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protocols::denovo_design::components Namespace Reference

Classes

class  Alias
 
class  BondInfo
 
class  BuildPhases
 
class  CompoundPerturber
 "mutates" a set of mixed architects More...
 
class  ConnectionPerturber
 "mutates" a connection More...
 
class  DivideAndConqueror
 Splits a denovo structure into pieces, and devises a strategy for folding the structure piece-by-piece. More...
 
class  EnumeratedVectorSelector
 Selects items sequentially from a vector. More...
 
class  EXCN_Fold
 Exception thrown by PoseFolder::apply to indicate folding was not successful. More...
 
class  EXCN_PoseInconsistent
 
class  EXCN_RemarksNotPresent
 
class  ExtendedPoseBuilder
 Builds a pose from StructureData. More...
 
class  FoldGraph
 
class  HelixPairing
 
class  HelixPerturber
 "mutates" a helix More...
 
class  HelixSheetPairing
 
class  IdealAbegoGenerator
 Logic for selection of abego values. More...
 
class  NamedSolution
 
class  NamedSolutions
 
class  NullPerturber
 Perturber that does nothing. More...
 
class  NullPoseFolder
 Folds a pose using random phi/psi torsions. More...
 
class  Picker
 class used for picking/caching fragments More...
 
class  PoseFolder
 Given a pose with all residues, and a StructureData object, assign a 3D conformation to the pose. More...
 
class  RandomTorsionPoseFolder
 Folds a pose using random phi/psi torsions. More...
 
class  RandomVectorSelector
 Selects items from a vector randomly. More...
 
class  RemodelLoopMoverPoseFolder
 Folds residues in a pose using RemodelLoopMover. More...
 
class  ResidueDihedrals
 
class  Segment
 manages information about segments of residues More...
 
class  SegmentCounts
 
class  SegmentPairing
 
class  SegmentPairSet
 
class  SheetDB
 class used to create/manipulate a database of sheets using a list of pdb files More...
 
class  SolutionPredicate
 
class  SolutionSorter
 
class  StrandPairing
 
class  StructureData
 
class  StructureDataCreator
 
class  StructureDataFactory
 Singleton for creating StructureData objects. More...
 
class  StructureDataObserver
 a cacheable observer that keeps track of what length events occured More...
 
class  StructureDataPerturber
 Classes for altering StructureData objects on the fly. More...
 
class  StructureSlice
 
class  StructureSlicePredicate
 
class  VectorSelector
 Selects items from a vector using different methods. More...
 
class  VLBProtected
 

Typedefs

typedef
utility::pointer::shared_ptr
< DivideAndConqueror
DivideAndConquerorOP
 
typedef
utility::pointer::shared_ptr
< DivideAndConqueror const > 
DivideAndConquerorCOP
 
typedef
utility::pointer::shared_ptr
< BuildPhases
BuildPhasesOP
 
typedef
utility::pointer::shared_ptr
< BuildPhases const > 
BuildPhasesCOP
 
typedef utility::vector1
< StructureSlice
StructureSlices
 
typedef utility::vector1
< StructureSlices
FoldingSolutions
 
typedef std::pair< SegmentName,
SegmentName
SegmentPair
 
typedef
utility::pointer::shared_ptr
< ExtendedPoseBuilder
ExtendedPoseBuilderOP
 
typedef
utility::pointer::shared_ptr
< ExtendedPoseBuilder const > 
ExtendedPoseBuilderCOP
 
typedef
utility::pointer::shared_ptr
< FoldGraph
FoldGraphOP
 
typedef
utility::pointer::shared_ptr
< FoldGraph const > 
FoldGraphCOP
 
typedef
utility::pointer::weak_ptr
< FoldGraph
FoldGraphAP
 
typedef
utility::pointer::weak_ptr
< FoldGraph const > 
FoldGraphCAP
 
typedef std::set< std::string > NamedNodeSet
 
typedef
utility::pointer::shared_ptr
< IdealAbegoGenerator
IdealAbegoGeneratorOP
 
typedef
utility::pointer::shared_ptr
< IdealAbegoGenerator const > 
IdealAbegoGeneratorCOP
 
