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protocols::calc_taskop_filters::RotamerBoltzmannWeight Class Reference

#include <RotamerBoltzmannWeight.hh>

Inheritance diagram for protocols::calc_taskop_filters::RotamerBoltzmannWeight:
Inheritance graph
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Public Member Functions

 RotamerBoltzmannWeight ()
 default ctor More...
 
bool apply (core::pose::Pose const &pose) const override
 Constructor with a single target residue. More...
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 
core::Real report_sm (core::pose::Pose const &pose) const override
 used to report filter internals through a score or silent file More...
 
protocols::filters::FilterOP clone () const override
 
protocols::filters::FilterOP fresh_instance () const override
 
core::Real compute (core::pose::Pose const &pose) const
 
 ~RotamerBoltzmannWeight () override
 
core::pack::task::TaskFactoryOP task_factory () const
 
void task_factory (core::pack::task::TaskFactoryOP task_factory)
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by FilterFactory when constructing new Filter. Takes care of the specific mover's parsing. More...
 
utility::vector1< core::Sizefirst_pass_ala_scan (core::pose::Pose const &pose) const
 
core::Real compute_Boltzmann_weight (core::pose::Pose const &pose, core::Size const resi) const
 
void rb_jump (core::Size const jump)
 
core::Size rb_jump () const
 
void sym_dof_names (std::string const &dof_names)
 
std::string sym_dof_names () const
 
void repacking_radius (core::Real const rad)
 
core::Real repacking_radius () const
 
core::Real ddG_threshold () const
 
void ddG_threshold (core::Real const ddG)
 
void scorefxn (core::scoring::ScoreFunctionOP scorefxn)
 
core::scoring::ScoreFunctionOP scorefxn () const
 
core::Real temperature () const
 
void temperature (core::Real const temp)
 
bool unbound () const
 
void unbound (bool const u)
 
void threshold_probability (core::chemical::AA const aa_type, core::Real const probability)
 
core::Real threshold_probability (core::chemical::AA const aa_type) const
 
void energy_reduction_factor (core::Real const factor)
 
core::Real energy_reduction_factor () const
 
core::Real interface_interaction_energy (core::pose::Pose const &pose, core::Size const res) const
 
bool compute_entropy_reduction () const
 
void compute_entropy_reduction (bool const cer)
 
void repack (bool const repack)
 
bool repack () const
 
bool skip_ala_scan () const
 
void skip_ala_scan (bool const s)
 
void no_modified_ddG (bool const no_ddg)
 
void target_residues (std::string const &target_residues_str)
 
std::string type () const
 
void type (std::string const &s)
 
bool write2pdb () const
 
void write2pdb (bool const write)
 
core::Real compute_modified_ddG (core::pose::Pose const &pose, std::ostream &out) const
 Note that compute( pose ) needs to have been run first. This merely sums over the probabilities. More...
 
void write_to_pdb (core::Size const residue, std::string const &residue_name, core::Real const boltzmann_weight) const
 Output per-residue Boltzmann weights to the output pdb file if desired. More...
 
std::string name () const override
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
 ~Filter () override
 
virtual std::string get_type () const
 
std::string get_user_defined_name () const
 
void set_user_defined_name (std::string const &name)
 
virtual void clear ()
 used to clear internal variables if needed. Using fresh_instance is preferred since it's a pure virtual More...
 
virtual core::Real score (core::pose::Pose &pose)
 
virtual bool filter_provides_citation_info () const
 Does this filter 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 filter_is_unpublished () const
 Does this filter 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 class_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 

Private Types

typedef protocols::filters::Filter parent
 

Private Member Functions

core::Real compute_boltz_probability () const
 

Private Attributes

core::pack::task::TaskFactoryOP task_factory_
 
core::Size rb_jump_
 
std::string sym_dof_names_
 
bool unbound_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Real temperature_
 
core::Real ddG_threshold_
 
core::Real repacking_radius_
 
utility::vector1< core::Realthreshold_probabilities_per_residue_
 
core::Real energy_reduction_factor_
 
bool compute_entropy_reduction_
 
bool compute_max_
 
bool repack_
 
std::map< core::Size, core::RealddGs_
 
std::map< core::Size, core::Realrotamer_probabilities_
 
std::string type_
 
bool skip_ala_scan_
 
bool skip_report_
 
bool fast_calc_
 
bool no_modified_ddG_
 
std::string target_residues_
 
bool write2pdb_
 

Additional Inherited Members

- Protected Attributes inherited from protocols::filters::Filter
std::string scorename_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::calc_taskop_filters::RotamerBoltzmannWeight::RotamerBoltzmannWeight ( )
protocols::calc_taskop_filters::RotamerBoltzmannWeight::~RotamerBoltzmannWeight ( )
overridedefault

Member Function Documentation

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::apply ( core::pose::Pose const &  pose) const
overridevirtual

Constructor with a single target residue.

Implements protocols::filters::Filter.

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::class_name ( )
static
protocols::filters::FilterOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::clone ( ) const
overridevirtual
core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute ( core::pose::Pose const &  pose) const
core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_boltz_probability ( ) const
private
core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_Boltzmann_weight ( core::pose::Pose const &  pose,
core::Size const  resi 
) const
bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_entropy_reduction ( ) const

References compute_entropy_reduction_.

Referenced by parse_my_tag().

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_entropy_reduction ( bool const  cer)
core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_modified_ddG ( core::pose::Pose const &  pose,
std::ostream &  out 
) const
core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::ddG_threshold ( ) const
void protocols::calc_taskop_filters::RotamerBoltzmannWeight::ddG_threshold ( core::Real const  ddG)

References ddG_threshold_.

