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core::fragment Namespace Reference

Namespaces

 picking_old
 

Classes

class  BaseCacheUnit
 
class  BBTorsionAndAnglesSRFD
 
class  BBTorsionSRFD
 
class  ConstantLengthFragSet
 A set of fragments that contains fragments of a constant length read in from a fragment file. More...
 
class  ConstantLengthFragSetIterator_
 
class  FragCache
 
class  MapCacheUnit
 
class  VectorCacheUnit
 
class  CacheWrapper
 
class  FragStore
 
class  FragData
 
class  AnnotatedFragData
 FragData that contains additional information. More...
 
class  FragID
 
class  FragID_Iterator
 
class  FragFactory
 
class  FragmentIO
 
class  FragmentRmsd
 
class  FragSet
 The FragSet: (Interface Definition – Virtual BaseClass ) More...
 
class  FragSetCollection
 
class  Frame
 Frame couples a list of FragData-instances to a certain alignment frame, i.e., position in sequence space A frame may be continous, i.e., its fragment data will be applied to all residues between start() and end() or ( in a specialized version inheriting this interface) may contain a loose list of sequence positions. More...
 
class  FrameIterator
 
class  FrameIteratorWorker_
 
class  FrameList
 
class  FrameListIterator_
 
class  IndependentBBTorsionSRFD
 A version of BBTorsionSRFD that considers each torsion independently during is_applicable() and apply() calls when passed a MoveMap (vs the all-torsions-must-be-moveable-or-nothing-is behavior in the original BBTorsionSRFD). More...
 
class  NonContinuousFrame
 JumpingFrame is a discontinuous frame i.e, the SRFDs stored in the FragData objects can be applied to residues anywhere a 5 7 9 Frame of a FragData containing three BBTorsionSRFDs would change torsions of 5 7 9 a 5 32 2 Frame of a FragData containing two BBTorsionSRFD and on JumpSRFD would change torsions of 5 and 32 and the RT of jump_nr 2 note that in the latter case the 2 is not coding for a residue number! More...
 
class  JumpingFrame
 JumpingFrame, so far there is nothing special about JumpingFrames. but I think we might want to have additionally information like the start and end residues that belong to a certain jump_nr.! okay: right now I require that the creator of a JumpingFrame sets start to the start-residue of the jump. More...
 
class  UpJumpSRFD
 
class  DownJumpSRFD
 
class  OrderedFragSet
 
class  OrderedFragSetIterator_
 
class  SecondaryStructure
 tiny helper class that knows the relative fractions of secondary structure L,H,E so far these fractions can be computed from a FragSet other input strategies are conceivable but not implemented, yet: eg. psipred files, a bunch of poses, More...
 
class  SecstructSRFD
 
class  SingleResidueFragData
 Base class for SRFD classes Instances of SRFD classes contain information on specific dofs in a single residue or a jump connected to a residue The classes' apply method will now how to implement the specified dofs in the give pose at the given residue position. More...
 
class  TorsionInfoSet
 

Typedefs

typedef
utility::pointer::owning_ptr
< BaseCacheUnit
BaseCacheUnitOP
 
typedef
utility::pointer::access_ptr
< BaseCacheUnit
BaseCacheUnitAP
 
typedef
utility::pointer::owning_ptr
< BBTorsionSRFD
BBTorsionSRFDOP
 
typedef
utility::pointer::owning_ptr
< BBTorsionSRFD const > 
BBTorsionSRFDCOP
 
typedef
utility::pointer::owning_ptr
< ConstantLengthFragSet
ConstantLengthFragSetOP
 
typedef
utility::pointer::owning_ptr
< ConstantLengthFragSet const > 
ConstantLengthFragSetCOP
 
typedef
utility::pointer::owning_ptr
< FragData
FragDataOP
 
typedef
utility::pointer::owning_ptr
< FragData const > 
FragDataCOP
 
typedef utility::vector1
< FragDataOP
FragDataList
 
typedef
utility::pointer::owning_ptr
< AnnotatedFragData
AnnotatedFragDataOP
 
typedef
utility::pointer::owning_ptr
< AnnotatedFragData const > 
AnnotatedFragDataCOP
 
