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protocols::seeded_abinitio Namespace Reference

Classes

class  CAcstGenerator
 
class  CAcstGeneratorCreator
 
class  CloseFold
 
class  CloseFoldCreator
 
class  CoordinateCst
 
class  CoordinateCstCreator
 
class  DefineMovableLoops
 
class  DefineMovableLoopsCreator
 
class  GrowPeptides
 
class  GrowPeptidesCreator
 
struct  GrowPeptidesSegment
 
class  SeedFoldTree
 
class  SeedFoldTreeCreator
 
class  SeedSetupMover
 
class  SeedSetupMoverCreator
 
class  SegmentHybridizer
 
class  SegmentHybridizerCreator
 
struct  SegmentSpec
 
class  SwapSegment
 
class  SwapSegmentCreator
 

Typedefs

using GrowPeptidesSegmentOP = utility::pointer::shared_ptr< GrowPeptidesSegment >
 
typedef
utility::pointer::shared_ptr
< SeedFoldTree
SeedFoldTreeOP
 
typedef
utility::pointer::shared_ptr
< SeedFoldTree const > 
SeedFoldTreeCOP
 

Functions

static basic::Tracer TR ("protocols.seeded_abinitio.CAcstGenerator")
 
bool is_part (utility::vector1< core::Size > &cut_points, core::Size &residue)
 
void add_dist_constraints (pose::Pose &pose, pose::PoseOP &pose_of_int, core::Size start_relevant_chain, core::scoring::constraints::ConstraintSetOP &cst, protocols::loops::Loops &seeds, protocols::loops::Loops &clear_area, utility::vector1< core::Size > cut_points, utility::vector1< core::Size > seed_exceptions, bool add_cst_seed, core::Real stddev, core::Size seq_separation, core::Real distance_cutoff)
 this method will get de-convoluted soon.... More...
 
static basic::Tracer TR ("protocols.seeded_abinitio.CoordinateCst")
 
static basic::Tracer TR_debug ("CoordinateCst.Debug")
 
void parse_spans (pose::Pose &pose, utility::vector1< std::pair< std::string, std::string > > const span_vector, std::set< core::Size > resi_collection)
 parse residues at run time, in case there was a lenght change More...
 
utility::vector1< core::Sizeadjust_residues (pose::Pose &pose, std::string design_residues)
 
void adjust_single_residues (pose::Pose &pose, std::string single_residues, std::set< core::Size > resi_collection)
 residue parsing at runtime More...
 
void add_coordinate_constraints (pose::Pose &pose, std::set< core::Size > const &constrain_residues, core::Size const anchor_resnum, core::Real const coord_sdev, std::string anchor_atom_name, std::string atom_name, core::scoring::func::HarmonicFuncOP &coord_cst_func)
 
void adjust_mm_to_length (core::pose::Pose const &pose, core::kinematics::MoveMapOP &mm)
 method to update numbering of a movemap if the pose length was changed previously only works if a LengthEventCollector is set in the pose's observer cache default behavior is to set everything new to be movable and adjust the numbering of the residues that were previously not allowed to move to the appropriate new numbering More...
 
protocols::loops::Loops parse_seeds (core::pose::Pose const &pose, utility::vector1< std::pair< std::string, std::string > > seed_vector)
 for runtime parsing of seeds More...
 
void combine_two_poses (core::pose::Pose design_pose, core::pose::PoseOP target_chain)
 
Size define_cut_point_stochasticly (core::Size start_resi, core::Size stop_resi, std::string secondarystruct_seq, core::Size start_fold_pose)
 
std::pair< core::Size, core::Sizeget_closest_residue_pair (core::Size seed_start, core::Size seed_stop, core::pose::PoseOP &target_seed_pose)
 
std::pair< core::Size, core::Sizefind_nearest_residue (core::Size anchor, pose::PoseOP &target_seed_pose)
 
static basic::Tracer TR ("protocols.seeded_abinitio.SeedSetupMover")
 
bool is_part (utility::vector1< core::Size > vec, core::Size pos)
 
void define_movemap_chains (core::pose::Pose &pose, core::kinematics::MoveMapOP &movemap, protocols::loops::Loops &seeds, bool chi_chain1, bool chi_chain2, bool interface_chi1, bool, core::Real interface_distance_cutoff)
 
utility::vector1< core::Sizeadjust_des_residues (pose::Pose &pose, std::string design_residues)
 adjustment since parse time specified residues are different numbered than run time residues More...
 
