protocols::rbsegment_relax Namespace Reference

Classes
class	CCDMoveWrapper
class	AutoRBMover
class	ConfChangeMover
class	ConfChangeMoverCreator
class	FragInsertAndAlignMover
	Performs a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply'. More...
class	IdealizeHelicesMover
class	IdealizeHelicesMoverCreator
class	MakeStarTopologyMover
class	MakeStarTopologyMoverCreator
class	OptimizeThreadingMover
class	OptimizeThreadingMoverCreator
class	RBResidueRange
	RB residue range. More...
class	RBSegment
	Rigid-body segments in a protein. More...
class	RB_lt
class	RBSegmentMover
	Performs a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply'. More...
class	HelicalGaussianMover
class	SequenceShiftMover
class	GaussianRBSegmentMover
class	StrandTwistingMover
class	RBSegmentRelax

Typedefs
using	CCDMoveWrapperOP = utility::pointer::shared_ptr< CCDMoveWrapper >
typedef utility::pointer::shared_ptr< ConfChangeMover >	ConfChangeMoverOP
typedef utility::pointer::shared_ptr< ConfChangeMover const >	ConfChangeMoverCOP
typedef utility::pointer::shared_ptr< FragInsertAndAlignMover >	FragInsertAndAlignMoverOP
typedef utility::pointer::shared_ptr< RBSegmentMover >	RBSegmentMoverOP
typedef utility::pointer::shared_ptr< RBSegment >	RBSegmentOP
typedef utility::vector1< RBSegment >	CompositeSegment
typedef utility::vector1< RBSegment >::iterator	RBIt
typedef utility::vector1< RBSegment >::const_iterator	RBConsIt

Enumerations
enum	RBSegmentType { RB_HELIX =1 , RB_SHEET , RB_DEFAULT }
	Enumeration of RB types. More...

Functions
static basic::Tracer	tr ("protocols.rbsegment_relax.RBSegment.AutoRBRelaxMover")
static basic::Tracer	TR ("protocols.rbsegment_relax.ConfChangeMover")
static basic::Tracer	TR ("FragInsertAndAlignMover")
static basic::Tracer	TR ("protocols.rbsegment_relax.IdealizeHelices")
static basic::Tracer	TR ("protocols.cryst.cryst_movers")
static basic::Tracer	TR ("protocols.rbsegment_relax.OptimizeThreading")
static basic::Tracer	TR_seg ("RBSegment")
core::Real	square (core::Real X)
	helper function More...
void	Tokenize (const std::string &str, utility::vector1< std::string > &tokens, const std::string &delimiters=" ")
	Helper function tokenizes a str. More...
void	read_RBSegment_file (utility::vector1< RBSegment > &rbsegs, protocols::loops::Loops &loops, std::string filename, bool autoGenerateLoops, int nres, utility::vector1< core::Size > cutpoints)
	Parses an RB segment file into a vector of RBsegments. More...
void	select_RBsegments (utility::vector1< RBSegment > const &rbsegs_in, protocols::loops::Loops const &loops_in, utility::vector1< RBSegment > &rbsegs_selected, protocols::loops::Loops &loops_selected)
	Select a single RB segment to perturb + attached loops. More...
static basic::Tracer	TR ("protocols::moves::RBSegmentMover")
static basic::Tracer	TS ("protocols.moves.RBSegmentRelax")
static basic::Tracer	TR ("protocols::moves::RBSegmentMover")
void	set_rb_constraints (core::pose::Pose &pose, core::pose::Pose const &cst_pose, utility::vector1< protocols::rbsegment_relax::RBSegment > const &rbsegs, core::id::SequenceMapping const &resmap, core::Real cst_width, core::Real cst_stdev, core::Size cst_seqwidth)
	set up constraints from RB segs currently uses bounded constraints on each CA ... make CST type flag-selectable???? More...
void	set_constraints (core::pose::Pose &pose, core::pose::Pose const &cst_pose, core::Real cst_width, core::Real cst_stdev, core::Size cst_seqwidth)
	set up constraints on complete pose (not just RB segments) currently uses bounded constraints ... make CST type flag-selectable???? More...
utility::vector1< core::Size >	setup_pose_rbsegs_keep_loops (core::pose::Pose &pose, utility::vector1< protocols::rbsegment_relax::RBSegment > const &rbsegs, loops::Loops const &loops, core::kinematics::MoveMapOP mm)
	Helper function to set up a pose; unlike alt version keep loops (use cutpoint variants) unlike version in loops_main, this uses RBSegment structure to build multi-level topology returns jump residues. More...
void	setup_star_topology (core::pose::Pose &pose)
	setup star-topology fold tree More...
void	setup_disconnected (core::pose::Pose &pose)
	build a pose where every residue is connected by jumps to vrt More...
void	setup_pose_from_rbsegs (utility::vector1< protocols::rbsegment_relax::RBSegment > const &rbsegs, core::pose::Pose const &pose_in, core::pose::Pose &pose_out, core::id::SequenceMapping &resmap, core::kinematics::MoveMap &mm, bool fix_ligand)
	Helper function to set up a loop-removed pose. More...
void	restore_pose_from_rbsegs (utility::vector1< protocols::rbsegment_relax::RBSegment > const &rbsegs, core::pose::Pose const &pose_in, core::pose::Pose &pose_out)
	Helper function to restore a fully-connected pose. More...
void	guess_rbsegs_from_pose (core::pose::Pose const &pose, utility::vector1< RBSegment > &rigid_segs, utility::vector1< RBSegment > &rb_chunks, protocols::loops::Loops &loops)
	use DSSP and simple rules to guess the asignment of rigid-body segments More...
void	remap_rb_segments (utility::vector1< RBSegment > const &rbsegs, utility::vector1< RBSegment > &rbsegs_remap, core::id::SequenceMapping const &resmap)
	@apply res mapping to rbsegments More...

Typedef Documentation

CCDMoveWrapperOP

using protocols::rbsegment_relax::CCDMoveWrapperOP = typedef utility::pointer::shared_ptr<CCDMoveWrapper>

CompositeSegment

typedef utility::vector1< RBSegment > protocols::rbsegment_relax::CompositeSegment

ConfChangeMoverCOP

typedef utility::pointer::shared_ptr<ConfChangeMover const> protocols::rbsegment_relax::ConfChangeMoverCOP

ConfChangeMoverOP

typedef utility::pointer::shared_ptr<ConfChangeMover> protocols::rbsegment_relax::ConfChangeMoverOP

FragInsertAndAlignMoverOP

typedef utility::pointer::shared_ptr< FragInsertAndAlignMover > protocols::rbsegment_relax::FragInsertAndAlignMoverOP

RBConsIt

typedef utility::vector1< RBSegment >::const_iterator protocols::rbsegment_relax::RBConsIt

RBIt

typedef utility::vector1< RBSegment >::iterator protocols::rbsegment_relax::RBIt

RBSegmentMoverOP

typedef utility::pointer::shared_ptr< RBSegmentMover > protocols::rbsegment_relax::RBSegmentMoverOP

RBSegmentOP

typedef utility::pointer::shared_ptr< RBSegment > protocols::rbsegment_relax::RBSegmentOP

Enumeration Type Documentation

RBSegmentType

enum protocols::rbsegment_relax::RBSegmentType

Enumeration of RB types.

