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Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::stepwise::modeler::options::StepWiseProteinModelerOptions Class Reference

#include <StepWiseProteinModelerOptions.hh>

Inheritance diagram for protocols::stepwise::modeler::options::StepWiseProteinModelerOptions:
Inheritance graph
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Public Member Functions

 StepWiseProteinModelerOptions ()
 
StepWiseProteinModelerOptionsOP clone () const
 clone the options More...
 
virtual void show (std::ostream &) const
 Describe this instance to a given output stream. More...
 
virtual void parse_my_tag (utility::tag::TagCOP)
 Initialize from the recursive "tag" structure. More...
 
virtual std::string type () const
 The class name (its type) for a particular ResourceOptions instance. This function allows for better error message delivery. More...
 
void initialize_from_command_line ()
 
void set_global_optimize (bool const &setting)
 
bool global_optimize () const
 
void set_sample_beta (bool const &setting)
 
bool sample_beta () const
 
void set_move_jumps_between_chains (bool const &setting)
 
bool move_jumps_between_chains () const
 
void set_disable_sampling_of_loop_takeoff (bool const &setting)
 
bool disable_sampling_of_loop_takeoff () const
 
void set_cart_min (bool const &setting)
 
bool cart_min () const
 
void set_n_sample (core::Size const &setting)
 
core::Size n_sample () const
 
void set_filter_native_big_bins (bool const &setting)
 
bool filter_native_big_bins () const
 
void set_allow_virtual_side_chains (bool const &setting)
 
bool allow_virtual_side_chains () const
 
void set_prepack (bool const &setting)
 
bool prepack () const
 
void set_pack_protein_side_chains (bool const &setting)
 
bool pack_protein_side_chains () const
 
void set_centroid_output (bool const &setting)
 
bool centroid_output () const
 
void set_centroid_screen (bool const &setting)
 
bool centroid_screen () const
 
void set_centroid_score_diff_cut (core::Real const &setting)
 
core::Real centroid_score_diff_cut () const
 
void set_centroid_weights (std::string const &setting)
 
std::string centroid_weights () const
 
void set_nstruct_centroid (core::Size const &setting)
 
core::Size nstruct_centroid () const
 
void set_ghost_loops (bool const &setting)
 
bool ghost_loops () const
 
void set_ccd_close (bool const &setting)
 
bool ccd_close () const
 
void set_cluster_by_all_atom_rmsd (bool const &setting)
 
bool cluster_by_all_atom_rmsd () const
 
void set_pack_weights (std::string const &setting)
 
std::string pack_weights () const
 
bool const & expand_loop_takeoff () const
 
void set_expand_loop_takeoff (bool const &setting)
 
bool const & skip_coord_constraints () const
 
void set_skip_coord_constraints (bool const &setting)
 
void set_frag_files (utility::vector1< std::string > const &setting)
 
utility::vector1< std::string > frag_files () const
 
void set_bridge_res (utility::vector1< core::Size > const &setting)
 
utility::vector1< core::Sizebridge_res () const
 

Protected Member Functions

void initialize_variables ()
 

Private Attributes

bool global_optimize_
 
bool sample_beta_
 
bool move_jumps_between_chains_
 
bool disable_sampling_of_loop_takeoff_
 
bool cart_min_
 
core::Size n_sample_
 
bool filter_native_big_bins_
 
bool allow_virtual_side_chains_
 
bool prepack_
 
bool pack_protein_side_chains_
 
bool centroid_output_
 
bool centroid_screen_
 
core::Real centroid_score_diff_cut_
 
std::string centroid_weights_
 
core::Size nstruct_centroid_
 
bool ghost_loops_
 
bool ccd_close_
 
bool cluster_by_all_atom_rmsd_
 
std::string pack_weights_
 
bool expand_loop_takeoff_
 
bool skip_coord_constraints_
 
utility::vector1< std::string > frag_files_
 
utility::vector1< core::Sizebridge_res_
 

Constructor & Destructor Documentation

protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::StepWiseProteinModelerOptions ( )

Member Function Documentation

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::allow_virtual_side_chains ( ) const
inline
utility::vector1< core::Size > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::bridge_res ( ) const
inline

References bridge_res_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cart_min ( ) const
inline

References cart_min_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ccd_close ( ) const
inline

References ccd_close_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_output ( ) const
inline

References centroid_output_.

core::Real protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_score_diff_cut ( ) const
inline
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_screen ( ) const
inline

References centroid_screen_.

std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_weights ( ) const
inline

References centroid_weights_.