typedef utility::vector1< SizePositionList
 
typedef utility::vector1< FragIDFragID_List
 
typedef
utility::pointer::owning_ptr
< FragmentRmsd
FragmentRmsdOP
 
typedef
utility::pointer::owning_ptr
< FragmentRmsd const > 
FragmentRmsdCOP
 
typedef
utility::pointer::owning_ptr
< FragSet
FragSetOP
 
typedef
utility::pointer::owning_ptr
< FragSet const > 
FragSetCOP
 
typedef std::pair< Size, SizeRange
 
typedef utility::vector1< SizeInsertMap
 
typedef utility::vector1< SizeInsertSize
 
typedef
utility::pointer::owning_ptr
< FragSetCollection
FragSetCollectionOP
 
typedef
utility::pointer::owning_ptr
< FragSetCollection const > 
FragSetCollectionCOP
 
typedef
utility::pointer::owning_ptr
< Frame
FrameOP
 
typedef
utility::pointer::owning_ptr
< Frame const > 
FrameCOP
 
typedef
utility::pointer::owning_ptr
< FrameIteratorWorker_
FrameIteratorWorker_OP
 
typedef
utility::pointer::access_ptr
< IndependentBBTorsionSRFD
IndependentBBTorsionSRFD_AP
 access pointer for IndependentBBTorsionSRFD More...
 
typedef
utility::pointer::access_ptr
< IndependentBBTorsionSRFD
const > 
IndependentBBTorsionSRFD_CAP
 const access pointer for IndependentBBTorsionSRFD More...
 
typedef
utility::pointer::owning_ptr
< IndependentBBTorsionSRFD
IndependentBBTorsionSRFD_OP
 owning pointer for IndependentBBTorsionSRFD More...
 
typedef
utility::pointer::owning_ptr
< IndependentBBTorsionSRFD
const > 
IndependentBBTorsionSRFD_COP
 const owning pointer for IndependentBBTorsionSRFD More...
 
typedef
utility::pointer::owning_ptr
< JumpingFrame
JumpingFrameOP
 
typedef
utility::pointer::owning_ptr
< JumpingFrame const > 
JumpingFrameCOP
 
typedef
utility::pointer::owning_ptr
< UpJumpSRFD
UpJumpSRFDOP
 
typedef
utility::pointer::owning_ptr
< UpJumpSRFD const > 
UpJumpSRFDCOP
 
typedef
utility::pointer::owning_ptr
< DownJumpSRFD
DownJumpSRFDOP
 
typedef
utility::pointer::owning_ptr
< DownJumpSRFD const > 
DownJumpSRFDCOP
 
typedef
utility::pointer::owning_ptr
< OrderedFragSet
OrderedFragSetOP
 
typedef
utility::pointer::owning_ptr
< OrderedFragSet const > 
OrderedFragSetCOP
 
typedef
utility::pointer::owning_ptr
< SecondaryStructure
SecondaryStructureOP
 
typedef
utility::pointer::owning_ptr
< SecondaryStructure const > 
SecondaryStructureCOP
 
typedef
utility::pointer::owning_ptr
< SingleResidueFragData
SingleResidueFragDataOP
 
typedef
utility::pointer::owning_ptr
< SingleResidueFragData const > 
SingleResidueFragDataCOP
 
typedef std::pair
< id::TorsionType, Size
TorsionInfo
 
typedef utility::vector1
< TorsionInfo
TorsionInfoList
 
typedef
utility::pointer::owning_ptr
< TorsionInfoSet const > 
TorsionInfoSetCOP
 

Functions

static basic::Tracer tr ("core.fragment.BBTorsionAndAnglesSRFD")
 
static basic::Tracer tr ("core.fragment")
 
static basic::Tracer tr ("core.fragments.ConstantLengthFragSet")
 
void make_pose_from_sequence_ (std::string sequence, chemical::ResidueTypeSet residue_set, pose::Pose &pose)
 
std::ostream & operator<< (std::ostream &out, FragData const &fr)
 
