Classes
class	CCDMoveWrapper

class	AutoRBMover

class	FragInsertAndAlignMover
	Performs a rigid-body movement on a segment of a protein Derived classes must implement 'getCoordinateTransform' and 'apply'. More...

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
typedef utility::pointer::owning_ptr < CCDMoveWrapper >	CCDMoveWrapperOP

typedef utility::pointer::owning_ptr < FragInsertAndAlignMover >	FragInsertAndAlignMoverOP

typedef utility::pointer::owning_ptr < RBSegmentMover >	RBSegmentMoverOP

typedef utility::pointer::owning_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
basic::Tracer	tr ("protocols.rbsegment_relax.RBSegment.AutoRBRelaxMover")

static numeric::random::RandomGenerator	rbseg_RG (18633)

static basic::Tracer	TR ("FragInsertAndAlignMover")

basic::Tracer	TR_seg ("RBSegment")

static numeric::random::RandomGenerator	RG (431112)

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 numeric::random::RandomGenerator	rbseg_RG (18632)

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

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

static numeric::random::RandomGenerator	rbseg_RG (186331)

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

void	set_rb_constraints (core::pose::Pose &pose, core::pose::Pose const &cst_pose, utility::vector1< 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< 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_pose_from_rbsegs (utility::vector1< 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< 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)
	res mapping to rbsegments More...

Typedef Documentation

typedef utility::pointer::owning_ptr< CCDMoveWrapper > protocols::rbsegment_relax::CCDMoveWrapperOP

Definition at line 100 of file AutoRBRelaxMover.cc.

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

Definition at line 35 of file RBSegment.fwd.hh.

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

Definition at line 41 of file FragInsertAndAlignMover.hh.

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

Definition at line 37 of file RBSegment.fwd.hh.

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

Definition at line 36 of file RBSegment.fwd.hh.

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

Definition at line 30 of file RBSegment.fwd.hh.

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

Definition at line 33 of file RBSegment.fwd.hh.

Enumeration Type Documentation

enum protocols::rbsegment_relax::RBSegmentType

Enumeration of RB types.

Enumerator
RB_HELIX
RB_SHEET
RB_DEFAULT

Definition at line 35 of file RBSegment.hh.

Function Documentation

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

Definition at line 435 of file util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_pro, core::conformation::Residue::atom(), protocols::loops::Loops::auto_choose_cutpoints(), protocols::loops::Loops::clear(), core::scoring::dssp::Dssp::dssp_reduced(), core::sequence::end, protocols::loops::Loops::push_back(), core::pose::Pose::residue(), protocols::loops::Loops::size(), protocols::loops::start, core::pose::Pose::total_residue(), TR(), protocols::loops::Loops::v_begin(), and protocols::loops::Loops::v_end().

Referenced by protocols::rbsegment_relax::AutoRBMover::setup_topology().

static numeric::random::RandomGenerator protocols::rbsegment_relax::rbseg_RG ( 18632 )

static

static numeric::random::RandomGenerator protocols::rbsegment_relax::rbseg_RG ( 18633 )

static

Referenced by protocols::rbsegment_relax::HelicalGaussianMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::rbsegment_relax::GaussianRBSegmentMover::apply(), and protocols::rbsegment_relax::StrandTwistingMover::apply().

static numeric::random::RandomGenerator protocols::rbsegment_relax::rbseg_RG ( 186331 )

static

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.

Definition at line 100 of file RBSegment.cc.

References protocols::loops::Loops::clear(), protocols::antibody2::l1, protocols::antibody2::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().

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

res mapping to rbsegments

Definition at line 615 of file util.cc.

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

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

void protocols::rbsegment_relax::restore_pose_from_rbsegs	(	utility::vector1< 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

Definition at line 374 of file util.cc.

References core::pose::Pose::append_residue_by_jump(), core::pose::Pose::copy_segment(), core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), core::chemical::ChemicalManager::get_instance(), core::kinematics::FoldTree::reorder(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::Pose::total_residue(), and TR().

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

static numeric::random::RandomGenerator protocols::rbsegment_relax::RG ( 431112 )

static

Referenced by 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.

Definition at line 342 of file RBSegment.cc.

References protocols::loops::Loops::clear(), protocols::loops::Loops::push_back(), RG(), and protocols::loops::Loops::size().

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

Definition at line 124 of file util.cc.

References core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), TR(), and core::conformation::Residue::xyz().

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

void protocols::rbsegment_relax::set_rb_constraints	(	core::pose::Pose &	pose,
		core::pose::Pose const &	cst_pose,
		utility::vector1< 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

Definition at line 69 of file util.cc.

References core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), core::conformation::Residue::is_protein(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), TR(), and core::conformation::Residue::xyz().

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

void protocols::rbsegment_relax::setup_pose_from_rbsegs	(	utility::vector1< 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 and setup star-topology fold tree

Definition at line 252 of file util.cc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clear(), core::conformation::ResidueFactory::create_residue(), core::sequence::end, core::kinematics::FoldTree::end(), core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), core::chemical::ChemicalManager::get_instance(), core::conformation::Residue::is_protein(), core::kinematics::Edge::PEPTIDE, 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::total_residue(), and TR().

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

utility::vector1< core::Size > protocols::rbsegment_relax::setup_pose_rbsegs_keep_loops	(	core::pose::Pose &	pose,
		utility::vector1< 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.

Definition at line 174 of file util.cc.

References core::pose::add_variant_type_to_pose_residue(), protocols::loops::Loops::begin(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, protocols::loops::Loops::end(), core::pose::Pose::fold_tree(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_upper_terminus(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), TR(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

Referenced by protocols::rbsegment_relax::AutoRBMover::setup_topology().

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

inline

helper function

Definition at line 51 of file RBSegment.cc.

References core::scoring::rna::X.

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

Helper function tokenizes a str.

Definition at line 59 of file RBSegment.cc.

Referenced by read_RBSegment_file().

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

static

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

static

Referenced by protocols::rbsegment_relax::FragInsertAndAlignMover::apply(), protocols::rbsegment_relax::HelicalGaussianMover::apply(), protocols::rbsegment_relax::SequenceShiftMover::apply(), protocols::rbsegment_relax::StrandTwistingMover::apply(), protocols::rbsegment_relax::HelicalGaussianMover::getCoordinateTransformation(), protocols::rbsegment_relax::StrandTwistingMover::getCoordinateTransformation(), guess_rbsegs_from_pose(), protocols::rbsegment_relax::FragInsertAndAlignMover::initialize_rb_fragments(), restore_pose_from_rbsegs(), set_constraints(), set_rb_constraints(), setup_pose_from_rbsegs(), and setup_pose_rbsegs_keep_loops().

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

static

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

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

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

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

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

Classes

Typedefs

Enumerations

Functions

Typedef Documentation

Enumeration Type Documentation

Function Documentation