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protocols::rna::denovo Namespace Reference

Namespaces

 coarse
 
 movers
 
 output
 

Classes

class  RNA_DeNovoPoseInitializer
 Object used in RNA_FragmentMonteCarlo to handle setup of pose & fold-tree, and jump changes. More...
 
class  RNA_DeNovoProtocol
 The RNA de novo structure modeling protocol. More...
 
class  RNA_DeNovoProtocolCreator
 
class  RNA_FragmentMonteCarlo
 

Typedefs

typedef
utility::pointer::shared_ptr
< RNA_DeNovoPoseInitializer
RNA_DeNovoPoseInitializerOP
 
typedef
utility::pointer::shared_ptr
< RNA_DeNovoPoseInitializer
const > 
RNA_DeNovoPoseInitializerCOP
 
typedef
utility::pointer::shared_ptr
< RNA_DeNovoProtocol
RNA_DeNovoProtocolOP
 
typedef
utility::pointer::shared_ptr
< RNA_DeNovoProtocol const > 
RNA_DeNovoProtocolCOP
 
typedef
utility::pointer::shared_ptr
< RNA_FragmentMonteCarlo
RNA_FragmentMonteCarloOP
 
typedef
utility::pointer::shared_ptr
< RNA_FragmentMonteCarlo const > 
RNA_FragmentMonteCarloCOP
 
typedef numeric::xyzVector
< core::Length
Vector
 

Functions

static basic::Tracer TR ("protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer")
 
static basic::Tracer TR ("protocols.rna.denovo.RNA_DeNovoProtocol")
 
std::ostream & operator<< (std::ostream &os, RNA_DeNovoProtocol const &mover)
 
void create_rna_vall_torsions (pose::Pose &pose, utility::io::ozstream &torsions_out, utility::vector1< core::Size > const &exclude_res_list)
 
void create_rna_vall_torsions (pose::Pose &pose, std::string const &outfile, utility::vector1< core::Size > const &exclude_res_list)
 
void ensure_phosphate_nomenclature_matches_mini (pose::Pose &pose)
 
void export_packer_results (utility::vector1< std::pair< Real, std::string > > &results, utility::vector1< pose::PoseOP > pose_list, scoring::ScoreFunctionOP &scorefxn, std::string const &outfile, bool const dump)
 
void check_base_pair (pose::Pose &pose, FArray1D_int &struct_type)
 
void setup_coarse_chainbreak_constraints (pose::Pose &pose, core::Size const &n)
 
void print_internal_coords (core::pose::Pose const &pose)
 
bool possible_root (core::kinematics::FoldTree const &f, core::Size const &n)
 
bool let_rigid_body_jumps_move (core::kinematics::MoveMap &movemap, pose::Pose const &pose, bool const &move_first_rigid_body, bool const &allow_single_rigid_body)
 
void translate_virtual_anchor_to_first_rigid_body (pose::Pose &pose)
 
bool involved_in_phosphate_torsion (std::string const &atomname)
 
void figure_out_base_pair_partner (pose::Pose &pose, std::map< core::Size, core::Size > &partner, bool const strict)
 
utility::vector1
< core::pose::rna::BasePair
classify_base_pairs_lores (pose::Pose const &pose_input)
 
void print_hbonds (pose::Pose &pose)
 
void get_default_allowed_bulge_res (utility::vector1< core::Size > &allow_bulge_res_list, core::pose::Pose const &pose, bool const verbose)
 
core::Size virtualize_bulges (core::pose::Pose &input_pose, utility::vector1< core::Size > const &in_allow_bulge_res_list, core::scoring::ScoreFunctionCOP const &scorefxn, std::string const &tag, bool const allow_pre_virtualize, bool const allow_consecutive_bulges, bool const verbose)
 
core::scoring::ScoreFunctionOP get_rna_hires_scorefxn (bool const &include_protein_terms)
 
utility::vector1< core::Sizeget_moving_res (core::pose::Pose const &pose, core::pose::toolbox::AtomLevelDomainMapCOP atom_level_domain_map)
 
void delete_non_protein_from_pose (core::pose::Pose &pose)
 
utility::vector1< core::Sizeget_residues_within_dist_of_RNA (core::pose::Pose const &pose, core::Real const &dist_cutoff)
 
core::kinematics::FoldTree get_rnp_docking_fold_tree (pose::Pose const &pose, bool const &with_density)
 
void export_packer_results (utility::vector1< std::pair< core::Real, std::string > > &results, utility::vector1< core::pose::PoseOP > pose_list, core::scoring::ScoreFunctionOP &scorefxn, std::string const &outfile, bool const dumo=false)
 
void check_base_pair (core::pose::Pose &pose, ObjexxFCL::FArray1D_int &struct_type)
 
bool is_num_in_list (core::Size const i, utility::vector1< core::Size > const &list)
 

Typedef Documentation

typedef utility::pointer::shared_ptr< RNA_DeNovoProtocol const > protocols::rna::denovo::RNA_DeNovoProtocolCOP
typedef utility::pointer::shared_ptr< RNA_DeNovoProtocol > protocols::rna::denovo::RNA_DeNovoProtocolOP
typedef utility::pointer::shared_ptr< RNA_FragmentMonteCarlo const > protocols::rna::denovo::RNA_FragmentMonteCarloCOP
typedef numeric::xyzVector< core::Length > protocols::rna::denovo::Vector

Function Documentation

void protocols::rna::denovo::check_base_pair ( core::pose::Pose pose,
ObjexxFCL::FArray1D_int &  struct_type 
)
void protocols::rna::denovo::check_base_pair ( pose::Pose pose,
FArray1D_int &  struct_type 
)
utility::vector1< core::pose::rna::BasePair > protocols::rna::denovo::classify_base_pairs_lores ( pose::Pose const &  pose_input)
void protocols::rna::denovo::create_rna_vall_torsions ( pose::Pose pose,
utility::io::ozstream &  torsions_out,
utility::vector1< core::Size > const &  exclude_res_list 
)
void protocols::rna::denovo::create_rna_vall_torsions ( pose::Pose pose,
std::string const &  outfile,
utility::vector1< core::Size > const &  exclude_res_list 
)
void protocols::rna::denovo::delete_non_protein_from_pose ( core::pose::Pose pose)
void protocols::rna::denovo::ensure_phosphate_nomenclature_matches_mini ( pose::Pose pose)
void protocols::rna::denovo::export_packer_results ( utility::vector1< std::pair< core::Real, std::string > > &  results,
utility::vector1< core::pose::PoseOP pose_list,
core::scoring::ScoreFunctionOP scorefxn,
std::string const &  outfile,
bool const  dumo = false 
)
void protocols::rna::denovo::export_packer_results ( utility::vector1< std::pair< Real, std::string > > &  results,
utility::vector1< pose::PoseOP pose_list,
scoring::ScoreFunctionOP scorefxn,
std::string const &  outfile,
bool const  dump 
)
void protocols::rna::denovo::figure_out_base_pair_partner ( pose::Pose pose,
std::map< core::Size, core::Size > &  partner,
bool const  strict 
)
void protocols::rna::denovo::get_default_allowed_bulge_res ( utility::vector1< core::Size > &  allow_bulge_res_list,
core::pose::Pose const &  pose,
bool const  verbose 
)
utility::vector1< core::Size > protocols::rna::denovo::get_moving_res ( core::pose::Pose const &  pose,
core::pose::toolbox::AtomLevelDomainMapCOP  atom_level_domain_map 
)
utility::vector1< core::Size > protocols::rna::denovo::get_residues_within_dist_of_RNA ( core::pose::Pose const &  pose,
core::Real const &  dist_cutoff 
)
core::scoring::ScoreFunctionOP protocols::rna::denovo::get_rna_hires_scorefxn ( bool const &  include_protein_terms)
core::kinematics::FoldTree protocols::rna::denovo::get_rnp_docking_fold_tree ( pose::Pose const &  pose,
bool const &  with_density 
)
bool protocols::rna::denovo::involved_in_phosphate_torsion ( std::string const &  atomname)
bool protocols::rna::denovo::is_num_in_list ( core::Size const  i,
utility::vector1< core::Size > const &  list 
)
inline
bool protocols::rna::denovo::let_rigid_body_jumps_move ( core::kinematics::MoveMap movemap,
pose::Pose const &  pose,
bool const &  move_first_rigid_body,
bool const &  allow_single_rigid_body 
)
std::ostream & protocols::rna::denovo::operator<< ( std::ostream &  os,
RNA_DeNovoProtocol const &  mover 
)
bool protocols::rna::denovo::possible_root ( core::kinematics::FoldTree const &  f,
core::Size const &  n 
)
void protocols::rna::denovo::print_hbonds ( pose::Pose pose)
void protocols::rna::denovo::print_internal_coords ( core::pose::Pose const &  pose)
void protocols::rna::denovo::setup_coarse_chainbreak_constraints ( pose::Pose pose,
core::Size const &  n 
)
static basic::Tracer protocols::rna::denovo::TR ( "protocols.rna.denovo.setup.RNA_DeNovoPoseInitializer"  )
static