Enumerator
RB_HELIX
RB_SHEET
RB_DEFAULT

Function Documentation

guess_rbsegs_from_pose()

void protocols::rbsegment_relax::guess_rbsegs_from_pose	(	core::pose::Pose const &	pose,
		utility::vector1< RBSegment > &	rigid_segs,
		utility::vector1< RBSegment > &	rb_chunks,
		protocols::loops::Loops &	loops
	)

use DSSP and simple rules to guess the asignment of rigid-body segments

References core::conformation::Residue::aa(), core::chemical::aa_pro, core::conformation::Residue::atom(), protocols::loops::Loops::auto_choose_cutpoints(), protocols::loops::Loops::clear(), core::kinematics::FoldTree::cutpoints(), core::scoring::dssp::Dssp::dssp_reduced(), core::sequence::end, protocols::loops::Loops::end(), core::pose::Pose::fold_tree(), core::chemical::ResidueType::is_lower_terminus(), core::conformation::Residue::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::conformation::Residue::is_upper_terminus(), protocols::mean_field::min(), protocols::loops::Loops::push_back(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::loops::Loops::size(), protocols::loops::start, protocols::loops::stop, TR(), protocols::loops::Loops::v_begin(), protocols::loops::Loops::v_end(), and core::conformation::Atom::xyz().

Referenced by setup_star_topology(), protocols::rbsegment_relax::AutoRBMover::setup_topology(), and protocols::rbsegment_relax::ConfChangeMover::stage1_pose_setup().

read_RBSegment_file()

void protocols::rbsegment_relax::read_RBSegment_file	(	utility::vector1< RBSegment > &	rbsegs,
		protocols::loops::Loops &	loops,
		std::string	filename,
		bool	autoGenerateLoops,
		int	nres,
		utility::vector1< core::Size >	cutpoints
	)

Parses an RB segment file into a vector of RBsegments.

References protocols::loops::Loops::clear(), protocols::abinitio::filename(), protocols::antibody::l1, protocols::antibody::l2, protocols::loops::Loops::push_back(), protocols::rbsegment_relax::RBSegment::set_movement(), protocols::loops::Loops::size(), protocols::loops::skip_rate, protocols::loops::start, protocols::loops::stop, Tokenize(), TR_seg(), protocols::loops::Loops::v_begin(), and protocols::loops::Loops::v_end().

Referenced by protocols::RBSegmentRelaxImpl::apply(), and protocols::rbsegment_relax::ConfChangeMover::stage1_pose_setup().

remap_rb_segments()

void protocols::rbsegment_relax::remap_rb_segments	(	utility::vector1< RBSegment > const &	rbsegs,
		utility::vector1< RBSegment > &	rbsegs_remap,
		core::id::SequenceMapping const &	resmap
	)

@apply res mapping to rbsegments

References protocols::rbsegment_relax::RBSegment::remap().

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply().

restore_pose_from_rbsegs()

void protocols::rbsegment_relax::restore_pose_from_rbsegs	(	utility::vector1< protocols::rbsegment_relax::RBSegment > const &	rbsegs,
		core::pose::Pose const &	pose_in,
		core::pose::Pose &	pose_out
	)

Helper function to restore a fully-connected pose.

restore loops from pose

References core::pose::addVirtualResAsRoot(), core::pose::Pose::copy_segment(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::reorder(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), and TR().

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply().

select_RBsegments()

void protocols::rbsegment_relax::select_RBsegments	(	utility::vector1< RBSegment > const &	rbsegs_in,
		protocols::loops::Loops const &	loops_in,
		utility::vector1< RBSegment > &	rbsegs_selected,
		protocols::loops::Loops &	loops_selected
	)

Select a single RB segment to perturb + attached loops.

References protocols::loops::Loops::clear(), protocols::loops::Loops::end(), protocols::loops::Loops::push_back(), core::scoring::rg, and protocols::loops::Loops::size().

set_constraints()

void protocols::rbsegment_relax::set_constraints	(	core::pose::Pose &	pose,
		core::pose::Pose const &	cst_pose,
		core::Real	cst_width,
		core::Real	cst_stdev,
		core::Size	cst_seqwidth
	)

set up constraints on complete pose (not just RB segments) currently uses bounded constraints ... make CST type flag-selectable????

set up constraints accounting for missing density in start pose

References core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), core::conformation::Residue::is_protein(), protocols::mean_field::max(), protocols::mean_field::min(), core::pose::Pose::residue(), core::pose::Pose::size(), TR(), and core::conformation::Residue::xyz().

