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protocols::moves::PyMolMover Class Reference

#include <PyMolMover.hh>

Inheritance diagram for protocols::moves::PyMolMover:
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Collaboration diagram for protocols::moves::PyMolMover:
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Public Member Functions

 PyMolMover ()
 
virtual ~PyMolMover ()
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual void apply (Pose &)
 
virtual void apply (Pose const &)
 Actually our mover does not change the Pose object, so we have additional const version... More...
 
void print (std::string const &message)
 Send message for PyMol to print. More...
 
void send_energy (Pose const &, core::scoring::ScoreType stype=core::scoring::total_score)
 Send specified energy to PyMOL. More...
 
void send_energy (Pose const &, std::string const &stype)
 Send specified energy to PyMOL. More...
 
void send_RAW_Energies (Pose const &, std::string energyType, utility::vector1< int > const &energies)
 Send RAW energy array for coloring by PyMOL. More...
 
virtual void send_colors (Pose const &, std::map< int, int > const &colors, X11Colors default_color=protocols::moves::XC_blue)
 Tell PyMOL to color protein with supplied custom colors. More...
 
bool update_energy ()
 
void update_energy (bool f)
 
core::scoring::ScoreType energy_type (void)
 
void energy_type (core::scoring::ScoreType t)
 
void keep_history (bool kh)
 Set the keep history flag. If set to True - PyMol will keep track of all frames that was sent. More...
 
bool keep_history (void)
 Return current keep_history flag. More...
 
void update_interval (core::Real t)
 Set current minimum update interval 't' in seconds. Mover will not send anyinformation to PyMOL before atleast 't' secons has passes since last packet was sent. default value is 0, - no packets are skipped. More...
 
core::Real update_interval ()
 Return current update interval. More...
 
- 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
 
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)
 
virtual MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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
 this function informs 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
 this function informs 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...
 
virtual MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

std::string get_PyMol_model_name (Pose const &pose) const
 
bool is_it_time ()
 

Private Attributes

UDPSocketClient link_
 Actual link object. More...
 
bool update_energy_
 
core::scoring::ScoreType energy_type_
 
bool keep_history_
 Should PyMol keep history of all models that was sent? - Default is false. More...
 
core::Real update_interval_
 Update interval in seconds. More...
 
core::Real last_packet_sent_time_
 Time stamp from where last packet was sent. More...
 
std::string name_
 Name of model in pymol. More...
 

Friends

std::ostream & operator<< (std::ostream &os, PyMolMover const &mover)
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 
- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...
 

Constructor & Destructor Documentation

protocols::moves::PyMolMover::PyMolMover ( )
inline
protocols::moves::PyMolMover::~PyMolMover ( )
virtual

Member Function Documentation

void protocols::moves::PyMolMover::apply ( Pose pose)
virtual
void protocols::moves::PyMolMover::apply ( Pose const &  pose)
virtual
core::scoring::ScoreType protocols::moves::PyMolMover::energy_type ( void  )
inline

References energy_type_.

void protocols::moves::PyMolMover::energy_type ( core::scoring::ScoreType  t)
inline
std::string protocols::moves::PyMolMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

std::string protocols::moves::PyMolMover::get_PyMol_model_name ( Pose const &  pose) const
private
bool protocols::moves::PyMolMover::is_it_time ( )
private
void protocols::moves::PyMolMover::keep_history ( bool  kh)
inline

Set the keep history flag. If set to True - PyMol will keep track of all frames that was sent.

References keep_history_.

bool protocols::moves::PyMolMover::keep_history ( void  )
inline

Return current keep_history flag.

References keep_history_.

void protocols::moves::PyMolMover::print ( std::string const &  message)

Send message for PyMol to print.

References is_it_time(), keep_history_, link_, and protocols::moves::UDPSocketClient::sendMessage().

void protocols::moves::PyMolMover::send_colors ( Pose const &  pose,
std::map< int, int > const &  colors,
X11Colors  default_color = protocols::moves::XC_blue 
)
virtual

Tell PyMOL to color protein with supplied custom colors.

References send_RAW_Energies(), core::pose::Pose::total_residue(), protocols::moves::XC_first_color, and protocols::moves::XC_last_color.

void protocols::moves::PyMolMover::send_energy ( Pose const &  pose,
core::scoring::ScoreType  stype = core::scoring::total_score 
)
void protocols::moves::PyMolMover::send_energy ( Pose const &  pose,
std::string const &  stype 
)

Send specified energy to PyMOL.

References core::scoring::ScoreTypeManager::score_type_from_name(), and send_energy().

void protocols::moves::PyMolMover::send_RAW_Energies ( Pose const &  pose,
std::string  energyType,
utility::vector1< int > const &  energies 
)
bool protocols::moves::PyMolMover::update_energy ( )
inline

References update_energy_.

void protocols::moves::PyMolMover::update_energy ( bool  f)
inline

References update_energy_.

void protocols::moves::PyMolMover::update_interval ( core::Real  t)
inline

Set current minimum update interval 't' in seconds. Mover will not send anyinformation to PyMOL before atleast 't' secons has passes since last packet was sent. default value is 0, - no packets are skipped.

References core::scoring::hbonds::t(), and update_interval_.

core::Real protocols::moves::PyMolMover::update_interval ( )
inline

Return current update interval.

References update_interval_.

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os,
PyMolMover const &  mover 
)
friend

Member Data Documentation

core::scoring::ScoreType protocols::moves::PyMolMover::energy_type_
private

Referenced by apply(), and energy_type().

bool protocols::moves::PyMolMover::keep_history_
private

Should PyMol keep history of all models that was sent? - Default is false.

Referenced by apply(), keep_history(), print(), send_energy(), and send_RAW_Energies().

core::Real protocols::moves::PyMolMover::last_packet_sent_time_
private

Time stamp from where last packet was sent.

Referenced by is_it_time().

UDPSocketClient protocols::moves::PyMolMover::link_
private

Actual link object.

Referenced by apply(), print(), send_energy(), and send_RAW_Energies().

std::string protocols::moves::PyMolMover::name_
private

Name of model in pymol.

Referenced by get_PyMol_model_name().

bool protocols::moves::PyMolMover::update_energy_
private

Referenced by apply(), and update_energy().

core::Real protocols::moves::PyMolMover::update_interval_
private

Update interval in seconds.

Referenced by is_it_time(), and update_interval().


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