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protocols::stepwise::modeler::rna::sugar Namespace Reference

Classes

class  SugarInstantiateMover
 
class  SugarModeling
 
class  SugarVirtualizeMover
 
class  VirtualSugarJustInTimeInstantiator
 
class  VirtualSugarSampler
 
class  VirtualSugarSamplerFromStringList
 

Typedefs

typedef
utility::pointer::shared_ptr
< SugarInstantiateMover
SugarInstantiateMoverOP
 
typedef
utility::pointer::shared_ptr
< SugarInstantiateMover const > 
SugarInstantiateMoverCOP
 
typedef
utility::pointer::shared_ptr
< SugarModeling
SugarModelingOP
 
typedef
utility::pointer::shared_ptr
< SugarModeling const > 
SugarModelingCOP
 
typedef
utility::pointer::shared_ptr
< SugarVirtualizeMover
SugarVirtualizeMoverOP
 
typedef
utility::pointer::shared_ptr
< SugarVirtualizeMover const > 
SugarVirtualizeMoverCOP
 
typedef
utility::pointer::shared_ptr
< VirtualSugarJustInTimeInstantiator
VirtualSugarJustInTimeInstantiatorOP
 
typedef
utility::pointer::shared_ptr
< VirtualSugarJustInTimeInstantiator
const > 
VirtualSugarJustInTimeInstantiatorCOP
 
typedef
utility::pointer::shared_ptr
< VirtualSugarSamplerFromStringList
VirtualSugarSamplerFromStringListOP
 
typedef
utility::pointer::shared_ptr
< VirtualSugarSamplerFromStringList
const > 
VirtualSugarSamplerFromStringListCOP
 

Functions

void minimize_all_sampled_floating_bases (core::pose::Pose &, utility::vector1< SugarModeling > const &modeling_list, utility::vector1< PoseOP > &pose_data_list, core::scoring::ScoreFunctionCOP const &scorefxn, working_parameters::StepWiseWorkingParametersCOP const &working_parameters_, bool const virtual_sugar_is_from_prior_step_)
 
bool is_sugar_virtual (core::pose::Pose const &pose, core::Size const sugar_res, core::Size const bulge_res)
 
bool is_sugar_virtual (core::pose::Pose const &pose, core::Size const sugar_res, core::Size const bulge_res, utility::vector1< core::Size > &bulge_residues_to_virtualize)
 
void modeler_starting_pose_data_list (utility::vector1< PoseOP > &starting_pose_data_list, utility::vector1< SugarModeling > const &sugar_modeling_list, core::pose::Pose const &pose)
 
std::map< core::Size, core::Sizeget_res_map (SugarModeling const &sugar_modeling)
 
void copy_bulge_res_and_sugar_torsion (SugarModeling const &sugar_modeling, core::pose::Pose &pose, core::pose::Pose const &template_pose, bool instantiate_sugar)
 
std::map< core::Size,
core::Size > const 
get_reference_res_for_each_virtual_sugar (pose::Pose const &pose, bool const check_for_non_jump, core::Size const moving_suite)
 
std::map< core::Size,
core::Size > const 
get_reference_res_for_each_virtual_sugar_without_fold_tree (pose::Pose const &pose, core::Size const moving_suite)
 
Size look_for_non_jump_reference_to_previous (core::Size const virtual_sugar_res, pose::Pose const &pose, core::Size const moving_suite)
 
Size look_for_non_jump_reference_to_next (core::Size const virtual_sugar_res, pose::Pose const &pose, core::Size const moving_suite)
 
utility::vector1< core::Sizeget_possible_reference_res_list_from_pose_without_fold_tree (core::Size const virtual_sugar_res, pose::Pose const &pose, core::Size const moving_suite)
 
std::map< core::Size,
core::Size > const 
get_reference_res_for_each_virtual_sugar_based_on_fold_tree (pose::Pose const &pose)
 
Size get_reference_res_for_virtual_sugar_based_on_fold_tree (pose::Pose const &pose, core::Size const n)
 
Size look_for_jumps (core::Size const n, pose::Pose const &pose, bool const force_upstream)
 
Size look_for_jumps_to_previous (core::Size const virtual_sugar_res, pose::Pose const &pose, bool const force_upstream)
 
Size look_for_jumps_to_next (core::Size const virtual_sugar_res, pose::Pose const &pose, bool const force_upstream)
 
sampler::copy_dofs::ResidueAlternativeSetOP convert_sugar_modeling_to_residue_alternative_set (SugarModeling const &sugar_modeling)
 
VirtualSugarJustInTimeInstantiatorOP instantiate_any_virtual_sugars (pose::Pose &pose, working_parameters::StepWiseWorkingParametersCOP working_parameters, core::scoring::ScoreFunctionCOP scorefxn, options::StepWiseModelerOptionsCOP options)
 
void minimize_all_sampled_floating_bases (core::pose::Pose &viewer_pose, utility::vector1< SugarModeling > const &modeling_list, utility::vector1< core::pose::PoseOP > &pose_data_list, core::scoring::ScoreFunctionCOP const &modeler_scorefxn, working_parameters::StepWiseWorkingParametersCOP const &working_parameters, bool const virtual_sugar_is_from_prior_step=true)
 
void modeler_starting_pose_data_list (utility::vector1< core::pose::PoseOP > &starting_pose_data_list, utility::vector1< SugarModeling > const &SugarModeling_list, core::pose::Pose const &pose)
 
bool is_sugar_virtual (pose::Pose const &pose, core::Size const &n)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< SugarModeling const > protocols::stepwise::modeler::rna::sugar::SugarModelingCOP

