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core::import_pose::FullModelPoseBuilder Class Reference

#include <FullModelPoseBuilder.hh>

Public Member Functions

 FullModelPoseBuilder ()
 
 ~FullModelPoseBuilder ()
 
void set_options (utility::options::OptionCollection const &options)
 
void set_input_poses (utility::vector1< pose::PoseOP > input_poses)
 
void set_input_resnum_and_chain_and_segid (std::tuple< utility::vector1< Size >, utility::vector1< char >, utility::vector1< std::string > > const &input_resnum_and_chain_and_segid)
 
void set_cutpoint_open_in_full_model (utility::vector1< Size > const &cutpoint_open_in_full_model)
 
void set_fasta_file (std::string const &fasta_file)
 
void set_full_model_parameters (core::pose::full_model_info::FullModelParametersOP const &full_model_parameters)
 
void set_extra_minimize_res (utility::vector1< Size > const &extra_minimize_res)
 
void set_sample_res (utility::vector1< Size > const &sample_res)
 
void set_working_res (utility::vector1< Size > const &working_res)
 
void set_terminal_res (utility::vector1< Size > const &terminal_res)
 
void set_block_stack_above_res (utility::vector1< Size > const &block_stack_above_res)
 
void set_block_stack_below_res (utility::vector1< Size > const &block_stack_below_res)
 
void set_preferred_root_res (utility::vector1< Size > const &preferred_root_res)
 
void set_jump_res (utility::vector1< Size > const &jump_res)
 
void set_cutpoint_closed (utility::vector1< Size > const &cutpoint_closed)
 
void set_cyclize_res (utility::vector1< Size > const &cyclize_res)
 
void set_twoprime_res (utility::vector1< Size > const &twoprime_res)
 
void set_fiveprime_res (utility::vector1< Size > const &fiveprime_res)
 
void set_bulge_res (utility::vector1< Size > const &bulge_res)
 
void set_extra_minimize_jump_res (utility::vector1< Size > const &extra_minimize_jump_res)
 
void set_virtual_sugar_res (utility::vector1< Size > const &virtual_sugar_res)
 
void set_alignment_anchor_res (utility::vector1< Size > const &alignment_anchor_res)
 
void set_calc_rms_res (utility::vector1< Size > const &calc_rms_res)
 
void set_rna_syn_chi (utility::vector1< Size > const &rna_syn_chi)
 
void set_rna_anti_chi (utility::vector1< Size > const &rna_anti_chi)
 
void set_rna_north_sugar (utility::vector1< Size > const &rna_north_sugar)
 
void set_rna_south_sugar (utility::vector1< Size > const &rna_south_sugar)
 
void set_rna_sample_sugar (utility::vector1< Size > const &rna_sample_sugar)
 
void set_global_seq_file (std::string const &global_seq_file)
 
void set_disulfide_file (std::string const &disulfide_file)
 
void set_constraint_file (std::string const &constraint_file)
 
void initialize_input_poses_from_options (core::chemical::ResidueTypeSetCOP rsd_set)
 
void initialize_further_from_options ()
 
void initialize_full_model_parameters ()
 
core::pose::PoseOP build ()
 

Private Member Functions

void fill_full_model_info (core::pose::Pose &pose)
 
void fill_full_model_info (utility::vector1< core::pose::PoseOP > &pose_ops)
 
void fill_full_model_info (core::pose::Pose &pose, utility::vector1< core::pose::PoseOP > &other_pose_ops)
 
void fill_full_model_info (utility::vector1< core::pose::Pose * > &pose_pointers)
 

Private Attributes

utility::options::OptionCollection options_
 
utility::vector1< pose::PoseOPinput_poses_
 
std::tuple< utility::vector1
< Size >, utility::vector1
< char >, utility::vector1
< std::string > > 
input_resnum_and_chain_and_segid_
 
utility::vector1< Sizecutpoint_open_in_full_model_
 
std::string fasta_file_ = ""
 
core::pose::full_model_info::FullModelParametersOP full_model_parameters_ = nullptr
 
utility::vector1< Sizeextra_minimize_res_
 
utility::vector1< Sizesample_res_
 
utility::vector1< Sizeworking_res_
 
utility::vector1< Sizeterminal_res_
 
utility::vector1< Sizeblock_stack_above_res_
 
utility::vector1< Sizeblock_stack_below_res_
 
utility::vector1< Sizepreferred_root_res_
 
utility::vector1< Sizejump_res_
 
utility::vector1< Sizecutpoint_closed_
 
utility::vector1< Sizecyclize_res_
 
utility::vector1< Sizetwoprime_res_
 
utility::vector1< Sizefiveprime_res_
 
utility::vector1< Sizebulge_res_
 
utility::vector1< Sizeextra_minimize_jump_res_
 
utility::vector1< Sizevirtual_sugar_res_
 
utility::vector1< Sizealignment_anchor_res_
 
utility::vector1< Sizecalc_rms_res_
 
utility::vector1< Sizerna_syn_chi_
 
utility::vector1< Sizerna_anti_chi_
 
utility::vector1< Sizerna_north_sugar_
 
utility::vector1< Sizerna_south_sugar_
 
utility::vector1< Sizerna_sample_sugar_
 
std::string global_seq_file_ = ""
 
std::string disulfide_file_ = ""
 
std::string constraint_file_ = ""
 