typedef
utility::pointer::shared_ptr
< NullPoseFolder
NullPoseFolderOP
 
typedef
utility::pointer::shared_ptr
< NullPoseFolder const > 
NullPoseFolderCOP
 
typedef
utility::pointer::shared_ptr
< Picker
PickerOP
 
typedef
utility::pointer::shared_ptr
< Picker const > 
PickerCOP
 
typedef
utility::pointer::weak_ptr
< Picker
PickerAP
 
typedef
utility::pointer::weak_ptr
< Picker const > 
PickerCAP
 
typedef
utility::pointer::shared_ptr
< PoseFolder
PoseFolderOP
 
typedef
utility::pointer::shared_ptr
< PoseFolder const > 
PoseFolderCOP
 
typedef
utility::pointer::shared_ptr
< RandomTorsionPoseFolder
RandomTorsionPoseFolderOP
 
typedef
utility::pointer::shared_ptr
< RandomTorsionPoseFolder
const > 
RandomTorsionPoseFolderCOP
 
typedef
utility::pointer::shared_ptr
< RemodelLoopMoverPoseFolder
RemodelLoopMoverPoseFolderOP
 
typedef
utility::pointer::shared_ptr
< RemodelLoopMoverPoseFolder
const > 
RemodelLoopMoverPoseFolderCOP
 
typedef long int SegmentResid
 
typedef
utility::pointer::shared_ptr
< Segment
SegmentOP
 
typedef
utility::pointer::shared_ptr
< Segment const > 
SegmentCOP
 
typedef
utility::pointer::weak_ptr
< Segment
SegmentAP
 
typedef
utility::pointer::weak_ptr
< Segment const > 
SegmentCAP
 
typedef utility::vector1
< SegmentOP
SegmentOPs
 
typedef utility::vector1
< SegmentCOP
SegmentCOPs
 
typedef utility::vector1
< StrandOrientation
StrandOrientations
 
typedef long int RegisterShift
 
typedef utility::vector1
< RegisterShift
RegisterShifts
 
typedef std::pair< core::Size,
core::Size
ResiduePair
 
typedef utility::vector1
< ResiduePair
ResiduePairs
 
typedef
utility::pointer::shared_ptr
< SegmentPairing
SegmentPairingOP
 
typedef
utility::pointer::shared_ptr
< SegmentPairing const > 
SegmentPairingCOP
 
typedef utility::vector1
< SegmentPairingOP
SegmentPairingOPs
 
typedef utility::vector1
< SegmentPairingCOP
SegmentPairingCOPs
 
typedef
utility::pointer::shared_ptr
< HelixPairing
HelixPairingOP
 
typedef
utility::pointer::shared_ptr
< HelixPairing const > 
HelixPairingCOP
 
typedef utility::vector1
< HelixPairingOP
HelixPairingOPs
 
typedef utility::vector1
< HelixPairingCOP
HelixPairingCOPs
 
typedef
utility::pointer::shared_ptr
< StrandPairing
StrandPairingOP
 
typedef
utility::pointer::shared_ptr
< StrandPairing const > 
StrandPairingCOP
 
typedef utility::vector1
< StrandPairingOP
StrandPairingOPs
 
typedef utility::vector1
< StrandPairingCOP
StrandPairingCOPs
 
typedef
utility::pointer::shared_ptr
< HelixSheetPairing
HelixSheetPairingOP
 
typedef
utility::pointer::shared_ptr
< HelixSheetPairing const > 
HelixSheetPairingCOP
 
typedef utility::vector1
< HelixSheetPairingOP
HelixSheetPairingOPs
 
typedef utility::vector1
< HelixSheetPairingCOP
HelixSheetPairingCOPs
 
typedef
utility::pointer::shared_ptr
< SheetDB
SheetDBOP
 
typedef
utility::pointer::shared_ptr
< SheetDB const > 
SheetDBCOP
 
typedef
utility::pointer::weak_ptr
< SheetDB
SheetDBAP
 
typedef
utility::pointer::weak_ptr
< SheetDB const > 
SheetDBCAP
 
typedef utility::vector1
< core::pose::PoseCOP
SheetList
 this is the actual map used to store the sheets More...
 
