefs
typedef numeric::xyzMatrix< Real >	Matrix
typedef utility::pointer::owning_ptr < CcdLoopClosureMover >	CcdLoopClosureMoverOP
typedef utility::pointer::owning_ptr < CcdLoopClosureMover const >	CcdLoopClosureMoverCOP
typedef utility::pointer::owning_ptr < CcdMover >	CcdMoverOP
typedef utility::pointer::owning_ptr < CcdMover const >	CcdMoverCOP
typedef utility::pointer::owning_ptr < FASelectSlidingWindowLoopClosure >	FASelectSlidingWindowLoopClosureOP
typedef utility::pointer::owning_ptr < FASelectSlidingWindowLoopClosure const >	FASelectSlidingWindowLoopClosureCOP
typedef utility::pointer::owning_ptr < LoopClosure >	LoopClosureOP
typedef utility::pointer::owning_ptr < LoopClosure const >	LoopClosureCOP
typedef utility::pointer::owning_ptr < ShortLoopClosure >	ShortLoopClosureOP
typedef utility::pointer::owning_ptr < ShortLoopClosure const >	ShortLoopClosureCOP
typedef utility::pointer::owning_ptr < SlidingWindowLoopClosure >	SlidingWindowLoopClosureOP
typedef utility::pointer::owning_ptr < SlidingWindowLoopClosure const >	SlidingWindowLoopClosureCOP

Functions
void	load_coords_and_torsions (pose::Pose const &pose, vector1< vector1< Vector > > &coords, vector1< vector1< Real > > &torsions)
	copy mainchain atoms xyz and torsions from pose to coords and torsions More...
void	copy_torsions_to_pose (pose::Pose &pose, int const loop_begin, int const loop_end, vector1< vector1< Real > > const &torsions)
	copy torsions into pose between residue loop_begin and loop_end More...
void	get_overlap_pos (vector1< vector1< Vector > > const &coords, vector1< vector1< Real > > const &torsions, int const cutpoint, int const direction, Real const bond_angle1, Real const bond_length, Real const bond_angle2, Matrix &M)
void	check_overlap_pos (vector1< vector1< Vector > > const &coords, vector1< vector1< Real > > const &torsions, int const cutpoint, int const direction, Real const bond_angle1, Real const ASSERT_ONLY(bond_length), Real const bond_angle2, Matrix const &M_in)
	check whether xyz coords of overlap position match internal coords More...
void	index_pair_in_range (int &pos, int &atom, int const nbb)
void	get_torsion_axis (vector1< vector1< Vector > > const &coords, int const seqpos, int const torsion, Vector &axis_atom, Vector &axis_vector)
void	refold_loop_torsion (Real const alpha, int const pos, int const torsion, int const dir, int const cutpoint, vector1< vector1< Vector > > &coords, Matrix &M)
void	calculate_ccd_angle (Matrix const &F, Matrix const &M, vector1< vector1< Vector > > const &coords, int const pos, int const torsion, int const direction, Real &angle, Real &dev)
void	check_torsions (int const loop_begin, int const loop_end, int const cutpoint, vector1< vector1< Real > > const &torsions, vector1< vector1< Vector > > const &coords)
int	fast_ccd_loop_closure (pose::Pose &pose, kinematics::MoveMap const &mm, int const loop_begin, int const loop_end, int const cutpoint, int const ii_cycles, Real const tolerance, bool const rama_check, Real const max_rama_score_increase, Real const max_total_delta_helix, Real const max_total_delta_strand, Real const max_total_delta_loop, Real &forward_deviation, Real &backward_deviation, Real &torsion_delta, Real &rama_delta)
void	ccd_moves (int const total_moves, core::pose::Pose &pose, core::kinematics::MoveMap const &mm, int const loop_begin, int const loop_end, int const cutpoint)
std::pair< core::Real, core::Real >	get_deviation (core::pose::Pose const &pose, int const cutpoint)
std::ostream &	operator<< (std::ostream &os, CcdLoopClosureMover const &mover)
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)

