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Rosetta 3.5
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Rosetta 3.5
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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 |
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 utility::pointer::owning_ptr< AnnotatedFragData const > core::fragment::AnnotatedFragDataCOP |
Definition at line 41 of file FragData.fwd.hh.
Definition at line 38 of file FragData.fwd.hh.
Definition at line 44 of file BaseCacheUnit.hh.
Definition at line 42 of file BaseCacheUnit.hh.
| typedef utility::pointer::owning_ptr< BBTorsionSRFD const > core::fragment::BBTorsionSRFDCOP |
Definition at line 29 of file BBTorsionSRFD.fwd.hh.
Definition at line 27 of file BBTorsionSRFD.fwd.hh.
| typedef utility::pointer::owning_ptr< ConstantLengthFragSet const > core::fragment::ConstantLengthFragSetCOP |
Definition at line 30 of file ConstantLengthFragSet.fwd.hh.
| typedef utility::pointer::owning_ptr< ConstantLengthFragSet > core::fragment::ConstantLengthFragSetOP |
Definition at line 27 of file ConstantLengthFragSet.fwd.hh.
| typedef utility::pointer::owning_ptr< DownJumpSRFD const > core::fragment::DownJumpSRFDCOP |
Definition at line 36 of file JumpSRFD.fwd.hh.
Definition at line 33 of file JumpSRFD.fwd.hh.
| typedef utility::pointer::owning_ptr< FragData const > core::fragment::FragDataCOP |
Definition at line 34 of file FragData.fwd.hh.
Definition at line 36 of file FragData.fwd.hh.
Definition at line 31 of file FragData.fwd.hh.
| typedef utility::vector1< FragID > core::fragment::FragID_List |
Definition at line 25 of file FragID.fwd.hh.
Definition at line 23 of file FragmentRmsd.fwd.hh.
Definition at line 21 of file FragmentRmsd.fwd.hh.
| typedef utility::pointer::owning_ptr< FragSetCollection const > core::fragment::FragSetCollectionCOP |
Definition at line 30 of file FragSetCollection.fwd.hh.
Definition at line 27 of file FragSetCollection.fwd.hh.
| typedef utility::pointer::owning_ptr< FragSet const > core::fragment::FragSetCOP |
Definition at line 38 of file FragSet.fwd.hh.
Definition at line 35 of file FragSet.fwd.hh.
| typedef utility::pointer::owning_ptr< Frame const > core::fragment::FrameCOP |
Definition at line 33 of file Frame.fwd.hh.
Definition at line 25 of file FrameIteratorWorker_.fwd.hh.
Definition at line 30 of file Frame.fwd.hh.
| typedef utility::pointer::access_ptr< IndependentBBTorsionSRFD > core::fragment::IndependentBBTorsionSRFD_AP |
access pointer for IndependentBBTorsionSRFD
Definition at line 28 of file IndependentBBTorsionSRFD.fwd.hh.
| typedef utility::pointer::access_ptr< IndependentBBTorsionSRFD const > core::fragment::IndependentBBTorsionSRFD_CAP |
const access pointer for IndependentBBTorsionSRFD
Definition at line 36 of file IndependentBBTorsionSRFD.fwd.hh.
| typedef utility::pointer::owning_ptr< IndependentBBTorsionSRFD const > core::fragment::IndependentBBTorsionSRFD_COP |
const owning pointer for IndependentBBTorsionSRFD
Definition at line 44 of file IndependentBBTorsionSRFD.fwd.hh.
| typedef utility::pointer::owning_ptr< IndependentBBTorsionSRFD > core::fragment::IndependentBBTorsionSRFD_OP |
owning pointer for IndependentBBTorsionSRFD
Definition at line 40 of file IndependentBBTorsionSRFD.fwd.hh.
| typedef utility::vector1< Size > core::fragment::InsertMap |
Definition at line 44 of file FragSet.fwd.hh.
| typedef utility::vector1< Size > core::fragment::InsertSize |
Definition at line 45 of file FragSet.fwd.hh.
| typedef utility::pointer::owning_ptr< JumpingFrame const > core::fragment::JumpingFrameCOP |
Definition at line 34 of file JumpingFrame.fwd.hh.
Definition at line 31 of file JumpingFrame.fwd.hh.
| typedef utility::pointer::owning_ptr< OrderedFragSet const > core::fragment::OrderedFragSetCOP |
Definition at line 31 of file OrderedFragSet.fwd.hh.
Definition at line 28 of file OrderedFragSet.fwd.hh.
| typedef utility::vector1< Size > core::fragment::PositionList |
Definition at line 45 of file FragData.hh.
| typedef std::pair< Size, Size > core::fragment::Range |
Definition at line 40 of file FragSet.fwd.hh.
| typedef utility::pointer::owning_ptr< SecondaryStructure const > core::fragment::SecondaryStructureCOP |
Definition at line 31 of file SecondaryStructure.fwd.hh.
