Rosetta 3.4
Public Member Functions | Protected Member Functions
protocols::simple_moves::ClassicFragmentMover Class Reference

A FragmentMover that applies uniform sampling of fragments. More...

#include <FragmentMover.hh>

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List of all members.

Public Member Functions

 ClassicFragmentMover (core::fragment::FragSetCOP fragset)
 
 ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap)
 
 ClassicFragmentMover (core::fragment::ConstantLengthFragSet const &fragset, core::kinematics::MoveMap const &movemap)
 Temp work around for PyRosetta code, until we found a way how to handle owning pointers in this case
 ~ClassicFragmentMover ()
void apply (core::pose::Pose &)
 Applies classic fragment insertion based on a FragSet.
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void set_check_ss (bool setting)
 check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)
bool check_ss () const
 accessor
core::Real end_bias () const
void set_end_bias (core::Real setting)
bool end_bias_check_enabled () const
void enable_end_bias_check (bool setting=true)
void set_min_overlap (Size setting)
 min_overlap controls the behaviour fragset->region()
void set_min_frag_length (Size setting)
 min_frag_length controls the behaviour fragset->region()
virtual bool apply_fragment (core::fragment::Frame const &frame, Size frag_num, core::kinematics::MoveMap const &movemap, core::pose::Pose &pose) const
 apply the chosen fragment, this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards
virtual void set_defaults ()
 set defaults
virtual bool choose_fragment (core::fragment::FrameList const &, core::pose::Pose const &, Size &frame_num, Size &frag_num) const
 given FrameList and pose, this method yields a fragment ( frame_num/ frag_num); return false if nothing suitable is found
void define_start_window (Size window_start)
 apply fragment at predefined position
virtual bool choose_window_start (core::pose::Pose const &, Size window_length, Size &window_start) const
 yields a start position (window_start) for fragment window to sample from ( return false, if nothing suitable is found )
virtual bool choose_window_length (core::pose::Pose const &, Size &window_length) const
 yields a length (window_length) of the fragment window to sample from ( return false, if no suitable length is found )
void on_new_fragments ()
 is called from set_fragments()
virtual bool end_bias_check (core::pose::Pose const &, Size window_start) const
virtual bool valid_ss (std::string const &new_ss) const
 returns true if the ss string is acceptable

Protected Member Functions

 ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, std::string type)
 alternative Constructor to be used by derived classes
 ClassicFragmentMover (core::fragment::FragSetCOP fragset, std::string type)
 alternative Constructor to be used by derived classes
virtual bool apply_frames (core::pose::Pose &, core::fragment::FrameList const &) const

Detailed Description

A FragmentMover that applies uniform sampling of fragments.


Constructor & Destructor Documentation

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover ( core::fragment::FragSetCOP  fragset)

References set_defaults().

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover ( core::fragment::FragSetCOP  fragset,
core::kinematics::MoveMapCOP  movemap 
)

References set_defaults().

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover ( core::fragment::ConstantLengthFragSet const &  fragset,
core::kinematics::MoveMap const &  movemap 
)

Temp work around for PyRosetta code, until we found a way how to handle owning pointers in this case

Note:
: temp work around for PyRosetta code, until we find a way to handle owning pointers in this case

References set_defaults().

protocols::simple_moves::ClassicFragmentMover::~ClassicFragmentMover ( )
protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover ( core::fragment::FragSetCOP  fragset,
core::kinematics::MoveMapCOP  movemap,
std::string  type 
) [protected]

alternative Constructor to be used by derived classes

References set_defaults().

protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover ( core::fragment::FragSetCOP  fragset,
std::string  type 
) [protected]

alternative Constructor to be used by derived classes

References set_defaults().


Member Function Documentation

void protocols::simple_moves::ClassicFragmentMover::apply ( core::pose::Pose pose) [virtual]

Applies classic fragment insertion based on a FragSet.

choose and insert a Fragment from the protocols::moves::Movers Fragment-Set into a Pose.

example: mover_3mer.apply(pose) See also: ClassicFragmentMover Pose ConstantLengthFragSet

Implements protocols::simple_moves::FragmentMover.

References apply_frames(), choose_window_length(), choose_window_start(), protocols::simple_moves::FragmentMover::fragset_, protocols::simple_moves::FragmentMover::insert_size_, protocols::simple_moves::FragmentMover::movemap(), protocols::simple_moves::tr(), and protocols::simple_moves::FragmentMover::update_insert_map().

virtual bool protocols::simple_moves::ClassicFragmentMover::apply_fragment ( core::fragment::Frame const &  frame,
Size  frag_num,
core::kinematics::MoveMap const &  movemap,
core::pose::Pose pose 
) const [virtual]

apply the chosen fragment, this can be overloaded to change action, e.,g., WobbleMover introduces chain-break before fragment insertion and does ccd-loop closure afterwards

Reimplemented in protocols::simple_moves::LoggedFragmentMover, protocols::simple_moves::SymmetricFragmentMover, and protocols::simple_moves::WobbleMover.