static basic::Tracer tr ("core.io.fragments")
 
static basic::Tracer tr ("core.fragment")
 
std::ostream & operator<< (std::ostream &out, FragSet const &cfrags)
 
static basic::Tracer tr ("core.fragment")
 
void make_pose_from_sequence_ (std::string sequence, chemical::ResidueTypeSet const &residue_set, pose::Pose &pose)
 
std::ostream & operator<< (std::ostream &out, Frame const &frame)
 
static basic::Tracer tr ("core.fragment")
 
std::ostream & operator<< (std::ostream &out, FrameList const &frags)
 
static basic::Tracer tr ("core.fragment.JumpSRFD")
 
static basic::Tracer tr ("core.fragments")
 
std::ostream & operator<< (std::ostream &os, SecondaryStructure const &t)
 output operator More...
 
static basic::Tracer tr ("core.fragment")
 
std::ostream & operator<< (std::ostream &out, SingleResidueFragData const &srfd)
 
std::istream & operator>> (std::istream &in, SingleResidueFragData &srfd)
 
static basic::Tracer tr ("core.fragment")
 
static
numeric::random::RandomGenerator 
RG (125923489)
 
void retain_top (core::Size k, FragSetOP fragments)
 Removes all but the top <k> fragments from <fragments> More...
 
void steal_constant_length_frag_set_from_pose (pose::Pose const &pose_in, ConstantLengthFragSet &fragset)
 
void steal_frag_set_from_pose (pose::Pose const &pose_in, FragSet &fragset, core::fragment::FragDataOP frag_type)
 
void steal_frag_set_from_pose (pose::Pose const &pose_in, Size const begin, Size const end, FragSet &fragset, core::fragment::FragDataOP frag_type)
 
void steal_frag_set_from_pose (pose::Pose const &pose_in, FragSet &fragset, core::fragment::FragDataOP frag_type, std::set< core::Size > const &selected_residues)
 
void chop_fragments (core::fragment::FragSet &source, core::fragment::FragSet &dest)
 Function for chopping the X-sized fragments in source into fragments that go into N-sized fragments in dest. Sizes are encoded by the value of max_frag_length() in both source and dest. More...
 
void compute_per_residue_coverage (core::fragment::FragSet const &_frags, utility::vector1< core::Size > &nr_frags)
 
void flatten_list (FrameList &frames, FragID_List &frag_ids)
 
FragSetOP merge_frags (FragSet const &good_frags, FragSet const &filling, Size min_nr_frags, bool bRandom)
 
void apply_best_scoring_fragdata (pose::Pose &pose, Frame const &frame, scoring::ScoreFunction const &sfxn)
 goes through all frag_data in the frame and puts the best scoring one into the pose, i.e. quenches the frame More...
 
void dump_frames_as_pdb (pose::Pose const &pose, utility::vector1< FrameOP > const &frames, std::string const filename, core::Size start_frag=1)
 writes FragData in multimodel pdb format start_tag can be used to only write a subset of the contained frag data More...
 
bool fill_template_frames_from_pdb (pose::Pose const &pose, utility::vector1< FrameOP > const &template_frames, std::string const filename)
 filling a frameset from a multimodel pdb file More...
 
void read_std_frags_from_cmd (FragSetOP &fragset_large, FragSetOP &fragset_small)
 
void make_simple_fold_tree_from_jump_frame (Frame const &frame, Size total_residue, kinematics::FoldTree &new_fold_tree)
 given a JumpFrame with Up and DownJumpSRFDs as LAST SRFDs this will make a fold-tree compatible with the Frame... this is NOT GOOD for sampling, since it introduces cut-points outside of fragments later for sampling: one could probably write a routine that looks if it can move existing Jumps in Fold-tree to fit the FRAME ... if not it returns failure... More...
 
void fragment_set_slice (ConstantLengthFragSetOP &fragset, Size const &min_res, Size const &max_res)
 
void FindBoundaries (const core::kinematics::FoldTree &tree, core::Size pos, core::Size *left, core::Size *right)
 Finds the fold tree boundaries to the left and right of <pos>. More...
 
