Rosetta Protocols  2014.35
Public Types | Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::simple_moves::ddG Class Reference

#include <ddG.hh>

Public Types

typedef core::Real Real
 
typedef core::scoring::ScoreType ScoreType
 
typedef core::pose::Pose Pose
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 

Public Member Functions

 ddG ()
 
 ddG (core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const jump=1)
 
 ddG (core::scoring::ScoreFunctionCOP scorefxn_in, core::Size const jump, utility::vector1< core::Size > const &chain_ids)
 
virtual void apply (Pose &pose)
 
void calculate (Pose const &pose_in)
 compute the energy of the repacked complex in the bound and unbound states More...
 
void report_ddG (std::ostream &out) const
 
Real sum_ddG () const
 
core::Size rb_jump () const
 
void rb_jump (core::Size j)
 
core::Size repeats () const
 
void repeats (core::Size repeats)
 
core::Real translate_by () const
 
void translate_by (core::Real translate_by)
 
virtual ~ddG ()
 
protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
void parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP relax_mover () const
 
void relax_mover (protocols::moves::MoverOP m)
 
protocols::filters::FilterOP filter () const
 
void filter (protocols::filters::FilterOP f)
 
void task_factory (core::pack::task::TaskFactoryOP task_factory)
 
core::pack::task::TaskFactoryOP task_factory () const
 
void use_custom_task (bool uct)
 
bool use_custom_task () const
 
void repack_bound (bool rpb)
 
bool repack_bound () const
 
void relax_bound (bool rlb)
 
bool relax_bound () const
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
void set_type (std::string const &setting)
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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
 
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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Member Functions

void unbind (Pose &pose) const
 Helper method to appropriately form unbound complex. More...
 
void setup_task (Pose const &pose)
 
void fill_energy_vector (Pose const &pose, std::map< ScoreType, Real > &energy_map)
 
void fill_per_residue_energy_vector (Pose const &pose, std::map< Size, Real > &energy_map)
 

Private Attributes

std::map< ScoreType, Realbound_energies_
 
std::map< ScoreType, Realunbound_energies_
 
std::map< Size, Realbound_per_residue_energies_
 
std::map< Size, Realunbound_per_residue_energies_
 
Real bound_total_energy_
 
Real unbound_total_energy_
 
Size repeats_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Size rb_jump_
 
utility::vector1< core::Sizechain_ids_
 
bool per_residue_ddg_
 
bool repack_
 
protocols::moves::MoverOP relax_mover_
 
protocols::filters::FilterOP filter_
 
core::pack::task::TaskFactoryOP task_factory_
 
core::pack::task::PackerTaskOP task_
 
bool use_custom_task_
 
bool repack_bound_
 
bool relax_bound_
 
core::scoring::methods::PBLifetimeCacheOP pb_cached_data_
 info carrier for poisson-boltzmann potential energy computation More...
 
bool pb_enabled_
 true when PB potential is part of scorefxn More...
 
core::Real translate_by_
 distance in A to separate moledules More...
 

Additional Inherited Members

- 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...
 
- 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::simple_moves::ddG::ddG ( )
protocols::simple_moves::ddG::ddG ( core::scoring::ScoreFunctionCOP  scorefxn_in,
core::Size const  jump = 1 
)
protocols::simple_moves::ddG::ddG ( core::scoring::ScoreFunctionCOP  scorefxn_in,
core::Size const  jump,
utility::vector1< core::Size > const &  chain_ids 
)
protocols::simple_moves::ddG::~ddG ( )
virtual

Member Function Documentation

void protocols::simple_moves::ddG::apply ( Pose pose)
virtual
void protocols::simple_moves::ddG::calculate ( pose::Pose const &  pose_original)
protocols::moves::MoverOP protocols::simple_moves::ddG::clone ( ) const
virtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References ddG().

void protocols::simple_moves::ddG::fill_energy_vector ( pose::Pose const &  pose,
std::map< ScoreType, Real > &  energy_map 
)
private
void protocols::simple_moves::ddG::fill_per_residue_energy_vector ( pose::Pose const &  pose,
std::map< Size, Real > &  energy_map 
)
private
protocols::filters::FilterOP protocols::simple_moves::ddG::filter ( ) const
void protocols::simple_moves::ddG::filter ( protocols::filters::FilterOP  f)

References filter_.

protocols::moves::MoverOP protocols::simple_moves::ddG::fresh_instance ( ) const
inlinevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References ddG().

std::string protocols::simple_moves::ddG::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::simple_moves::ddG::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References chain_ids_, core::scoring::ScoreFunction::clone(), filter(), core::pose::get_chain_id_from_chain(), protocols::rosetta_scripts::parse_filter(), protocols::rosetta_scripts::parse_mover(), protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), core::scoring::PB_elec, pb_enabled_, per_residue_ddg_, rb_jump_, relax_bound_, relax_mover(), repack_, repack_bound_, repeats_, scorefxn_, utility::string_split(), task_factory(), protocols::simple_moves::TR, translate_by_, and use_custom_task().

core::Size protocols::simple_moves::ddG::rb_jump ( ) const
inline

References rb_jump_.

void protocols::simple_moves::ddG::rb_jump ( core::Size  j)
inline

References rb_jump_.

void protocols::simple_moves::ddG::relax_bound ( bool  rlb)
inline
bool protocols::simple_moves::ddG::relax_bound ( ) const
inline

References relax_bound_.

Referenced by calculate().

protocols::moves::MoverOP protocols::simple_moves::ddG::relax_mover ( ) const
inline
void protocols::simple_moves::ddG::relax_mover ( protocols::moves::MoverOP  m)
inline

References relax_mover_.

void protocols::simple_moves::ddG::repack_bound ( bool  rpb)
inline
bool protocols::simple_moves::ddG::repack_bound ( ) const
inline

References repack_bound_.

Referenced by calculate().

core::Size protocols::simple_moves::ddG::repeats ( ) const
inline

References repeats_.

void protocols::simple_moves::ddG::repeats ( core::Size  repeats)
inline

References repeats(), and repeats_.

Referenced by repeats().

void protocols::simple_moves::ddG::report_ddG ( std::ostream &  out) const
void protocols::simple_moves::ddG::setup_task ( pose::Pose const &  pose)
private
Real protocols::simple_moves::ddG::sum_ddG ( ) const
void protocols::simple_moves::ddG::task_factory ( core::pack::task::TaskFactoryOP  task_factory)
inline
core::pack::task::TaskFactoryOP protocols::simple_moves::ddG::task_factory ( ) const
inline

References task_factory_.

Referenced by parse_my_tag().

core::Real protocols::simple_moves::ddG::translate_by ( ) const
inline
void protocols::simple_moves::ddG::translate_by ( core::Real  translate_by)
inline

References translate_by(), and translate_by_.

Referenced by translate_by().

void protocols::simple_moves::ddG::unbind ( pose::Pose pose) const
private
void protocols::simple_moves::ddG::use_custom_task ( bool  uct)
inline
bool protocols::simple_moves::ddG::use_custom_task ( ) const
inline

References use_custom_task_.

Referenced by parse_my_tag(), and setup_task().

Member Data Documentation

std::map< ScoreType, Real > protocols::simple_moves::ddG::bound_energies_
private

Referenced by calculate(), ddG(), report_ddG(), and sum_ddG().

std::map< Size, Real > protocols::simple_moves::ddG::bound_per_residue_energies_
private

Referenced by apply(), calculate(), and ddG().

Real protocols::simple_moves::ddG::bound_total_energy_
private
utility::vector1<core::Size> protocols::simple_moves::ddG::chain_ids_
private

Referenced by ddG(), parse_my_tag(), setup_task(), and unbind().

protocols::filters::FilterOP protocols::simple_moves::ddG::filter_
private
core::scoring::methods::PBLifetimeCacheOP protocols::simple_moves::ddG::pb_cached_data_
private

info carrier for poisson-boltzmann potential energy computation

Referenced by apply(), and calculate().

bool protocols::simple_moves::ddG::pb_enabled_
private

true when PB potential is part of scorefxn

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

bool protocols::simple_moves::ddG::per_residue_ddg_
private

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

core::Size protocols::simple_moves::ddG::rb_jump_
private
bool protocols::simple_moves::ddG::relax_bound_
private

Referenced by parse_my_tag(), and relax_bound().

protocols::moves::MoverOP protocols::simple_moves::ddG::relax_mover_
private

Referenced by relax_mover().

bool protocols::simple_moves::ddG::repack_
private

Referenced by calculate(), and parse_my_tag().

bool protocols::simple_moves::ddG::repack_bound_
private

Referenced by parse_my_tag(), and repack_bound().

Size protocols::simple_moves::ddG::repeats_
private

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

core::scoring::ScoreFunctionOP protocols::simple_moves::ddG::scorefxn_
private
core::pack::task::PackerTaskOP protocols::simple_moves::ddG::task_
private

Referenced by calculate(), and setup_task().

core::pack::task::TaskFactoryOP protocols::simple_moves::ddG::task_factory_
private

Referenced by setup_task(), and task_factory().

core::Real protocols::simple_moves::ddG::translate_by_
private

distance in A to separate moledules

Referenced by parse_my_tag(), translate_by(), and unbind().

std::map< ScoreType, Real > protocols::simple_moves::ddG::unbound_energies_
private

Referenced by calculate(), ddG(), report_ddG(), and sum_ddG().

std::map< Size, Real > protocols::simple_moves::ddG::unbound_per_residue_energies_
private

Referenced by apply(), calculate(), and ddG().

Real protocols::simple_moves::ddG::unbound_total_energy_
private
bool protocols::simple_moves::ddG::use_custom_task_
private

Referenced by use_custom_task().


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