Definition at line 27 of file SecondaryStructure.fwd.hh.
| typedef utility::pointer::owning_ptr< SingleResidueFragData const > core::fragment::SingleResidueFragDataCOP |
Definition at line 30 of file SingleResidueFragData.fwd.hh.
| typedef utility::pointer::owning_ptr< SingleResidueFragData > core::fragment::SingleResidueFragDataOP |
Definition at line 27 of file SingleResidueFragData.fwd.hh.
| typedef std::pair< id::TorsionType, Size > core::fragment::TorsionInfo |
Definition at line 46 of file TorsionSRFD.hh.
Definition at line 48 of file TorsionSRFD.hh.
| typedef utility::pointer::owning_ptr< TorsionInfoSet const > core::fragment::TorsionInfoSetCOP |
Definition at line 50 of file TorsionSRFD.hh.
| typedef utility::pointer::owning_ptr< UpJumpSRFD const > core::fragment::UpJumpSRFDCOP |
Definition at line 31 of file JumpSRFD.fwd.hh.
Definition at line 28 of file JumpSRFD.fwd.hh.
| 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
Definition at line 273 of file util.cc.
References core::fragment::Frame::apply(), and core::fragment::Frame::nr_frags().
| void core::fragment::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.
Definition at line 175 of file util.cc.
References core::fragment::FragSet::add(), core::fragment::Frame::add_fragment(), core::fragment::FragSet::begin(), core::fragment::FragSet::end(), core::fragment::Frame::end(), core::fragment::Frame::fragment(), core::fragment::FragSet::max_frag_length(), core::fragment::FragSet::max_pos(), core::fragment::Frame::nr_frags(), and core::fragment::Frame::start().
Referenced by protocols::hybridization::HybridizeProtocol::check_and_create_fragments(), protocols::hybridization::FoldTreeHybridize::FoldTreeHybridize(), and protocols::loops::read_loop_fragments().
| void core::fragment::compute_per_residue_coverage | ( | core::fragment::FragSet const & | _frags, |
| utility::vector1< core::Size > & | nr_frags | ||
| ) |
Definition at line 200 of file util.cc.
References core::fragment::FragSet::begin(), core::fragment::FragSet::end(), and core::fragment::FragSet::max_pos().
Referenced by merge_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
Definition at line 311 of file util.cc.
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
Definition at line 360 of file util.cc.
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>.
Definition at line 549 of file util.cc.
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 | ||
| ) |
Definition at line 215 of file util.cc.
References core::fragment::FrameList::flat_size().
Referenced by merge_frags().
| core::kinematics::Stub core::fragment::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 | ||
| ) |
Definition at line 574 of file util.cc.
References core::kinematics::Stub::M, and core::kinematics::Stub::v.
Referenced by make_pose_from_frags().
| void core::fragment::make_pose_from_frags | ( | pose::Pose & | pose, |
| std::string | sequence, | ||
| utility::vector1< FragDataCOP > | frags, | ||
| bool | chains | ||
| ) |
Definition at line 601 of file util.cc.
References core::kinematics::FoldTree::check_fold_tree(), core::pose::Pose::clear(), core::pose::Pose::conformation(), FindBoundaries(), core::pose::Pose::fold_tree(), getxform(), core::conformation::idealize_position(), core::conformation::Conformation::insert_chain_ending(), core::pose::make_pose_from_sequence(), core::pose::Pose::residue(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::pose::Pose::total_residue(), xform_pose(), and core::conformation::Residue::xyz().
Referenced by protocols::frag_picker::FragmentPicker::nonlocal_pairs(), and protocols::frag_picker::FragmentCandidate::output_silent().
| void core::fragment::make_pose_from_sequence_ | ( | std::string | sequence, |
| chemical::ResidueTypeSet | residue_set, | ||
| pose::Pose & | pose | ||
| ) |
Definition at line 46 of file FragData.cc.
References core::chemical::aa_from_oneletter_code(), core::chemical::ResidueTypeSet::aa_map(), core::pose::Pose::clear(), and core::conformation::ResidueFactory::create_residue().
Referenced by core::fragment::Frame::fragment_as_pose().
| void core::fragment::make_pose_from_sequence_ | ( | std::string | sequence, |
| chemical::ResidueTypeSet const & | residue_set, | ||
| pose::Pose & | pose | ||
| ) |
Definition at line 55 of file Frame.cc.
References core::chemical::aa_from_oneletter_code(), core::chemical::ResidueTypeSet::aa_map(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::clear(), and core::conformation::ResidueFactory::create_residue().
| 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
Definition at line 486 of file util.cc.
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 | ||
| ) |
Definition at line 224 of file util.cc.
References core::fragment::FragSet::clone(), compute_per_residue_coverage(), flatten_list(), core::fragment::FragSet::frames(), core::fragment::FragSet::max_pos(), RG(), and tr().