core::kinematics::Stub getxform (numeric::xyzVector< core::Real > m1, numeric::xyzVector< core::Real > m2, numeric::xyzVector< core::Real > m3, numeric::xyzVector< core::Real > f1, numeric::xyzVector< core::Real > f2, numeric::xyzVector< core::Real > f3)
 
void xform_pose (core::pose::Pose &pose, const core::kinematics::Stub &s, core::Size sres, core::Size eres)
 
void make_pose_from_frags (pose::Pose &pose, std::string sequence, utility::vector1< FragDataCOP > frags, bool chains)
 

Typedef Documentation

access pointer for IndependentBBTorsionSRFD

const access pointer for IndependentBBTorsionSRFD

const owning pointer for IndependentBBTorsionSRFD

owning pointer for IndependentBBTorsionSRFD

typedef std::pair< Size, Size > core::fragment::Range

Function Documentation

void core::fragment::apply_best_scoring_fragdata ( pose::Pose pose,
Frame const &  frame,
scoring::ScoreFunction const &  sfxn 
)

goes through all frag_data in the frame and puts the best scoring one into the pose, i.e. quenches the frame

References core::fragment::Frame::apply(), and core::fragment::Frame::nr_frags().

void core::fragment::chop_fragments ( core::fragment::FragSet source,
core::fragment::FragSet dest 
)
void core::fragment::compute_per_residue_coverage ( core::fragment::FragSet const &  _frags,
utility::vector1< core::Size > &  nr_frags 
)
void core::fragment::dump_frames_as_pdb ( pose::Pose const &  pose,
utility::vector1< FrameOP > const &  frames,
std::string const  filename,
Size const  start_frag 
)

writes FragData in multimodel pdb format start_tag can be used to only write a subset of the contained frag data

References core::io::pdb::dump_pdb_residue(), and core::pose::Pose::residue().

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::apply().

bool core::fragment::fill_template_frames_from_pdb ( pose::Pose const &  pose,
utility::vector1< FrameOP > const &  template_frames,
std::string const  filename 
)

filling a frameset from a multimodel pdb file

this is a little tricky: this should support functionality for both creating a frameset entirely from

the input pdb (i.e. with no prior information about frag data length or srfds ), but it should also

be possible to pass in non_empty frames such that the information in the pdb will generate FragData

objects that are compatible to the ones already in the passed in frames. hmpf

returns true if no error occured

References core::pose::Pose::copy_segment(), core::pose::Pose::pdb_info(), core::import_pose::pose_from_pdb(), and protocols::loops::start.

Referenced by protocols::enzdes::EnzdesFlexBBProtocol::recover_loops_from_file().

void core::fragment::FindBoundaries ( const core::kinematics::FoldTree tree,
core::Size  pos,
core::Size left,
core::Size right 
)

Finds the fold tree boundaries to the left and right of <pos>.

References core::kinematics::FoldTree::cutpoint(), core::kinematics::FoldTree::nres(), and core::kinematics::FoldTree::num_cutpoint().

Referenced by make_pose_from_frags().

void core::fragment::flatten_list ( FrameList &  frames,
FragID_List &  frag_ids 
)
void core::fragment::fragment_set_slice ( ConstantLengthFragSetOP &  fragset,
Size const &  min_res,
Size const &  max_res 
)
void core::fragment::make_pose_from_frags ( pose::Pose pose,
std::string  sequence,
utility::vector1< FragDataCOP >  frags,
bool  chains 
)
void core::fragment::make_pose_from_sequence_ ( std::string  sequence,
chemical::ResidueTypeSet  residue_set,
pose::Pose pose 
)
void core::fragment::make_pose_from_sequence_ ( std::string  sequence,
chemical::ResidueTypeSet const &  residue_set,
pose::Pose pose 
)
void core::fragment::make_simple_fold_tree_from_jump_frame ( Frame const &  frame,
Size  total_residue,
kinematics::FoldTree &  new_fold_tree 
)

given a JumpFrame with Up and DownJumpSRFDs as LAST SRFDs this will make a fold-tree compatible with the Frame... this is NOT GOOD for sampling, since it introduces cut-points outside of fragments later for sampling: one could probably write a routine that looks if it can move existing Jumps in Fold-tree to fit the FRAME ... if not it returns failure...