Referenced by protocols::simple_moves::SymmetricFragmentMover::apply_fragment(), protocols::simple_moves::LoggedFragmentMover::apply_fragment(), and apply_frames().

bool protocols::simple_moves::ClassicFragmentMover::apply_frames ( core::pose::Pose ,
core::fragment::FrameList const &   
) const [protected, virtual]
bool protocols::simple_moves::ClassicFragmentMover::check_ss ( ) const [inline]

accessor

Referenced by apply_frames().

virtual bool protocols::simple_moves::ClassicFragmentMover::choose_fragment ( core::fragment::FrameList const &  ,
core::pose::Pose const &  ,
Size frame_num,
Size frag_num 
) const [virtual]

given FrameList and pose, this method yields a fragment ( frame_num/ frag_num); return false if nothing suitable is found

Reimplemented in protocols::simple_moves::SmoothFragmentMover, and protocols::simple_moves::SmoothSymmetricFragmentMover.

Referenced by apply_frames().

virtual bool protocols::simple_moves::ClassicFragmentMover::choose_window_length ( core::pose::Pose const &  ,
Size window_length 
) const [inline, virtual]

yields a length (window_length) of the fragment window to sample from ( return false, if no suitable length is found )

Referenced by apply().

bool protocols::simple_moves::ClassicFragmentMover::choose_window_start ( core::pose::Pose const &  pose,
Size  window_length,
Size window_start 
) const [virtual]

yields a start position (window_start) for fragment window to sample from ( return false, if nothing suitable is found )

References end_bias_check(), protocols::simple_moves::FragmentMover::insert_map_, protocols::simple_moves::FragmentMover::insert_size_, protocols::simple_moves::RG(), and protocols::simple_moves::tr().

Referenced by apply().

void protocols::simple_moves::ClassicFragmentMover::define_start_window ( Size  window_start)

apply fragment at predefined position

void protocols::simple_moves::ClassicFragmentMover::enable_end_bias_check ( bool  setting = true) [inline]
core::Real protocols::simple_moves::ClassicFragmentMover::end_bias ( ) const [inline]

Referenced by end_bias_check().

bool protocols::simple_moves::ClassicFragmentMover::end_bias_check ( core::pose::Pose const &  pose,
Size  begin 
) const [virtual]

accept with probability 1 if the fragment window is centered on the center of the protein. accept with probability .3677 if the fragment window is centered end-bias residues away from the center of the protein

References make_table_of_pilot_apps::begin, core::kinematics::FoldTree::count_fixed_residues(), end_bias(), core::pose::Pose::fold_tree(), protocols::simple_moves::FragmentMover::insert_size_, core::pose::symmetry::is_symmetric(), protocols::simple_moves::RG(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and protocols::simple_moves::tr().

Referenced by choose_window_start().

bool protocols::simple_moves::ClassicFragmentMover::end_bias_check_enabled ( ) const [inline]
std::string protocols::simple_moves::ClassicFragmentMover::get_name ( ) const [virtual]
void protocols::simple_moves::ClassicFragmentMover::on_new_fragments ( ) [inline, virtual]

is called from set_fragments()

Reimplemented from protocols::simple_moves::FragmentMover.

void protocols::simple_moves::ClassicFragmentMover::set_check_ss ( bool  setting) [inline]
void protocols::simple_moves::ClassicFragmentMover::set_defaults ( ) [virtual]

set defaults

Reimplemented in protocols::simple_moves::WobbleMover.

Referenced by ClassicFragmentMover().

void protocols::simple_moves::ClassicFragmentMover::set_end_bias ( core::Real  setting) [inline]
void protocols::simple_moves::ClassicFragmentMover::set_min_frag_length ( Size  setting) [inline]

min_frag_length controls the behaviour fragset->region()

void protocols::simple_moves::ClassicFragmentMover::set_min_overlap ( Size  setting) [inline]

min_overlap controls the behaviour fragset->region()

bool protocols::simple_moves::ClassicFragmentMover::valid_ss ( std::string const &  new_ss) const [virtual]

returns true if the ss string is acceptable

DONT ALLOW HELICES OF LESS THAN 3 OR STRANDS OF LESS THAN 2 Fix this: inserting length two helices at the chain end is allowed as is inserting length 1 strands... For the moment, preserving r++'s incorrect behavior.

References protocols::simple_moves::tr().

Referenced by apply_frames().


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