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protocols::anchored_design::AnchoredDesignMover Class Reference

#include <AnchorMovers.hh>

Inheritance diagram for protocols::anchored_design::AnchoredDesignMover:
Inheritance graph
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Public Member Functions

 AnchoredDesignMover (protocols::anchored_design::AnchorMoversDataOP interface_in)
 constructor with arguments More...
 
 AnchoredDesignMover ()
 ctor with no arguments More...
 
 AnchoredDesignMover (AnchoredDesignMover const &rhs)
 copy ctor More...
 
AnchoredDesignMoveroperator= (AnchoredDesignMover const &rhs)
 assignment operator More...
 
 ~AnchoredDesignMover () override
 
void apply (core::pose::Pose &pose) override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
bool reinitialize_for_new_input () const override
 
bool reinitialize_for_each_job () const override
 Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void set_fold_tree_and_cutpoints (core::pose::Pose &pose)
 creates the anchored design fold tree and applies it to the pose More...
 
void filter (core::pose::Pose &pose)
 runs varous filtering checks on the finished pose; sets MoverStatus for failure as needed More...
 
void forget_initial_loops (core::pose::Pose &pose)
 implements the "extended" field of the loop file specification - sets extended phi/psi as needed More...
 
void calculate_rmsd (core::pose::Pose const &pose, core::pose::PoseCOP start_pose)
 calculate RMSD if desired; protected internally More...
 
void randomize_input_sequence (core::pose::Pose &pose) const
 randomize the input loop sequence. Useful if you have reason to believe the starting loop sequence is biasing to a particular unwanted structure in centroid mode. Acts only on designable positions. More...
 
void delete_interface_native_sidechains (core::pose::Pose &pose) const
 This function repacks the interface with use_input_sc forcibly off for benchmarking purposes. More...
 
void perturb_anchor (core::pose::Pose &pose) const
 handles perturbing the initial anchor placement More...
 
bool get_rmsd () const
 run RMSD calculations More...
 
std::string const & get_RMSD_only_this () const
 run only RMSD calculations against this input, don't do actual AnchoredDesign More...
 
bool get_delete_interface_native_sidechains () const
 delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode More...
 
bool get_show_extended () const
 show_extended demonstrates that the code really forgets the input structure More...
 
bool get_randomize_input_sequence () const
 randomize_input_sequence to complement loop extension in forgetting the input More...
 
bool get_vary_cutpoints () const
 pick a different cutpoint than the input; useful when you want to sample cutpoints More...
 
bool get_refine_only () const
 skip the perturbation step - useful when you already have a good structure More...
 
core::Real get_filter_score () const
 filter based on total complex score More...
 
core::Real get_filter_SASA () const
 filter based on complex SASA More...
 
bool get_filter_omega () const
 filter based on omega angles in the loops - filter out cis omegas More...
 
bool get_autoinitialize () const
 whether to automatically initialize from the options system; defaults to true More...
 
void set_rmsd (bool const rmsd)
 run RMSD calculations More...
 
void set_RMSD_only_this (std::string const &RMSD_only_this)
 run only RMSD calculations against this input, don't do actual AnchoredDesign More...
 
void set_delete_interface_native_sidechains (bool const delete_interface_native_sidechains)
 delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode More...
 
void set_show_extended (bool const show_extended)
 show_extended demonstrates that the code really forsets the input structure More...
 
void set_randomize_input_sequence (bool const randomize_input_sequence)
 randomize_input_sequence to complement loop extension in forgetting the input More...
 
void set_vary_cutpoints (bool const vary_cutpoints)
 pick a different cutpoint than the input; useful when you want to sample cutpoints More...
 
void set_refine_only (bool const refine_only)
 skip the perturbation step - useful when you already have a good structure More...
 
void set_filter_score (core::Real const filter_score)
 filter based on total complex score More...
 
void set_filter_SASA (core::Real const filter_SASA)
 filter based on complex SASA More...
 
void set_filter_omega (bool const filter_omega)
 filter based on omega angles in the loops - filter out cis omegas More...
 
void set_autoinitialize (bool const autoinitialize)
 whether to automatically initialize from the options system; defaults to true More...
 
void read_options ()
 read in options from the options system 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...
 
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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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...
 

Private Member Functions

void init_on_new_input (core::pose::Pose const &pose)
 internals; must wait for a pose to initialize More...
 