one little assumption: create frames always like this: contigues piece JUMP contig. piec JUMP contig. piece. then good candidates for cutpoints are the last contig.piece residue before a jump

References protocols::loops::cut_point, core::fragment::Frame::fragment(), core::fragment::Frame::length(), core::fragment::Frame::nr_frags(), core::fragment::Frame::seqpos(), and core::kinematics::FoldTree::tree_from_jumps_and_cuts().

FragSetOP core::fragment::merge_frags ( FragSet const &  good_frags,
FragSet const &  filling,
Size  min_nr_frags,
bool  bRandom 
)
std::ostream & core::fragment::operator<< ( std::ostream &  out,
FrameList const &  frags 
)
std::ostream& core::fragment::operator<< ( std::ostream &  out,
SingleResidueFragData const &  srfd 
)
inline
std::ostream& core::fragment::operator<< ( std::ostream &  os,
SecondaryStructure const &  t 
)
inline

output operator

References core::fragment::SecondaryStructure::show().

std::ostream& core::fragment::operator<< ( std::ostream &  out,
FragData const &  fr 
)
inline
std::ostream& core::fragment::operator<< ( std::ostream &  out,
FragSet const &  cfrags 
)
std::ostream& core::fragment::operator<< ( std::ostream &  out,
Frame const &  frame 
)
inline
std::istream& core::fragment::operator>> ( std::istream &  in,
SingleResidueFragData &  srfd 
)
inline
void core::fragment::read_std_frags_from_cmd ( FragSetOP &  fragset_large,
FragSetOP &  fragset_small 
)
void core::fragment::retain_top ( core::Size  k,
FragSetOP  fragments 
)

Removes all but the top <k> fragments from <fragments>

References core::fragment::Frame::add_fragment().

Referenced by protocols::nonlocal::PolicyFactory::get_policy().

static numeric::random::RandomGenerator core::fragment::RG ( 125923489  )
static

Referenced by merge_frags().

void core::fragment::steal_constant_length_frag_set_from_pose ( pose::Pose const &  pose_in,
ConstantLengthFragSet &  fragset 
)
void core::fragment::steal_frag_set_from_pose ( pose::Pose const &  pose_in,
FragSet &  fragset,
core::fragment::FragDataOP  frag_type 
)
void core::fragment::steal_frag_set_from_pose ( pose::Pose const &  pose_in,
Size const  begin,
Size const  end,
FragSet &  fragset,
core::fragment::FragDataOP  frag_type 
)
void core::fragment::steal_frag_set_from_pose ( pose::Pose const &  pose_in,
FragSet &  fragset,
core::fragment::FragDataOP  frag_type,
std::set< core::Size > const &  selected_residues 
)
static basic::Tracer core::fragment::tr ( "core.fragment"  )
static
static basic::Tracer core::fragment::tr ( "core.fragment.BBTorsionAndAnglesSRFD"  )
static
static basic::Tracer core::fragment::tr ( "core.fragment"  )
static
static basic::Tracer core::fragment::tr ( "core.fragment"  )
static
static basic::Tracer core::fragment::tr ( "core.fragment"  )
static
static basic::Tracer core::fragment::tr ( "core.fragments"  )
static
static basic::Tracer core::fragment::tr ( "core.fragment.JumpSRFD"  )
static
static basic::Tracer core::fragment::tr ( "core.io.fragments"  )
static
static basic::Tracer core::fragment::tr ( "core.fragment"  )
static
static basic::Tracer core::fragment::tr ( "core.fragments.ConstantLengthFragSet"  )
static
static basic::Tracer core::fragment::tr ( "core.fragment"  )
static
void core::fragment::xform_pose ( core::pose::Pose pose,
const core::kinematics::Stub s,
core::Size  sres,
core::Size  eres 
)