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply().

set_rb_constraints()

void protocols::rbsegment_relax::set_rb_constraints	(	core::pose::Pose &	pose,
		core::pose::Pose const &	cst_pose,
		utility::vector1< protocols::rbsegment_relax::RBSegment > const &	rbsegs,
		core::id::SequenceMapping const &	resmap,
		core::Real	cst_width,
		core::Real	cst_stdev,
		core::Size	cst_seqwidth
	)

set up constraints from RB segs currently uses bounded constraints on each CA ... make CST type flag-selectable????

set up constraints over RB segments only; allow ambiguity in sequence threading

References core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), core::conformation::Residue::is_protein(), protocols::mean_field::max(), protocols::mean_field::min(), core::pose::Pose::residue(), core::pose::Pose::size(), TR(), and core::conformation::Residue::xyz().

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply().

setup_disconnected()

void protocols::rbsegment_relax::setup_disconnected

(

core::pose::Pose &

pose

)

build a pose where every residue is connected by jumps to vrt

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::pose::add_variant_type_to_pose_residue(), core::chemical::element::B, core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::pose::Pose::fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::natoms(), core::kinematics::FoldTree::nres(), core::pose::Pose::pdb_info(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::pose::symmetry::set_asymm_unit_fold_tree(), TR(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

Referenced by protocols::rbsegment_relax::MakeStarTopologyMover::apply().

setup_pose_from_rbsegs()

void protocols::rbsegment_relax::setup_pose_from_rbsegs	(	utility::vector1< protocols::rbsegment_relax::RBSegment > const &	rbsegs,
		core::pose::Pose const &	pose_in,
		core::pose::Pose &	pose_out,
		core::id::SequenceMapping &	resmap,
		core::kinematics::MoveMap &	mm,
		bool	fix_ligand
	)

Helper function to set up a loop-removed pose.

remove loops from pose

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::kinematics::FoldTree::add_edge(), core::pose::addVirtualResAsRoot(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clear(), core::kinematics::FoldTree::end(), core::pose::Pose::fold_tree(), core::conformation::Residue::is_protein(), core::kinematics::Edge::PEPTIDE, core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::id::SequenceMapping::resize(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_jump(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), and TR().

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply().

setup_pose_rbsegs_keep_loops()

utility::vector1< core::Size > protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops	(	core::pose::Pose &	pose,
		utility::vector1< protocols::rbsegment_relax::RBSegment > const &	rbsegs,
		loops::Loops const &	loops,
		core::kinematics::MoveMapOP	mm
	)

Helper function to set up a pose; unlike alt version keep loops (use cutpoint variants) unlike version in loops_main, this uses RBSegment structure to build multi-level topology returns jump residues.

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::pose::add_variant_type_to_pose_residue(), core::chemical::element::B, core::kinematics::FoldTree::clear(), core::pose::Pose::conformation(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::kinematics::FoldTree::cutpoints(), core::pose::Pose::fold_tree(), core::conformation::symmetry::get_asymm_unit_fold_tree(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_lower_terminus(), core::conformation::Residue::is_upper_terminus(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::natoms(), core::kinematics::FoldTree::nres(), core::pose::Pose::pdb_info(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::pose::symmetry::set_asymm_unit_fold_tree(), TR(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

Referenced by setup_star_topology(), protocols::rbsegment_relax::AutoRBMover::setup_topology(), and protocols::rbsegment_relax::ConfChangeMover::stage1_pose_setup().

setup_star_topology()

void protocols::rbsegment_relax::setup_star_topology

(

core::pose::Pose &

pose

)

setup star-topology fold tree

References core::pose::symmetry::extract_asymmetric_unit(), guess_rbsegs_from_pose(), and setup_pose_rbsegs_keep_loops().