Variables
basic::Tracer	tccd ("protocols.loops.loop_closure.ccd.ccd_closure")
static basic::Tracer	tr ("protocols.loops.loop_closure.ccd.FASelectSlidingWindowLoopClosure")
const Real	REALLY_BAD_SCORE (1000000000.0)
static numeric::random::RandomGenerator	RG (9781212)
static basic::Tracer	tr ("protocols.loops.loop_closure.ccd.LoopClosure")
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
std::string const	SCORE_FRAG_STORE
std::string const	RMSD_FRAG_STORE

Typedef Documentation

typedef utility::pointer::owning_ptr< CcdLoopClosureMover const > protocols::loops::loop_closure::ccd::CcdLoopClosureMoverCOP

typedef utility::pointer::owning_ptr< CcdLoopClosureMover > protocols::loops::loop_closure::ccd::CcdLoopClosureMoverOP

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

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

typedef utility::pointer::owning_ptr< FASelectSlidingWindowLoopClosure const > protocols::loops::loop_closure::ccd::FASelectSlidingWindowLoopClosureCOP

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

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

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

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

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

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

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

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

Function Documentation

void protocols::loops::loop_closure::ccd::calculate_ccd_angle	(	Matrix const &	F,
		Matrix const &	M,
		vector1< vector1< Vector > > const &	coords,
		int const	pos,
		int const	torsion,
		int const	direction,
		Real &	angle,
		Real &	dev
	)

References protocols::rigid::c2n, numeric::xyzMatrix< class >::col(), cross(), numeric::conversions::degrees(), degrees(), dot(), get_torsion_axis(), numeric::xyzVector< class >::is_unit(), numeric::xyzVector< class >::length(), protocols::rigid::n2c, protocols::comparative_modeling::features::O, numeric::conversions::radians(), radians(), and utility_exit_with_message.

Referenced by ccd_moves(), and fast_ccd_loop_closure().

void protocols::loops::loop_closure::ccd::ccd_moves	(	int const	total_moves,
		core::pose::Pose &	pose,
		core::kinematics::MoveMap const &	mm,
		int const	loop_begin,
		int const	loop_end,
		int const	cutpoint
	)

References core::pose::Pose::aa(), BB, protocols::rigid::c2n, calculate_ccd_angle(), check_overlap_pos(), numeric::xyzMatrix< class >::col(), copy_torsions_to_pose(), core::chemical::AtomICoor::d(), core::kinematics::MoveMap::get(), get_overlap_pos(), core::chemical::ResidueConnection::icoor(), j, load_coords_and_torsions(), core::conformation::Residue::lower_connect(), core::conformation::Residue::mainchain_atoms(), protocols::rigid::n2c, nres, basic::periodic_range(), rama, refold_loop_torsion(), core::pose::Pose::residue(), core::pose::Pose::secstruct(), size(), ss, tccd, core::chemical::AtomICoor::theta(), torsion(), core::pose::Pose::total_residue(), total_weight, numeric::random::uniform(), core::conformation::Residue::upper_connect(), and weight.

Referenced by protocols::rbsegment_relax::AutoRBMover::apply(), protocols::antibody::CloseOneCDRLoop::apply(), protocols::antibody::H3PerturbCCD::apply(), protocols::rbsegment_relax::CCDMoveWrapper::apply(), protocols::loops::loop_closure::ccd::CcdMover::apply(), protocols::antibody_legacy::LoopRlxMover::apply(), protocols::forge::remodel::RemodelLoopMover::boost_closure_stage(), protocols::LoopRebuild::build_loop_with_ccd_closure(), protocols::antibody_legacy::CloseOneMover::close_one_loop_stem(), protocols::antibody::H3RefineCCD::finalize_setup(), protocols::forge::remodel::RemodelLoopMover::independent_stage(), protocols::antibody::RefineOneCDRLoopCentroid::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax(), protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(), protocols::forge::remodel::RemodelLoopMover::loophash_stage(), protocols::loops::loop_mover::perturb::LoopMover_Perturb_QuickCCD_Moves::model_loop(), protocols::antibody_legacy::CDRH3Modeler::scored_frag_close(), and protocols::forge::remodel::RemodelLoopMover::simultaneous_stage().