Referenced by protocols::abinitio::AbrelaxApplication::setup_fragments().
| std::ostream & core::fragment::operator<< | ( | std::ostream & | out, |
| FrameList const & | frags | ||
| ) |
Definition at line 69 of file FrameList.cc.
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Definition at line 161 of file SingleResidueFragData.hh.
References core::fragment::SingleResidueFragData::show().
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output operator
Definition at line 185 of file SecondaryStructure.hh.
References core::fragment::SecondaryStructure::show().
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Definition at line 235 of file FragData.hh.
References core::fragment::FragData::show().
| std::ostream& core::fragment::operator<< | ( | std::ostream & | out, |
| FragSet const & | cfrags | ||
| ) |
Definition at line 248 of file FragSet.cc.
References core::fragment::FragSet::begin(), and core::fragment::FragSet::end().
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Definition at line 323 of file Frame.hh.
References core::fragment::Frame::show().
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Definition at line 166 of file SingleResidueFragData.hh.
References core::fragment::SingleResidueFragData::read_data().
| void core::fragment::read_std_frags_from_cmd | ( | FragSetOP & | fragset_large, |
| FragSetOP & | fragset_small | ||
| ) |
Definition at line 411 of file util.cc.
References core::import_pose::pose_from_pdb(), core::fragment::FragmentIO::read_data(), core::pose::set_ss_from_phipsi(), steal_frag_set_from_pose(), and tr().
Referenced by protocols::topology_broker::add_cmdline_claims().
| void core::fragment::retain_top | ( | core::Size | k, |
| FragSetOP | fragments | ||
| ) |
Removes all but the top <k> fragments from <fragments>
Definition at line 81 of file util.cc.
References core::fragment::Frame::add_fragment().
Referenced by protocols::nonlocal::PolicyFactory::get_policy().
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Referenced by merge_frags().
| void core::fragment::steal_constant_length_frag_set_from_pose | ( | pose::Pose const & | pose_in, |
| ConstantLengthFragSet & | fragset | ||
| ) |
Definition at line 97 of file util.cc.
References core::fragment::FragSet::add(), core::kinematics::FoldTree::cutpoint(), core::pose::Pose::fold_tree(), core::fragment::FragSet::max_frag_length(), core::kinematics::FoldTree::num_cutpoint(), core::pose::set_ss_from_phipsi(), and core::pose::Pose::total_residue().
Referenced by protocols::abinitio::IterativeBase::gen_resample_fragments().
| void core::fragment::steal_frag_set_from_pose | ( | pose::Pose const & | pose_in, |
| FragSet & | fragset, | ||
| core::fragment::FragDataOP | frag_type | ||
| ) |
Definition at line 126 of file util.cc.
References core::fragment::FragSet::add(), core::pose::set_ss_from_phipsi(), and core::pose::Pose::total_residue().
Referenced by protocols::topology_broker::StartStructClaimer::generate_init_frags(), protocols::loops::read_loop_fragments(), read_std_frags_from_cmd(), protocols::jd2::parser::FragmentReader::set_fragments(), and protocols::abinitio::AbrelaxApplication::setup_fragments().
| 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 | ||
| ) |
Definition at line 140 of file util.cc.
References core::fragment::FragSet::add(), and core::pose::set_ss_from_phipsi().
| 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 | ||
| ) |
Definition at line 154 of file util.cc.
References core::fragment::FragSet::add(), and core::pose::set_ss_from_phipsi().
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Referenced by core::fragment::FragSet::add(), core::fragment::Frame::align(), core::fragment::DownJumpSRFD::apply(), core::fragment::FragmentIO::clean_frag_cache(), core::fragment::SecondaryStructure::compute_fractions(), core::fragment::FragSet::generate_insert_map(), core::fragment::FragSet::insert_fragID_list(), core::fragment::BBTorsionSRFD::is_applicable(), merge_frags(), core::fragment::DownJumpSRFD::read(), core::fragment::FragmentIO::read_data(), core::fragment::FragmentIO::read_frag_data(), core::fragment::SecondaryStructure::read_from_file(), core::fragment::FragmentIO::read_next_frames(), core::fragment::SecondaryStructure::read_psipred_ss2(), read_std_frags_from_cmd(), core::fragment::SecondaryStructure::read_talos_ss(), and core::fragment::Frame::steal().
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| void core::fragment::xform_pose | ( | core::pose::Pose & | pose, |
| const core::kinematics::Stub & | s, | ||
| core::Size | sres, | ||
| core::Size | eres | ||
| ) |
Definition at line 586 of file util.cc.
References core::kinematics::Stub::local2global(), core::pose::Pose::n_residue(), core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), core::pose::Pose::set_xyz(), and core::pose::Pose::xyz().
Referenced by make_pose_from_frags().
1.8.4