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

#include <RenderGridsToKinemage.hh>

Public Member Functions

 RenderGridsToKinemage ()
 RenderGridsToKinemage (RenderGridsToKinemage const &mover)
virtual ~RenderGridsToKinemage ()
virtual moves::MoverOP clone () const
 Return a clone of the Mover object. More...
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
virtual void apply (core::pose::Pose &pose)
virtual void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data, filters::Filters_map const &filters, protocols::moves::Movers_map const &movers, core::pose::Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. 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
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...
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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 setup_colors ()
void setup_one_color_scheme ()
void setup_two_color_scheme ()
void setup_three_color_scheme ()
void write_points (utility::io::ozstream &kin_file)
void write_colors (utility::io::ozstream &kin_file)
void write_header (utility::io::ozstream &kin_file)

Private Attributes

std::string filename_
core::Size color_mode_
core::Size gradient_bins_
core::Size stride_
std::string grid_name_
numeric::xyzVector< core::Realcolor_
numeric::xyzVector< core::Reallow_color_
numeric::xyzVector< core::Realzero_color_
numeric::xyzVector< core::Realhigh_color_
utility::vector1< ColorGradientcolor_data_
scoring_grid::SingleGridOP grid_

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
typedef core::pose::Pose Pose
typedef core::pose::PoseCOP PoseCOP
typedef std::list< std::stringStrings
- 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...

Constructor & Destructor Documentation

protocols::qsar::RenderGridsToKinemage::RenderGridsToKinemage ( )

Referenced by clone().

protocols::qsar::RenderGridsToKinemage::RenderGridsToKinemage ( RenderGridsToKinemage const &  mover)
protocols::qsar::RenderGridsToKinemage::~RenderGridsToKinemage ( )

Member Function Documentation

void protocols::qsar::RenderGridsToKinemage::apply ( core::pose::Pose pose)
protocols::moves::MoverOP protocols::qsar::RenderGridsToKinemage::clone ( ) const

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 RenderGridsToKinemage().

std::string protocols::qsar::RenderGridsToKinemage::get_name ( ) const

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

Implements protocols::moves::Mover.

void protocols::qsar::RenderGridsToKinemage::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data,
filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 

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 color_, color_mode_, utility::pointer::dynamic_pointer_cast(), filename_, protocols::qsar::scoring_grid::GridManager::get_grid(), protocols::qsar::scoring_grid::GridManager::get_instance(), gradient_bins_, grid_, grid_name_, high_color_, low_color_, stride_, and zero_color_.

void protocols::qsar::RenderGridsToKinemage::setup_colors ( )
void protocols::qsar::RenderGridsToKinemage::setup_one_color_scheme ( )

References color_, color_data_, grid_, and grid_name_.

Referenced by setup_colors().

void protocols::qsar::RenderGridsToKinemage::setup_three_color_scheme ( )
void protocols::qsar::RenderGridsToKinemage::setup_two_color_scheme ( )
void protocols::qsar::RenderGridsToKinemage::write_colors ( utility::io::ozstream kin_file)
void protocols::qsar::RenderGridsToKinemage::write_header ( utility::io::ozstream kin_file)

Referenced by apply().

void protocols::qsar::RenderGridsToKinemage::write_points ( utility::io::ozstream kin_file)

Member Data Documentation

numeric::xyzVector<core::Real> protocols::qsar::RenderGridsToKinemage::color_
utility::vector1<ColorGradient> protocols::qsar::RenderGridsToKinemage::color_data_
core::Size protocols::qsar::RenderGridsToKinemage::color_mode_

Referenced by parse_my_tag(), and setup_colors().

std::string protocols::qsar::RenderGridsToKinemage::filename_

Referenced by apply(), and parse_my_tag().

core::Size protocols::qsar::RenderGridsToKinemage::gradient_bins_
scoring_grid::SingleGridOP protocols::qsar::RenderGridsToKinemage::grid_
std::string protocols::qsar::RenderGridsToKinemage::grid_name_
numeric::xyzVector<core::Real> protocols::qsar::RenderGridsToKinemage::high_color_
numeric::xyzVector<core::Real> protocols::qsar::RenderGridsToKinemage::low_color_
core::Size protocols::qsar::RenderGridsToKinemage::stride_

Referenced by parse_my_tag(), and write_points().

numeric::xyzVector<core::Real> protocols::qsar::RenderGridsToKinemage::zero_color_

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