typedef std::map< std::string,
SheetList
MapByLengths
 
typedef std::map< std::string,
MapByLengths
MapByOrientations
 
typedef std::map< core::Size,
MapByOrientations
MapByStrands
 
typedef core::Size MovableGroup
 
typedef
utility::pointer::shared_ptr
< StructureData
StructureDataOP
 
typedef
utility::pointer::shared_ptr
< StructureData const > 
StructureDataCOP
 
typedef
utility::pointer::weak_ptr
< StructureData
StructureDataAP
 
typedef
utility::pointer::weak_ptr
< StructureData const > 
StructureDataCAP
 
typedef utility::vector1
< StructureDataOP
StructureDataOPs
 
typedef utility::vector1
< StructureDataCOP
StructureDataCOPs
 
typedef std::map< std::string,
std::string > 
StringMap
 
typedef std::map< std::string,
Segment
SegmentMap
 
typedef std::map< std::string,
Alias
AliasMap
 
typedef utility::vector1
< BondInfo
BondInfos
 
typedef utility::vector1
< core::Size
Cutpoints
 
typedef utility::vector1
< MovableGroup
MovableGroups
 
typedef
utility::pointer::shared_ptr
< StructureDataFactory
StructureDataFactoryOP
 
typedef
utility::pointer::shared_ptr
< StructureDataFactory const > 
StructureDataFactoryCOP
 
typedef
utility::pointer::shared_ptr
< StructureDataObserver
StructureDataObserverOP
 
typedef
utility::pointer::shared_ptr
< StructureDataObserver const > 
StructureDataObserverCOP
 
typedef
utility::pointer::weak_ptr
< StructureDataObserver
StructureDataObserverAP
 
typedef
utility::pointer::weak_ptr
< StructureDataObserver const > 
StructureDataObserverCAP
 
typedef
utility::pointer::shared_ptr
< StructureDataPerturber
StructureDataPerturberOP
 
typedef
utility::pointer::shared_ptr
< StructureDataPerturber const > 
StructureDataPerturberCOP
 
typedef utility::vector1
< StructureDataPerturber
StructureDataPerturbers
 
typedef utility::vector1
< StructureDataPerturberOP
StructureDataPerturberOPs
 
typedef utility::vector1
< StructureDataPerturberCOP
StructureDataPerturberCOPs
 
typedef
utility::pointer::shared_ptr
< ConnectionPerturber
ConnectionPerturberOP
 
typedef
utility::pointer::shared_ptr
< ConnectionPerturber const > 
ConnectionPerturberCOP
 
typedef
utility::pointer::shared_ptr
< CompoundPerturber
CompoundPerturberOP
 
typedef
utility::pointer::shared_ptr
< CompoundPerturber const > 
CompoundPerturberCOP
 
typedef
utility::pointer::shared_ptr
< HelixPerturber
HelixPerturberOP
 
typedef
utility::pointer::shared_ptr
< HelixPerturber const > 
HelixPerturberCOP
 

Enumerations

enum  StrandOrientation { UP = 1, DOWN = 2, ORIENTATIONS_END = 3 }
 Individual strands are oriented pointing either "UP" or "DOWN" If two adjacent strands have the same orientation, they are parallel If two adjacent strands have different orientation, they are antiparallel. More...
 

Functions

std::ostream & operator<< (std::ostream &os, SegmentPairSet const &pairs)
 
std::ostream & operator<< (std::ostream &os, StructureSlice const &slice)
 
void add_terminus_variants (core::pose::Pose &pose, ExtendedPoseBuilder::Resids const &endings)
 
core::conformation::ResidueOP rsd_op (core::pose::Pose const &pose, std::string const &res_type)
 helper function to create a ValineOP in the same typeset as the pose More...
 
void append_new_chain_from_template_segment (core::pose::Pose &pose, Segment const &segment)
 
void append_residues_from_template_segment (core::pose::Pose &pose, Segment const &prev_segment, Segment const &segment)
 
core::kinematics::FoldTree modify_ft_for_residue_insertion (core::pose::Pose &pose, core::Size const safe_res)
 modifies teh ft in the pose, returns the original More...
 