static basic::Tracer TR ("protocols.seeded_abinitio.movers.SegmentHybridizer")
 
static basic::Tracer TR_ccd ("protocols.seeded_abinitio.movers.SegmentHybridizer_ccd")
 
static basic::Tracer TR ("protocols.seeded_abinitio.util")
 
void superposition_transform (utility::vector1< numeric::xyzVector< numeric::Real > > &init_coords, utility::vector1< numeric::xyzVector< numeric::Real > > &ref_coords, numeric::xyzMatrix< numeric::Real > &rotation, numeric::xyzVector< numeric::Real > &toCenter, numeric::xyzVector< numeric::Real > &toFitCenter)
 
template<typename T >
void vector_vector_to_FArray2 (utility::vector1< numeric::xyzVector< T > > &from, ObjexxFCL::FArray2D< T > &to)
 

Typedef Documentation

using protocols::seeded_abinitio::GrowPeptidesSegmentOP = typedef utility::pointer::shared_ptr< GrowPeptidesSegment >
typedef utility::pointer::shared_ptr<SeedFoldTree const> protocols::seeded_abinitio::SeedFoldTreeCOP
typedef utility::pointer::shared_ptr<SeedFoldTree> protocols::seeded_abinitio::SeedFoldTreeOP

Function Documentation

void protocols::seeded_abinitio::add_coordinate_constraints ( pose::Pose pose,
std::set< core::Size > const &  constrain_residues,
core::Size const  anchor_resnum,
core::Real const  coord_sdev,
std::string  anchor_atom_name,
std::string  atom_name,
core::scoring::func::HarmonicFuncOP coord_cst_func 
)
void protocols::seeded_abinitio::add_dist_constraints ( pose::Pose pose,
pose::PoseOP pose_of_int,
core::Size  start_relevant_chain,
core::scoring::constraints::ConstraintSetOP cst,
protocols::loops::Loops seeds,
protocols::loops::Loops clear_area,
utility::vector1< core::Size cut_points,
utility::vector1< core::Size seed_exceptions,
bool  add_cst_seed,
core::Real  stddev,
core::Size  seq_separation,
core::Real  distance_cutoff 
)
utility::vector1< core::Size > protocols::seeded_abinitio::adjust_des_residues ( pose::Pose pose,
std::string  design_residues 
)

adjustment since parse time specified residues are different numbered than run time residues

References core::pose::parse_resnum(), and TR().

Referenced by protocols::seeded_abinitio::SeedSetupMover::apply().

void protocols::seeded_abinitio::adjust_mm_to_length ( core::pose::Pose const &  pose,
core::kinematics::MoveMapOP mm 
)

method to update numbering of a movemap if the pose length was changed previously only works if a LengthEventCollector is set in the pose's observer cache default behavior is to set everything new to be movable and adjust the numbering of the residues that were previously not allowed to move to the appropriate new numbering

to readjust the move map after length changes

References core::id::combine_sequence_mappings(), core::pose::datacache::LENGTH_EVENT_COLLECTOR, core::pose::Pose::observer_cache(), core::pose::Pose::size(), and TR().

utility::vector1< core::Size > protocols::seeded_abinitio::adjust_residues ( pose::Pose pose,
std::string  design_residues 
)
void protocols::seeded_abinitio::adjust_single_residues ( pose::Pose pose,
std::string  single_residues,
std::set< core::Size resi_collection 
)

residue parsing at runtime

References core::pose::parse_resnum().

Referenced by protocols::seeded_abinitio::CoordinateCst::apply().

void protocols::seeded_abinitio::combine_two_poses ( core::pose::Pose  design_pose,
core::pose::PoseOP  target_chain 
)
Size protocols::seeded_abinitio::define_cut_point_stochasticly ( core::Size  start_resi,
core::Size  stop_resi,
std::string  secondarystruct_seq,
core::Size  start_fold_pose 
)
void protocols::seeded_abinitio::define_movemap_chains ( core::pose::Pose pose,
core::kinematics::MoveMapOP movemap,
protocols::loops::Loops seeds,
bool  chi_chain1,
bool  chi_chain2,
bool  interface_chi1,
bool  ,
core::Real  interface_distance_cutoff 
)
std::pair< core::Size, core::Size > protocols::seeded_abinitio::find_nearest_residue ( core::Size  anchor,
pose::PoseOP target_seed_pose 
)
std::pair< core::Size, core::Size > protocols::seeded_abinitio::get_closest_residue_pair ( core::Size  seed_start,
core::Size  seed_stop,
core::pose::PoseOP target_seed_pose 
)
bool protocols::seeded_abinitio::is_part ( utility::vector1< core::Size > &  cut_points,
core::Size residue 
)
bool protocols::seeded_abinitio::is_part ( utility::vector1< core::Size vec,
core::Size  pos 
)
protocols::loops::Loops protocols::seeded_abinitio::parse_seeds ( core::pose::Pose const &  pose,
utility::vector1< std::pair< std::string, std::string > >  seed_vector 
)
void protocols::seeded_abinitio::parse_spans ( pose::Pose pose,
utility::vector1< std::pair< std::string, std::string > > const  span_vector,
std::set< core::Size resi_collection 
)

