Rosetta Protocols  2014.35
Public Member Functions | Private Attributes | List of all members
protocols::simple_filters::TaskAwareAlaScan Class Reference

#include <TaskAwareAlaScan.hh>

Public Member Functions

 TaskAwareAlaScan ()
 default constructor More...
 
 TaskAwareAlaScan (core::pack::task::TaskFactoryOP task_factory, core::pack::task::TaskFactoryOP ddG_task_factory, bool use_custom_task, core::Size const jump, std::string const sym_dof_name, core::Size const repeats, core::scoring::ScoreFunctionCOP scorefxn, bool repack, bool report_diffs)
 constructor with arguments More...
 
 TaskAwareAlaScan (TaskAwareAlaScan const &rval)
 copy constructor More...
 
virtual
protocols::filters::FilterOP 
clone () const
 
virtual
protocols::filters::FilterOP 
fresh_instance () const
 
virtual ~TaskAwareAlaScan ()
 destructor More...
 
virtual std::string name () const
 
void task_factory (core::pack::task::TaskFactoryOP task_factory)
 
void ddG_task_factory (core::pack::task::TaskFactoryOP ddG_task_factory)
 
void use_custom_task (bool const uct)
 
void jump (core::Size const j)
 
void sym_dof_name (std::string const j)
 
void repeats (core::Size const r)
 
void scorefxn (core::scoring::ScoreFunctionOP const scorefxn)
 
void repack (bool const repack)
 
void report_diffs (bool const report_diffs)
 
void write2pdb (bool const write)
 
core::pack::task::TaskFactoryOP task_factory () const
 
core::pack::task::TaskFactoryOP ddG_task_factory () const
 
bool use_custom_task () const
 
core::Size jump () const
 
std::string sym_dof_name () const
 
core::Size repeats () const
 
bool repack () const
 
bool report_diffs () const
 
bool write2pdb () const
 
virtual bool apply (core::pose::Pose const &) const
 Dummy Filter apply function. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 parse xml More...
 
void parse_ddG_task_operations (utility::tag::TagCOP tag, basic::datacache::DataMap const &data)
 
void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks)
 
core::Real ddG_for_single_residue (core::pose::Pose const &const_pose, core::Size const resi) const
 Calculate the ddG for an alanine mutation at the specified position. More...
 
void report (std::ostream &out, core::pose::Pose const &pose) const
 calculate and report the per-residue ddGs More...
 
void write_to_pdb (core::pose::Pose const &pose, core::Size const &residue, std::string const &residue_name, core::Real const &ddG) const
 
- Public Member Functions inherited from protocols::filters::Filter
 Filter ()
 
 Filter (std::string const &)
 
 Filter (Filter const &)
 
virtual ~Filter ()
 
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 void apply (core::io::serialization::PipeMap &pmap)
 
virtual void score (core::io::serialization::PipeMap &pmap)
 
virtual core::Real score (core::pose::Pose &pose)
 

Private Attributes

core::pack::task::TaskFactoryOP task_factory_
 
core::pack::task::TaskFactoryOP ddG_task_factory_
 
bool use_custom_task_
 
core::Size jump_
 
std::string sym_dof_name_
 
core::Size repeats_
 
core::scoring::ScoreFunctionOP scorefxn_
 
bool repack_
 
bool report_diffs_
 
std::set< std::stringexempt_identities_
 
bool write2pdb_
 

Additional Inherited Members

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

Constructor & Destructor Documentation

protocols::simple_filters::TaskAwareAlaScan::TaskAwareAlaScan ( )
protocols::simple_filters::TaskAwareAlaScan::TaskAwareAlaScan ( core::pack::task::TaskFactoryOP  task_factory,
core::pack::task::TaskFactoryOP  ddG_task_factory,
bool  use_custom_task,
core::Size const  jump,
std::string const  sym_dof_name,
core::Size const  repeats,
core::scoring::ScoreFunctionCOP  scorefxn,
bool  repack,
bool  report_diffs 
)

constructor with arguments

protocols::simple_filters::TaskAwareAlaScan::TaskAwareAlaScan ( TaskAwareAlaScan const &  rval)

copy constructor

protocols::simple_filters::TaskAwareAlaScan::~TaskAwareAlaScan ( )
virtual

destructor

Member Function Documentation

bool protocols::simple_filters::TaskAwareAlaScan::apply ( core::pose::Pose const &  ) const
virtual

Dummy Filter apply function.

Implements protocols::filters::Filter.

protocols::filters::FilterOP protocols::simple_filters::TaskAwareAlaScan::clone ( ) const
virtual

Implements protocols::filters::Filter.

References TaskAwareAlaScan().

Referenced by parse_def().

core::Real protocols::simple_filters::TaskAwareAlaScan::ddG_for_single_residue ( core::pose::Pose const &  const_pose,
core::Size const  resi 
) const
void protocols::simple_filters::TaskAwareAlaScan::ddG_task_factory ( core::pack::task::TaskFactoryOP  ddG_task_factory)
core::pack::task::TaskFactoryOP protocols::simple_filters::TaskAwareAlaScan::ddG_task_factory ( ) const
protocols::filters::FilterOP protocols::simple_filters::TaskAwareAlaScan::fresh_instance ( ) const
virtual
void protocols::simple_filters::TaskAwareAlaScan::jump ( core::Size const  j)

References jump_.

core::Size protocols::simple_filters::TaskAwareAlaScan::jump ( ) const
virtual std::string protocols::simple_filters::TaskAwareAlaScan::name ( ) const
inlinevirtual

Reimplemented from protocols::filters::Filter.

