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core::import_pose::RNA_DeNovoSetup Class Reference

#include <RNA_DeNovoSetup.hh>

Inheritance diagram for core::import_pose::RNA_DeNovoSetup:
Inheritance graph
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Public Member Functions

 RNA_DeNovoSetup ()
 
 ~RNA_DeNovoSetup () override
 
void initialize_from_options (utility::options::OptionCollection const &opts)
 
void initialize_from_command_line ()
 
core::import_pose::options::RNA_DeNovoProtocolOptionsCOP options () const
 
core::import_pose::RNA_DeNovoParametersCOP rna_params () const
 
void initialize_inputs_from_options (utility::options::OptionCollection const &opts)
 Initialize particular inputs first – like PDB files. More...
 
void set_fasta_files (utility::vector1< std::string > const &fasta_files)
 
void set_input_pdbs (utility::vector1< std::string > const &input_pdbs)
 
void set_input_silent_files (utility::vector1< std::string > const &input_silent_files)
 
void set_sequence_strings (utility::vector1< std::string > const &sequence_strings)
 
void set_minimize_rna (bool const minimize_rna)
 
void set_native_pose (core::pose::PoseOP native_pose)
 
void set_align_pdb (std::string const &align_pdb)
 
void set_nstruct (Size const nstruct)
 
void set_silent_file (std::string const &silent_file)
 
utility::vector1
< core::pose::PoseOP > const & 
refine_pose_list () const
 
core::pose::PoseOP pose ()
 
core::pose::PoseCOP native_pose ()
 

Static Public Member Functions

static void list_options_read (utility::options::OptionKeyList &opts)
 

Private Member Functions

void de_novo_setup_from_command_line ()
 
void de_novo_setup_from_options (utility::options::OptionCollection const &opts)
 
void de_novo_setup_from_command_line_legacy ()
 
void setup_refine_pose_list (utility::options::OptionCollection const &opts)
 
utility::vector1
< core::pose::PoseOP
get_refine_pose_list (std::string const &input_silent_file, std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &output_res_and_chain_segid, core::chemical::ResidueTypeSetCOP rsd_set) const
 
utility::vector1< core::Sizeworking_res_map (utility::vector1< core::Size > const &vec, utility::vector1< core::Size > const &working_res, bool const leave_out_last_working_residue=false) const
 
std::string working_res_map (std::string const &seq, utility::vector1< core::Size > const &working_res, bool const annotations_in_brackets=true) const
 
core::pose::rna::RNA_SecStruct working_res_map (core::pose::rna::RNA_SecStruct const &seq, utility::vector1< core::Size > const &working_res) const
 
void get_seq_and_resnum (std::string const &pdb, std::string &seq, utility::vector1< int > &resnum, utility::vector1< char > &chain, utility::vector1< std::string > &segid) const
 
std::string get_silent_seq (std::string const &silent_file) const
 
std::tuple< utility::vector1
< int >, utility::vector1
< char >, utility::vector1
< std::string > > 
get_silent_resnum (std::string const &silent_file) const
 
bool already_listed_in_obligate_pair (utility::vector1< core::Size > const &new_pair, utility::vector1< core::Size > const &obligate_pair) const
 
bool already_listed_in_obligate_pair (utility::vector1< Size > const &new_pair, utility::vector1< Size > const &obligate_pair, utility::vector1< Size > const &obligate_pair_explicit) const
 
void update_working_obligate_pairs_with_stems (utility::vector1< core::pose::rna::BasePair > &working_obligate_pairs, utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &working_stems, utility::vector1< core::Size > const &working_input_res) const
 

Private Attributes

core::import_pose::options::RNA_DeNovoProtocolOptionsOP options_
 
core::import_pose::RNA_DeNovoParametersOP rna_params_
 
core::chemical::ResidueTypeSetCOP rsd_set_
 
core::pose::PoseOP pose_
 
core::pose::PoseOP native_pose_
 
utility::vector1
< core::pose::PoseOP
refine_pose_list_
 
utility::vector1< std::string > fasta_files_
 
utility::vector1< std::string > input_pdbs_
 
utility::vector1< std::string > input_silent_files_
 
utility::vector1< std::string > sequence_strings_
 
bool minimize_rna_
 
bool minimize_rna_has_been_specified_ = false
 
utility::vector1< std::string > helical_substructs_
 
utility::vector1< std::string > dock_chunks_
 
utility::vector1< std::string > input_initialization_pdbs_
 

Constructor & Destructor Documentation

core::import_pose::RNA_DeNovoSetup::RNA_DeNovoSetup ( )
core::import_pose::RNA_DeNovoSetup::~RNA_DeNovoSetup ( )
overridedefault

