Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::loop_modeling::LoopBuilder Class Reference

Build loops from scratch. More...

#include <LoopBuilder.hh>

Public Member Functions

 LoopBuilder ()
 Default constructor. More...
 
string get_name () const
 Return the name of this mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, protocols::filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, Pose const &pose)
 Configure from a RosettaScripts tag. More...
 
void use_fragments (utility::vector1< core::fragment::FragSetCOP > const &frag_libs)
 Use the given fragment libraries when building the loop. More...
 
void set_max_attempts (Size attempts)
 Specify how many time to invoke KIC before giving up. More...
 
Size get_max_attempts () const
 Return the number of times KIC will be invoked before the LoopBuilder gives up. More...
 
- Public Member Functions inherited from protocols::loop_modeling::LoopMover
 LoopMover ()
 Default constructor. More...
 
 ~LoopMover ()
 Default destructor. More...
 
void apply (Pose &pose)
 Sample the pose in the regions specified by get_loops(). More...
 
bool was_successful () const
 Return true if the previous move was successful. More...
 
Loops get_loops () const
 Return the loops to be sampled on the next call to apply(). More...
 
core::scoring::ScoreFunctionCOP get_score_function () const
 Return the score function to be used on the next call to apply(). More...
 
core::scoring::ScoreFunctionOP get_score_function ()
 Return the score function to be used on the next call to apply() (non-const access). More...
 
void set_loop (Loop const &loop)
 Set the loop to be sampled on the next call to apply(). More...
 
void set_loops (Loops const &loops)
 Set the loops to be sampled on the next call to apply(). More...
 
void set_score_function (core::scoring::ScoreFunctionOP sfxn)
 Set the score function to be used on the next call to apply(). More...
 
virtual FoldTreeRequest request_fold_tree () const
 Return an enum representing the kind of fold tree that is compatible with this mover. More...
 
void trust_fold_tree ()
 Promise that the calling code will setup a fold tree compatible with request_fold_tree(). If this method is not called, most movers will setup a fold tree on their own the first time apply() is called. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (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...
 
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 MoverOP clone () const
 Return a clone of the Mover object. 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 Stringsinfo ()
 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Protected Member Functions

bool do_apply (Pose &pose, Loop const &loop)
 Attempt to find a reasonable loop conformation without using any information from the original coordinates. More...
 
- Protected Member Functions inherited from protocols::loop_modeling::LoopMover
virtual bool do_apply (Pose &pose)
 Perform the loop sampling move. This method can be overwritten in child classes. More...
 
void dont_manage_score_function ()
 Disable all the LoopMover score function related methods. More...
 
template<class LoopMoverSubclassOP >
LoopMoverSubclassOP register_nested_loop_mover (LoopMoverSubclassOP mover)
 Indicate that the given loop mover is used within do_apply(). More...
 
void deregister_nested_loop_movers ()
 Drop association with any currently registered loop movers. More...
 
vector1< LoopMoverOP > const & get_nested_loop_movers () const
 Return a reference to the list of nested loop movers. More...
 
- Protected Member Functions inherited from protocols::moves::Mover
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

protocols::kinematic_closure::KicMoverOP kic_mover_
 
refiners::MinimizationRefinerOP minimizer_
 
Size max_attempts_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
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::stringStrings
 
- Static Public Member Functions inherited from protocols::loop_modeling::LoopMover
static void setup_fold_tree (Pose &pose, Loops const &loops, FoldTreeRequest request)
 Setup the given pose with a fold tree that is compatible with the given loops and requests. More...
 
- Static Public Member Functions inherited from protocols::moves::Mover
static std::string name ()
 
static void register_options ()
 Overload this static method if you access options within the mover. More...
 

Detailed Description

Build loops from scratch.

Author
Kale Kundert
Roland A. Pache, PhD

Building a loop from scratch is useful in two scenarios. The first is when there's missing density that needs to be modeled, and the second is when the whole loop modeling algorithm needs to be benchmarked. This mover uses kinematic closure (KIC) to build loops. By default, the loop are built by picking phi and psi values from a Ramachandran distribution and setting all other DOFs to ideal values. Phi and psi values can also be picked using fragment libraries. Loop building succeeds when a model is found that passes a more-lenient-than-usual bump check. If no such model is found after 1000 iterations, the mover gives up and reports failure.

This process can be very slow for long loops, because there's nothing guiding the algorithm towards the right solution. By default, torsions are just being randomly picked, and they often won't fit in the relatively narrow space that's available. The problem is worse for interior loops than it is for surface loops, of course. This algorithm seems to work well enough on 12 residue loops, but beyond that it may be necessary to develop a smarter algorithm that preferentially builds into free space.

Constructor & Destructor Documentation

protocols::loop_modeling::LoopBuilder::LoopBuilder ( )

Default constructor.

References option.

Member Function Documentation

bool protocols::loop_modeling::LoopBuilder::do_apply ( Pose pose,
Loop const &  loop 
)
protectedvirtual

Attempt to find a reasonable loop conformation without using any information from the original coordinates.

Reimplemented from protocols::loop_modeling::LoopMover.

References protocols::loops::Loop::is_extended(), and tr.

Size protocols::loop_modeling::LoopBuilder::get_max_attempts ( ) const

Return the number of times KIC will be invoked before the LoopBuilder gives up.

string protocols::loop_modeling::LoopBuilder::get_name ( ) const
inlinevirtual

Return the name of this mover.

Reimplemented from protocols::loop_modeling::LoopMover.

void protocols::loop_modeling::LoopBuilder::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
Pose const &  pose 
)
virtual

Configure from a RosettaScripts tag.

Reimplemented from protocols::moves::Mover.

void protocols::loop_modeling::LoopBuilder::set_max_attempts ( Size  attempts)

Specify how many time to invoke KIC before giving up.

void protocols::loop_modeling::LoopBuilder::use_fragments ( utility::vector1< core::fragment::FragSetCOP > const &  frag_libs)

Use the given fragment libraries when building the loop.

Member Data Documentation

protocols::kinematic_closure::KicMoverOP protocols::loop_modeling::LoopBuilder::kic_mover_
private
Size protocols::loop_modeling::LoopBuilder::max_attempts_
private
refiners::MinimizationRefinerOP protocols::loop_modeling::LoopBuilder::minimizer_
private

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