Function Documentation

sampler::copy_dofs::ResidueAlternativeSetOP protocols::stepwise::modeler::rna::sugar::convert_sugar_modeling_to_residue_alternative_set ( SugarModeling const &  sugar_modeling)
void protocols::stepwise::modeler::rna::sugar::copy_bulge_res_and_sugar_torsion ( SugarModeling const &  sugar_modeling,
core::pose::Pose pose,
core::pose::Pose const &  template_pose,
bool  instantiate_sugar 
)
utility::vector1< core::Size > protocols::stepwise::modeler::rna::sugar::get_possible_reference_res_list_from_pose_without_fold_tree ( core::Size const  virtual_sugar_res,
pose::Pose const &  pose,
core::Size const  moving_suite 
)
std::map< core::Size, core::Size > const protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar ( pose::Pose const &  pose,
bool const  check_for_non_jump,
core::Size const  moving_suite 
)
std::map< core::Size, core::Size > const protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_based_on_fold_tree ( pose::Pose const &  pose)
std::map< core::Size, core::Size > const protocols::stepwise::modeler::rna::sugar::get_reference_res_for_each_virtual_sugar_without_fold_tree ( pose::Pose const &  pose,
core::Size const  moving_suite 
)
core::Size protocols::stepwise::modeler::rna::sugar::get_reference_res_for_virtual_sugar_based_on_fold_tree ( pose::Pose const &  pose,
core::Size const  n 
)
std::map< core::Size, core::Size > protocols::stepwise::modeler::rna::sugar::get_res_map ( SugarModeling const &  sugar_modeling)
VirtualSugarJustInTimeInstantiatorOP protocols::stepwise::modeler::rna::sugar::instantiate_any_virtual_sugars ( pose::Pose pose,
working_parameters::StepWiseWorkingParametersCOP  working_parameters,
core::scoring::ScoreFunctionCOP  scorefxn,
options::StepWiseModelerOptionsCOP  options 
)
bool protocols::stepwise::modeler::rna::sugar::is_sugar_virtual ( core::pose::Pose const &  pose,
core::Size const  sugar_res,
core::Size const  bulge_res 
)
bool protocols::stepwise::modeler::rna::sugar::is_sugar_virtual ( core::pose::Pose const &  pose,
core::Size const  sugar_res,
core::Size const  bulge_res,
utility::vector1< core::Size > &  bulge_residues_to_virtualize 
)
bool protocols::stepwise::modeler::rna::sugar::is_sugar_virtual ( pose::Pose const &  pose,
core::Size const &  n 
)
core::Size protocols::stepwise::modeler::rna::sugar::look_for_jumps ( core::Size const  n,
pose::Pose const &  pose,
bool const  force_upstream 
)
core::Size protocols::stepwise::modeler::rna::sugar::look_for_jumps_to_next ( core::Size const  virtual_sugar_res,
pose::Pose const &  pose,
bool const  force_upstream 
)
core::Size protocols::stepwise::modeler::rna::sugar::look_for_jumps_to_previous ( core::Size const  virtual_sugar_res,
pose::Pose const &  pose,
bool const  force_upstream 
)
core::Size protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_next ( core::Size const  virtual_sugar_res,
pose::Pose const &  pose,
core::Size const  moving_suite 
)
core::Size protocols::stepwise::modeler::rna::sugar::look_for_non_jump_reference_to_previous ( core::Size const  virtual_sugar_res,
pose::Pose const &  pose,
core::Size const  moving_suite 
)
void protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases ( core::pose::Pose viewer_pose,
utility::vector1< SugarModeling > const &  modeling_list,
utility::vector1< core::pose::PoseOP > &  pose_data_list,
core::scoring::ScoreFunctionCOP const &  modeler_scorefxn,
working_parameters::StepWiseWorkingParametersCOP const &  working_parameters,
bool const  virtual_sugar_is_from_prior_step = true 
)
void protocols::stepwise::modeler::rna::sugar::minimize_all_sampled_floating_bases ( core::pose::Pose ,
utility::vector1< SugarModeling > const &  modeling_list,
utility::vector1< PoseOP > &  pose_data_list,
core::scoring::ScoreFunctionCOP const &  scorefxn,
working_parameters::StepWiseWorkingParametersCOP const &  working_parameters_,
bool const  virtual_sugar_is_from_prior_step_ 
)
void protocols::stepwise::modeler::rna::sugar::modeler_starting_pose_data_list ( utility::vector1< core::pose::PoseOP > &  starting_pose_data_list,
utility::vector1< SugarModeling > const &  SugarModeling_list,
core::pose::Pose const &  pose 
)
void protocols::stepwise::modeler::rna::sugar::modeler_starting_pose_data_list ( utility::vector1< PoseOP > &  starting_pose_data_list,
utility::vector1< SugarModeling > const &  sugar_modeling_list,
core::pose::Pose const &  pose 
)