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protocols::helical_bundle::BackboneGridSampler Class Reference

#include <BackboneGridSampler.hh>

Inheritance diagram for protocols::helical_bundle::BackboneGridSampler:
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Public Types

typedef
protocols::cyclic_peptide::PeptideStubMover 
PeptideStubMover
 
typedef
protocols::cyclic_peptide::PeptideStubMoverOP 
PeptideStubMoverOP
 
typedef
protocols::cyclic_peptide::PeptideStubMoverCOP 
PeptideStubMoverCOP
 
typedef
protocols::helical_bundle::BackboneGridSamplerHelper 
BackboneGridSamplerHelper
 
typedef
protocols::helical_bundle::BackboneGridSamplerHelperOP 
BackboneGridSamplerHelperOP
 
typedef
protocols::helical_bundle::BackboneGridSamplerHelperCOP 
BackboneGridSamplerHelperCOP
 
- 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
 

Public Member Functions

 BackboneGridSampler ()
 Creator for BackboneGridSampler mover. More...
 
 BackboneGridSampler (BackboneGridSampler const &src)
 Copy constructor for BackboneGridSampler mover. More...
 
 ~BackboneGridSampler () override
 Destructor for BackboneGridSampler mover. More...
 
protocols::moves::MoverOP clone () const override
 Clone operator to create a pointer to a fresh BackboneGridSampler object that copies this one. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Fresh_instance operator to create a pointer to a fresh BackboneGridSampler object that does NOT copy this one. More...
 
void apply (core::pose::Pose &pose) override
 Actually apply the mover to the pose. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Returns the name of this mover ("BackboneGridSampler"). More...
 
void set_max_samples (core::Size const val)
 Set the maximum number of samples for the mover. More...
 
core::Size max_samples () const
 Get the maximum number of samples for the mover. More...
 
void set_selection_low (bool const val)
 Sets whether the selection should be for the lowest score value (true) or highest (false). More...
 
bool selection_low ()
 Returns whether the selection should be for the lowest score value (true) or highest (false). More...
 
void set_prescoring_mover (protocols::moves::MoverOP mover)
 Sets the mover that will be applied to all helical bundles generated prior to energy evaluation. More...
 
void set_prescoring_filter (protocols::filters::FilterOP filter)
 Sets the filter that will be applied to all helical bundles generated prior to energy evaluation. More...
 
bool prescoring_mover_exists () const
 Returns "true" if and only if a preselection mover has been assigned. More...
 
bool prescoring_filter_exists () const
 Returns "true" if and only if a preselection filter has been assigned. More...
 
void set_pdb_output (bool const val)
 Set whether the mover dumps pdbs or not. More...
 
bool pdb_output () const
 Returns whether the mover dumps pdbs or not. More...
 
void set_pdb_prefix (std::string const &prefix)
 Sets the filename prefix for PDB output. More...
 
std::string pdb_prefix ()
 Access the filename prefix for PDB output. More...
 
void set_sfxn (core::scoring::ScoreFunctionOP sfxn_in)
 Sets the scorefunction for this mover. More...
 
bool sfxn_set () const
 Returns whether the scorefunction has been set. More...
 
void set_nstruct_mode (bool const &val)
 Set the nstruct mode. More...
 
bool nstruct_mode () const
 Get the nstruct mode. More...
 
void set_nstruct_repeats (core::Size const val)
 Set the nstruct repeats. More...
 
core::Size nstruct_repeats () const
 Get the nstruct repeats. More...
 
void add_torsion_to_sample (core::Size const residue_index, core::Size const torsion_index, core::Real const &start_of_range, core::Real const &end_of_range, core::Size const samples)
 Add a mainchain torsion to sample, the range of values that will be sampled, and the number of samples. More...
 
void add_torsion_to_fix (core::Size const residue_index, core::Size const torsion_index, core::Real const &torsion_value)
 Add a mainchain torsion to fix, and that torsion's value. More...
 
void set_nres (core::Size const nres_in)
 Set the number of residues in the pose to build. More...
 
core::Size nres () const
 Get the number of residues in the pose to build. More...
 
void set_resname (core::Size const res_index, std::string const &resname_in)
 Set the residue type. More...
 