Referenced by protocols::rbsegment_relax::MakeStarTopologyMover::apply().

square()

core::Real protocols::rbsegment_relax::square ( core::Real  X )

inline

helper function

References protocols::comparative_modeling::features::X.

Tokenize()

void protocols::rbsegment_relax::Tokenize	(	const std::string &	str,
		utility::vector1< std::string > &	tokens,
		const std::string &	delimiters = " "
	)

Helper function tokenizes a str.

References protocols::kinmatch::str().

Referenced by read_RBSegment_file().

TR() [1/7]

static basic::Tracer protocols::rbsegment_relax::TR ( "FragInsertAndAlignMover"  )

static

TR() [2/7]

static basic::Tracer protocols::rbsegment_relax::TR ( "protocols.cryst.cryst_movers"  )

static

TR() [3/7]

static basic::Tracer protocols::rbsegment_relax::TR ( "protocols.rbsegment_relax.ConfChangeMover"  )

static

Referenced by protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts(), protocols::rbsegment_relax::ConfChangeMover::add_dihedral_csts_to_rb(), protocols::rbsegment_relax::ConfChangeMover::apply(), protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::rbsegment_relax::OptimizeThreadingMover::apply(), protocols::rbsegment_relax::HelicalGaussianMover::apply(), protocols::rbsegment_relax::StrandTwistingMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::rbsegment_relax::ConfChangeMover::get_additional_output(), protocols::rbsegment_relax::HelicalGaussianMover::getCoordinateTransformation(), protocols::rbsegment_relax::StrandTwistingMover::getCoordinateTransformation(), guess_rbsegs_from_pose(), protocols::rbsegment_relax::FragInsertAndAlignMover::initialize_rb_fragments(), protocols::rbsegment_relax::ConfChangeMover::parse_my_tag(), protocols::rbsegment_relax::MakeStarTopologyMover::parse_my_tag(), restore_pose_from_rbsegs(), set_constraints(), set_rb_constraints(), setup_disconnected(), setup_pose_from_rbsegs(), setup_pose_rbsegs_keep_loops(), protocols::rbsegment_relax::ConfChangeMover::stage1(), protocols::rbsegment_relax::ConfChangeMover::stage1_pose_setup(), and protocols::rbsegment_relax::ConfChangeMover::stage2().

TR() [4/7]

static basic::Tracer protocols::rbsegment_relax::TR ( "protocols.rbsegment_relax.IdealizeHelices"  )

static

TR() [5/7]

static basic::Tracer protocols::rbsegment_relax::TR ( "protocols.rbsegment_relax.OptimizeThreading"  )

static

tr()

static basic::Tracer protocols::rbsegment_relax::tr ( "protocols.rbsegment_relax.RBSegment.AutoRBRelaxMover"  )

static

Referenced by protocols::rbsegment_relax::AutoRBMover::apply(), and protocols::rbsegment_relax::AutoRBMover::grow_flexible().

TR() [6/7]

static basic::Tracer protocols::rbsegment_relax::TR ( "protocols::moves::RBSegmentMover"  )

static

TR() [7/7]

static basic::Tracer protocols::rbsegment_relax::TR ( "protocols::moves::RBSegmentMover"  )

static

TR_seg()

static basic::Tracer protocols::rbsegment_relax::TR_seg ( "RBSegment"  )

static

Referenced by protocols::rbsegment_relax::RBSegment::RBSegment(), read_RBSegment_file(), protocols::rbsegment_relax::RBSegment::remap(), and protocols::rbsegment_relax::RBSegment::set_movement().

TS()

static basic::Tracer protocols::rbsegment_relax::TS ( "protocols.moves.RBSegmentRelax"  )

static

Referenced by protocols::rbsegment_relax::RBSegmentRelax::apply().