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protocols::swa::protein::StepWiseProteinPoseSetup Class Reference

#include <StepWiseProteinPoseSetup.hh>

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Public Member Functions

 StepWiseProteinPoseSetup (std::string const &desired_sequence, utility::vector1< std::string > const &start_tags, utility::vector1< std::string > const &silent_files_in)
 
 ~StepWiseProteinPoseSetup ()
 
virtual void apply (core::pose::Pose &pose_to_visualize)
 Apply the minimizer to one pose. More...
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
utility::vector1< core::Size >
const & 
moving_residues () const
 
void set_n_terminus (bool const setting)
 
void set_c_terminus (bool const setting)
 
void set_sample_junction (bool const setting)
 
void set_add_peptide_plane (bool const &setting)
 
- 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

void match_specific_variants (core::pose::Pose const &pose, core::Size const &pose_res, core::pose::Pose &scratch_pose, core::Size const &scratch_pose_res, utility::vector1< core::chemical::VariantType > const &variant_types) const
 
void match_end_variants (core::pose::Pose const &pose, core::pose::Pose &scratch_pose, core::Size const &start_res, core::Size const &end_res) const
 
void add_end_variants (core::pose::Pose &pose)
 
Size figure_out_nested_positions (std::string const &inside_sequence, std::string const &desired_sequence) const
 
void initialize_from_scratch (core::pose::Pose &pose)
 
void prepend_residues (core::pose::Pose &pose)
 
void append_residues (core::pose::Pose &pose, core::pose::Pose const &start_pose)
 

Private Attributes

std::string const desired_sequence_
 
utility::vector1< std::string >
const 
start_tags_
 
utility::vector1< std::string >
const 
silent_files_in_
 
core::chemical::ResidueTypeSetCAP rsd_set_
 
Size const nres_
 
ObjexxFCL::FArray1D< boolinput_residue_array_
 
ObjexxFCL::FArray1D< booljunction_residue_array_
 
ObjexxFCL::FArray1D< boolmoving_residue_array_
 
bool sample_junction_
 
utility::vector1< core::Sizemoving_residues_
 
bool n_terminus_
 
bool c_terminus_
 
bool add_peptide_plane_
 
bool verbose_
 

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::swa::protein::StepWiseProteinPoseSetup::StepWiseProteinPoseSetup ( std::string const &  desired_sequence,
utility::vector1< std::string > const &  start_tags,
utility::vector1< std::string > const &  silent_files_in 
)
protocols::swa::protein::StepWiseProteinPoseSetup::~StepWiseProteinPoseSetup ( )

Member Function Documentation

void protocols::swa::protein::StepWiseProteinPoseSetup::add_end_variants ( core::pose::Pose pose)
private
void protocols::swa::protein::StepWiseProteinPoseSetup::append_residues ( core::pose::Pose pose,
core::pose::Pose const &  start_pose 
)
private
void protocols::swa::protein::StepWiseProteinPoseSetup::apply ( core::pose::Pose pose_to_visualize)
virtual
Size protocols::swa::protein::StepWiseProteinPoseSetup::figure_out_nested_positions ( std::string const &  inside_sequence,
std::string const &  desired_sequence 
) const
private

References input_residue_array_.

Referenced by apply().

std::string protocols::swa::protein::StepWiseProteinPoseSetup::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::swa::protein::StepWiseProteinPoseSetup::initialize_from_scratch ( core::pose::Pose pose)
private
void protocols::swa::protein::StepWiseProteinPoseSetup::match_end_variants ( core::pose::Pose const &  pose,
core::pose::Pose scratch_pose,
core::Size const &  start_res,
core::Size const &  end_res 
) const
private
void protocols::swa::protein::StepWiseProteinPoseSetup::match_specific_variants ( core::pose::Pose const &  pose,
core::Size const &  pose_res,
core::pose::Pose scratch_pose,
core::Size const &  scratch_pose_res,
utility::vector1< core::chemical::VariantType > const &  variant_types 
) const
private
utility::vector1< core::Size > const & protocols::swa::protein::StepWiseProteinPoseSetup::moving_residues ( ) const

References moving_residues_.

void protocols::swa::protein::StepWiseProteinPoseSetup::prepend_residues ( core::pose::Pose pose)
private
void protocols::swa::protein::StepWiseProteinPoseSetup::set_add_peptide_plane ( bool const &  setting)

References add_peptide_plane_.

void protocols::swa::protein::StepWiseProteinPoseSetup::set_c_terminus ( bool const  setting)
inline

References c_terminus_.

void protocols::swa::protein::StepWiseProteinPoseSetup::set_n_terminus ( bool const  setting)
inline

References n_terminus_.

void protocols::swa::protein::StepWiseProteinPoseSetup::set_sample_junction ( bool const  setting)
inline

References sample_junction_.

Member Data Documentation

bool protocols::swa::protein::StepWiseProteinPoseSetup::add_peptide_plane_
private
bool protocols::swa::protein::StepWiseProteinPoseSetup::c_terminus_
private

Referenced by add_end_variants(), and set_c_terminus().

std::string const protocols::swa::protein::StepWiseProteinPoseSetup::desired_sequence_
private

Referenced by apply().

ObjexxFCL::FArray1D< bool > protocols::swa::protein::StepWiseProteinPoseSetup::input_residue_array_
private
ObjexxFCL::FArray1D< bool > protocols::swa::protein::StepWiseProteinPoseSetup::junction_residue_array_
private

Referenced by apply().

ObjexxFCL::FArray1D< bool > protocols::swa::protein::StepWiseProteinPoseSetup::moving_residue_array_
private

Referenced by apply().

utility::vector1< core::Size > protocols::swa::protein::StepWiseProteinPoseSetup::moving_residues_
private

Referenced by apply(), and moving_residues().

bool protocols::swa::protein::StepWiseProteinPoseSetup::n_terminus_
private

Referenced by add_end_variants(), and set_n_terminus().

Size const protocols::swa::protein::StepWiseProteinPoseSetup::nres_
private

Referenced by apply().

core::chemical::ResidueTypeSetCAP protocols::swa::protein::StepWiseProteinPoseSetup::rsd_set_
private

Referenced by apply().

bool protocols::swa::protein::StepWiseProteinPoseSetup::sample_junction_
private

Referenced by apply(), and set_sample_junction().

utility::vector1< std::string > const protocols::swa::protein::StepWiseProteinPoseSetup::silent_files_in_
private

Referenced by apply().

utility::vector1< std::string > const protocols::swa::protein::StepWiseProteinPoseSetup::start_tags_
private

Referenced by apply().

bool protocols::swa::protein::StepWiseProteinPoseSetup::verbose_
private

Referenced by apply().


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