std::string resname (core::Size const res_index) const
 Get the residue type. More...
 
void set_cap_ends (bool cap)
 Set whether then ends should be capped (N-acetyl, C-methylamide). More...
 
bool cap_ends () const
 Return whether the ends should be capped (N-acetyl, C-methylamide). More...
 
void set_up_peptide_stub_mover ()
 Set up the PeptideStubMover object that will be used to build geometry. More...
 
bool peptide_stub_mover_initialized () const
 Has the PeptideStubMover been initialized? More...
 
void reset_and_initialize_data ()
 Reset the torsions_to_sample_, torsions_to_fix_, and resname_ vectors, and initialize them based on the value of residues_per_repeat_. More...
 
void set_residues_per_repeat (core::Size const val)
 Set the number of residues per repeat. More...
 
core::Size residues_per_repeat () const
 Get the number of residues per repeat. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const override
 Provides citation info for any published pre-scoring movers or filters, though this mover is unpublished and has no citation information of its own. More...
 
bool mover_is_unpublished () const override
 Indicate that this mover is unpublished. More...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provide authorship information for an unpublished Rosetta module. 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 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...
 
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...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Member Functions

bool is_in_list (core::Size const val, utility::vector1< core::Size > const &list) const
 Is a value in a list? More...
 
core::Size calculate_total_samples () const
 Calculate the number of grid points that will be sampled, based on the options set by the user. More...
 

Private Attributes

bool nstruct_mode_
 Should the parallel sampling be done based on the job (nstruct number)? More...
 
core::Size nstruct_mode_repeats_
 If nstruct_mode_ is true, how many times should each set of mainchain torsion values be repeated? More...
 
bool select_low_
 The selection type. If false, the pose with the highest score value is selected. If true, the pose with the lowest score value is selected. True by default. More...
 
core::Size max_samples_
 The maximum number of gridpoints allowed. More...
 
protocols::moves::MoverOP pre_scoring_mover_
 Owning pointer for an (optional) pre-selection mover applied to all helical bundles before energy evaluation. More...
 
bool pre_scoring_mover_exists_
 Bool determining whether there exists a pre-selection mover that wlil be applied. More...
 
protocols::filters::FilterOP pre_scoring_filter_
 Owning pointer for an (optional) pre-selection filter applied to all helical bundles after the pre-selection mover but before picking the lowest-energy solution. If PDBs are dumped, only those passing filters are dumped. More...
 
bool pre_scoring_filter_exists_
 Bool determining whether a pre-selection filter has been set. More...
 
bool dump_pdbs_
 Dump a PDB file for each bundle generated? False by default. More...
 
std::string pdb_prefix_
 PDB filename prefix. Filename will be of the form <prefix>_#####.pdb. More...
 
bool sfxn_set_
 Has the scorefunction been set? More...
 
core::scoring::ScoreFunctionOP sfxn_
 The scorefunction that this mover will use to pick the lowest-energy bundle. More...
 
core::Size residues_per_repeat_
 The number of residues in the repeating unit. More...
 
utility::vector1
< utility::vector1< std::pair
< core::Size, std::pair
< std::pair< core::Real,
core::Real >, core::Size > > > > 
torsions_to_sample_
 The list of mainchain torsions to sample, and the range of values. More...
 
utility::vector1
< utility::vector1< std::pair
< core::Size, core::Real > > > 
torsions_to_fix_
 The list of mainchain torsions to fix, and the values at which to fix them. More...
 
core::Size nres_
 The number of residues in the pose to build. More...
 
utility::vector1< std::string > resname_
 The residue type (full name) for the pose to build. More...
 
bool cap_ends_
 Should we add terminal caps (N-acetyl, C-methylamidation) to the polymer? More...
 
PeptideStubMoverOP peptide_stub_mover_
 A PeptideStubMover used to build the new pose. More...
 
bool peptide_stub_mover_initialized_
 Has the PeptideStubMover been initialized? More...
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::helical_bundle::BackboneGridSampler::BackboneGridSampler ( )

Creator for BackboneGridSampler mover.

References resname_, torsions_to_fix_, and torsions_to_sample_.

protocols::helical_bundle::BackboneGridSampler::BackboneGridSampler ( BackboneGridSampler const &  src)

Copy constructor for BackboneGridSampler mover.

protocols::helical_bundle::BackboneGridSampler::~BackboneGridSampler ( )
overridedefault

Destructor for BackboneGridSampler mover.

Member Function Documentation

void protocols::helical_bundle::BackboneGridSampler::add_torsion_to_fix ( core::Size const  residue_index,
core::Size const  torsion_index,
core::Real const &  torsion_value 
)

Add a mainchain torsion to fix, and that torsion's value.

The residue_index is the index of the residue in the repeating unit (1st, 2nd, 3rd, etc.). The torsion_index is the mainchain torsion index in this residue, and the torsion_value is the value at which to fix this residue.

References residues_per_repeat(), torsions_to_fix_, and torsions_to_sample_.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::add_torsion_to_sample ( core::Size const  residue_index,
core::Size const  torsion_index,
core::Real const &  start_of_range,
core::Real const &  end_of_range,
core::Size const  samples 
)

Add a mainchain torsion to sample, the range of values that will be sampled, and the number of samples.

The residue_index is the index in the repeating unit (1st residue, 2nd residue, etc.). The torsion_index is the mainchain torsion index in this residue. Sampled values will go from start_of_range to end_of_range, with the total number of samples given by the samples parameter. If the range is -180 to 180, the samples are adjusted so that 180 is not sampled twice.

References protocols::sic_dock::range(), residues_per_repeat(), torsions_to_fix_, and torsions_to_sample_.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::apply ( core::pose::Pose pose)
overridevirtual
core::Size protocols::helical_bundle::BackboneGridSampler::calculate_total_samples ( ) const
private

Calculate the number of grid points that will be sampled, based on the options set by the user.

References torsions_to_sample_.

Referenced by apply().

bool protocols::helical_bundle::BackboneGridSampler::cap_ends ( ) const
inline

Return whether the ends should be capped (N-acetyl, C-methylamide).

References cap_ends_.

Referenced by apply(), and parse_my_tag().

protocols::moves::MoverOP protocols::helical_bundle::BackboneGridSampler::clone ( ) const
overridevirtual

Clone operator to create a pointer to a fresh BackboneGridSampler object that copies this one.

Reimplemented from protocols::moves::Mover.

Referenced by parse_my_tag().

protocols::moves::MoverOP protocols::helical_bundle::BackboneGridSampler::fresh_instance ( ) const
overridevirtual

Fresh_instance operator to create a pointer to a fresh BackboneGridSampler object that does NOT copy this one.

Reimplemented from protocols::moves::Mover.

std::string protocols::helical_bundle::BackboneGridSampler::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

bool protocols::helical_bundle::BackboneGridSampler::is_in_list ( core::Size const  val,
utility::vector1< core::Size > const &  list 
) const
private

Is a value in a list?

core::Size protocols::helical_bundle::BackboneGridSampler::max_samples ( ) const
inline

Get the maximum number of samples for the mover.

If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted.

References max_samples_.

Referenced by apply().

bool protocols::helical_bundle::BackboneGridSampler::mover_is_unpublished ( ) const
overridevirtual

Indicate that this mover is unpublished.

Returns
True.

Reimplemented from protocols::moves::Mover.

std::string protocols::helical_bundle::BackboneGridSampler::mover_name ( )
static
core::Size protocols::helical_bundle::BackboneGridSampler::nres ( ) const
inline

Get the number of residues in the pose to build.

This is actually the number of REPEATS. If there are two residues per repeat, you'd have twice this number of resiudes.

References nres_.

Referenced by apply(), parse_my_tag(), and set_up_peptide_stub_mover().

bool protocols::helical_bundle::BackboneGridSampler::nstruct_mode ( ) const
inline

Get the nstruct mode.

If true, each job samples one set of mainchain torsion values. If false, every job samples every set of mainchain torsion values. False by default.

References nstruct_mode_.

Referenced by apply().

core::Size protocols::helical_bundle::BackboneGridSampler::nstruct_repeats ( ) const
inline

Get the nstruct repeats.

This is set to 1 by default, which means that each nstruct number correspnds to a different set of mainchain torsion values. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same mainchain torsion values. This allows combinatorially combining this mover's sampling with another, similar mover's sampling.

References nstruct_mode_repeats_.

Referenced by apply().

void protocols::helical_bundle::BackboneGridSampler::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data_map 
)
overridevirtual
bool protocols::helical_bundle::BackboneGridSampler::pdb_output ( ) const
inline

Returns whether the mover dumps pdbs or not.

References dump_pdbs_.

Referenced by apply().

std::string protocols::helical_bundle::BackboneGridSampler::pdb_prefix ( )
inline

Access the filename prefix for PDB output.

PDB files are of the form <prefix>_#####.pdb.

References pdb_prefix_.

Referenced by apply().

bool protocols::helical_bundle::BackboneGridSampler::peptide_stub_mover_initialized ( ) const
inline

Has the PeptideStubMover been initialized?

References peptide_stub_mover_initialized_.

Referenced by apply().

bool protocols::helical_bundle::BackboneGridSampler::prescoring_filter_exists ( ) const
inline

Returns "true" if and only if a preselection filter has been assigned.

References pre_scoring_filter_exists_.

Referenced by apply().

bool protocols::helical_bundle::BackboneGridSampler::prescoring_mover_exists ( ) const
inline

Returns "true" if and only if a preselection mover has been assigned.

References pre_scoring_mover_exists_.

Referenced by apply().

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::helical_bundle::BackboneGridSampler::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provide authorship information for an unpublished Rosetta module.

Also provides authorship information for unpublished pre-scoring movers or filters, if provided.

Reimplemented from protocols::moves::Mover.

References pre_scoring_filter_, and pre_scoring_mover_.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::helical_bundle::BackboneGridSampler::provide_citation_info ( ) const
overridevirtual

Provides citation info for any published pre-scoring movers or filters, though this mover is unpublished and has no citation information of its own.

Author
Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tute.nosp@m..org)

Reimplemented from protocols::moves::Mover.

References pre_scoring_filter_, and pre_scoring_mover_.

void protocols::helical_bundle::BackboneGridSampler::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::helical_bundle::BackboneGridSampler::reset_and_initialize_data ( )

Reset the torsions_to_sample_, torsions_to_fix_, and resname_ vectors, and initialize them based on the value of residues_per_repeat_.

References residues_per_repeat(), resname_, torsions_to_fix_, and torsions_to_sample_.

Referenced by set_residues_per_repeat().

core::Size protocols::helical_bundle::BackboneGridSampler::residues_per_repeat ( ) const
inline
std::string protocols::helical_bundle::BackboneGridSampler::resname ( core::Size const  res_index) const
inline

Get the residue type.

Returns the residue type (full name string) for the nth residue in the list of residues defining the repeating unit.

References resname_.

Referenced by apply(), parse_my_tag(), and set_up_peptide_stub_mover().

bool protocols::helical_bundle::BackboneGridSampler::selection_low ( )
inline

Returns whether the selection should be for the lowest score value (true) or highest (false).

References select_low_.

void protocols::helical_bundle::BackboneGridSampler::set_cap_ends ( bool  cap)
inline

Set whether then ends should be capped (N-acetyl, C-methylamide).

References cap_ends_.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_max_samples ( core::Size const  val)
inline

Set the maximum number of samples for the mover.

If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted.

References max_samples_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_nres ( core::Size const  nres_in)
inline

Set the number of residues in the pose to build.

This is actually the number of REPEATS. If there are two residues per repeat, you'd have twice this number of resiudes.

References nres_.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_nstruct_mode ( bool const &  val)
inline

Set the nstruct mode.

If true, each job samples one set of mainchain torsion values. If false, every job samples every set of mainchain torsion values. False by default.

References nstruct_mode_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_nstruct_repeats ( core::Size const  val)
inline

Set the nstruct repeats.

This is set to 1 by default, which means that each nstruct number correspnds to a different set of mainchain torsion values. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same mainchain torsion values. This allows combinatorially combining this mover's sampling with another, similar mover's sampling.

References nstruct_mode_repeats_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_pdb_output ( bool const  val)
inline

Set whether the mover dumps pdbs or not.

References dump_pdbs_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_pdb_prefix ( std::string const &  prefix)
inline

Sets the filename prefix for PDB output.

PDB files are of the form <prefix>_#####.pdb.

References pdb_prefix_.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_prescoring_filter ( protocols::filters::FilterOP  filter)

Sets the filter that will be applied to all helical bundles generated prior to energy evaluation.

See the pre_scoring_filter_ private member variable for details.

References pre_scoring_filter_, and pre_scoring_filter_exists_.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_prescoring_mover ( protocols::moves::MoverOP  mover)

Sets the mover that will be applied to all helical bundles generated prior to energy evaluation.

Note: if this is used, there is no guarantee that the resulting geometry will still lie within the parameter space. (That is, this mover could move the backbone.)

References pre_scoring_mover_, and pre_scoring_mover_exists_.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_residues_per_repeat ( core::Size const  val)

Set the number of residues per repeat.

This resets the torsions_to_sample_, torsions_to_fix_, and resname_ vectors, and must therefore be called BEFORE setting up the torsions to sample, torsions to fix, or residue types.

References reset_and_initialize_data(), residues_per_repeat_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_resname ( core::Size const  res_index,
std::string const &  resname_in 
)
inline

Set the residue type.

Sets the residue type for the nth residue in the list of residues defining the repeating unit.

References resname_.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_selection_low ( bool const  val)
inline

Sets whether the selection should be for the lowest score value (true) or highest (false).

References select_low_, and protocols::hybridization::val.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_sfxn ( core::scoring::ScoreFunctionOP  sfxn_in)
inline

Sets the scorefunction for this mover.

This must be done before calling the apply() function.

References sfxn_, and sfxn_set_.

Referenced by parse_my_tag().

void protocols::helical_bundle::BackboneGridSampler::set_up_peptide_stub_mover ( )

Set up the PeptideStubMover object that will be used to build geometry.

References nres(), peptide_stub_mover_, peptide_stub_mover_initialized_, residues_per_repeat(), and resname().

Referenced by apply().

bool protocols::helical_bundle::BackboneGridSampler::sfxn_set ( ) const
inline

Returns whether the scorefunction has been set.

References sfxn_set_.

Member Data Documentation

bool protocols::helical_bundle::BackboneGridSampler::cap_ends_
private

Should we add terminal caps (N-acetyl, C-methylamidation) to the polymer?

If false, the ends are just the regular terminal types (NH3+, COO-). False by default.

Referenced by cap_ends(), and set_cap_ends().

bool protocols::helical_bundle::BackboneGridSampler::dump_pdbs_
private

Dump a PDB file for each bundle generated? False by default.

Referenced by pdb_output(), and set_pdb_output().

core::Size protocols::helical_bundle::BackboneGridSampler::max_samples_
private

The maximum number of gridpoints allowed.

If the number of gridpoints based on user options exceeds this number, an error is thrown and the mover aborts. This is to prevent unreasonably large calculations from being attempted. Default value is ten thousand (10,000).

Referenced by max_samples(), and set_max_samples().

core::Size protocols::helical_bundle::BackboneGridSampler::nres_
private

The number of residues in the pose to build.

This is actually the number of REPEATS. If there are two residues per repeat, you'd have twice this number of resiudes.

Referenced by nres(), and set_nres().

bool protocols::helical_bundle::BackboneGridSampler::nstruct_mode_
private

Should the parallel sampling be done based on the job (nstruct number)?

If true, each job samples one set of mainchain torsion values. If false, every job samples every set of mainchain torsion values. False by default.

Referenced by nstruct_mode(), and set_nstruct_mode().

core::Size protocols::helical_bundle::BackboneGridSampler::nstruct_mode_repeats_
private

If nstruct_mode_ is true, how many times should each set of mainchain torsion values be repeated?

This is set to 1 by default, which means that each nstruct number correspnds to a different set of mainchain torsion values. If set greater than 1, then multiple consecutive nstruct numbers will correspond to the same mainchain torsion values. This allows combinatorially combining this mover's sampling with another, similar mover's sampling.