Constructor & Destructor Documentation

core::import_pose::FullModelPoseBuilder::FullModelPoseBuilder ( )
core::import_pose::FullModelPoseBuilder::~FullModelPoseBuilder ( )
inline

Member Function Documentation

PoseOP core::import_pose::FullModelPoseBuilder::build ( )
void core::import_pose::FullModelPoseBuilder::fill_full_model_info ( core::pose::Pose pose)
private

Referenced by build(), and fill_full_model_info().

void core::import_pose::FullModelPoseBuilder::fill_full_model_info ( utility::vector1< core::pose::PoseOP > &  pose_ops)
private
void core::import_pose::FullModelPoseBuilder::fill_full_model_info ( core::pose::Pose pose,
utility::vector1< core::pose::PoseOP > &  other_pose_ops 
)
private
void core::import_pose::FullModelPoseBuilder::fill_full_model_info ( utility::vector1< core::pose::Pose * > &  pose_pointers)
private

References core::import_pose::add_block_stack_variants(), core::pose::full_model_info::ALIGNMENT_ANCHOR_RES, alignment_anchor_res_, block_stack_above_res_, block_stack_below_res_, bulge_res_, core::pose::full_model_info::CALC_RMS, calc_rms_res_, core::import_pose::check_extra_minimize_res_are_input(), core::import_pose::check_working_res(), constraint_file_, cutpoint_closed_, core::pose::full_model_info::CUTPOINT_OPEN, cutpoint_open_in_full_model_, core::pose::full_model_info::CYCLIZE_RES, cyclize_res_, disulfide_file_, core::pose::full_model_info::DOCK_DOMAIN, core::pose::full_model_info::EXTRA_MINIMIZE, core::pose::full_model_info::EXTRA_MINIMIZE_JUMP, extra_minimize_jump_res_, extra_minimize_res_, core::import_pose::figure_out_dock_domain_map(), core::import_pose::figure_out_fixed_domain_map(), core::import_pose::figure_out_motif_mode(), core::import_pose::figure_out_sample_res(), core::import_pose::figure_out_working_res(), core::chemical::FIVEPRIME_CAP, fiveprime_res_, core::pose::fix_up_residue_type_variants(), core::pose::copydofs::FIXED_DOMAIN, full_model_parameters_, core::pose::full_model_info::get_chains_from_pdb_info(), core::pose::full_model_info::get_res_num_from_pdb_info(), core::pose::full_model_info::get_segids_from_pdb_info(), global_seq_file_, core::pose::full_model_info::INPUT_DOMAIN, jump_res_, options_, core::pose::full_model_info::PREFERRED_ROOT, preferred_root_res_, core::pose::rna::remove_bracketed(), core::import_pose::reorder_pose(), core::pose::full_model_info::RNA_ANTI_CHI, rna_anti_chi_, core::pose::full_model_info::RNA_BLOCK_STACK_ABOVE, core::pose::full_model_info::RNA_BLOCK_STACK_BELOW, core::pose::full_model_info::RNA_BULGE, core::pose::full_model_info::RNA_NORTH_SUGAR, rna_north_sugar_, core::pose::full_model_info::RNA_SAMPLE_SUGAR, rna_sample_sugar_, core::pose::full_model_info::RNA_SOUTH_SUGAR, rna_south_sugar_, core::pose::full_model_info::RNA_SYN_CHI, rna_syn_chi_, core::pose::full_model_info::RNA_TERMINAL, core::pose::full_model_info::SAMPLE, sample_res_, core::pose::full_model_info::set_full_model_info(), core::import_pose::setup_fold_trees(), core::import_pose::setup_for_density_scoring(), core::pose::Pose::size(), terminal_res_, core::pose::full_model_info::TWOPRIME_RES, twoprime_res_, core::pose::full_model_info::update_pose_objects_from_full_model_info(), virtual_sugar_res_, core::pose::full_model_info::WORKING, and working_res_.

void core::import_pose::FullModelPoseBuilder::initialize_full_model_parameters ( )
void core::import_pose::FullModelPoseBuilder::initialize_further_from_options ( )
void core::import_pose::FullModelPoseBuilder::initialize_input_poses_from_options ( core::chemical::ResidueTypeSetCOP  rsd_set)
void core::import_pose::FullModelPoseBuilder::set_alignment_anchor_res ( utility::vector1< Size > const &  alignment_anchor_res)
inline
void core::import_pose::FullModelPoseBuilder::set_block_stack_above_res ( utility::vector1< Size > const &  block_stack_above_res)
inline
void core::import_pose::FullModelPoseBuilder::set_block_stack_below_res ( utility::vector1< Size > const &  block_stack_below_res)
inline
void core::import_pose::FullModelPoseBuilder::set_bulge_res ( utility::vector1< Size > const &  bulge_res)
inline