Member Function Documentation

bool core::import_pose::RNA_DeNovoSetup::already_listed_in_obligate_pair ( utility::vector1< core::Size > const &  new_pair,
utility::vector1< core::Size > const &  obligate_pair 
) const
private
bool core::import_pose::RNA_DeNovoSetup::already_listed_in_obligate_pair ( utility::vector1< Size > const &  new_pair,
utility::vector1< Size > const &  obligate_pair,
utility::vector1< Size > const &  obligate_pair_explicit 
) const
private
void core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_command_line ( )
private
void core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_command_line_legacy ( )
private
void core::import_pose::RNA_DeNovoSetup::de_novo_setup_from_options ( utility::options::OptionCollection const &  opts)
private

References core::pose::addVirtualResAsRoot(), already_listed_in_obligate_pair(), core::chemical::rna::ANTIPARALLEL, core::chemical::rna::ANY_BASE_DOUBLET_ORIENTATION, core::chemical::rna::ANY_BASE_EDGE, core::pose::rna::RNA_SecStruct::base_pairs(), core::pose::rna::RNA_SecStruct::blank(), core::pack::dunbrack::c, core::pose::rna::RNA_SecStruct::check_compatible_with_sequence(), chr_chains(), core::pose::full_model_info::CUTPOINT_OPEN, dock_chunks_, core::import_pose::dump_stems(), core::pose::full_model_info::EXTRA_MINIMIZE, fasta_files_, core::io::rna::RNA_DataReader::fill_rna_data_info(), core::pose::copydofs::FIXED_DOMAIN, core::pose::rna::get_base_doublet_orientation_from_LW(), core::chemical::rna::get_edge_from_char(), core::import_pose::get_extra_cutpoints_from_names(), core::chemical::rna::get_LW_orientation_from_char(), core::chemical::rna::get_orientation_from_char(), get_seq_and_resnum(), core::import_pose::get_sequence_information(), get_silent_resnum(), get_silent_seq(), helical_substructs_, core::import_pose::initialize_native_and_align_pose(), core::pose::full_model_info::INPUT_DOMAIN, input_initialization_pdbs_, input_pdbs_, input_silent_files_, core::pose::make_pose_from_sequence(), protocols::mean_field::max(), protocols::mean_field::min(), minimize_rna_, minimize_rna_has_been_specified_, core::conformation::named_atom_id_to_atom_id(), native_pose_, options_, core::sequence::parse_out_non_standard_residues(), protocols::hybridization::path, core::import_pose::PDB_file, core::pose::pdbslice(), pose_, core::import_pose::pose_from_file(), core::chemical::rings::q, refine_pose_list(), core::pose::rna::RNA_SecStruct::remove_pair(), core::pose::full_model_info::RNA_ANTI_CHI, core::pose::full_model_info::RNA_BLOCK_STACK_ABOVE, core::pose::full_model_info::RNA_BLOCK_STACK_BELOW, rna_params_, core::pose::full_model_info::RNA_SYN_CHI, rsd_set_, sequence_strings_, core::pose::full_model_info::set_full_model_info(), core::pose::set_output_res_and_chain(), core::sequence::strip_spacers(), core::import_pose::TR(), update_working_obligate_pairs_with_stems(), core::chemical::rna::WATSON_CRICK, and working_res_map().

Referenced by de_novo_setup_from_command_line(), and initialize_from_options().

vector1< pose::PoseOP > core::import_pose::RNA_DeNovoSetup::get_refine_pose_list ( std::string const &  input_silent_file,
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > const &  output_res_and_chain_segid,
core::chemical::ResidueTypeSetCOP  rsd_set 
) const
private
void core::import_pose::RNA_DeNovoSetup::get_seq_and_resnum ( std::string const &  pdb,
std::string &  seq,
utility::vector1< int > &  resnum,
utility::vector1< char > &  chain,
utility::vector1< std::string > &  segid 
) const
private
std::tuple< utility::vector1< int >, utility::vector1< char >, utility::vector1< std::string > > core::import_pose::RNA_DeNovoSetup::get_silent_resnum ( std::string const &  silent_file) const
private
std::string core::import_pose::RNA_DeNovoSetup::get_silent_seq ( std::string const &  silent_file) const
private
void core::import_pose::RNA_DeNovoSetup::initialize_from_command_line ( )
void core::import_pose::RNA_DeNovoSetup::initialize_from_options ( utility::options::OptionCollection const &  opts)
void core::import_pose::RNA_DeNovoSetup::initialize_inputs_from_options ( utility::options::OptionCollection const &  opts)

Initialize particular inputs first – like PDB files.

the idea is that these are most likely to be unspecified on the command line in a pyrosetta type of context, and this way we could re-spec them later.