Private Attributes

protocols::anchored_design::AnchorMoversDataOP interface_
 
core::pose::PoseCOP RMSD_only_this_pose_
 
protocols::analysis::InterfaceAnalyzerMoverOP IAM_
 
bool rmsd_
 run RMSD calculations More...
 
std::string RMSD_only_this_
 run only RMSD calculations against this input, don't do actual AnchoredDesign More...
 
bool delete_interface_native_sidechains_
 delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode More...
 
bool show_extended_
 show_extended demonstrates that the code really forgets the input structure More...
 
bool randomize_input_sequence_
 randomize_input_sequence to complement loop extension in forgetting the input More...
 
bool vary_cutpoints_
 pick a different cutpoint than the input; useful when you want to sample cutpoints More...
 
bool refine_only_
 skip the perturbation step - useful when you already have a good structure More...
 
core::Real filter_score_
 filter based on total complex score More...
 
bool use_filter_score_
 filter based on total complex score More...
 
core::Real filter_SASA_
 filter based on complex SASA More...
 
bool use_filter_SASA_
 filter based on complex SASA More...
 
bool use_filter_omega_
 filter based on omega angles in the loops - filter out cis omegas More...
 
bool autoinitialize_
 whether to automatically initialize from the options system; defaults to true More...
 
bool init_for_input_yet_
 used to determine the validity of the rest of the internals, especially the interface_ object More...
 

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
 
- 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 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...
 

Constructor & Destructor Documentation

protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover ( protocols::anchored_design::AnchorMoversDataOP  interface_in)

constructor with arguments

References protocols::moves::Mover::type().

protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover ( )

ctor with no arguments

References protocols::moves::Mover::type().

protocols::anchored_design::AnchoredDesignMover::AnchoredDesignMover ( AnchoredDesignMover const &  rhs)

copy ctor

protocols::anchored_design::AnchoredDesignMover::~AnchoredDesignMover ( )
overridedefault

Member Function Documentation

void protocols::anchored_design::AnchoredDesignMover::apply ( core::pose::Pose pose)
overridevirtual
void protocols::anchored_design::AnchoredDesignMover::calculate_rmsd ( core::pose::Pose const &  pose,
core::pose::PoseCOP  start_pose 
)
protocols::moves::MoverOP protocols::anchored_design::AnchoredDesignMover::clone ( ) const
overridevirtual

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.

void protocols::anchored_design::AnchoredDesignMover::delete_interface_native_sidechains ( core::pose::Pose pose) const

This function repacks the interface with use_input_sc forcibly off for benchmarking purposes.

For benchmarking, it is a minor sin to allow native sidechains to leak through from the starting structure. AnchoredDesign runs best with use_input_sc because it does sidechain minimization, not because it needs starting sidechains. This function deletes the native sidechains by repacking the interface with use_input_sc forcibly off. DO NOT USE THIS FUNCTION for proper designs - it is meant for a specific benchmarking purpose.

References core::sequence::end, core::pack::task::EX_ONE_STDDEV, interface_, and core::pose::Pose::size().

Referenced by apply(), and set_delete_interface_native_sidechains().

void protocols::anchored_design::AnchoredDesignMover::filter ( core::pose::Pose pose)
void protocols::anchored_design::AnchoredDesignMover::forget_initial_loops ( core::pose::Pose pose)

implements the "extended" field of the loop file specification - sets extended phi/psi as needed

implements the is_extended boolean for the Loop class. If the boolean is on, this function resets phi/psi for those regions to be extended (-150phi, 150psi). This function does not affect omega, or residues outside of defined loops, or the anchor.

References interface_, core::pose::Pose::set_phi(), and core::pose::Pose::set_psi().

Referenced by apply().

protocols::moves::MoverOP protocols::anchored_design::AnchoredDesignMover::fresh_instance ( ) const
overridevirtual

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.

bool protocols::anchored_design::AnchoredDesignMover::get_autoinitialize ( ) const

whether to automatically initialize from the options system; defaults to true

References autoinitialize_.

Referenced by operator=().

bool protocols::anchored_design::AnchoredDesignMover::get_delete_interface_native_sidechains ( ) const

delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode

References delete_interface_native_sidechains_.

Referenced by operator=().

bool protocols::anchored_design::AnchoredDesignMover::get_filter_omega ( ) const

filter based on omega angles in the loops - filter out cis omegas

References use_filter_omega_.

Referenced by operator=().

core::Real protocols::anchored_design::AnchoredDesignMover::get_filter_SASA ( ) const

filter based on complex SASA

References filter_SASA_.

Referenced by operator=().

core::Real protocols::anchored_design::AnchoredDesignMover::get_filter_score ( ) const

filter based on total complex score

References filter_score_.