References bulge_res_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_calc_rms_res ( utility::vector1< Size > const &  calc_rms_res)
inline
void core::import_pose::FullModelPoseBuilder::set_constraint_file ( std::string const &  constraint_file)
inline
void core::import_pose::FullModelPoseBuilder::set_cutpoint_closed ( utility::vector1< Size > const &  cutpoint_closed)
inline
void core::import_pose::FullModelPoseBuilder::set_cutpoint_open_in_full_model ( utility::vector1< Size > const &  cutpoint_open_in_full_model)
inline
void core::import_pose::FullModelPoseBuilder::set_cyclize_res ( utility::vector1< Size > const &  cyclize_res)
inline

References cyclize_res_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_disulfide_file ( std::string const &  disulfide_file)
inline
void core::import_pose::FullModelPoseBuilder::set_extra_minimize_jump_res ( utility::vector1< Size > const &  extra_minimize_jump_res)
void core::import_pose::FullModelPoseBuilder::set_extra_minimize_res ( utility::vector1< Size > const &  extra_minimize_res)
inline
void core::import_pose::FullModelPoseBuilder::set_fasta_file ( std::string const &  fasta_file)
inline

References fasta_file_.

void core::import_pose::FullModelPoseBuilder::set_fiveprime_res ( utility::vector1< Size > const &  fiveprime_res)
inline
void core::import_pose::FullModelPoseBuilder::set_full_model_parameters ( core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters)
inline
void core::import_pose::FullModelPoseBuilder::set_global_seq_file ( std::string const &  global_seq_file)
inline
void core::import_pose::FullModelPoseBuilder::set_input_poses ( utility::vector1< pose::PoseOP input_poses)
inline
void core::import_pose::FullModelPoseBuilder::set_input_resnum_and_chain_and_segid ( std::tuple< utility::vector1< Size >, utility::vector1< char >, utility::vector1< std::string > > const &  input_resnum_and_chain_and_segid)
inline
void core::import_pose::FullModelPoseBuilder::set_jump_res ( utility::vector1< Size > const &  jump_res)
inline

References jump_res_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_options ( utility::options::OptionCollection const &  options)
inline
void core::import_pose::FullModelPoseBuilder::set_preferred_root_res ( utility::vector1< Size > const &  preferred_root_res)
inline
void core::import_pose::FullModelPoseBuilder::set_rna_anti_chi ( utility::vector1< Size > const &  rna_anti_chi)
inline
void core::import_pose::FullModelPoseBuilder::set_rna_north_sugar ( utility::vector1< Size > const &  rna_north_sugar)
inline
void core::import_pose::FullModelPoseBuilder::set_rna_sample_sugar ( utility::vector1< Size > const &  rna_sample_sugar)
inline
void core::import_pose::FullModelPoseBuilder::set_rna_south_sugar ( utility::vector1< Size > const &  rna_south_sugar)
inline
void core::import_pose::FullModelPoseBuilder::set_rna_syn_chi ( utility::vector1< Size > const &  rna_syn_chi)
inline

References rna_syn_chi_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_sample_res ( utility::vector1< Size > const &  sample_res)
inline

References sample_res_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_terminal_res ( utility::vector1< Size > const &  terminal_res)
inline
void core::import_pose::FullModelPoseBuilder::set_twoprime_res ( utility::vector1< Size > const &  twoprime_res)
inline
void core::import_pose::FullModelPoseBuilder::set_virtual_sugar_res ( utility::vector1< Size > const &  virtual_sugar_res)
inline
void core::import_pose::FullModelPoseBuilder::set_working_res ( utility::vector1< Size > const &  working_res)
inline

References working_res_.

Referenced by initialize_further_from_options().

Member Data Documentation

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::alignment_anchor_res_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::block_stack_above_res_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::block_stack_below_res_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::bulge_res_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::calc_rms_res_
private
std::string core::import_pose::FullModelPoseBuilder::constraint_file_ = ""
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::cutpoint_closed_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::cutpoint_open_in_full_model_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::cyclize_res_
private
std::string core::import_pose::FullModelPoseBuilder::disulfide_file_ = ""
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::extra_minimize_jump_res_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::extra_minimize_res_
private
std::string core::import_pose::FullModelPoseBuilder::fasta_file_ = ""
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::fiveprime_res_
private
core::pose::full_model_info::FullModelParametersOP core::import_pose::FullModelPoseBuilder::full_model_parameters_ = nullptr
private
std::string core::import_pose::FullModelPoseBuilder::global_seq_file_ = ""
private
utility::vector1< pose::PoseOP > core::import_pose::FullModelPoseBuilder::input_poses_
private
std::tuple< utility::vector1< Size >, utility::vector1< char >, utility::vector1< std::string > > core::import_pose::FullModelPoseBuilder::input_resnum_and_chain_and_segid_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::jump_res_
private
utility::options::OptionCollection core::import_pose::FullModelPoseBuilder::options_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::preferred_root_res_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::rna_anti_chi_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::rna_north_sugar_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::rna_sample_sugar_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::rna_south_sugar_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::rna_syn_chi_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::sample_res_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::terminal_res_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::twoprime_res_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::virtual_sugar_res_
private
utility::vector1< Size > core::import_pose::FullModelPoseBuilder::working_res_
private

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