Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::stepwise::modeler::options::StepWiseProteinModelerOptions Class Reference

#include <StepWiseProteinModelerOptions.hh>

Public Member Functions

 StepWiseProteinModelerOptions ()
 
 StepWiseProteinModelerOptions (StepWiseProteinModelerOptions const &src)
 copy constructor More...
 
 ~StepWiseProteinModelerOptions ()
 
StepWiseProteinModelerOptionsOP clone () const
 clone the options More...
 
StepWiseProteinModelerOptionsoperator= (StepWiseProteinModelerOptions const &src)
 
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_mapfile_activated (bool const &setting)
 
bool mapfile_activated () 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 (Size const &setting)
 
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_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 (Real const &setting)
 
Real centroid_score_diff_cut () const
 
void set_centroid_weights (std::string const &setting)
 
std::string centroid_weights () const
 
void set_nstruct_centroid (Size const &setting)
 
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
 
void set_use_packer_instead_of_rotamer_trials (bool const &setting)
 
bool use_packer_instead_of_rotamer_trials () const
 
void set_min_type (std::string const &setting)
 
std::string min_type () const
 
void set_min_tolerance (Real const &setting)
 
Real min_tolerance () 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::stringfrag_files () const
 
void set_bridge_res (utility::vector1< Size > const &setting)
 
utility::vector1< Sizebridge_res () const
 

Protected Member Functions

void initialize_variables ()
 

Private Attributes

bool global_optimize_
 
bool mapfile_activated_
 
bool sample_beta_
 
bool move_jumps_between_chains_
 
bool disable_sampling_of_loop_takeoff_
 
bool cart_min_
 
Size n_sample_
 
bool filter_native_big_bins_
 
bool allow_virtual_side_chains_
 
bool prepack_
 
bool centroid_output_
 
bool centroid_screen_
 
Real centroid_score_diff_cut_
 
std::string centroid_weights_
 
Size nstruct_centroid_
 
bool ghost_loops_
 
bool ccd_close_
 
bool cluster_by_all_atom_rmsd_
 
std::string pack_weights_
 
bool use_packer_instead_of_rotamer_trials_
 
std::string min_type_
 
Real min_tolerance_
 
bool expand_loop_takeoff_
 
bool skip_coord_constraints_
 
utility::vector1< std::stringfrag_files_
 
utility::vector1< Sizebridge_res_
 

Constructor & Destructor Documentation

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

Referenced by clone().

protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::StepWiseProteinModelerOptions ( StepWiseProteinModelerOptions const &  src)

copy constructor

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

Member Function Documentation

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::allow_virtual_side_chains ( ) const
inline
utility::vector1< Size > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::bridge_res ( ) const
inline
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cart_min ( ) const
inline
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ccd_close ( ) const
inline
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_output ( ) const
inline
Real protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_score_diff_cut ( ) const
inline
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_screen ( ) const
inline
std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_weights ( ) const
inline
StepWiseProteinModelerOptionsOP protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::clone ( ) const

clone the options

References StepWiseProteinModelerOptions().

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

References basic::options::OptionKeys::stepwise::protein::allow_virtual_side_chains, allow_virtual_side_chains_, bridge_res_, basic::options::OptionKeys::stepwise::protein::cart_min, cart_min_, basic::options::OptionKeys::stepwise::protein::ccd_close, ccd_close_, basic::options::OptionKeys::stepwise::protein::centroid_output, centroid_output_, basic::options::OptionKeys::stepwise::protein::centroid_score_diff_cut, centroid_score_diff_cut_, basic::options::OptionKeys::stepwise::protein::centroid_screen, centroid_screen_, basic::options::OptionKeys::stepwise::protein::centroid_weights, centroid_weights_, basic::options::OptionKeys::stepwise::protein::cluster_by_all_atom_rmsd, cluster_by_all_atom_rmsd_, basic::options::OptionKeys::stepwise::protein::disable_sampling_of_loop_takeoff, disable_sampling_of_loop_takeoff_, basic::options::OptionKeys::stepwise::protein::expand_loop_takeoff, expand_loop_takeoff_, basic::options::OptionKeys::stepwise::protein::filter_native_big_bins, filter_native_big_bins_, frag_files_, basic::options::OptionKeys::stepwise::protein::ghost_loops, ghost_loops_, basic::options::OptionKeys::stepwise::protein::global_optimize, global_optimize_, edensity::mapfile, mapfile_activated_, basic::options::OptionKeys::stepwise::protein::min_tolerance, min_tolerance_, basic::options::OptionKeys::stepwise::protein::min_type, min_type_, basic::options::OptionKeys::stepwise::protein::move_jumps_between_chains, move_jumps_between_chains_, basic::options::OptionKeys::stepwise::protein::n_sample, n_sample_, basic::options::OptionKeys::stepwise::protein::nstruct_centroid, nstruct_centroid_, option, score::pack_weights, basic::options::OptionKeys::score::pack_weights, pack_weights_, prepack_, basic::options::OptionKeys::stepwise::protein::protein_prepack, basic::options::OptionKeys::stepwise::protein::sample_beta, sample_beta_, skip_coord_constraints_, basic::options::OptionKeys::stepwise::protein::use_packer_instead_of_rotamer_trials, use_packer_instead_of_rotamer_trials_, and user.

Referenced by protocols::stepwise::modeler::options::StepWiseModelerOptions::initialize_from_command_line().

void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::initialize_variables ( )
protected
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::mapfile_activated ( ) const
inline
Real protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::min_tolerance ( ) const
inline
std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::min_type ( ) const
inline
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::move_jumps_between_chains ( ) const
inline
Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::n_sample ( ) const
inline
Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::nstruct_centroid ( ) const
inline
StepWiseProteinModelerOptions & protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::operator= ( StepWiseProteinModelerOptions const &  src)
std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_weights ( ) const
inline
virtual void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::parse_my_tag ( utility::tag::TagCOP  )
inlinevirtual

Initialize from the recursive "tag" structure.

Implements basic::resource_manager::ResourceOptions.

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

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::prepack ( ) const
inline
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::sample_beta ( ) const
inline
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< Size > const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_cart_min ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_ccd_close ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_output ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_score_diff_cut ( Real const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_screen ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_centroid_weights ( std::string const &  setting)
inline
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
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
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_ghost_loops ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_global_optimize ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_mapfile_activated ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_min_tolerance ( Real const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_min_type ( std::string const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_move_jumps_between_chains ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_n_sample ( Size const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_nstruct_centroid ( Size const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_pack_weights ( std::string const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_prepack ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_sample_beta ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_skip_coord_constraints ( bool const &  setting)
inline
void protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::set_use_packer_instead_of_rotamer_trials ( 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.

Implements basic::resource_manager::ResourceOptions.

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

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

Member Data Documentation

bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::allow_virtual_side_chains_
private
utility::vector1< Size > protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::bridge_res_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::cart_min_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ccd_close_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::centroid_output_
private
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
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::ghost_loops_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::global_optimize_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::mapfile_activated_
private
Real protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::min_tolerance_
private
std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::min_type_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::move_jumps_between_chains_
private
Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::n_sample_
private
Size protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::nstruct_centroid_
private
std::string protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::pack_weights_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::prepack_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::sample_beta_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::skip_coord_constraints_
private
bool protocols::stepwise::modeler::options::StepWiseProteinModelerOptions::use_packer_instead_of_rotamer_trials_
private

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