Referenced by operator=().

std::string protocols::anchored_design::AnchoredDesignMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

bool protocols::anchored_design::AnchoredDesignMover::get_randomize_input_sequence ( ) const

randomize_input_sequence to complement loop extension in forgetting the input

References randomize_input_sequence_.

Referenced by operator=().

bool protocols::anchored_design::AnchoredDesignMover::get_refine_only ( ) const

skip the perturbation step - useful when you already have a good structure

References refine_only_.

Referenced by operator=().

bool protocols::anchored_design::AnchoredDesignMover::get_rmsd ( ) const

run RMSD calculations

References rmsd_.

Referenced by operator=().

std::string const & protocols::anchored_design::AnchoredDesignMover::get_RMSD_only_this ( ) const

run only RMSD calculations against this input, don't do actual AnchoredDesign

References RMSD_only_this_.

Referenced by operator=().

bool protocols::anchored_design::AnchoredDesignMover::get_show_extended ( ) const

show_extended demonstrates that the code really forgets the input structure

References show_extended_.

Referenced by operator=().

bool protocols::anchored_design::AnchoredDesignMover::get_vary_cutpoints ( ) const

pick a different cutpoint than the input; useful when you want to sample cutpoints

References vary_cutpoints_.

Referenced by operator=().

void protocols::anchored_design::AnchoredDesignMover::init_on_new_input ( core::pose::Pose const &  pose)
private
AnchoredDesignMover & protocols::anchored_design::AnchoredDesignMover::operator= ( AnchoredDesignMover const &  rhs)
void protocols::anchored_design::AnchoredDesignMover::perturb_anchor ( core::pose::Pose pose) const
void protocols::anchored_design::AnchoredDesignMover::randomize_input_sequence ( core::pose::Pose pose) const

randomize the input loop sequence. Useful if you have reason to believe the starting loop sequence is biasing to a particular unwanted structure in centroid mode. Acts only on designable positions.

This is crazy. Sometimes loop redesign is overly biased by the starting loop sequence, because the centroid phase won't change the sequence, and the rama term may remember the conformation to well due to sequence preferences. This restricts sampling. So, this function creates a random sequence in the designable positions, based on what the design PackerTask thinks they can become. This code special cases histidine (to avoid double-allowing histidine, based on its two protonations).

References core::chemical::aa_his, protocols::mean_field::add(), core::pose::Pose::conformation(), interface_, core::pose::Pose::replace_residue(), core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::size(), T_design(), and protocols::moves::Mover::type().

Referenced by apply(), and set_randomize_input_sequence().

void protocols::anchored_design::AnchoredDesignMover::read_options ( )
bool protocols::anchored_design::AnchoredDesignMover::reinitialize_for_each_job ( ) const
overridevirtual

Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use.

Movers default to not regenerating

Reimplemented from protocols::moves::Mover.

bool protocols::anchored_design::AnchoredDesignMover::reinitialize_for_new_input ( ) const
overridevirtual

generally returns true; will return false for RMSD_only_this mode

Reimplemented from protocols::moves::Mover.

References protocols::anchored_design::EMPTY_STRING(), and RMSD_only_this_.

void protocols::anchored_design::AnchoredDesignMover::set_autoinitialize ( bool const  autoinitialize)

whether to automatically initialize from the options system; defaults to true

References autoinitialize_.

void protocols::anchored_design::AnchoredDesignMover::set_delete_interface_native_sidechains ( bool const  delete_interface_native_sidechains)

delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode

References delete_interface_native_sidechains(), and delete_interface_native_sidechains_.

void protocols::anchored_design::AnchoredDesignMover::set_filter_omega ( bool const  filter_omega)

filter based on omega angles in the loops - filter out cis omegas

References use_filter_omega_.

void protocols::anchored_design::AnchoredDesignMover::set_filter_SASA ( core::Real const  filter_SASA)

filter based on complex SASA

References filter_SASA_, and use_filter_SASA_.

void protocols::anchored_design::AnchoredDesignMover::set_filter_score ( core::Real const  filter_score)

filter based on total complex score

References filter_score_, and use_filter_score_.

void protocols::anchored_design::AnchoredDesignMover::set_fold_tree_and_cutpoints ( core::pose::Pose pose)
void protocols::anchored_design::AnchoredDesignMover::set_randomize_input_sequence ( bool const  randomize_input_sequence)

randomize_input_sequence to complement loop extension in forgetting the input

References randomize_input_sequence(), and randomize_input_sequence_.

void protocols::anchored_design::AnchoredDesignMover::set_refine_only ( bool const  refine_only)

skip the perturbation step - useful when you already have a good structure

References refine_only_.

void protocols::anchored_design::AnchoredDesignMover::set_rmsd ( bool const  rmsd)

run RMSD calculations

References rmsd_.