References dock_chunks_, fasta_files_, helical_substructs_, input_initialization_pdbs_, input_pdbs_, input_silent_files_, minimize_rna_, minimize_rna_has_been_specified_, and sequence_strings_.

Referenced by initialize_from_options().

void core::import_pose::RNA_DeNovoSetup::list_options_read ( utility::options::OptionKeyList &  opts)
static
core::pose::PoseCOP core::import_pose::RNA_DeNovoSetup::native_pose ( )
inline
core::import_pose::options::RNA_DeNovoProtocolOptionsCOP core::import_pose::RNA_DeNovoSetup::options ( ) const
inline

References options_.

core::pose::PoseOP core::import_pose::RNA_DeNovoSetup::pose ( )
inline

References pose_.

Referenced by get_seq_and_resnum().

utility::vector1< core::pose::PoseOP > const& core::import_pose::RNA_DeNovoSetup::refine_pose_list ( ) const
inline
core::import_pose::RNA_DeNovoParametersCOP core::import_pose::RNA_DeNovoSetup::rna_params ( ) const
inline

References rna_params_.

void core::import_pose::RNA_DeNovoSetup::set_align_pdb ( std::string const &  align_pdb)

References options_.

void core::import_pose::RNA_DeNovoSetup::set_fasta_files ( utility::vector1< std::string > const &  fasta_files)
inline

References fasta_files_.

void core::import_pose::RNA_DeNovoSetup::set_input_pdbs ( utility::vector1< std::string > const &  input_pdbs)

References input_pdbs_, and options_.

void core::import_pose::RNA_DeNovoSetup::set_input_silent_files ( utility::vector1< std::string > const &  input_silent_files)

References input_silent_files_, and options_.

void core::import_pose::RNA_DeNovoSetup::set_minimize_rna ( bool const  minimize_rna)
inline
void core::import_pose::RNA_DeNovoSetup::set_native_pose ( core::pose::PoseOP  native_pose)
inline

References native_pose(), and native_pose_.

void core::import_pose::RNA_DeNovoSetup::set_nstruct ( Size const  nstruct)

References options_.

void core::import_pose::RNA_DeNovoSetup::set_sequence_strings ( utility::vector1< std::string > const &  sequence_strings)
inline

References sequence_strings_.

void core::import_pose::RNA_DeNovoSetup::set_silent_file ( std::string const &  silent_file)

References options_.

void core::import_pose::RNA_DeNovoSetup::setup_refine_pose_list ( utility::options::OptionCollection const &  opts)
private
void core::import_pose::RNA_DeNovoSetup::update_working_obligate_pairs_with_stems ( utility::vector1< core::pose::rna::BasePair > &  working_obligate_pairs,
utility::vector1< utility::vector1< std::pair< core::Size, core::Size > > > const &  working_stems,
utility::vector1< core::Size > const &  working_input_res 
) const
private
utility::vector1< core::Size > core::import_pose::RNA_DeNovoSetup::working_res_map ( utility::vector1< core::Size > const &  vec,
utility::vector1< core::Size > const &  working_res,
bool const  leave_out_last_working_residue = false 
) const
private
std::string core::import_pose::RNA_DeNovoSetup::working_res_map ( std::string const &  seq,
utility::vector1< core::Size > const &  working_res,
bool const  annotations_in_brackets = true 
) const
private
core::pose::rna::RNA_SecStruct core::import_pose::RNA_DeNovoSetup::working_res_map ( core::pose::rna::RNA_SecStruct const &  seq,
utility::vector1< core::Size > const &  working_res 
) const
private

Member Data Documentation

utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::dock_chunks_
private
utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::fasta_files_
private
utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::helical_substructs_
private
utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::input_initialization_pdbs_
private
utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::input_pdbs_
private
utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::input_silent_files_
private
bool core::import_pose::RNA_DeNovoSetup::minimize_rna_
private
bool core::import_pose::RNA_DeNovoSetup::minimize_rna_has_been_specified_ = false
private
core::pose::PoseOP core::import_pose::RNA_DeNovoSetup::native_pose_
private
core::import_pose::options::RNA_DeNovoProtocolOptionsOP core::import_pose::RNA_DeNovoSetup::options_
private
core::pose::PoseOP core::import_pose::RNA_DeNovoSetup::pose_
private
utility::vector1< core::pose::PoseOP > core::import_pose::RNA_DeNovoSetup::refine_pose_list_
private
core::import_pose::RNA_DeNovoParametersOP core::import_pose::RNA_DeNovoSetup::rna_params_
private
core::chemical::ResidueTypeSetCOP core::import_pose::RNA_DeNovoSetup::rsd_set_
private
utility::vector1< std::string > core::import_pose::RNA_DeNovoSetup::sequence_strings_
private

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