parse residues at run time, in case there was a lenght change

References core::sequence::end, core::pose::parse_resnum(), and TR().

Referenced by protocols::seeded_abinitio::CoordinateCst::apply().

void protocols::seeded_abinitio::superposition_transform ( utility::vector1< numeric::xyzVector< numeric::Real > > &  init_coords,
utility::vector1< numeric::xyzVector< numeric::Real > > &  ref_coords,
numeric::xyzMatrix< numeric::Real > &  rotation,
numeric::xyzVector< numeric::Real > &  toCenter,
numeric::xyzVector< numeric::Real > &  toFitCenter 
)
static basic::Tracer protocols::seeded_abinitio::TR ( "protocols.seeded_abinitio.util"  )
static
static basic::Tracer protocols::seeded_abinitio::TR ( "protocols.seeded_abinitio.CAcstGenerator"  )
static

Referenced by add_coordinate_constraints(), adjust_des_residues(), adjust_mm_to_length(), adjust_residues(), protocols::seeded_abinitio::CoordinateCst::apply(), protocols::seeded_abinitio::DefineMovableLoops::apply(), protocols::seeded_abinitio::SeedSetupMover::apply(), protocols::seeded_abinitio::CloseFold::apply(), protocols::seeded_abinitio::SeedFoldTree::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply(), protocols::seeded_abinitio::SwapSegment::apply(), protocols::seeded_abinitio::SegmentHybridizer::apply_frame(), protocols::seeded_abinitio::SeedFoldTree::best_by_ala_scan(), combine_two_poses(), protocols::seeded_abinitio::SwapSegment::copying_side_chains(), define_cut_point_stochasticly(), define_movemap_chains(), protocols::seeded_abinitio::DefineMovableLoops::find_loops(), protocols::seeded_abinitio::CloseFold::find_loops(), find_nearest_residue(), get_closest_residue_pair(), protocols::seeded_abinitio::CoordinateCst::parse_my_tag(), protocols::seeded_abinitio::DefineMovableLoops::parse_my_tag(), protocols::seeded_abinitio::SeedSetupMover::parse_my_tag(), protocols::seeded_abinitio::CloseFold::parse_my_tag(), protocols::seeded_abinitio::SegmentHybridizer::parse_my_tag(), protocols::seeded_abinitio::SwapSegment::parse_my_tag(), protocols::seeded_abinitio::SeedFoldTree::parse_my_tag(), parse_seeds(), parse_spans(), protocols::seeded_abinitio::CloseFold::quick_closure(), protocols::seeded_abinitio::SeedFoldTree::set_foldtree(), protocols::seeded_abinitio::SeedSetupMover::set_packerTasks_target_and_seeds(), protocols::seeded_abinitio::SwapSegment::swap_chain(), and protocols::seeded_abinitio::SwapSegment::swap_segment().

static basic::Tracer protocols::seeded_abinitio::TR ( "protocols.seeded_abinitio.SeedSetupMover"  )
static
static basic::Tracer protocols::seeded_abinitio::TR ( "protocols.seeded_abinitio.CoordinateCst"  )
static
static basic::Tracer protocols::seeded_abinitio::TR ( "protocols.seeded_abinitio.movers.SegmentHybridizer"  )
static
static basic::Tracer protocols::seeded_abinitio::TR_ccd ( "protocols.seeded_abinitio.movers.SegmentHybridizer_ccd"  )
static
static basic::Tracer protocols::seeded_abinitio::TR_debug ( "CoordinateCst.Debug"  )
static
template<typename T >
void protocols::seeded_abinitio::vector_vector_to_FArray2 ( utility::vector1< numeric::xyzVector< T > > &  from,
ObjexxFCL::FArray2D< T > &  to 
)

Referenced by superposition_transform().