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Rosetta
2016.11
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A FragmentMover that applies uniform sampling of fragments. More...
#include <FragmentMover.hh>
Public Member Functions | |
ClassicFragmentMover () | |
Empty constructor. More... | |
ClassicFragmentMover (core::fragment::FragSetCOP fragset) | |
Constructor with supplied FragSet. More... | |
ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap) | |
Constructor with supplied FragSet and MoveMap. More... | |
ClassicFragmentMover (core::fragment::ConstantLengthFragSet const &fragset, core::kinematics::MoveMap const &movemap) | |
Constructor with supplied ConstantLengthFragSet and MoveMap. More... | |
~ClassicFragmentMover () | |
virtual void | apply (core::pose::Pose &) |
Applies classic fragment insertion based on a FragSet. More... | |
virtual std::string | get_name () const |
Each derived class must specify its name. The class name. More... | |
virtual void | show (std::ostream &output=std::cout) const |
Outputs details about the Mover, including current settings. More... | |
virtual protocols::moves::MoverOP | clone () const |
Return a clone of the Mover object. More... | |
virtual protocols::moves::MoverOP | fresh_instance () const |
Generates a new Mover object freshly created with the default ctor. More... | |
void | set_check_ss (bool setting) |
check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2) More... | |
bool | check_ss () const |
accessor More... | |
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() More... | |
void | set_min_frag_length (Size setting) |
min_frag_length controls the behaviour fragset->region() More... | |
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 More... | |
virtual void | set_defaults () |
set defaults More... | |
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 More... | |
void | define_start_window (Size window_start) |
apply fragment at predefined position More... | |
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 ) More... | |
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 ) More... | |
void | on_new_fragments () |
is called from set_fragments() More... | |
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 More... | |
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~FragmentMover () | |
virtual bool | apply (core::pose::Pose &, Size pos) const |
apply a fragment at pos to movemable dofs More... | |
virtual Size | apply_at_all_positions (core::pose::Pose &) const |
apply at all movemable positions — honors movemap More... | |
core::fragment::FragSetCOP | fragments () const |
accessor to the fragment set More... | |
virtual void | set_fragments (core::fragment::FragSetCOP new_frags_) |
setter for the fragment set More... | |
virtual void | set_movemap (core::kinematics::MoveMapCOP movemap) |
setter for the movemap More... | |
core::kinematics::MoveMapCOP | movemap () const |
core::fragment::InsertMap const & | insert_map () const |
core::fragment::InsertSize const & | insert_size () const |
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MoveMapMover () | |
MoveMapMover (std::string const &name) | |
MoveMapMover (MoveMapMover const &other) | |
virtual | ~MoveMapMover () |
virtual void | initialize (core::pose::Pose &) |
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Mover () | |
virtual | ~Mover () |
virtual MoverOP | create () |
MoverCOP | get_self_ptr () const |
MoverOP | get_self_ptr () |
MoverCAP | get_self_weak_ptr () const |
MoverAP | get_self_weak_ptr () |
Mover (std::string const &type_name) | |
sets the type for a mover; name_ has been removed (2010/05/14) More... | |
Mover (Mover const &other) | |
Mover & | operator= (Mover const &other) |
assignment operator More... | |
virtual core::Real | last_proposal_density_ratio () |
std::string const & | type () const |
void | set_type (std::string const &setting) |
std::string | get_current_tag () const |
A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More... | |
virtual void | set_current_tag (std::string const &new_tag) |
virtual void | set_input_pose (PoseCOP pose) |
setter for poses contained for rms More... | |
virtual void | set_native_pose (PoseCOP pose) |
setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More... | |
PoseCOP | get_input_pose () const |
PoseCOP | get_native_pose () const |
virtual void | test_move (Pose &pose) |
: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More... | |
void | type (const std::string &type_in) |
virtual void | parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose) |
Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More... | |
std::string | get_type () const |
MoverStatus | get_last_move_status () const |
end parser interface, start Job Distributor interface///////////// More... | |
void | reset_status () |
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More... | |