void set_dihedrals (core::pose::Pose &pose, core::Size const resid, ResidueDihedrals const &dihedrals)
 
void prepend_new_residues (core::pose::Pose &pose, core::Size num_residues, core::Size insert_pos, core::Size const , std::string const &type, ResidueDihedrals const &lower_dihedrals)
 
void append_new_residues (core::pose::Pose &pose, core::Size num_residues, core::Size insert_pos, core::Size const, std::string const &type, ResidueDihedrals const &upper_dihedrals)
 
template<class T >
void insert_mg (std::map< core::Size, std::list< T > > &fixed_mgs, core::Size const mg, T const &segname)
 
std::map< core::Size,
std::list< core::Size > > 
map_mgs (StructureData const &sd, FoldGraph const &fg)
 
std::map< core::Size, core::Sizemap_nodes (StructureData const &sd, FoldGraph const &fg)
 
std::ostream & operator<< (std::ostream &os, NamedSolutions const &solutions)
 
std::ostream & operator<< (std::ostream &os, NamedSolution const &s)
 
utility::vector1< std::string > truncate_abego (utility::vector1< std::string > const &complete_abego, core::Size const closest_chain_ending)
 
core::Size get_closest_chain_ending (utility::vector1< core::Size > const &chain_endings, core::Size total_residue, core::Size const end_res)
 
void check_residue (core::select::residue_selector::ResidueSubset const &subset, core::Size const resid)
 checks to ensure a residue is in the ResidueSubset exits with error if not More...
 
void check_residue_subset (core::select::residue_selector::ResidueSubset const &subset, protocols::loops::Loops const &loops)
 checks to ensure loops are contained within the ResidueSubset exits with error if not More...
 
bool residue_is_compatible (core::conformation::Residue const &rsd)
 
std::ostream & operator<< (std::ostream &os, Segment const &res)
 output residueinfo More...
 
std::ostream & operator<< (std::ostream &os, SegmentPairing const &pairing)
 
core::select::residue_selector::ResidueVector get_strand_residues (StrandOrientation const &orient, core::Size const start, core::Size const stop, core::select::residue_selector::ResidueVector const &bulges)
 
core::select::residue_selector::ResidueVector get_bulges (core::Size const start, core::Size const stop, std::string const &abego)
 
void add_paired_residues (StructureData const &sd, StrandPairing const &p, protocols::fldsgn::topology::SS_Info2 const &ss_info, ResiduePairs &pairs)
 
core::Size count_bulges (protocols::fldsgn::topology::Strand const &strand, std::string const &abego)
 
bool pose_matches_description (core::pose::Pose const &pose, std::string const &in_lengths_shifts)
 tells whether the given pose matches up with the given descriptor More...
 
std::string orientations_str (StrandOrientations const &orientations)
 
utility::graph::Graph graph_from_strandpairings (protocols::fldsgn::topology::StrandPairings const &spairs, std::map< core::Size, core::Size > &node_to_strand)
 
int add_to_pose (core::pose::PoseOP newpose, core::pose::Pose const &pose, core::Size s_start, core::Size s_stop)
 
utility::vector1
< core::pose::PoseOP
extract_sheets_from_strandlist (utility::vector1< core::pose::PoseOP > const &strands, core::Size const nstrands)
 
core::pose::PoseOP reorder_chains (core::pose::Pose &pose)
 
utility::vector1
< core::pose::PoseOP
extract_sheets_from_pose (core::pose::Pose const &pose, protocols::fldsgn::topology::StrandPairings const &spairs, protocols::fldsgn::topology::SS_Info2 const &ss_info, bool const idealize)
 
utility::vector1< boolcalc_paired_residues (core::pose::Pose &pose, protocols::fldsgn::topology::StrandPairingSet const &spairs)
 creates a list of whether a pose residue is beta-sheet-type paired to anything More...
 
std::string make_strand_info_str (architects::Lengths const &lengths, RegisterShifts const &shifts)
 creates a string key for lengths/shifts based on the given vectors for strand lengths and register shifts More...
 
std::string make_lengths_str (core::pose::Pose const &pose, utility::vector1< bool > const &paired, Lengths const &lengths, StrandOrientations const &orients, protocols::fldsgn::topology::StrandPairingSet const &spairs)
 
std::pair< std::string,
std::string > 
prune_unpaired_residues (core::pose::Pose &pose)
 using the pose secondary structure, remove residues that aren't paired. returns a list of paired strand lengths, which do not necessarily correspond to pose lengths due to beta-bulges and other weird things. More...
 
