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protocols::jumping::JumpSample Class Reference

#include <JumpSample.hh>

Public Member Functions

 JumpSample ()
 
 ~JumpSample ()=default
 
 JumpSample (JumpSetup const &)
 
 JumpSample (core::Size total_residue, core::Size njump, ObjexxFCL::FArray2D_int jumps, ObjexxFCL::FArray1D_int cuts, core::Size root=1)
 
 JumpSample (core::Size total_residue, core::Size njump, ObjexxFCL::FArray2D_int jumps, ObjexxFCL::FArray2D< std::string > jump_atoms, ObjexxFCL::FArray1D_int cuts, core::Size root=1)
 
 JumpSample (core::Size total_residue, core::scoring::dssp::PairingsList const &jumps, ObjexxFCL::FArray1D_float const &cut_probability, core::Size root=1)
 
 JumpSample (core::Size total_residue, core::scoring::dssp::PairingsList const &jumps, core::fragment::SecondaryStructure const &ss_def, core::Size root=1)
 
 JumpSample (core::kinematics::FoldTree const &f)
 
 JumpSample (core::kinematics::FoldTreeOP f)
 
bool is_valid () const
 
void resize (core::Size njump)
 
void set_fold_tree_in_pose (core::pose::Pose &pose) const
 
void safe_secstruct (core::pose::Pose &pose) const
 
void transfer_jumps (core::pose::Pose &pose, core::pose::Pose &native_pose) const
 
void steal_jumps (core::pose::Pose &native_pose, core::fragment::FrameIterator const &begin, core::fragment::FrameIterator const &end) const
 
void generate_jump_frames (core::fragment::FrameList &, core::kinematics::MoveMap const &, bool bWithTorsion=true) const
 
void steal_orientation_and_pleating (core::pose::Pose &native_pose)
 
void generate_jump_frags (PairingLibrary const &pairings, core::kinematics::MoveMap const &, bool bWithTorsion, core::fragment::FrameList &) const
 
void add_chainbreaks (core::pose::Pose &pose) const
 
void add_chainbreaks (core::pose::Pose &pose, core::Size max_dist, core::kinematics::ShortestPathInFoldTree const &) const
 
void add_chainbreaks_as_distance_constraint (core::pose::Pose &pose) const
 
void add_chainbreaks_as_distance_constraint (core::pose::Pose &pose, core::Size max_dist, core::kinematics::ShortestPathInFoldTree const &sp) const
 
void remove_chainbreaks (core::pose::Pose &pose) const
 
void set_fold_tree_and_chainbreaks (core::pose::Pose &pose) const
 
core::Size downstream_res_nr (core::Size jump_nr) const
 
core::Size size () const
 
ObjexxFCL::FArray2D
< core::Size > const & 
jumps () const
 
ObjexxFCL::FArray1D
< core::Size > const & 
cuts () const
 
ObjexxFCL::FArray2D
< std::string > const & 
jump_atoms () const
 
bool has_orientation_and_pleating () const
 
core::kinematics::FoldTree const & fold_tree () const
 
core::Size total_residue () const
 
void dump_pymol (std::string fn) const
 dump file with little pymol script that shows jumps and cuts More...
 
core::scoring::dssp::Pairing get_pairing (core::Size res1, core::Size res2) const
 

Private Member Functions

void generate_tree_from_jumps_and_cuts (core::Size root=1)
 
void generate_random_tree_from_jumps (ObjexxFCL::FArray1D_float const &prob, core::Size root=1)
 
void apply_to (core::kinematics::FoldTreeOP f)
 
void jumps2pairings ()
 
void correct_jump_atoms_for_fragments () const
 

Private Attributes

core::Size total_residue_
 
core::Size njump_
 
core::scoring::dssp::PairingsList jump_pairings_
 
ObjexxFCL::FArray2D< core::Sizejumps_
 
ObjexxFCL::FArray2D< std::string > jump_atoms_
 
ObjexxFCL::FArray1D< core::Sizecuts_
 
core::kinematics::FoldTreeOP fold_tree_
 
bool bValidTree_
 

Friends

std::ostream & operator<< (std::ostream &os, JumpSample const &t)
 output operator More...
 

Constructor & Destructor Documentation

protocols::jumping::JumpSample::JumpSample ( )
inline
protocols::jumping::JumpSample::~JumpSample ( )
default
protocols::jumping::JumpSample::JumpSample ( JumpSetup const &  def)
protocols::jumping::JumpSample::JumpSample ( core::Size  total_residue,
core::Size  njump,
ObjexxFCL::FArray2D_int  jumps,
ObjexxFCL::FArray1D_int  cuts,
core::Size  root = 1 
)
protocols::jumping::JumpSample::JumpSample ( core::Size  total_residue,
core::Size  njump,
ObjexxFCL::FArray2D_int  jumps,
ObjexxFCL::FArray2D< std::string >  jump_atoms,
ObjexxFCL::FArray1D_int  cuts,
core::Size  root = 1 
)
protocols::jumping::JumpSample::JumpSample ( core::Size  total_residue,
core::scoring::dssp::PairingsList const &  jumps,
ObjexxFCL::FArray1D_float const &  cut_probability,
core::Size  root = 1 
)
protocols::jumping::JumpSample::JumpSample ( core::Size  total_residue,
core::scoring::dssp::PairingsList const &  jumps,
core::fragment::SecondaryStructure const &  ss_def,
core::Size  root = 1 
)
protocols::jumping::JumpSample::JumpSample ( core::kinematics::FoldTree const &  f)
protocols::jumping::JumpSample::JumpSample ( core::kinematics::FoldTreeOP  f)