Referenced by write_to_pdb().

void protocols::simple_filters::TaskAwareAlaScan::parse_ddG_task_operations ( utility::tag::TagCOP  tag,
basic::datacache::DataMap const &  data 
)

Adapted from protocols/rosetta_scripts/util.cc Since RosettaScripts can only return one TaskFactory from one set of task_operations, a separate function is needed to provide an auxiliary TaskFactory that can be passed along to the ddG mover to control repacking during ddG calculations.

Note
Do NOT use STMStoredTasks generated by the StoreTaskMover as ddG_task_operations. These will prevent mutation of the residue in question to alanine.

References ddG_task_factory(), end, basic::datacache::DataMap::get(), basic::datacache::DataMap::has(), core::pack::task::TaskFactory::push_back(), utility::string_split(), protocols::simple_filters::TR, and utility_exit_with_message.

Referenced by parse_my_tag().

void protocols::simple_filters::TaskAwareAlaScan::parse_def ( utility::lua::LuaObject const &  def,
utility::lua::LuaObject const &  score_fxns,
utility::lua::LuaObject const &  tasks 
)
virtual
void protocols::simple_filters::TaskAwareAlaScan::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &   
)
virtual
void protocols::simple_filters::TaskAwareAlaScan::repack ( bool const  repack)

References repack(), and repack_.

bool protocols::simple_filters::TaskAwareAlaScan::repack ( ) const

References repack_.

Referenced by parse_def(), parse_my_tag(), and repack().

void protocols::simple_filters::TaskAwareAlaScan::repeats ( core::Size const  r)

References repeats_.

core::Size protocols::simple_filters::TaskAwareAlaScan::repeats ( ) const
void protocols::simple_filters::TaskAwareAlaScan::report ( std::ostream &  out,
core::pose::Pose const &  pose 
) const
virtual
void protocols::simple_filters::TaskAwareAlaScan::report_diffs ( bool const  report_diffs)

References report_diffs(), and report_diffs_.

bool protocols::simple_filters::TaskAwareAlaScan::report_diffs ( ) const

References report_diffs_.

Referenced by parse_def(), parse_my_tag(), report(), and report_diffs().

void protocols::simple_filters::TaskAwareAlaScan::scorefxn ( core::scoring::ScoreFunctionOP const  scorefxn)

References scorefxn_.

void protocols::simple_filters::TaskAwareAlaScan::sym_dof_name ( std::string const  j)

References sym_dof_name_.

std::string protocols::simple_filters::TaskAwareAlaScan::sym_dof_name ( ) const
void protocols::simple_filters::TaskAwareAlaScan::task_factory ( core::pack::task::TaskFactoryOP  task_factory)

References task_factory(), and task_factory_.

core::pack::task::TaskFactoryOP protocols::simple_filters::TaskAwareAlaScan::task_factory ( ) const

References task_factory_.

Referenced by parse_def(), parse_my_tag(), and task_factory().

void protocols::simple_filters::TaskAwareAlaScan::use_custom_task ( bool const  uct)

References use_custom_task_.

bool protocols::simple_filters::TaskAwareAlaScan::use_custom_task ( ) const
void protocols::simple_filters::TaskAwareAlaScan::write2pdb ( bool const  write)

References write2pdb_.

bool protocols::simple_filters::TaskAwareAlaScan::write2pdb ( ) const

References write2pdb_.

Referenced by parse_def(), parse_my_tag(), and report().

void protocols::simple_filters::TaskAwareAlaScan::write_to_pdb ( core::pose::Pose const &  pose,
core::Size const &  residue,
std::string const &  residue_name,
core::Real const &  ddG 
) const

Member Data Documentation

core::pack::task::TaskFactoryOP protocols::simple_filters::TaskAwareAlaScan::ddG_task_factory_
private

Referenced by ddG_task_factory().

std::set< std::string > protocols::simple_filters::TaskAwareAlaScan::exempt_identities_
private
core::Size protocols::simple_filters::TaskAwareAlaScan::jump_
private

Referenced by jump().

bool protocols::simple_filters::TaskAwareAlaScan::repack_
private

Referenced by repack().

core::Size protocols::simple_filters::TaskAwareAlaScan::repeats_
private

Referenced by repeats().

bool protocols::simple_filters::TaskAwareAlaScan::report_diffs_
private

Referenced by report_diffs().

core::scoring::ScoreFunctionOP protocols::simple_filters::TaskAwareAlaScan::scorefxn_
private
std::string protocols::simple_filters::TaskAwareAlaScan::sym_dof_name_
private

Referenced by sym_dof_name().

core::pack::task::TaskFactoryOP protocols::simple_filters::TaskAwareAlaScan::task_factory_
private

Referenced by report(), and task_factory().

bool protocols::simple_filters::TaskAwareAlaScan::use_custom_task_
private

Referenced by use_custom_task().

bool protocols::simple_filters::TaskAwareAlaScan::write2pdb_
private

Referenced by write2pdb().


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