Referenced by nstruct_repeats(), and set_nstruct_repeats().

std::string protocols::helical_bundle::BackboneGridSampler::pdb_prefix_
private

PDB filename prefix. Filename will be of the form <prefix>_#####.pdb.

Defaults to "bgs_out".

Referenced by pdb_prefix(), and set_pdb_prefix().

PeptideStubMoverOP protocols::helical_bundle::BackboneGridSampler::peptide_stub_mover_
private

A PeptideStubMover used to build the new pose.

Referenced by apply(), and set_up_peptide_stub_mover().

bool protocols::helical_bundle::BackboneGridSampler::peptide_stub_mover_initialized_
private

Has the PeptideStubMover been initialized?

Referenced by peptide_stub_mover_initialized(), and set_up_peptide_stub_mover().

protocols::filters::FilterOP protocols::helical_bundle::BackboneGridSampler::pre_scoring_filter_
private

Owning pointer for an (optional) pre-selection filter applied to all helical bundles after the pre-selection mover but before picking the lowest-energy solution. If PDBs are dumped, only those passing filters are dumped.

Referenced by apply(), provide_authorship_info_for_unpublished(), provide_citation_info(), and set_prescoring_filter().

bool protocols::helical_bundle::BackboneGridSampler::pre_scoring_filter_exists_
private

Bool determining whether a pre-selection filter has been set.

Referenced by prescoring_filter_exists(), and set_prescoring_filter().

protocols::moves::MoverOP protocols::helical_bundle::BackboneGridSampler::pre_scoring_mover_
private

Owning pointer for an (optional) pre-selection mover applied to all helical bundles before energy evaluation.

Referenced by apply(), provide_authorship_info_for_unpublished(), provide_citation_info(), and set_prescoring_mover().

bool protocols::helical_bundle::BackboneGridSampler::pre_scoring_mover_exists_
private

Bool determining whether there exists a pre-selection mover that wlil be applied.

Referenced by prescoring_mover_exists(), and set_prescoring_mover().

core::Size protocols::helical_bundle::BackboneGridSampler::residues_per_repeat_
private

The number of residues in the repeating unit.

The repeating unit in the helix need not be a single residue, particularly if the helix is composed of residues of an alternating type.

Referenced by residues_per_repeat(), and set_residues_per_repeat().

utility::vector1<std::string> protocols::helical_bundle::BackboneGridSampler::resname_
private

The residue type (full name) for the pose to build.

This is a vector of strings, with one entry for each residue in the repeating unit.

Referenced by BackboneGridSampler(), reset_and_initialize_data(), resname(), and set_resname().

bool protocols::helical_bundle::BackboneGridSampler::select_low_
private

The selection type. If false, the pose with the highest score value is selected. If true, the pose with the lowest score value is selected. True by default.

Referenced by apply(), selection_low(), and set_selection_low().

core::scoring::ScoreFunctionOP protocols::helical_bundle::BackboneGridSampler::sfxn_
private

The scorefunction that this mover will use to pick the lowest-energy bundle.

Must be set prior to calling apply() function.

Referenced by apply(), and set_sfxn().

bool protocols::helical_bundle::BackboneGridSampler::sfxn_set_
private

Has the scorefunction been set?

False by default.

Referenced by set_sfxn(), and sfxn_set().

utility::vector1< utility::vector1 < std::pair <core::Size , core::Real > > > protocols::helical_bundle::BackboneGridSampler::torsions_to_fix_
private

The list of mainchain torsions to fix, and the values at which to fix them.

The outer vecotr corresponds to the list of residues in the repeating unit.

Referenced by add_torsion_to_fix(), add_torsion_to_sample(), apply(), BackboneGridSampler(), and reset_and_initialize_data().

utility::vector1< utility::vector1 < std::pair <core::Size , std::pair < std::pair < core::Real , core::Real >, core::Size > > > > protocols::helical_bundle::BackboneGridSampler::torsions_to_sample_
private

The list of mainchain torsions to sample, and the range of values.

The outer vector corresponds to the list of residues in the repeating unit.

Referenced by add_torsion_to_fix(), add_torsion_to_sample(), apply(), BackboneGridSampler(), calculate_total_samples(), and reset_and_initialize_data().


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