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protocols::denovo_design::movers Namespace Reference

Classes

class  AddSegmentDataMover
 Adds a segment to the structuredata. More...
 
class  AddSegmentDataMoverCreator
 
class  AlignResiduesMover
 Aligns one residue onto another. More...
 
class  AlignResiduesMoverCreator
 
class  BridgeChainsCreator
 
class  BridgeChainsMover
 Creates a bridge connection between two chains using remodel. More...
 
class  BridgeChainsMoverCreator
 
class  BuildDeNovoBackboneMover
 Mover that builds and folds a structure via fragment insertion. More...
 
class  BuildDeNovoBackboneMoverCreator
 
struct  CutAndJump
 
class  DeclareStructureDataCovalentBondMover
 declares covalent bond More...
 
class  DeclareStructureDataCovalentBondMoverCreator
 
class  EXCN_FilterFailed
 
class  EXCN_NothingToFold
 
class  ExtendChainMover
 
class  ExtendChainMoverCreator
 
class  FastDesign
 
class  FastDesignCreator
 
class  FoldTreeFromFoldGraphMover
 Creates and sets a new fold tree for the pose by traversing a FoldGraph. More...
 
class  FoldTreeFromFoldGraphMoverCreator
 
class  MakeAsymmetricStructureDataMover
 Converts a StructureData for a symmetric pose into an asymmetric representation. More...
 
class  MakeAsymmetricStructureDataMoverCreator
 
struct  RelaxScriptCommand
 
class  RotateSegmentMover
 Rotates a segment in the pose. More...
 
class  RotateSegmentMoverCreator
 
class  RotationRange
 
class  SealFoldTreeMover
 Creates a sealed foldtree, and removes all cutpoints from the pose. More...
 
class  SealFoldTreeMoverCreator
 
class  SetPoseSecstructFromStructureDataMover
 
class  SetResidueAliasMover
 Sets a residue alias in the StructureData. More...
 
class  SetResidueAliasMoverCreator
 

Typedefs

typedef
utility::pointer::shared_ptr
< AddSegmentDataMover
AddSegmentDataMoverOP
 
typedef
utility::pointer::shared_ptr
< AddSegmentDataMover const > 
AddSegmentDataMoverCOP
 
typedef
utility::pointer::shared_ptr
< AlignResiduesMover
AlignResiduesMoverOP
 
typedef
utility::pointer::shared_ptr
< AlignResiduesMover const > 
AlignResiduesMoverCOP
 
typedef
utility::pointer::shared_ptr
< BridgeChainsMover
BridgeChainsMoverOP
 
typedef
utility::pointer::shared_ptr
< BridgeChainsMover const > 
BridgeChainsMoverCOP
 
typedef
utility::pointer::shared_ptr
< BuildDeNovoBackboneMover
BuildDeNovoBackboneMoverOP
 
typedef
utility::pointer::shared_ptr
< BuildDeNovoBackboneMover
const > 
BuildDeNovoBackboneMoverCOP
 
typedef
utility::pointer::shared_ptr
< DeclareStructureDataCovalentBondMover
DeclareStructureDataCovalentBondMoverOP
 
typedef
utility::pointer::shared_ptr
< DeclareStructureDataCovalentBondMover
const > 
DeclareStructureDataCovalentBondMoverCOP
 
typedef
utility::pointer::shared_ptr
< ExtendChainMover
ExtendChainMoverOP
 
typedef
utility::pointer::shared_ptr
< ExtendChainMover const > 
ExtendChainMoverCOP
 
typedef
utility::pointer::weak_ptr
< ExtendChainMover
ExtendChainMoverAP
 
typedef
utility::pointer::weak_ptr
< ExtendChainMover const > 
ExtendChainMoverCAP
 
