Rosetta 3.4
Public Member Functions
protocols::rna::RNA_DeNovoProtocol Class Reference

The RNA de novo structure modeling protocol. More...

#include <RNA_DeNovoProtocol.hh>

Inheritance diagram for protocols::rna::RNA_DeNovoProtocol:
Inheritance graph
Collaboration diagram for protocols::rna::RNA_DeNovoProtocol:
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List of all members.

Public Member Functions

 RNA_DeNovoProtocol (Size const nstruct, Size const monte_carlo_cycles, std::string const silent_file, bool const heat_structure=true, bool const minimize_structure=false, bool const relax_structure=false)
 Construct the protocol object given the RNA fragment library to use.
 ~RNA_DeNovoProtocol ()
virtual protocols::moves::MoverOP clone () const
 Clone this object.
void apply (core::pose::Pose &pose)
 Apply the RNA denovo modeling protocol to the input pose.
virtual std::string get_name () const
 Each derived class must specify its name. The class name.
void set_dump_pdb (bool const setting)
void set_jump_library_file (std::string const jump_library_file)
void set_all_rna_fragments_file (std::string const file)
void set_vall_torsions_file (std::string const file)
void set_rna_params_file (std::string const file)
void set_rna_data_file (std::string const file)
void set_chunk_silent_files (utility::vector1< std::string > const &chunk_silent_files)
void set_chunk_res (utility::vector1< Size > const &chunk_res)
void ignore_secstruct (bool const setting)
void jump_change_frequency (core::Real const value)
void set_close_loops (bool const setting)
void set_close_loops_after_each_move (bool const setting)
void simple_rmsd_cutoff_relax (bool const setting)
void output_lores_silent_file (bool const setting)
void set_filter_lores_base_pairs (bool const setting)
void set_binary_rna_output (bool const setting)
void set_lores_scorefxn (std::string const &lores_scorefxn)
void set_vary_bond_geometry (bool const setting)
void output_to_silent_file (core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag, bool const score_only=false) const
void align_and_output_to_silent_file (core::pose::Pose &pose, std::string const &silent_file, std::string const &out_file_tag) const
void set_staged_constraints (bool const setting)

Detailed Description

The RNA de novo structure modeling protocol.

Constructor & Destructor Documentation

protocols::rna::RNA_DeNovoProtocol::RNA_DeNovoProtocol ( Size const  nstruct,
Size const  monte_carlo_cycles,
std::string const  silent_file,
bool const  heat_structure = true,
bool const  minimize_structure = false,
bool const  relax_structure = false 

Construct the protocol object given the RNA fragment library to use.

References core::scoring::rna::RNA_LowResolutionPotential::more_precise_base_pair_classification(), and protocols::moves::Mover::type().

Referenced by clone().

protocols::rna::RNA_DeNovoProtocol::~RNA_DeNovoProtocol ( )

Member Function Documentation

void protocols::rna::RNA_DeNovoProtocol::align_and_output_to_silent_file ( core::pose::Pose pose,
std::string const &  silent_file,
std::string const &  out_file_tag 
) const
void protocols::rna::RNA_DeNovoProtocol::apply ( core::pose::Pose pose) [virtual]
protocols::moves::MoverOP protocols::rna::RNA_DeNovoProtocol::clone ( ) const [virtual]

Clone this object.

Reimplemented from protocols::moves::Mover.

References RNA_DeNovoProtocol().

std::string protocols::rna::RNA_DeNovoProtocol::get_name ( ) const [virtual]

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

Implements protocols::moves::Mover.

void protocols::rna::RNA_DeNovoProtocol::ignore_secstruct ( bool const  setting) [inline]
void protocols::rna::RNA_DeNovoProtocol::jump_change_frequency ( core::Real const  value) [inline]
void protocols::rna::RNA_DeNovoProtocol::output_lores_silent_file ( bool const  setting) [inline]
void protocols::rna::RNA_DeNovoProtocol::output_to_silent_file ( core::pose::Pose pose,
std::string const &  silent_file,
std::string const &  out_file_tag,
bool const  score_only = false 
) const
void protocols::rna::RNA_DeNovoProtocol::set_all_rna_fragments_file ( std::string const  file) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_binary_rna_output ( bool const  setting) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_chunk_res ( utility::vector1< Size > const &  chunk_res) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_chunk_silent_files ( utility::vector1< std::string > const &  chunk_silent_files) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_close_loops ( bool const  setting) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_close_loops_after_each_move ( bool const  setting) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_dump_pdb ( bool const  setting) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_filter_lores_base_pairs ( bool const  setting) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_jump_library_file ( std::string const  jump_library_file) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_lores_scorefxn ( std::string const &  lores_scorefxn) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_rna_data_file ( std::string const  file) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_rna_params_file ( std::string const  file) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_staged_constraints ( bool const  setting) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_vall_torsions_file ( std::string const  file) [inline]
void protocols::rna::RNA_DeNovoProtocol::set_vary_bond_geometry ( bool const  setting) [inline]
void protocols::rna::RNA_DeNovoProtocol::simple_rmsd_cutoff_relax ( bool const  setting) [inline]

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