core::Size num_strands (core::pose::Pose const &pose)
 counts number of strands based on number of jumps. Pose must be a disconnected sheet More...
 
std::pair< std::string,
std::string > 
find_orientations_and_lengths (core::pose::Pose const &pose)
 gets a pair of strings, which refer to orientations, and lengths/shifts. Pose secstruct MUST be set More...
 
std::string reverse_orientations (std::string const &orient)
 
utility::vector1< boolparse_orientations (std::string const &orientations)
 
std::pair< utility::vector1
< core::Size >
, utility::vector1< int > > 
parse_lengths (std::string const &lengths)
 
std::string reverse_lengths (std::string const &orientations, std::string const &lengths)
 
std::pair< std::string,
std::string > 
canonicalize (std::string const &orientations, std::string const &lengths)
 
std::string const & choose_canonical (std::string const &l1, std::string const &l2)
 
core::pose::PoseOP reverse_chains (core::pose::Pose const &pose)
 
std::ostream & operator<< (std::ostream &os, BondInfo const &b)
 
template<class T >
void set_map_data (std::map< std::string, T > &map, std::string const &key, T const &value, bool const overwrite)
 
utility::vector1< core::Sizecompute_cutpoints (core::pose::Pose const &pose)
 
utility::vector1< core::Sizecompute_chain_beginnings (core::pose::Pose const &pose)
 
void advance_past_virtual_residues (core::pose::Pose const &pose, utility::vector1< core::Size >::const_iterator &cur_resid, utility::vector1< core::Size >::const_iterator const &end_resids)
 
std::ostream & operator<< (std::ostream &os, StructureData const &perm)
 output More...
 
std::ostream & operator<< (std::ostream &os, Alias const &alias)
 
std::string add_segment (StructureData &sd, Segment &seg, char const ss_type, SegmentCounts &counts)
 
void add_segments_for_chain (std::string const &id_val, StructureData &sd, std::string const &chain_ss, std::string const &chain_abego, SegmentCounts &counts)
 Adds segments to the given SD. More...
 
basic::datacache::WriteableCacheableMap
const & 
get_writeable_cacheable_map (core::pose::Pose const &pose)
 
basic::datacache::WriteableCacheableMap & get_writeable_cacheable_map (core::pose::Pose &pose)
 
void clean_from_storage (std::string &st)
 prepare a string that was stored in string datacache More...
 
void clean_for_storage (std::string &ss)
 prepare a string to be stored in the string datacache More...
 

Typedef Documentation

typedef std::map< std::string, Alias > protocols::denovo_design::components::AliasMap
typedef utility::pointer::shared_ptr< BuildPhases const > protocols::denovo_design::components::BuildPhasesCOP
typedef utility::pointer::shared_ptr< BuildPhases > protocols::denovo_design::components::BuildPhasesOP
typedef utility::pointer::weak_ptr< FoldGraph > protocols::denovo_design::components::FoldGraphAP
typedef utility::pointer::weak_ptr< FoldGraph const > protocols::denovo_design::components::FoldGraphCAP
typedef utility::pointer::shared_ptr< FoldGraph const > protocols::denovo_design::components::FoldGraphCOP
typedef utility::pointer::shared_ptr< FoldGraph > protocols::denovo_design::components::FoldGraphOP
typedef utility::pointer::shared_ptr< HelixPairing const > protocols::denovo_design::components::HelixPairingCOP
typedef utility::pointer::shared_ptr< HelixPairing > protocols::denovo_design::components::HelixPairingOP
typedef utility::pointer::shared_ptr< HelixPerturber const > protocols::denovo_design::components::HelixPerturberCOP
typedef std::set< std::string > protocols::denovo_design::components::NamedNodeSet
typedef utility::pointer::shared_ptr< NullPoseFolder const > protocols::denovo_design::components::NullPoseFolderCOP
typedef utility::pointer::weak_ptr< Picker > protocols::denovo_design::components::PickerAP
typedef utility::pointer::weak_ptr< Picker const > protocols::denovo_design::components::PickerCAP
typedef utility::pointer::shared_ptr< Picker const > protocols::denovo_design::components::PickerCOP
typedef utility::pointer::shared_ptr< Picker > protocols::denovo_design::components::PickerOP
typedef utility::pointer::shared_ptr< PoseFolder const > protocols::denovo_design::components::PoseFolderCOP
typedef utility::pointer::shared_ptr< PoseFolder > protocols::denovo_design::components::PoseFolderOP
typedef utility::pointer::weak_ptr< Segment > protocols::denovo_design::components::SegmentAP
typedef utility::pointer::weak_ptr< Segment const > protocols::denovo_design::components::SegmentCAP
typedef utility::pointer::shared_ptr< Segment const > protocols::denovo_design::components::SegmentCOP
typedef utility::pointer::shared_ptr< Segment > protocols::denovo_design::components::SegmentOP
typedef utility::pointer::shared_ptr< SegmentPairing const > protocols::denovo_design::components::SegmentPairingCOP
typedef utility::pointer::weak_ptr< SheetDB > protocols::denovo_design::components::SheetDBAP
typedef utility::pointer::weak_ptr< SheetDB const > protocols::denovo_design::components::SheetDBCAP
typedef utility::pointer::shared_ptr< SheetDB const > protocols::denovo_design::components::SheetDBCOP
typedef utility::pointer::shared_ptr< SheetDB > protocols::denovo_design::components::SheetDBOP

