Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::simple_ddg::DdGScan Class Reference

#include <DdGScan.hh>

Inheritance diagram for protocols::simple_ddg::DdGScan:
Inheritance graph

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 () 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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

◆ DdGScan() [1/3]

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

default constructor

References initialize().

◆ DdGScan() [2/3]

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().

◆ DdGScan() [3/3]

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

copy constructor

◆ ~DdGScan()

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


Member Function Documentation

◆ apply()

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

Dummy Filter apply function.

Implements protocols::filters::Filter.

◆ calculate()

utility::vector1< ddG_data_tuple > protocols::simple_ddg::DdGScan::calculate ( std::ostream &  out,
core::pose::Pose const &  pose 
) const

◆ class_name()

std::string protocols::simple_ddg::DdGScan::class_name ( )

◆ clone()

protocols::filters::FilterOP protocols::simple_ddg::DdGScan::clone ( ) const

◆ ddG_for_single_residue()

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().

◆ ddG_mover() [1/2]

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

References ddG_mover_.

Referenced by initialize(), and parse_my_tag().

◆ ddG_mover() [2/2]

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

References ddG_mover_.

◆ fresh_instance()

protocols::filters::FilterOP protocols::simple_ddg::DdGScan::fresh_instance ( ) const

◆ initialize()

void protocols::simple_ddg::DdGScan::initialize ( )

References ddG_mover().

Referenced by DdGScan().

◆ name()

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

Reimplemented from protocols::filters::Filter.

References class_name().

Referenced by write_to_pdb().

◆ parse_my_tag()

void protocols::simple_ddg::DdGScan::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data 

◆ provide_xml_schema()

void protocols::simple_ddg::DdGScan::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ repeats() [1/2]

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

References repeats_.

Referenced by ddG_for_single_residue(), and parse_my_tag().

◆ repeats() [2/2]

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

References repeats_.

◆ report()

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

Implementation of virtual report function.

Calls report function with return value

Reimplemented from protocols::filters::Filter.

References calculate(), and core::conformation::membrane::out.

◆ report_diffs() [1/2]

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

References report_diffs_.

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

◆ report_diffs() [2/2]

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

References report_diffs(), and report_diffs_.

◆ scorefxn()

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

References scorefxn_.

◆ task_factory() [1/2]

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

References task_factory_.

Referenced by parse_my_tag(), and task_factory().

◆ task_factory() [2/2]

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

References task_factory(), and task_factory_.

◆ write2pdb() [1/2]

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

References write2pdb_.

Referenced by calculate(), and parse_my_tag().

◆ write2pdb() [2/2]

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

References write2pdb_.

◆ write_to_pdb()

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

◆ ddG_mover_

protocols::simple_ddg::ddGOP protocols::simple_ddg::DdGScan::ddG_mover_

◆ repeats_

core::Size protocols::simple_ddg::DdGScan::repeats_

Referenced by repeats().

◆ report_diffs_

bool protocols::simple_ddg::DdGScan::report_diffs_

Referenced by report_diffs().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::simple_ddg::DdGScan::scorefxn_

◆ task_factory_

core::pack::task::TaskFactoryOP protocols::simple_ddg::DdGScan::task_factory_

Referenced by calculate(), and task_factory().

◆ write2pdb_

bool protocols::simple_ddg::DdGScan::write2pdb_

Referenced by write2pdb().

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