typedef
utility::pointer::shared_ptr
< FastDesign
FastDesignOP
 
typedef
utility::pointer::shared_ptr
< FastDesign const > 
FastDesignCOP
 
typedef
utility::pointer::weak_ptr
< FastDesign
FastDesignAP
 
typedef
utility::pointer::weak_ptr
< FastDesign const > 
FastDesignCAP
 
typedef
utility::pointer::shared_ptr
< FoldTreeFromFoldGraphMover
FoldTreeFromFoldGraphMoverOP
 
typedef
utility::pointer::shared_ptr
< FoldTreeFromFoldGraphMover
const > 
FoldTreeFromFoldGraphMoverCOP
 
typedef utility::vector1
< CutAndJump
JumpInfo
 
typedef
utility::pointer::shared_ptr
< MakeAsymmetricStructureDataMover
MakeAsymmetricStructureDataMoverOP
 
typedef
utility::pointer::shared_ptr
< MakeAsymmetricStructureDataMover
const > 
MakeAsymmetricStructureDataMoverCOP
 
typedef
utility::pointer::shared_ptr
< RotateSegmentMover
RotateSegmentMoverOP
 
typedef
utility::pointer::shared_ptr
< RotateSegmentMover const > 
RotateSegmentMoverCOP
 
typedef
utility::pointer::shared_ptr
< SealFoldTreeMover
SealFoldTreeMoverOP
 
typedef
utility::pointer::shared_ptr
< SealFoldTreeMover const > 
SealFoldTreeMoverCOP
 
typedef
utility::pointer::shared_ptr
< SetResidueAliasMover
SetResidueAliasMoverOP
 
typedef
utility::pointer::shared_ptr
< SetResidueAliasMover const > 
SetResidueAliasMoverCOP
 

Functions

std::ostream & operator<< (std::ostream &os, AddSegmentDataMover const &mover)
 
AlignResiduesMover::ResidueSelectorCOPs parse_residue_selectors (std::string const &selector_name_str, basic::datacache::DataMap const &data)
 
std::ostream & operator<< (std::ostream &os, AlignResiduesMover const &mover)
 
AlignResiduesMover::ResidueVectors compute_residues_from_selectors (core::pose::Pose const &pose, AlignResiduesMover::ResidueSelectorCOPs const &selectors)
 
std::ostream & operator<< (std::ostream &os, BridgeChainsMover const &mover)
 
std::string pdb_filename (core::Size const phase_num)
 given an build phase number, returns a pdb filename for checkpointing Example filename: iter_01_20160718133800.pdb More...
 
core::scoring::ScoreFunctionOP get_score_function (core::pose::Pose const &)
 
utility::tag::XMLSchemaSimpleSubelementList pre_and_post_fold_mover_subelements ()
 
BuildDeNovoBackboneMover::ResidueVector add_overlap_to_loops (protocols::loops::Loops &loops, core::Size const overlap, core::pose::Pose const &pose)
 goes through loops and adds overlapping residues More...
 
std::ostream & operator<< (std::ostream &os, DeclareStructureDataCovalentBondMover const &mover)
 
std::ostream & operator<< (std::ostream &os, FoldTreeFromFoldGraphMover const &mover)
 
int new_jump_and_cutpoint (core::pose::Pose &pose, core::Size const saferes1, core::Size const saferes2, core::Size const cutres)
 
std::ostream & operator<< (std::ostream &os, MakeAsymmetricStructureDataMover const &mover)
 
std::string new_id (core::Size const subunit, std::string const &orig_name)
 
core::Real calc_dihedral (core::Vector const &p1, core::Vector const &p2, core::Vector const &p3, core::Vector const &p4)
 
std::ostream & operator<< (std::ostream &os, SealFoldTreeMover const &mover)
 