this is the actual map used to store the sheets

typedef utility::pointer::shared_ptr< StrandPairing const > protocols::denovo_design::components::StrandPairingCOP
typedef std::map< std::string, std::string > protocols::denovo_design::components::StringMap
typedef utility::pointer::weak_ptr< StructureData const > protocols::denovo_design::components::StructureDataCAP
typedef utility::pointer::shared_ptr< StructureData const > protocols::denovo_design::components::StructureDataCOP

Enumeration Type Documentation

Individual strands are oriented pointing either "UP" or "DOWN" If two adjacent strands have the same orientation, they are parallel If two adjacent strands have different orientation, they are antiparallel.

Enumerator
UP 
DOWN 
ORIENTATIONS_END 

Function Documentation

void protocols::denovo_design::components::add_paired_residues ( StructureData const &  sd,
StrandPairing const &  p,
protocols::fldsgn::topology::SS_Info2 const &  ss_info,
ResiduePairs &  pairs 
)
std::string protocols::denovo_design::components::add_segment ( StructureData &  sd,
Segment &  seg,
char const  ss_type,
SegmentCounts &  counts 
)
void protocols::denovo_design::components::add_segments_for_chain ( std::string const &  id_val,
StructureData &  sd,
std::string const &  chain_ss,
std::string const &  chain_abego,
SegmentCounts &  counts 
)

Adds segments to the given SD.

Parameters
[in]id_valParent ID of the segments. Can be empty
[in,out]sdStructureData to be modified
[in]chain_ssSecondary structure of the full chain
[in]chain_abegoAbego for the full chain
[in,out]countsSecondary structure element counters for naming segments

References core::pose::motif::a(), add_segment(), protocols::denovo_design::components::StructureData::mark_connected(), and protocols::TR().

Referenced by protocols::denovo_design::components::StructureDataFactory::create_from_motifs(), protocols::denovo_design::architects::BlueprintArchitect::design(), and protocols::denovo_design::components::StructureDataFactory::infer_from_pose().

void protocols::denovo_design::components::add_terminus_variants ( core::pose::Pose pose,
ExtendedPoseBuilder::Resids const &  endings 
)
int protocols::denovo_design::components::add_to_pose ( core::pose::PoseOP  newpose,
core::pose::Pose const &  pose,
core::Size  s_start,
core::Size  s_stop 
)
void protocols::denovo_design::components::advance_past_virtual_residues ( core::pose::Pose const &  pose,
utility::vector1< core::Size >::const_iterator &  cur_resid,
utility::vector1< core::Size >::const_iterator const &  end_resids 
)
void protocols::denovo_design::components::append_new_chain_from_template_segment ( core::pose::Pose pose,
Segment const &  segment 
)
void protocols::denovo_design::components::append_new_residues ( core::pose::Pose pose,
core::Size  num_residues,
core::Size  insert_pos,
core::Size  const,
std::string const &  type,
ResidueDihedrals const &  upper_dihedrals 
)
void protocols::denovo_design::components::append_residues_from_template_segment ( core::pose::Pose pose,
Segment const &  prev_segment,
Segment const &  segment 
)
utility::vector1< bool > protocols::denovo_design::components::calc_paired_residues ( core::pose::Pose pose,
protocols::fldsgn::topology::StrandPairingSet const &  spairs 
)
std::pair< std::string, std::string > protocols::denovo_design::components::canonicalize ( std::string const &  orientations,
std::string const &  lengths 
)
void protocols::denovo_design::components::check_residue ( core::select::residue_selector::ResidueSubset const &  subset,
core::Size const  resid 
)

