Rosetta Protocols  2014.35
Classes | Typedefs | Enumerations | Functions | Variables
protocols::rbsegment_relax Namespace Reference

Classes

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

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

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...
 
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::Sizesetup_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)
 res mapping to rbsegments More...
 

Variables

basic::Tracer tr ("protocols.rbsegment_relax.RBSegment.AutoRBRelaxMover")
 
static
numeric::random::RandomGenerator 
rbseg_RG (18633)
 
static basic::Tracer TR ("FragInsertAndAlignMover")
 
static basic::Tracer TR ("protocols.rbsegment_relax.IdealizeHelices")
 
static
numeric::random::RandomGenerator 
RG (8411111)
 
static basic::Tracer TR ("protocols.cryst.cryst_movers")
 
static basic::Tracer TR ("protocols.rbsegment_relax.OptimizeThreading")
 
basic::Tracer TR_seg ("RBSegment")
 
static
numeric::random::RandomGenerator 
RG (431112)
 
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")
 

Typedef Documentation

Enumeration Type Documentation

Enumeration of RB types.

Enumerator
RB_HELIX 
RB_SHEET 
RB_DEFAULT 

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 
)
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 
)
void protocols::rbsegment_relax::remap_rb_segments ( utility::vector1< RBSegment > const &  rbsegs,
utility::vector1< RBSegment > &  rbsegs_remap,
core::id::SequenceMapping const &  resmap 
)
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 
)
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 
)
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::scoring::constraints::ConstraintSet::add_constraint(), core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), core::conformation::Residue::is_protein(), length, nres, 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< 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::scoring::constraints::ConstraintSet::add_constraint(), core::conformation::Residue::atom_index(), core::pose::Pose::constraint_set(), core::conformation::Residue::is_protein(), length, 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_disconnected ( core::pose::Pose pose)
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 
)
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 
)
void protocols::rbsegment_relax::setup_star_topology ( core::pose::Pose pose)
core::Real protocols::rbsegment_relax::square ( core::Real  X)
inline
void protocols::rbsegment_relax::Tokenize ( const std::string str,
utility::vector1< std::string > &  tokens,
const std::string delimiters = " " 
)

Helper function tokenizes a str.

Referenced by read_RBSegment_file().

Variable Documentation

numeric::random::RandomGenerator protocols::rbsegment_relax::rbseg_RG(18632)
static
numeric::random::RandomGenerator protocols::rbsegment_relax::rbseg_RG(18633)
static
numeric::random::RandomGenerator protocols::rbsegment_relax::rbseg_RG(186331)
static
numeric::random::RandomGenerator protocols::rbsegment_relax::RG(431112)
static
numeric::random::RandomGenerator protocols::rbsegment_relax::RG(8411111)
static
basic::Tracer protocols::rbsegment_relax::TR("protocols::moves::RBSegmentMover")
static
basic::Tracer protocols::rbsegment_relax::TR("protocols.cryst.cryst_movers")
static
basic::Tracer protocols::rbsegment_relax::TR("FragInsertAndAlignMover")
static
basic::Tracer protocols::rbsegment_relax::TR("protocols::moves::RBSegmentMover")
static
basic::Tracer protocols::rbsegment_relax::TR("protocols.rbsegment_relax.OptimizeThreading")
static
basic::Tracer protocols::rbsegment_relax::tr("protocols.rbsegment_relax.RBSegment.AutoRBRelaxMover")
basic::Tracer protocols::rbsegment_relax::TR("protocols.rbsegment_relax.IdealizeHelices")
static
basic::Tracer protocols::rbsegment_relax::TR_seg("RBSegment")
basic::Tracer protocols::rbsegment_relax::TS("protocols.moves.RBSegmentRelax")