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protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup Class Reference

#include <StepWiseRNA_PoseSetup.hh>

Inheritance diagram for protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup:
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Public Member Functions

 StepWiseRNA_PoseSetup (stepwise::modeler::working_parameters::StepWiseWorkingParametersOP &working_parameters)
 
 ~StepWiseRNA_PoseSetup () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
std::string get_name () const override
 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_output_pdb (bool const setting)
 
void set_apply_virtual_res_variant_at_dinucleotide (bool const setting)
 
void set_align_to_native (bool const setting)
 
void set_use_phenix_geo (bool const setting)
 
void update_fold_tree_at_virtual_sugars (core::pose::Pose &pose)
 
void setup_full_model_info (core::pose::Pose &pose) const
 
void setup_vdw_cached_rep_screen_info (core::pose::Pose &pose) const
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
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...
 
virtual MoverOP clone () const
 Return a clone of the Mover object. 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...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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 parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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 mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Private Member Functions

void Import_pose (core::Size const &i, core::pose::Pose &import_pose) const
 
void make_extended_pose (core::pose::Pose &pose)
 
void create_starting_pose (core::pose::Pose &pose)
 
void create_pose_from_input_poses (core::pose::Pose &pose)
 
void read_input_pose_and_copy_dofs (core::pose::Pose &pose)
 
void apply_cutpoint_variants (core::pose::Pose &pose)
 
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 additional_setup_for_floating_base (core::pose::Pose &pose) const
 
void instantiate_residue_if_rebuilding_bulge (core::pose::Pose &pose)
 
void virtualize_sugar_and_backbone_at_moving_res (core::pose::Pose &pose) const
 
void apply_virtual_res_variant (core::pose::Pose &pose) const
 
void do_checks_and_apply_protonated_H1_adenosine_variant (core::pose::Pose &pose, core::pose::Pose const &start_pose_with_variant, core::Size const &n, core::Size const &i, utility::vector1< core::Size > const &input_res, std::map< core::Size, core::Size > &full_to_sub)
 
void correctly_copy_HO2prime_positions (core::pose::Pose &full_pose, utility::vector1< core::pose::Pose > const &start_pose_list)
 
core::Real get_nearest_dist_to_O2prime (core::Size const O2prime_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_
 
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP working_parameters_
 
bool copy_DOF_
 
bool verbose_
 
utility::vector1< core::Sizebulge_res_
 
utility::vector1< core::Sizevirtual_res_list_
 
utility::vector1< core::Sizenative_virtual_res_list_
 
bool output_pdb_
 
bool apply_virtual_res_variant_at_dinucleotide_
 
bool align_to_native_
 
bool use_phenix_geo_
 

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::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. 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::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::StepWiseRNA_PoseSetup ( stepwise::modeler::working_parameters::StepWiseWorkingParametersOP working_parameters)
protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::~StepWiseRNA_PoseSetup ( )
overridedefault

Member Function Documentation

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_aa_virt_rsd_as_root ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_protonated_H1_adenosine_variants ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::add_terminal_res_repulsion ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::additional_setup_for_floating_base ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply ( core::pose::Pose )
overridevirtual
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_bulge_variants ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_cutpoint_variants ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_phosphate_variants ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::correctly_copy_HO2prime_positions ( core::pose::Pose full_pose,
utility::vector1< core::pose::Pose > const &  start_pose_list 
)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::create_pose_from_input_poses ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::create_starting_pose ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::do_checks_and_apply_protonated_H1_adenosine_variant ( core::pose::Pose pose,
core::pose::Pose const &  start_pose_with_variant,
core::Size const &  n,
core::Size const &  i,
utility::vector1< core::Size > const &  input_res,
std::map< core::Size, core::Size > &  full_to_sub 
)
private
std::string protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

core::Real protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::get_nearest_dist_to_O2prime ( core::Size const  O2prime_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::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::Import_pose ( core::Size const &  i,
core::pose::Pose import_pose 
) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::instantiate_residue_if_rebuilding_bulge ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::make_extended_pose ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::read_input_pose_and_copy_dofs ( core::pose::Pose pose)
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_align_to_native ( bool const  setting)
inline

References align_to_native_.

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

References bulge_res_.

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_copy_DOF ( bool const  setting)
inline

References copy_DOF_.

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

References input_tags_.

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

References output_pdb_.

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

References silent_files_in_.

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_use_phenix_geo ( bool const  setting)
inline

References use_phenix_geo_.

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::set_verbose ( bool const  setting)
inline

References verbose_.

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

References virtual_res_list_.

void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_full_model_info ( core::pose::Pose pose) const
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_native_pose ( core::pose::Pose pose)
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::setup_vdw_cached_rep_screen_info ( core::pose::Pose pose) const
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::update_fold_tree_at_virtual_sugars ( core::pose::Pose pose)
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verify_protonated_H1_adenosine_variants ( core::pose::Pose pose) const
private
void protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::virtualize_sugar_and_backbone_at_moving_res ( core::pose::Pose pose) const
private

Member Data Documentation

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::align_to_native_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::apply_virtual_res_variant_at_dinucleotide_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::bulge_res_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::copy_DOF_
private
utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::input_tags_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::native_virtual_res_list_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::output_pdb_
private
core::chemical::ResidueTypeSetCAP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::rsd_set_
private

Referenced by Import_pose(), and make_extended_pose().

utility::vector1< std::string > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::silent_files_in_
private
bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::use_phenix_geo_
private

Referenced by apply(), and set_use_phenix_geo().

bool protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::verbose_
private
utility::vector1< core::Size > protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::virtual_res_list_
private
stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::rna::StepWiseRNA_PoseSetup::working_parameters_
private

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