void protocols::loops::loop_closure::ccd::check_overlap_pos	(	vector1< vector1< Vector > > const &	coords,
		vector1< vector1< Real > > const &	torsions,
		int const	cutpoint,
		int const	direction,
		Real const	bond_angle1,
		Real const	ASSERT_ONLYbond_length,
		Real const	bond_angle2,
		Matrix const &	M_in
	)

check whether xyz coords of overlap position match internal coords

References angles, ASSERT_ONLY, numeric::xyzMatrix< class >::col(), dihedral_radians(), distance(), dot(), length, numeric::conversions::radians(), radians(), size(), subtract_radian_angles(), and basic::subtract_radian_angles().

Referenced by ccd_moves(), and fast_ccd_loop_closure().

void protocols::loops::loop_closure::ccd::check_torsions	(	int const	loop_begin,
		int const	loop_end,
		int const	cutpoint,
		vector1< vector1< Real > > const &	torsions,
		vector1< vector1< Vector > > const &	coords
	)

References numeric::dihedral_degrees(), index_pair_in_range(), size(), basic::subtract_degree_angles(), tccd, torsion(), and protocols::kinmatch::xyz().

Referenced by fast_ccd_loop_closure().

void protocols::loops::loop_closure::ccd::copy_torsions_to_pose	(	pose::Pose &	pose,
		int const	loop_begin,
		int const	loop_end,
		vector1< vector1< Real > > const &	torsions
	)

copy torsions into pose between residue loop_begin and loop_end

References j, and core::pose::Pose::set_torsion().

Referenced by ccd_moves(), and fast_ccd_loop_closure().

int protocols::loops::loop_closure::ccd::fast_ccd_loop_closure	(	pose::Pose &	pose,
		kinematics::MoveMap const &	mm,
		int const	loop_begin,
		int const	loop_end,
		int const	cutpoint,
		int const	ii_cycles,
		Real const	tolerance,
		bool const	rama_check,
		Real const	max_rama_score_increase,
		Real const	max_total_delta_helix,
		Real const	max_total_delta_strand,
		Real const	max_total_delta_loop,
		Real &	forward_deviation,
		Real &	backward_deviation,
		Real &	torsion_delta,
		Real &	rama_delta
	)

tolerance in Angstroms, forward and backward splice RMS over N,CA,C must be less than tolerance for an early return. otherwise goes through the loop ii_cycles, each time both forward and backward returns the number of cycles actually taken

References core::pose::Pose::aa(), BB, protocols::rigid::c2n, calculate_ccd_angle(), basic::CCD_CLOSE, check_overlap_pos(), check_torsions(), numeric::xyzMatrix< class >::col(), copy_torsions_to_pose(), core::chemical::AtomICoor::d(), numeric::xyzVector< class >::distance_squared(), core::kinematics::MoveMap::get(), get_overlap_pos(), protocols::abinitio::abscript::I, core::chemical::ResidueConnection::icoor(), j, load_coords_and_torsions(), core::conformation::Residue::lower_connect(), core::conformation::Residue::mainchain_atoms(), protocols::rigid::n2c, nres, basic::periodic_range(), PROF_START, PROF_STOP, rama, refold_loop_torsion(), repeat, core::pose::Pose::residue(), core::pose::Pose::secstruct(), size(), numeric::square(), basic::subtract_degree_angles(), tccd, core::chemical::AtomICoor::theta(), torsion(), core::pose::Pose::total_residue(), numeric::random::uniform(), core::conformation::Residue::upper_connect(), and utility_exit_with_message.