Member Function Documentation

void protocols::jumping::JumpSample::add_chainbreaks ( core::pose::Pose pose) const
void protocols::jumping::JumpSample::add_chainbreaks ( core::pose::Pose pose,
core::Size  max_dist,
core::kinematics::ShortestPathInFoldTree const &  sp 
) const
void protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint ( core::pose::Pose pose) const
void protocols::jumping::JumpSample::add_chainbreaks_as_distance_constraint ( core::pose::Pose pose,
core::Size  max_dist,
core::kinematics::ShortestPathInFoldTree const &  sp 
) const
void protocols::jumping::JumpSample::apply_to ( core::kinematics::FoldTreeOP  f)
private
void protocols::jumping::JumpSample::correct_jump_atoms_for_fragments ( ) const
private

we want N-CA-C as the stub atoms for the jump to achieve that we have to set the upstream jump atom according to folding direction N2C –> JumpAtom C C2N –> JumpAtom N since the AtomTree automatically uses the parent and grand-parent as second and third stub atom

References bValidTree_, fold_tree_, jump_atoms_, and njump_.

Referenced by generate_random_tree_from_jumps(), generate_tree_from_jumps_and_cuts(), and JumpSample().

ObjexxFCL::FArray1D< core::Size > const& protocols::jumping::JumpSample::cuts ( ) const
inline
core::Size protocols::jumping::JumpSample::downstream_res_nr ( core::Size  jump_nr) const
inline

References fold_tree_.

void protocols::jumping::JumpSample::dump_pymol ( std::string  fn) const

dump file with little pymol script that shows jumps and cuts

References cuts_, jumps_, core::conformation::membrane::out, and size().

core::kinematics::FoldTree const& protocols::jumping::JumpSample::fold_tree ( ) const
inline
void protocols::jumping::JumpSample::generate_jump_frags ( PairingLibrary const &  pairings,
core::kinematics::MoveMap const &  mm,
bool  bWithTorsion,
core::fragment::FrameList all_frames 
) const
void protocols::jumping::JumpSample::generate_jump_frames ( core::fragment::FrameList all_frames,
core::kinematics::MoveMap const &  mm,
bool  bWithTorsion = true 
) const
void protocols::jumping::JumpSample::generate_random_tree_from_jumps ( ObjexxFCL::FArray1D_float const &  prob,
core::Size  root = 1 
)
private
void protocols::jumping::JumpSample::generate_tree_from_jumps_and_cuts ( core::Size  root = 1)
private
core::scoring::dssp::Pairing protocols::jumping::JumpSample::get_pairing ( core::Size  res1,
core::Size  res2 
) const
bool protocols::jumping::JumpSample::has_orientation_and_pleating ( ) const
bool protocols::jumping::JumpSample::is_valid ( ) const
inline
ObjexxFCL::FArray2D< std::string > const& protocols::jumping::JumpSample::jump_atoms ( ) const
inline
ObjexxFCL::FArray2D< core::Size > const& protocols::jumping::JumpSample::jumps ( ) const
inline
void protocols::jumping::JumpSample::jumps2pairings ( )
private

References jump_pairings_, jumps_, and size().

Referenced by apply_to(), and JumpSample().

void protocols::jumping::JumpSample::remove_chainbreaks ( core::pose::Pose pose) const
void protocols::jumping::JumpSample::resize ( core::Size  njump)

References cuts_, jump_atoms_, jump_pairings_, and jumps_.

Referenced by apply_to(), and JumpSample().

void protocols::jumping::JumpSample::safe_secstruct ( core::pose::Pose pose) const
void protocols::jumping::JumpSample::set_fold_tree_and_chainbreaks ( core::pose::Pose pose) const
inline
void protocols::jumping::JumpSample::set_fold_tree_in_pose ( core::pose::Pose pose) const
core::Size protocols::jumping::JumpSample::size ( ) const
inline
void protocols::jumping::JumpSample::steal_jumps ( core::pose::Pose native_pose,
core::fragment::FrameIterator const &  begin,
core::fragment::FrameIterator const &  end 
) const
void protocols::jumping::JumpSample::steal_orientation_and_pleating ( core::pose::Pose native_pose)
core::Size protocols::jumping::JumpSample::total_residue ( ) const
inline

References total_residue_.

Referenced by JumpSample().

void protocols::jumping::JumpSample::transfer_jumps ( core::pose::Pose pose,
core::pose::Pose native_pose 
) const

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
JumpSample const &  t 
)
friend

output operator

Member Data Documentation

bool protocols::jumping::JumpSample::bValidTree_
private
ObjexxFCL::FArray1D< core::Size > protocols::jumping::JumpSample::cuts_
private
core::kinematics::FoldTreeOP protocols::jumping::JumpSample::fold_tree_
private
ObjexxFCL::FArray2D< std::string > protocols::jumping::JumpSample::jump_atoms_
private
core::scoring::dssp::PairingsList protocols::jumping::JumpSample::jump_pairings_
private
ObjexxFCL::FArray2D< core::Size > protocols::jumping::JumpSample::jumps_
private
core::Size protocols::jumping::JumpSample::njump_
private
core::Size protocols::jumping::JumpSample::total_residue_
private

The documentation for this class was generated from the following files: