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protocols::loop_modeling::LoopBuilder Class Reference

Build loops from scratch. More...

#include <LoopBuilder.hh>

Inheritance diagram for protocols::loop_modeling::LoopBuilder:
Inheritance graph
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Public Member Functions

 LoopBuilder ()
 Default constructor. More...
 
 ~LoopBuilder () override
 Default destructor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Return the name of this mover. More...
 
void use_fragments (utility::vector1< core::fragment::FragSetCOP > const &frag_libs)
 Use the given fragment libraries when building the loop. More...
 
core::Size get_max_attempts () const
 Return the number of times KIC will be invoked before the LoopBuilder gives up. More...
 
void set_max_attempts (core::Size attempts)
 Specify how many time to invoke KIC before giving up. More...
 
core::scoring::ScoreFunctionOP get_score_function () const
 Get the score function to be used on the next call to apply(). More...
 
void set_score_function (core::scoring::ScoreFunctionOP score_function)
 Set the score function to be used on the next call to apply(). More...
 
utilities::TrajectoryLoggerOP get_logger () const
 Return the object that report on the progress of the protocol. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
- Public Member Functions inherited from protocols::loop_modeling::LoopMover
 LoopMover ()
 Default constructor. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Configure from a RosettaScripts tag. More...
 
void apply (Pose &pose) override
 Sample the pose in the regions specified by get_loops(). More...
 
string get_name () const override
 Return the name of this mover. More...
 
virtual void get_children_names (utility::vector1< std::string > &names, std::string indent="") const
 Add the names of all the algorithms invoked by this loop mover to the given list. Indentation is used to represent hierarchy. More...
 
bool was_successful () const
 Return true if the previous move was successful. More...
 
void was_successful (bool value)
 Set the success status of a loop mover. More...
 
LoopsOP get_loops ()
 Return the loops to be sampled on the next call to apply(). More...
 
LoopsCOP get_loops () const
 Return the loops to be sampled on the next call to apply(). More...
 
Loop const & get_loop (core::Size index) const
 Return the specified loop. More...
 
void set_loops (LoopsOP loops)
 Set the loops 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_loop (Loop const &loop)
 Set the loop to be sampled on the next call to apply(). More...
 
template<typename ToolTypeOP >
ToolTypeOP get_tool (std::string key) const
 Request a tool from this mover or any of its parents. More...
 
template<typename ToolTypeOP >
ToolTypeOP get_tool (std::string key, ToolTypeOP fallback) const
 Request a tool from this mover or any of its parents. More...
 
template<typename ToolTypeOP >
ToolTypeOP set_tool (std::string key, ToolTypeOP value)
 Provide a tool for this mover or any of its children to use. 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, this mover will setup a fold tree on its own every time apply() is called. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 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...
 
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...
 
virtual MoverOP clone () const
 Return a clone of the Mover object. 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...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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 show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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 mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static void get_score_function_attributes (utility::tag::AttributeList &attlist)
 
- Static Public Member Functions inherited from protocols::loop_modeling::LoopMover
static void setup_fold_tree (Pose &pose, LoopsCOP loops, FoldTreeRequest request)
 Setup the given pose with a fold tree that is compatible with the given loops and requests. More...
 
static void define_composition_schema (utility::tag::XMLSchemaDefinition &xsd, utility::tag::XMLSchemaComplexTypeGenerator &ct_gen, utility::tag::XMLSchemaSimpleSubelementList &subelements)
 
- 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...
 

Protected Member Functions

bool do_apply (Pose &pose, Loop const &loop) override
 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...
 
template<typename ChildSubclassOP >
ChildSubclassOP add_child (ChildSubclassOP child)
 Add a child to this mover. More...
 
void remove_child (LoopMoverOP child)
 Remove a child from this mover. More...
 
void clear_children ()
 Remove all children from this mover. More...
 
LoopMoverOPs get_children () const
 Return all of this mover's children. More...
 
core::Size count_children () const
 Return the number of children this mover has. 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 Member Functions

void idealize_loop (Pose &pose, Loop const &loop, core::kinematics::FoldTree &ft) const
 Idealize the loop with a give fold tree The fold tree of the pose is restored after the idealization. More...
 

Private Attributes

protocols::kinematic_closure::KicMoverOP kic_mover_
 
refiners::MinimizationRefinerOP minimizer_
 
utilities::TrajectoryLoggerOP logger_
 
core::Size max_attempts_
 

Friends

class ::LoopModelerTests
 

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 std::list< std::string > Strings
 

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.

protocols::loop_modeling::LoopBuilder::~LoopBuilder ( )
overridedefault

Default destructor.

Member Function Documentation

bool protocols::loop_modeling::LoopBuilder::do_apply ( Pose pose,
Loop const &  loop 
)
overrideprotectedvirtual
utilities::TrajectoryLoggerOP protocols::loop_modeling::LoopBuilder::get_logger ( ) const

Return the object that report on the progress of the protocol.

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
overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

ScoreFunctionOP protocols::loop_modeling::LoopBuilder::get_score_function ( ) const

Get the score function to be used on the next call to apply().

void protocols::loop_modeling::LoopBuilder::get_score_function_attributes ( utility::tag::AttributeList &  attlist)
static
void protocols::loop_modeling::LoopBuilder::idealize_loop ( Pose pose,
Loop const &  loop,
core::kinematics::FoldTree ft 
) const
private

Idealize the loop with a give fold tree The fold tree of the pose is restored after the idealization.

References core::pose::Pose::fold_tree(), and protocols::loops::idealize_loop().

string protocols::loop_modeling::LoopBuilder::mover_name ( )
static
void protocols::loop_modeling::LoopBuilder::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Return the name of this mover.

Configure from a RosettaScripts tag.

Reimplemented from protocols::moves::Mover.

References protocols::loop_modeling::utilities::set_scorefxn_from_tag().

void protocols::loop_modeling::LoopBuilder::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::loop_modeling::LoopBuilder::set_max_attempts ( core::Size  attempts)

Specify how many time to invoke KIC before giving up.

void protocols::loop_modeling::LoopBuilder::set_score_function ( core::scoring::ScoreFunctionOP  score_function)

Set the score function to be used on the next call to apply().

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

Use the given fragment libraries when building the loop.

Friends And Related Function Documentation

friend class ::LoopModelerTests
friend

Member Data Documentation

protocols::kinematic_closure::KicMoverOP protocols::loop_modeling::LoopBuilder::kic_mover_
private
utilities::TrajectoryLoggerOP protocols::loop_modeling::LoopBuilder::logger_
private
core::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: