Rosetta  2020.37
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protocols::simple_ddg::DdGScan Class Reference

#include <DdGScan.hh>

Inheritance diagram for protocols::simple_ddg::DdGScan:
Inheritance graph
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Public Member Functions

 DdGScan ()
 default constructor More...
 
 DdGScan (core::pack::task::TaskFactoryOP task_factory, core::Size const repeats, core::scoring::ScoreFunctionCOP scorefxn, bool report_diffs, bool write2pdb)
 constructor with arguments More...
 
 DdGScan (DdGScan const &rval)
 copy constructor More...
 
protocols::filters::FilterOP clone () const override
 
protocols::filters::FilterOP fresh_instance () const override
 
 ~DdGScan () override
 destructor More...
 
void initialize ()
 
void task_factory (core::pack::task::TaskFactoryOP task_factory)
 
void repeats (core::Size const r)
 
void scorefxn (core::scoring::ScoreFunctionOP const scorefxn)
 
void report_diffs (bool const report_diffs)
 
void write2pdb (bool const write)
 
void ddG_mover (protocols::simple_ddg::ddGOP const ddG_mover_op)
 
core::pack::task::TaskFactoryOP task_factory () const
 
core::Size repeats () const
 
bool report_diffs () const
 
bool write2pdb () const
 
protocols::simple_ddg::ddGOP ddG_mover () const
 
bool apply (core::pose::Pose const &) const override
 Dummy Filter apply function. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 parse xml More...
 
core::Real ddG_for_single_residue (core::pose::Pose const &const_pose, core::Size const resi, core::pack::task::PackerTaskOP const general_task, core::pose::Pose &pose_to_mutate) const
 Calculate the binding ddG for a mutation at the specified position (or wildtype no-mutant if resi is 0) More...
 
void write_to_pdb (core::pose::Pose const &pose, core::Size const &residue, core::Size const &output_resi, std::string const &residue_name, core::Real const &ddG) const
 
void report (std::ostream &out, core::pose::Pose const &pose) const override
 Implementation of virtual report function. More...
 
utility::vector1< ddG_data_tuplecalculate (std::ostream &out, core::pose::Pose const &pose) const
 calculate and report the per-residue ddGs 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 core::Real report_sm (core::pose::Pose const &) const
 used to report filter internals through a score or silent file More...
 
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 Attributes

core::pack::task::TaskFactoryOP task_factory_
 
core::Size repeats_
 
core::scoring::ScoreFunctionOP scorefxn_
 
bool report_diffs_
 
bool write2pdb_
 
protocols::simple_ddg::ddGOP ddG_mover_
 

Additional Inherited Members

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

Constructor & Destructor Documentation

protocols::simple_ddg::DdGScan::DdGScan ( )

default constructor

References initialize().

protocols::simple_ddg::DdGScan::DdGScan ( core::pack::task::TaskFactoryOP  task_factory,
core::Size const  repeats,
core::scoring::ScoreFunctionCOP  scorefxn,
bool  report_diffs,
bool  write2pdb 
)

constructor with arguments

References initialize().

protocols::simple_ddg::DdGScan::DdGScan ( DdGScan const &  rval)
default

copy constructor

protocols::simple_ddg::DdGScan::~DdGScan ( )
overridedefault

destructor

Member Function Documentation

bool protocols::simple_ddg::DdGScan::apply ( core::pose::Pose const &  ) const
overridevirtual

Dummy Filter apply function.

Implements protocols::filters::Filter.

utility::vector1< ddG_data_tuple > protocols::simple_ddg::DdGScan::calculate ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
std::string protocols::simple_ddg::DdGScan::class_name ( )
static
protocols::filters::FilterOP protocols::simple_ddg::DdGScan::clone ( ) const
overridevirtual
core::Real protocols::simple_ddg::DdGScan::ddG_for_single_residue ( core::pose::Pose const &  const_pose,
core::Size const  resi,
core::pack::task::PackerTaskOP const  general_task,
core::pose::Pose pose_to_mutate 
) const

Calculate the binding ddG for a mutation at the specified position (or wildtype no-mutant if resi is 0)

References protocols::jd2::current_output_name(), ddG_mover_, core::conformation::Residue::name3(), core::pack::pack_rotamers(), repeats(), core::pose::Pose::residue(), scorefxn_, core::pose::Pose::size(), and protocols::simple_ddg::TR().

Referenced by calculate().

void protocols::simple_ddg::DdGScan::ddG_mover ( protocols::simple_ddg::ddGOP const  ddG_mover_op)

References ddG_mover_.

protocols::simple_ddg::ddGOP protocols::simple_ddg::DdGScan::ddG_mover ( ) const

References ddG_mover_.

Referenced by initialize(), and parse_my_tag().

protocols::filters::FilterOP protocols::simple_ddg::DdGScan::fresh_instance ( ) const
overridevirtual
void protocols::simple_ddg::DdGScan::initialize ( )

References ddG_mover().

Referenced by DdGScan().

std::string protocols::simple_ddg::DdGScan::name ( ) const
overridevirtual

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by write_to_pdb().

void protocols::simple_ddg::DdGScan::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::simple_ddg::DdGScan::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::simple_ddg::DdGScan::repeats ( core::Size const  r)

References repeats_.

core::Size protocols::simple_ddg::DdGScan::repeats ( ) const

References repeats_.

Referenced by ddG_for_single_residue(), and parse_my_tag().

void protocols::simple_ddg::DdGScan::report ( std::ostream &  out,
core::pose::Pose const &  const_pose 
) const
overridevirtual

Implementation of virtual report function.

Calls report function with return value

Reimplemented from protocols::filters::Filter.

References calculate().

void protocols::simple_ddg::DdGScan::report_diffs ( bool const  report_diffs)

References report_diffs(), and report_diffs_.

bool protocols::simple_ddg::DdGScan::report_diffs ( ) const

References report_diffs_.

Referenced by calculate(), parse_my_tag(), and report_diffs().

void protocols::simple_ddg::DdGScan::scorefxn ( core::scoring::ScoreFunctionOP const  scorefxn)

References scorefxn_.

void protocols::simple_ddg::DdGScan::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

References task_factory(), and task_factory_.

core::pack::task::TaskFactoryOP protocols::simple_ddg::DdGScan::task_factory ( ) const

References task_factory_.

Referenced by parse_my_tag(), and task_factory().

void protocols::simple_ddg::DdGScan::write2pdb ( bool const  write)

References write2pdb_.

bool protocols::simple_ddg::DdGScan::write2pdb ( ) const

References write2pdb_.

Referenced by calculate(), and parse_my_tag().

void protocols::simple_ddg::DdGScan::write_to_pdb ( core::pose::Pose const &  pose,
core::Size const &  residue,
core::Size const &  output_resi,
std::string const &  residue_name,
core::Real const &  ddG 
) const

Member Data Documentation

protocols::simple_ddg::ddGOP protocols::simple_ddg::DdGScan::ddG_mover_
private
core::Size protocols::simple_ddg::DdGScan::repeats_
private

Referenced by repeats().

bool protocols::simple_ddg::DdGScan::report_diffs_
private

Referenced by report_diffs().

core::scoring::ScoreFunctionOP protocols::simple_ddg::DdGScan::scorefxn_
private
core::pack::task::TaskFactoryOP protocols::simple_ddg::DdGScan::task_factory_
private

Referenced by calculate(), and task_factory().

bool protocols::simple_ddg::DdGScan::write2pdb_
private

Referenced by write2pdb().


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