virtual core::pose::PoseOP | get_additional_output () |
Mechanism by which a mover may return multiple output poses from a single input pose. More... | |
virtual void | clear_info () |
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More... | |
virtual Strings & | info () |
non-const accessor More... | |
virtual Strings const & | info () const |
const accessor More... | |
virtual bool | reinitialize_for_each_job () const |
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More... | |
virtual bool | reinitialize_for_new_input () const |
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More... | |
void | set_current_job (protocols::jobdist::BasicJobCOP job) |
jobdist::BasicJobCOP | get_current_job () const |
Protected Member Functions | |
ClassicFragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, std::string type) | |
alternative Constructor to be used by derived classes More... | |
ClassicFragmentMover (core::fragment::FragSetCOP fragset, std::string type) | |
alternative Constructor to be used by derived classes More... | |
virtual bool | apply_frames (core::pose::Pose &, core::fragment::FrameList const &) const |
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FragmentMover (std::string type) | |
Empty constructor. More... | |
FragmentMover (core::fragment::FragSetCOP fragset, std::string type) | |
FragmentMover (core::fragment::FragSetCOP fragset, core::kinematics::MoveMapCOP movemap, std::string type) | |
constructor More... | |
void | update_insert_map () |
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void | set_last_move_status (MoverStatus status) |
nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More... | |
Private Attributes | |
Size | min_overlap_ |
Size | min_frag_length_ |
bool | check_ss_ |
core::Real | end_bias_ |
bool | bApplyEndBias_ |
bool | use_predefined_window_start_ |
Size | predefined_window_start_ |
Additional Inherited Members | |
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typedef utility::tag::TagCOP | TagCOP |
typedef core::pose::Pose | Pose |
typedef core::pose::PoseCOP | PoseCOP |
typedef protocols::filters::Filters_map | Filters_map |
typedef std::list< std::string > | Strings |
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static std::string | name () |
static void | register_options () |
Overload this static method if you access options within the mover. More... | |
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core::fragment::FragSetCOP | fragset_ |
core::kinematics::MoveMapCOP | movemap_ |
core::fragment::InsertMap | insert_map_ |
core::fragment::InsertSize | insert_size_ |
A FragmentMover that applies uniform sampling of fragments.
protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover | ( | ) |
protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover | ( | core::fragment::FragSetCOP | fragset | ) |
Constructor with supplied FragSet.
References set_defaults().
protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover | ( | core::fragment::FragSetCOP | fragset, |
core::kinematics::MoveMapCOP | movemap | ||
) |
Constructor with supplied FragSet and MoveMap.
References set_defaults().
protocols::simple_moves::ClassicFragmentMover::ClassicFragmentMover | ( | core::fragment::ConstantLengthFragSet const & | fragset, |
core::kinematics::MoveMap const & | movemap | ||
) |
Constructor with supplied ConstantLengthFragSet and MoveMap.
References set_defaults().
protocols::simple_moves::ClassicFragmentMover::~ClassicFragmentMover | ( | ) |
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alternative Constructor to be used by derived classes
References set_defaults().
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alternative Constructor to be used by derived classes
References set_defaults().
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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::moves::Mover.
References apply_frames(), choose_window_length(), choose_window_start(), protocols::simple_moves::FragmentMover::fragset_, protocols::simple_moves::FragmentMover::insert_size_, min_frag_length_, min_overlap_, protocols::simple_moves::FragmentMover::movemap(), predefined_window_start_, protocols::simple_moves::tr(), protocols::simple_moves::FragmentMover::update_insert_map(), and use_predefined_window_start_.
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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::WobbleMover, and protocols::simple_moves::SymmetricFragmentMover.
Referenced by protocols::simple_moves::SymmetricFragmentMover::apply_fragment(), protocols::simple_moves::LoggedFragmentMover::apply_fragment(), protocols::simple_moves::ResTypeFragmentMover::apply_frames(), and apply_frames().
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Implements protocols::simple_moves::FragmentMover.
Reimplemented in protocols::simple_moves::ResTypeFragmentMover.