Referenced by protocols::rna::denovo::RNA_FragmentMonteCarlo::align_pose(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::append_virtual_anchor(), protocols::rna::denovo::movers::RNA_HelixMover::apply(), protocols::rna::denovo::movers::RNA_Minimizer::apply(), protocols::rna::denovo::RNA_FragmentMonteCarlo::apply(), protocols::rna::denovo::movers::RNP_HighResMover::apply(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply(), protocols::rna::denovo::movers::RNA_Relaxer::apply(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::apply_after_jump_change(), protocols::rna::denovo::RNA_DeNovoProtocol::calc_rmsds(), protocols::rna::denovo::RNA_FragmentMonteCarlo::check_for_loop_modeling_case(), protocols::rna::denovo::RNA_FragmentMonteCarlo::check_score_filter(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::close_at_all_cutpoints(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::close_the_loop(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::do_random_moves(), protocols::rna::denovo::coarse::CoarseRNA_LoopCloser::figure_out_pivot_res_and_scratch_res(), protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::finalize(), protocols::rna::denovo::movers::RNA_Relaxer::find_fragment_by_simple_rmsd_cutoff(), protocols::rna::denovo::coarse::CoarseRNA_Fragments::find_source_positions(), protocols::rna::denovo::output::RNA_FragmentMonteCarloOutputter::initialize(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::initialize_secstruct(), protocols::rna::denovo::movers::RNA_Relaxer::lores_monte_carlo(), protocols::rna::denovo::movers::RNA_Minimizer::o2prime_trials(), protocols::rna::denovo::RNA_DeNovoProtocol::output_silent_struct(), protocols::rna::denovo::RNA_DeNovoProtocol::output_to_silent_file(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::override_secstruct(), protocols::rna::denovo::movers::RNA_Minimizer::packing_trials(), protocols::rna::denovo::coarse::CoarseRNA_Fragments::pick_random_fragment(), protocols::rna::denovo::movers::RNP_HighResMover::protein_sidechain_packing(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_chainbreak_variants(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_fold_tree_through_build_full_model_info(), protocols::rna::denovo::RNA_DeNovoPoseInitializer::setup_jumps(), protocols::rna::denovo::RNA_FragmentMonteCarlo::setup_monte_carlo_cycles(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rigid_body_mover(), protocols::rna::denovo::movers::RNA_DeNovoMasterMover::setup_rna_protein_docking_mover(), protocols::rna::denovo::RNA_FragmentMonteCarlo::update_pose_constraints(), and protocols::rna::denovo::RNA_FragmentMonteCarlo::update_rna_denovo_master_mover().

static basic::Tracer protocols::rna::denovo::TR ( "protocols.rna.denovo.RNA_DeNovoProtocol"  )
static
void protocols::rna::denovo::translate_virtual_anchor_to_first_rigid_body ( pose::Pose pose)
core::Size protocols::rna::denovo::virtualize_bulges ( core::pose::Pose input_pose,
utility::vector1< core::Size > const &  in_allow_bulge_res_list,
core::scoring::ScoreFunctionCOP const &  scorefxn,
std::string const &  tag,
bool const  allow_pre_virtualize,
bool const  allow_consecutive_bulges,
bool const  verbose 
)