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::energy_reduction_factor ( core::Real const  factor)
core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::energy_reduction_factor ( ) const
utility::vector1< core::Size > protocols::calc_taskop_filters::RotamerBoltzmannWeight::first_pass_ala_scan ( core::pose::Pose const &  pose) const
protocols::filters::FilterOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::fresh_instance ( ) const
overridevirtual
core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::interface_interaction_energy ( core::pose::Pose const &  pose,
core::Size const  res 
) const
std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::no_modified_ddG ( bool const  no_ddg)

References no_modified_ddG_.

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::parse_my_tag ( utility::tag::TagCOP  ,
basic::datacache::DataMap &   
)
overridevirtual
void protocols::calc_taskop_filters::RotamerBoltzmannWeight::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::calc_taskop_filters::RotamerBoltzmannWeight::rb_jump ( core::Size const  jump)

References rb_jump_.

core::Size protocols::calc_taskop_filters::RotamerBoltzmannWeight::rb_jump ( ) const
void protocols::calc_taskop_filters::RotamerBoltzmannWeight::repack ( bool const  repack)

References repack(), and repack_.

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::repack ( ) const
void protocols::calc_taskop_filters::RotamerBoltzmannWeight::repacking_radius ( core::Real const  rad)
core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::repacking_radius ( ) const
void protocols::calc_taskop_filters::RotamerBoltzmannWeight::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
overridevirtual
core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::report_sm ( core::pose::Pose const &  ) const
overridevirtual

used to report filter internals through a score or silent file

Reimplemented from protocols::filters::Filter.

References compute(), compute_boltz_probability(), compute_modified_ddG(), no_modified_ddG_, and protocols::calc_taskop_filters::TR().

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::scorefxn ( core::scoring::ScoreFunctionOP  scorefxn)
core::scoring::ScoreFunctionOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::scorefxn ( ) const
bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::skip_ala_scan ( ) const

References skip_ala_scan_.

Referenced by first_pass_ala_scan(), and parse_my_tag().

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::skip_ala_scan ( bool const  s)

References skip_ala_scan_.

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::sym_dof_names ( std::string const &  dof_names)

References sym_dof_names_.

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::sym_dof_names ( ) const

References sym_dof_names_.

Referenced by compute(), and parse_my_tag().

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::target_residues ( std::string const &  target_residues_str)

References target_residues_.

core::pack::task::TaskFactoryOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::task_factory ( ) const
void protocols::calc_taskop_filters::RotamerBoltzmannWeight::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

References task_factory(), and task_factory_.

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::temperature ( ) const
void protocols::calc_taskop_filters::RotamerBoltzmannWeight::temperature ( core::Real const  temp)

References temperature_.

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::threshold_probability ( core::chemical::AA const  aa_type,
core::Real const  probability 
)
core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::threshold_probability ( core::chemical::AA const  aa_type) const
std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::type ( ) const

References type_.

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::type ( std::string const &  s)

References type_.

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::unbound ( ) const

References unbound_.

Referenced by compute(), compute_Boltzmann_weight(), and parse_my_tag().

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::unbound ( bool const  u)
bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::write2pdb ( ) const

References write2pdb_.

Referenced by compute(), and parse_my_tag().

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::write2pdb ( bool const  write)

References write2pdb_.

void protocols::calc_taskop_filters::RotamerBoltzmannWeight::write_to_pdb ( core::Size const  residue,
std::string const &  residue_name,
core::Real const  boltzmann_weight 
) const

Output per-residue Boltzmann weights to the output pdb file if desired.

References protocols::jd2::add_string_to_current_job(), and protocols::filters::Filter::get_user_defined_name().

Referenced by compute().

Member Data Documentation

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_entropy_reduction_
private
bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::compute_max_
private
core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::ddG_threshold_
private

Referenced by ddG_threshold().

std::map< core::Size, core::Real > protocols::calc_taskop_filters::RotamerBoltzmannWeight::ddGs_
mutableprivate

the following are mutable b/c they only sum up data in the filter. They do not affect how the filter is run (so the filter will remain logically constant, despite these variables) Mutability here allows the variables to be changed even in const methods.

Referenced by compute(), compute_modified_ddG(), and first_pass_ala_scan().

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::energy_reduction_factor_
private

Referenced by energy_reduction_factor().

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::fast_calc_
private

Referenced by compute(), and parse_my_tag().

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::no_modified_ddG_
private
core::Size protocols::calc_taskop_filters::RotamerBoltzmannWeight::rb_jump_
private

Referenced by rb_jump().

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::repack_
private

Referenced by repack().

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::repacking_radius_
private

Referenced by repacking_radius().

std::map< core::Size, core::Real > protocols::calc_taskop_filters::RotamerBoltzmannWeight::rotamer_probabilities_
mutableprivate
core::scoring::ScoreFunctionOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::scorefxn_
private
bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::skip_ala_scan_
private

Referenced by skip_ala_scan().

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::skip_report_
private

Referenced by parse_my_tag(), and report().

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::sym_dof_names_
private

Referenced by sym_dof_names().

std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::target_residues_
private
core::pack::task::TaskFactoryOP protocols::calc_taskop_filters::RotamerBoltzmannWeight::task_factory_
private

Referenced by task_factory().

core::Real protocols::calc_taskop_filters::RotamerBoltzmannWeight::temperature_
private

Referenced by temperature().

utility::vector1< core::Real > protocols::calc_taskop_filters::RotamerBoltzmannWeight::threshold_probabilities_per_residue_
private
std::string protocols::calc_taskop_filters::RotamerBoltzmannWeight::type_
private

Referenced by compute(), parse_my_tag(), report(), and type().

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::unbound_
private

Referenced by unbound().

bool protocols::calc_taskop_filters::RotamerBoltzmannWeight::write2pdb_
private

Referenced by write2pdb().


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