References apply_fragment(), check_ss(), choose_fragment(), protocols::simple_moves::FragmentMover::movemap_, core::pose::Pose::secstruct(), core::pose::Pose::total_residue(), protocols::simple_moves::tr(), and valid_ss().
Referenced by apply().
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accessor
References check_ss_.
Referenced by protocols::simple_moves::ResTypeFragmentMover::apply_frames(), and apply_frames().
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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::SmoothSymmetricFragmentMover, and protocols::simple_moves::SmoothFragmentMover.
References core::chemical::element::N, and core::scoring::rg.
Referenced by protocols::simple_moves::ResTypeFragmentMover::apply_frames(), and apply_frames().
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yields a length (window_length) of the fragment window to sample from ( return false, if no suitable length is found )
Referenced by apply().
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yields a start position (window_start) for fragment window to sample from ( return false, if nothing suitable is found )
References bApplyEndBias_, end_bias_check(), protocols::simple_moves::FragmentMover::insert_map_, protocols::simple_moves::FragmentMover::insert_size_, core::scoring::rg, and protocols::simple_moves::tr().
Referenced by apply().
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Return a clone of the Mover object.
clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.
Reimplemented from protocols::moves::Mover.
References ClassicFragmentMover().
void protocols::simple_moves::ClassicFragmentMover::define_start_window | ( | Size | window_start | ) |
apply fragment at predefined position
References predefined_window_start_, and use_predefined_window_start_.
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References bApplyEndBias_.
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References end_bias_.
Referenced by end_bias_check().
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References core::kinematics::FoldTree::count_fixed_residues(), end_bias(), core::pose::Pose::fold_tree(), protocols::simple_moves::FragmentMover::insert_size_, core::pose::symmetry::is_symmetric(), core::scoring::rg, core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and protocols::simple_moves::tr().
Referenced by choose_window_start().
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References bApplyEndBias_.
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Generates a new Mover object freshly created with the default ctor.
fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.
Reimplemented from protocols::moves::Mover.
References ClassicFragmentMover().
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Each derived class must specify its name. The class name.
Reimplemented from protocols::simple_moves::FragmentMover.
Reimplemented in protocols::simple_moves::LoggedFragmentMover, protocols::simple_moves::SmoothSymmetricFragmentMover, protocols::simple_moves::SmoothFragmentMover, protocols::simple_moves::WobbleMover, and protocols::simple_moves::SymmetricFragmentMover.
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is called from set_fragments()
Reimplemented from protocols::simple_moves::FragmentMover.
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check_ss controls whether fragment insertions are rejected that create short helices (<3) or strands (<2)
References check_ss_.
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set defaults
Reimplemented in protocols::simple_moves::WobbleMover.
References bApplyEndBias_, check_ss_, end_bias_, min_frag_length_, min_overlap_, predefined_window_start_, and use_predefined_window_start_.
Referenced by ClassicFragmentMover().
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References end_bias_.
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min_frag_length controls the behaviour fragset->region()
References min_frag_length_.
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min_overlap controls the behaviour fragset->region()
References min_overlap_.
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Outputs details about the Mover, including current settings.
Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.
Reimplemented from protocols::moves::Mover.
Reimplemented in protocols::simple_moves::LoggedFragmentMover.
References bApplyEndBias_, check_ss_, end_bias_, min_frag_length_, min_overlap_, protocols::simple_moves::FragmentMover::movemap(), predefined_window_start_, protocols::moves::Mover::show(), and use_predefined_window_start_.
Referenced by protocols::simple_moves::operator<<().
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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 protocols::simple_moves::ResTypeFragmentMover::apply_frames(), and apply_frames().
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Referenced by choose_window_start(), enable_end_bias_check(), end_bias_check_enabled(), set_defaults(), and show().
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Referenced by check_ss(), set_check_ss(), set_defaults(), and show().
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Referenced by end_bias(), set_defaults(), set_end_bias(), and show().
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Referenced by apply(), set_defaults(), set_min_frag_length(), and show().
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Referenced by apply(), set_defaults(), set_min_overlap(), and show().
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Referenced by apply(), define_start_window(), set_defaults(), and show().
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Referenced by apply(), define_start_window(), set_defaults(), and show().