StepWiseProteinModelerOptionsOP protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::clone ( ) const

clone the options

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cluster_by_all_atom_rmsd ( ) const
inline
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::disable_sampling_of_loop_takeoff ( ) const
inline
bool const& protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::expand_loop_takeoff ( ) const
inline

References expand_loop_takeoff_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::filter_native_big_bins ( ) const
inline
utility::vector1< std::string > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::frag_files ( ) const
inline

References frag_files_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ghost_loops ( ) const
inline

References ghost_loops_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::global_optimize ( ) const
inline

References global_optimize_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::initialize_from_command_line ( )
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::initialize_variables ( )
protected
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::move_jumps_between_chains ( ) const
inline
core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::n_sample ( ) const
inline

References n_sample_.

core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::nstruct_centroid ( ) const
inline

References nstruct_centroid_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_protein_side_chains ( ) const
inline
std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_weights ( ) const
inline

References pack_weights_.

virtual void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::parse_my_tag ( utility::tag::TagCOP  )
inlinevirtual

Initialize from the recursive "tag" structure.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::prepack ( ) const
inline

References prepack_.

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::sample_beta ( ) const
inline

References sample_beta_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_allow_virtual_side_chains ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_bridge_res ( utility::vector1< core::Size > const &  setting)
inline

References bridge_res_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_cart_min ( bool const &  setting)
inline

References cart_min_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_ccd_close ( bool const &  setting)
inline

References ccd_close_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_output ( bool const &  setting)
inline

References centroid_output_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_score_diff_cut ( core::Real const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_screen ( bool const &  setting)
inline

References centroid_screen_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_weights ( std::string const &  setting)
inline

References centroid_weights_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_cluster_by_all_atom_rmsd ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_disable_sampling_of_loop_takeoff ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_expand_loop_takeoff ( bool const &  setting)
inline

References expand_loop_takeoff_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_filter_native_big_bins ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_frag_files ( utility::vector1< std::string > const &  setting)
inline

References frag_files_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_ghost_loops ( bool const &  setting)
inline

References ghost_loops_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_global_optimize ( bool const &  setting)
inline

References global_optimize_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_move_jumps_between_chains ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_n_sample ( core::Size const &  setting)
inline

References n_sample_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_nstruct_centroid ( core::Size const &  setting)
inline

References nstruct_centroid_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_pack_protein_side_chains ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_pack_weights ( std::string const &  setting)
inline

References pack_weights_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_prepack ( bool const &  setting)
inline

References prepack_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_sample_beta ( bool const &  setting)
inline

References sample_beta_.

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_skip_coord_constraints ( bool const &  setting)
inline
virtual void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::show ( std::ostream &  ) const
inlinevirtual

Describe this instance to a given output stream.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

bool const& protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::skip_coord_constraints ( ) const
inline
virtual std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::type ( ) const
inlinevirtual

The class name (its type) for a particular ResourceOptions instance. This function allows for better error message delivery.

Reimplemented in protocols::stepwise::modeler::options::StepWiseModelerOptions.

Member Data Documentation

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::allow_virtual_side_chains_
private
utility::vector1< core::Size > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::bridge_res_
private

Referenced by bridge_res(), and set_bridge_res().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cart_min_
private

Referenced by cart_min(), and set_cart_min().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ccd_close_
private

Referenced by ccd_close(), and set_ccd_close().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_output_
private
core::Real protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_score_diff_cut_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_screen_
private
std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_weights_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cluster_by_all_atom_rmsd_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::disable_sampling_of_loop_takeoff_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::expand_loop_takeoff_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::filter_native_big_bins_
private
utility::vector1< std::string > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::frag_files_
private

Referenced by frag_files(), and set_frag_files().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ghost_loops_
private

Referenced by ghost_loops(), and set_ghost_loops().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::global_optimize_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::move_jumps_between_chains_
private
core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::n_sample_
private

Referenced by n_sample(), and set_n_sample().

core::Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::nstruct_centroid_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_protein_side_chains_
private
std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_weights_
private

Referenced by pack_weights(), and set_pack_weights().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::prepack_
private

Referenced by prepack(), and set_prepack().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::sample_beta_
private

Referenced by sample_beta(), and set_sample_beta().

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::skip_coord_constraints_
private

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