Referenced by protocols::loops::loop_closure::ccd::CcdLoopClosureMover::apply(), protocols::loops::ccd_close_loops(), protocols::simple_moves::WobbleMover::ccd_closure(), protocols::stepwise::sampling::protein::StepWiseProteinCCD_Closer::CCD_loop_close(), protocols::LoopRebuild::fast_ccd_close_loops(), and protocols::loops::loop_mover::perturb::fast_ccd_close_loops().

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

References protocols::rigid::c2n, numeric::xyzMatrix< class >::col(), core::chemical::AtomICoor::d(), get_overlap_pos(), core::chemical::ResidueConnection::icoor(), j, load_coords_and_torsions(), core::conformation::Residue::lower_connect(), core::conformation::Residue::mainchain_atoms(), protocols::rigid::n2c, core::pose::Pose::residue(), numeric::square(), core::chemical::AtomICoor::theta(), and core::conformation::Residue::upper_connect().

void protocols::loops::loop_closure::ccd::get_overlap_pos	(	vector1< vector1< Vector > > const &	coords,
		vector1< vector1< Real > > const &	torsions,
		int const	cutpoint,
		int const	direction,
		Real const	bond_angle1,
		Real const	bond_length,
		Real const	bond_angle2,
		Matrix &	M
	)

References angles, ASSERT_ONLY, numeric::xyzMatrix< class >::col(), dihedral_radians(), distance(), dot(), length, radians(), numeric::conversions::radians(), numeric::rotation_matrix_radians(), size(), basic::subtract_radian_angles(), and subtract_radian_angles().

Referenced by ccd_moves(), fast_ccd_loop_closure(), and get_deviation().

void protocols::loops::loop_closure::ccd::get_torsion_axis	(	vector1< vector1< Vector > > const &	coords,
		int const	seqpos,
		int const	torsion,
		Vector &	axis_atom,
		Vector &	axis_vector
	)

References index_pair_in_range(), and size().

Referenced by calculate_ccd_angle(), and refold_loop_torsion().

void protocols::loops::loop_closure::ccd::index_pair_in_range	(	int &	pos,
		int &	atom,
		int const	nbb
	)

Referenced by check_torsions(), get_torsion_axis(), and refold_loop_torsion().

void protocols::loops::loop_closure::ccd::load_coords_and_torsions	(	pose::Pose const &	pose,
		vector1< vector1< Vector > > &	coords,
		vector1< vector1< Real > > &	torsions
	)

copy mainchain atoms xyz and torsions from pose to coords and torsions

References core::conformation::Residue::atom(), j, nres, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and protocols::kinmatch::xyz().

Referenced by ccd_moves(), fast_ccd_loop_closure(), and get_deviation().

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

)

void protocols::loops::loop_closure::ccd::refold_loop_torsion	(	Real const	alpha,
		int const	pos,
		int const	torsion,
		int const	dir,
		int const	cutpoint,
		vector1< vector1< Vector > > &	coords,
		Matrix &	M
	)

References numeric::xyzMatrix< class >::col(), get_torsion_axis(), index_pair_in_range(), j, numeric::conversions::radians(), numeric::rotation_matrix_degrees(), and size().

Referenced by ccd_moves(), and fast_ccd_loop_closure().

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"

)

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

(

"closure_loop_vdw"

)

Variable Documentation

const Real protocols::loops::loop_closure::ccd::REALLY_BAD_SCORE(1000000000.0)

(

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().

numeric::random::RandomGenerator protocols::loops::loop_closure::ccd::RG(9781212)

static

Referenced by protocols::loops::loop_closure::ccd::LoopClosure::do_frag_cycles().

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().

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

Referenced by ccd_moves(), check_torsions(), and fast_ccd_loop_closure().

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

static

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

static

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

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().

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

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().