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protocols::swa::rna::StepWiseRNA_PoseSetup Class Reference

#include <StepWiseRNA_PoseSetup.hh>

Inheritance diagram for protocols::swa::rna::StepWiseRNA_PoseSetup:
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Public Member Functions

 StepWiseRNA_PoseSetup (StepWiseRNA_JobParametersOP &job_parameters)
 
 ~StepWiseRNA_PoseSetup ()
 
virtual void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void set_input_tags (utility::vector1< std::string > const &setting)
 
void set_silent_files_in (utility::vector1< std::string > const &setting)
 
void set_bulge_res (utility::vector1< core::Size > const &bulge_res)
 
void set_virtual_res (utility::vector1< core::Size > const &virtual_res_list)
 
void set_native_virtual_res (utility::vector1< core::Size > const &native_virtual_res_list)
 
void set_copy_DOF (bool const setting)
 
void set_verbose (bool const setting)
 
void setup_native_pose (core::pose::Pose &pose)
 
void set_rebuild_bulge_mode (bool const setting)
 
void set_output_pdb (bool const setting)
 
void set_apply_virtual_res_variant_at_dinucleotide (bool const setting)
 
void set_align_to_native (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 Import_pose (Size const &i, core::pose::Pose &import_pose) const
 
void make_pose (core::pose::Pose &pose)
 
void read_input_pose_and_copy_dofs (core::pose::Pose &pose)
 
void apply_cutpoint_variants (core::pose::Pose &pose, core::pose::Pose &pose_without_cutpoints)
 
void apply_bulge_variants (core::pose::Pose &pose) const
 
void apply_virtual_phosphate_variants (core::pose::Pose &pose) const
 
void add_terminal_res_repulsion (core::pose::Pose &pose) const
 
void apply_virtual_res_variant (core::pose::Pose &pose) const
 
void correctly_copy_HO2star_positions (core::pose::Pose &full_pose, utility::vector1< core::pose::Pose > const &start_pose_list)
 
core::Real get_nearest_dist_to_O2star (core::Size const O2star_seq_num, core::pose::Pose const &input_pose, utility::vector1< core::Size > const input_res_list, utility::vector1< core::Size > const &common_res_list)
 
void add_protonated_H1_adenosine_variants (core::pose::Pose &pose) const
 
void verify_protonated_H1_adenosine_variants (core::pose::Pose &pose) const
 
void add_aa_virt_rsd_as_root (core::pose::Pose &pose)
 

Private Attributes

core::chemical::ResidueTypeSetCAP rsd_set_
 
utility::vector1< std::string > input_tags_
 
utility::vector1< std::string > silent_files_in_
 
StepWiseRNA_JobParametersOP job_parameters_
 
bool copy_DOF_
 
bool verbose_
 
utility::vector1< Sizebulge_res_
 
utility::vector1< Sizevirtual_res_list_
 
utility::vector1< Sizenative_virtual_res_list_
 
bool rebuild_bulge_mode_
 
bool output_pdb_
 
bool apply_virtual_res_variant_at_dinucleotide_
 
bool align_to_native_
 

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::rna::StepWiseRNA_PoseSetup::StepWiseRNA_PoseSetup ( StepWiseRNA_JobParametersOP job_parameters)
protocols::swa::rna::StepWiseRNA_PoseSetup::~StepWiseRNA_PoseSetup ( )

Member Function Documentation

void protocols::swa::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root ( core::pose::Pose pose)
private
void protocols::swa::rna::StepWiseRNA_PoseSetup::add_protonated_H1_adenosine_variants ( core::pose::Pose pose) const
private
void protocols::swa::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion ( core::pose::Pose pose) const
private
void protocols::swa::rna::StepWiseRNA_PoseSetup::apply ( core::pose::Pose pose)
virtual
void protocols::swa::rna::StepWiseRNA_PoseSetup::apply_bulge_variants ( core::pose::Pose pose) const
private
void protocols::swa::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants ( core::pose::Pose pose,
core::pose::Pose pose_without_cutpoints 
)
private
void protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants ( core::pose::Pose pose) const
private
void protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant ( core::pose::Pose pose) const
private
void protocols::swa::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2star_positions ( core::pose::Pose full_pose,
utility::vector1< core::pose::Pose > const &  start_pose_list 
)
private
std::string protocols::swa::rna::StepWiseRNA_PoseSetup::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

core::Real protocols::swa::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2star ( core::Size const  O2star_seq_num,
core::pose::Pose const &  input_pose,
utility::vector1< core::Size > const  input_res_list,
utility::vector1< core::Size > const &  common_res_list 
)
private
void protocols::swa::rna::StepWiseRNA_PoseSetup::Import_pose ( Size const &  i,
core::pose::Pose import_pose 
) const
private
void protocols::swa::rna::StepWiseRNA_PoseSetup::make_pose ( core::pose::Pose pose)
private
void protocols::swa::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs ( core::pose::Pose pose)
private
void protocols::swa::rna::StepWiseRNA_PoseSetup::set_align_to_native ( bool const  setting)
inline

References align_to_native_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_apply_virtual_res_variant_at_dinucleotide ( bool const  setting)
inline
void protocols::swa::rna::StepWiseRNA_PoseSetup::set_bulge_res ( utility::vector1< core::Size > const &  bulge_res)
inline

References bulge_res_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_copy_DOF ( bool const  setting)
inline

References copy_DOF_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_input_tags ( utility::vector1< std::string > const &  setting)
inline

References input_tags_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_native_virtual_res ( utility::vector1< core::Size > const &  native_virtual_res_list)
inline
void protocols::swa::rna::StepWiseRNA_PoseSetup::set_output_pdb ( bool const  setting)
inline

References output_pdb_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_rebuild_bulge_mode ( bool const  setting)
inline

References rebuild_bulge_mode_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_silent_files_in ( utility::vector1< std::string > const &  setting)
inline

References silent_files_in_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_verbose ( bool const  setting)
inline

References verbose_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::set_virtual_res ( utility::vector1< core::Size > const &  virtual_res_list)
inline

References virtual_res_list_.

void protocols::swa::rna::StepWiseRNA_PoseSetup::setup_native_pose ( core::pose::Pose pose)
void protocols::swa::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants ( core::pose::Pose pose) const
private

Member Data Documentation

bool protocols::swa::rna::StepWiseRNA_PoseSetup::align_to_native_
private
bool protocols::swa::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant_at_dinucleotide_
private
utility::vector1< Size > protocols::swa::rna::StepWiseRNA_PoseSetup::bulge_res_
private
bool protocols::swa::rna::StepWiseRNA_PoseSetup::copy_DOF_
private
utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_PoseSetup::input_tags_
private
StepWiseRNA_JobParametersOP protocols::swa::rna::StepWiseRNA_PoseSetup::job_parameters_
private
utility::vector1< Size > protocols::swa::rna::StepWiseRNA_PoseSetup::native_virtual_res_list_
private
bool protocols::swa::rna::StepWiseRNA_PoseSetup::output_pdb_
private
bool protocols::swa::rna::StepWiseRNA_PoseSetup::rebuild_bulge_mode_
private
core::chemical::ResidueTypeSetCAP protocols::swa::rna::StepWiseRNA_PoseSetup::rsd_set_
private

Referenced by Import_pose(), and make_pose().

utility::vector1< std::string > protocols::swa::rna::StepWiseRNA_PoseSetup::silent_files_in_
private
bool protocols::swa::rna::StepWiseRNA_PoseSetup::verbose_
private
utility::vector1< Size > protocols::swa::rna::StepWiseRNA_PoseSetup::virtual_res_list_
private

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