checks to ensure a residue is in the ResidueSubset exits with error if not

References protocols::denovo_design::components::RandomTorsionPoseFolder::class_name().

Referenced by check_residue_subset().

void protocols::denovo_design::components::check_residue_subset ( core::select::residue_selector::ResidueSubset const &  subset,
protocols::loops::Loops const &  loops 
)

checks to ensure loops are contained within the ResidueSubset exits with error if not

References check_residue().

Referenced by protocols::denovo_design::components::RandomTorsionPoseFolder::apply().

std::string const & protocols::denovo_design::components::choose_canonical ( std::string const &  l1,
std::string const &  l2 
)
void protocols::denovo_design::components::clean_for_storage ( std::string &  ss)

prepare a string to be stored in the string datacache

Referenced by protocols::denovo_design::components::StructureData::write().

void protocols::denovo_design::components::clean_from_storage ( std::string &  st)

prepare a string that was stored in string datacache

Referenced by protocols::denovo_design::components::StructureDataFactory::create_from_cacheable_data().

utility::vector1< core::Size > protocols::denovo_design::components::compute_chain_beginnings ( core::pose::Pose const &  pose)
utility::vector1< core::Size > protocols::denovo_design::components::compute_cutpoints ( core::pose::Pose const &  pose)
core::Size protocols::denovo_design::components::count_bulges ( protocols::fldsgn::topology::Strand const &  strand,
std::string const &  abego 
)
utility::vector1< core::pose::PoseOP > protocols::denovo_design::components::extract_sheets_from_pose ( core::pose::Pose const &  pose,
protocols::fldsgn::topology::StrandPairings const &  spairs,
protocols::fldsgn::topology::SS_Info2 const &  ss_info,
bool const  idealize 
)
utility::vector1< core::pose::PoseOP > protocols::denovo_design::components::extract_sheets_from_strandlist ( utility::vector1< core::pose::PoseOP > const &  strands,
core::Size const  nstrands 
)
std::pair< std::string, std::string > protocols::denovo_design::components::find_orientations_and_lengths ( core::pose::Pose const &  pose)
core::select::residue_selector::ResidueVector protocols::denovo_design::components::get_bulges ( core::Size const  start,
core::Size const  stop,
std::string const &  abego 
)

References protocols::loops::stop.

Referenced by add_paired_residues().