std::ostream & operator<< (std::ostream &os, SetResidueAliasMover const &mover)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< AlignResiduesMover const > protocols::denovo_design::movers::AlignResiduesMoverCOP
typedef utility::pointer::shared_ptr< BridgeChainsMover const > protocols::denovo_design::movers::BridgeChainsMoverCOP
typedef utility::pointer::weak_ptr< ExtendChainMover const > protocols::denovo_design::movers::ExtendChainMoverCAP
typedef utility::pointer::shared_ptr< ExtendChainMover const > protocols::denovo_design::movers::ExtendChainMoverCOP
typedef utility::pointer::weak_ptr< FastDesign > protocols::denovo_design::movers::FastDesignAP
typedef utility::pointer::weak_ptr< FastDesign const > protocols::denovo_design::movers::FastDesignCAP
typedef utility::pointer::shared_ptr< FastDesign const > protocols::denovo_design::movers::FastDesignCOP
typedef utility::pointer::shared_ptr< FastDesign > protocols::denovo_design::movers::FastDesignOP
typedef utility::pointer::shared_ptr< RotateSegmentMover const > protocols::denovo_design::movers::RotateSegmentMoverCOP
typedef utility::pointer::shared_ptr< SealFoldTreeMover const > protocols::denovo_design::movers::SealFoldTreeMoverCOP

Function Documentation

BuildDeNovoBackboneMover::ResidueVector protocols::denovo_design::movers::add_overlap_to_loops ( protocols::loops::Loops loops,
core::Size const  overlap,
core::pose::Pose const &  pose 
)
core::Real protocols::denovo_design::movers::calc_dihedral ( core::Vector const &  p1,
core::Vector const &  p2,
core::Vector const &  p3,
core::Vector const &  p4 
)
AlignResiduesMover::ResidueVectors protocols::denovo_design::movers::compute_residues_from_selectors ( core::pose::Pose const &  pose,
AlignResiduesMover::ResidueSelectorCOPs const &  selectors 
)
core::scoring::ScoreFunctionOP protocols::denovo_design::movers::get_score_function ( core::pose::Pose const &  )
std::string protocols::denovo_design::movers::new_id ( core::Size const  subunit,
std::string const &  orig_name 
)
int protocols::denovo_design::movers::new_jump_and_cutpoint ( core::pose::Pose pose,
core::Size const  saferes1,
core::Size const  saferes2,
core::Size const  cutres 
)
std::ostream & protocols::denovo_design::movers::operator<< ( std::ostream &  os,
MakeAsymmetricStructureDataMover const &  mover 
)
std::ostream & protocols::denovo_design::movers::operator<< ( std::ostream &  os,
SetResidueAliasMover const &  mover 
)
std::ostream & protocols::denovo_design::movers::operator<< ( std::ostream &  os,
AddSegmentDataMover const &  mover 
)
std::ostream & protocols::denovo_design::movers::operator<< ( std::ostream &  os,
FoldTreeFromFoldGraphMover const &  mover 
)
std::ostream & protocols::denovo_design::movers::operator<< ( std::ostream &  os,
SealFoldTreeMover const &  mover 
)
std::ostream & protocols::denovo_design::movers::operator<< ( std::ostream &  os,
BridgeChainsMover const &  mover 
)
std::ostream & protocols::denovo_design::movers::operator<< ( std::ostream &  os,
AlignResiduesMover const &  mover 
)
std::ostream & protocols::denovo_design::movers::operator<< ( std::ostream &  os,
DeclareStructureDataCovalentBondMover const &  mover 
)
AlignResiduesMover::ResidueSelectorCOPs protocols::denovo_design::movers::parse_residue_selectors ( std::string const &  selector_name_str,
basic::datacache::DataMap const &  data 
)
std::string protocols::denovo_design::movers::pdb_filename ( core::Size const  phase_num)

given an build phase number, returns a pdb filename for checkpointing Example filename: iter_01_20160718133800.pdb

Parameters
[in]phase_numBuild phase number

References protocols::abinitio::filename().

Referenced by protocols::denovo_design::movers::BuildDeNovoBackboneMover::build_in_phases(), and protocols::stepwise::legacy::modeler::rna::get_tag_from_pdb_filename().

utility::tag::XMLSchemaSimpleSubelementList protocols::denovo_design::movers::pre_and_post_fold_mover_subelements ( )