void protocols::anchored_design::AnchoredDesignMover::set_RMSD_only_this ( std::string const &  RMSD_only_this)

run only RMSD calculations against this input, don't do actual AnchoredDesign

References RMSD_only_this_.

void protocols::anchored_design::AnchoredDesignMover::set_show_extended ( bool const  show_extended)

show_extended demonstrates that the code really forsets the input structure

References show_extended_.

void protocols::anchored_design::AnchoredDesignMover::set_vary_cutpoints ( bool const  vary_cutpoints)

pick a different cutpoint than the input; useful when you want to sample cutpoints

pick a different cutpoint than the input { _ = ;} useful when you want to sample cutpoints

References vary_cutpoints_.

Member Data Documentation

bool protocols::anchored_design::AnchoredDesignMover::autoinitialize_
private

whether to automatically initialize from the options system; defaults to true

Referenced by get_autoinitialize(), init_on_new_input(), operator=(), and set_autoinitialize().

bool protocols::anchored_design::AnchoredDesignMover::delete_interface_native_sidechains_
private

delete the input sidechains (independently from use_input_sc in the packer) - used to prevent leakage of sidechains in benchmarking mode

Referenced by apply(), get_delete_interface_native_sidechains(), operator=(), read_options(), and set_delete_interface_native_sidechains().

core::Real protocols::anchored_design::AnchoredDesignMover::filter_SASA_
private

filter based on complex SASA

Referenced by filter(), get_filter_SASA(), operator=(), read_options(), and set_filter_SASA().

core::Real protocols::anchored_design::AnchoredDesignMover::filter_score_
private

filter based on total complex score

Referenced by filter(), get_filter_score(), operator=(), read_options(), and set_filter_score().

protocols::analysis::InterfaceAnalyzerMoverOP protocols::anchored_design::AnchoredDesignMover::IAM_
private

Referenced by apply(), and operator=().

bool protocols::anchored_design::AnchoredDesignMover::init_for_input_yet_
private

used to determine the validity of the rest of the internals, especially the interface_ object

Referenced by apply(), init_on_new_input(), and operator=().

protocols::anchored_design::AnchorMoversDataOP protocols::anchored_design::AnchoredDesignMover::interface_
private
bool protocols::anchored_design::AnchoredDesignMover::randomize_input_sequence_
private

randomize_input_sequence to complement loop extension in forgetting the input

Referenced by apply(), get_randomize_input_sequence(), operator=(), read_options(), and set_randomize_input_sequence().

bool protocols::anchored_design::AnchoredDesignMover::refine_only_
private

skip the perturbation step - useful when you already have a good structure

Referenced by apply(), get_refine_only(), operator=(), read_options(), and set_refine_only().

bool protocols::anchored_design::AnchoredDesignMover::rmsd_
private

run RMSD calculations

Referenced by apply(), calculate_rmsd(), get_rmsd(), operator=(), read_options(), and set_rmsd().

std::string protocols::anchored_design::AnchoredDesignMover::RMSD_only_this_
private

run only RMSD calculations against this input, don't do actual AnchoredDesign

Referenced by apply(), get_RMSD_only_this(), init_on_new_input(), operator=(), read_options(), reinitialize_for_new_input(), and set_RMSD_only_this().

core::pose::PoseCOP protocols::anchored_design::AnchoredDesignMover::RMSD_only_this_pose_
private

used for RMSD comparisons with RMSD_only_this mode

Referenced by apply(), init_on_new_input(), and operator=().

bool protocols::anchored_design::AnchoredDesignMover::show_extended_
private

show_extended demonstrates that the code really forgets the input structure

Referenced by apply(), get_show_extended(), operator=(), read_options(), and set_show_extended().

bool protocols::anchored_design::AnchoredDesignMover::use_filter_omega_
private

filter based on omega angles in the loops - filter out cis omegas

Referenced by filter(), get_filter_omega(), operator=(), read_options(), and set_filter_omega().

bool protocols::anchored_design::AnchoredDesignMover::use_filter_SASA_
private

filter based on complex SASA

Referenced by filter(), operator=(), read_options(), and set_filter_SASA().

bool protocols::anchored_design::AnchoredDesignMover::use_filter_score_
private

filter based on total complex score

Referenced by filter(), operator=(), read_options(), and set_filter_score().

bool protocols::anchored_design::AnchoredDesignMover::vary_cutpoints_
private

pick a different cutpoint than the input; useful when you want to sample cutpoints

Referenced by apply(), get_vary_cutpoints(), operator=(), read_options(), and set_vary_cutpoints().


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