core::Size protocols::denovo_design::components::get_closest_chain_ending ( utility::vector1< core::Size > const &  chain_endings,
core::Size  total_residue,
core::Size const  end_res 
)
core::select::residue_selector::ResidueVector protocols::denovo_design::components::get_strand_residues ( StrandOrientation const &  orient,
core::Size const  start,
core::Size const  stop,
core::select::residue_selector::ResidueVector const &  bulges 
)
basic::datacache::WriteableCacheableMap const& protocols::denovo_design::components::get_writeable_cacheable_map ( core::pose::Pose const &  pose)
basic::datacache::WriteableCacheableMap& protocols::denovo_design::components::get_writeable_cacheable_map ( core::pose::Pose pose)
utility::graph::Graph protocols::denovo_design::components::graph_from_strandpairings ( protocols::fldsgn::topology::StrandPairings const &  spairs,
std::map< core::Size, core::Size > &  node_to_strand 
)
template<class T >
void protocols::denovo_design::components::insert_mg ( std::map< core::Size, std::list< T > > &  fixed_mgs,
core::Size const  mg,
T const &  segname 
)
std::string protocols::denovo_design::components::make_lengths_str ( core::pose::Pose const &  pose,
utility::vector1< bool > const &  paired,
Lengths const &  lengths,
StrandOrientations const &  orients,
protocols::fldsgn::topology::StrandPairingSet const &  spairs 
)
std::string protocols::denovo_design::components::make_strand_info_str ( Lengths const &  lengths,
RegisterShifts const &  shifts 
)
std::map< core::Size, std::list< core::Size > > protocols::denovo_design::components::map_mgs ( StructureData const &  sd,
FoldGraph const &  fg 
)
std::map< core::Size, core::Size > protocols::denovo_design::components::map_nodes ( StructureData const &  sd,
FoldGraph const &  fg 
)
core::kinematics::FoldTree protocols::denovo_design::components::modify_ft_for_residue_insertion ( core::pose::Pose pose,
core::Size const  safe_res 
)
core::Size protocols::denovo_design::components::num_strands ( core::pose::Pose const &  pose)
std::ostream& protocols::denovo_design::components::operator<< ( std::ostream &  os,
SegmentPairSet const &  pairs 
)
std::ostream& protocols::denovo_design::components::operator<< ( std::ostream &  os,
StructureSlice const &  slice 
)
std::ostream& protocols::denovo_design::components::operator<< ( std::ostream &  os,
SegmentPairing const &  pairing 
)
std::ostream& protocols::denovo_design::components::operator<< ( std::ostream &  os,
BondInfo const &  b 
)
std::ostream& protocols::denovo_design::components::operator<< ( std::ostream &  os,
Segment const &  res 
)
std::ostream& protocols::denovo_design::components::operator<< ( std::ostream &  os,
NamedSolutions const &  solutions 
)
std::ostream& protocols::denovo_design::components::operator<< ( std::ostream &  os,
NamedSolution const &  s 
)
std::ostream& protocols::denovo_design::components::operator<< ( std::ostream &  os,
StructureData const &  perm 
)
std::ostream& protocols::denovo_design::components::operator<< ( std::ostream &  os,
Alias const &  alias 
)
std::string protocols::denovo_design::components::orientations_str ( StrandOrientations const &  orientations)
std::pair< utility::vector1< core::Size >, utility::vector1< int > > protocols::denovo_design::components::parse_lengths ( std::string const &  lengths)
utility::vector1< bool > protocols::denovo_design::components::parse_orientations ( std::string const &  orientations)

References protocols::TR().

Referenced by reverse_lengths().

bool protocols::denovo_design::components::pose_matches_description ( core::pose::Pose const &  pose,
std::string const &  in_lengths_shifts 
)
void protocols::denovo_design::components::prepend_new_residues ( core::pose::Pose pose,
core::Size  num_residues,
core::Size  insert_pos,
core::Size  const,
std::string const &  type,
ResidueDihedrals const &  lower_dihedrals 
)
std::pair< std::string, std::string > protocols::denovo_design::components::prune_unpaired_residues ( core::pose::Pose pose)
core::pose::PoseOP protocols::denovo_design::components::reorder_chains ( core::pose::Pose pose)
bool protocols::denovo_design::components::residue_is_compatible ( core::conformation::Residue const &  rsd)
core::pose::PoseOP protocols::denovo_design::components::reverse_chains ( core::pose::Pose const &  pose)
std::string protocols::denovo_design::components::reverse_lengths ( std::string const &  orientations,
std::string const &  lengths 
)
std::string protocols::denovo_design::components::reverse_orientations ( std::string const &  orient)
core::conformation::ResidueOP protocols::denovo_design::components::rsd_op ( core::pose::Pose const &  pose,
std::string const &  res_type 
)
void protocols::denovo_design::components::set_dihedrals ( core::pose::Pose pose,
core::Size const  resid,
ResidueDihedrals const &  dihedrals 
)
template<class T >
void protocols::denovo_design::components::set_map_data ( std::map< std::string, T > &  map,
std::string const &  key,
T const &  value,
bool const  overwrite 
)
utility::vector1< std::string > protocols::denovo_design::components::truncate_abego ( utility::vector1< std::string > const &  complete_abego,
core::Size const  closest_chain_ending 
)