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

(

)

References fill_full_model_info(), input_poses_, input_resnum_and_chain_and_segid_, core::pose::Pose::pdb_info(), and core::pose::Pose::size().

Referenced by core::import_pose::initialize_pose_and_other_poses_from_options().

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

References fill_full_model_info().

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

private

References fill_full_model_info(), core::pose::full_model_info::nonconst_full_model_info(), and core::pose::full_model_info::FullModelInfo::set_other_pose_list().

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

(

)

References cutpoint_open_in_full_model_, fasta_file_, full_model_parameters_, core::import_pose::get_sequence_information(), input_poses_, and options_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::initialize_further_from_options

(

)

References full_model_parameters_, initialize_full_model_parameters(), options_, set_alignment_anchor_res(), set_block_stack_above_res(), set_block_stack_below_res(), set_bulge_res(), set_calc_rms_res(), set_constraint_file(), set_cutpoint_closed(), set_cutpoint_open_in_full_model(), set_cyclize_res(), set_disulfide_file(), set_extra_minimize_jump_res(), set_extra_minimize_res(), set_fiveprime_res(), set_global_seq_file(), set_input_resnum_and_chain_and_segid(), set_jump_res(), set_preferred_root_res(), set_rna_anti_chi(), set_rna_north_sugar(), set_rna_sample_sugar(), set_rna_south_sugar(), set_rna_syn_chi(), set_sample_res(), set_terminal_res(), set_twoprime_res(), set_virtual_sugar_res(), and set_working_res().

Referenced by core::import_pose::initialize_pose_and_other_poses_from_options().

void core::import_pose::FullModelPoseBuilder::initialize_input_poses_from_options

(

core::chemical::ResidueTypeSetCOP

rsd_set

)

References core::io::silent::SilentFileData::begin(), core::import_pose::get_other_poses(), core::import_pose::get_pdb_and_cleanup(), input_poses_, options_, and core::io::silent::SilentFileData::read_file().

Referenced by core::import_pose::initialize_pose_and_other_poses_from_options().

void core::import_pose::FullModelPoseBuilder::set_alignment_anchor_res ( utility::vector1< Size > const &  alignment_anchor_res )

inline

References alignment_anchor_res_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_block_stack_above_res ( utility::vector1< Size > const &  block_stack_above_res )

inline

References block_stack_above_res_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_block_stack_below_res ( utility::vector1< Size > const &  block_stack_below_res )

inline

References block_stack_below_res_.

Referenced by initialize_further_from_options().

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

References calc_rms_res_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_constraint_file ( std::string const &  constraint_file )

inline

References constraint_file_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_cutpoint_closed ( utility::vector1< Size > const &  cutpoint_closed )

inline

References cutpoint_closed_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_cutpoint_open_in_full_model ( utility::vector1< Size > const &  cutpoint_open_in_full_model )

inline

References cutpoint_open_in_full_model_.

Referenced by initialize_further_from_options().

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

References disulfide_file_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_extra_minimize_jump_res

(

utility::vector1< Size > const &

extra_minimize_jump_res

)

References extra_minimize_jump_res_, jump_res_, and core::chemical::rings::q.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_extra_minimize_res ( utility::vector1< Size > const &  extra_minimize_res )

inline

References extra_minimize_res_.

Referenced by initialize_further_from_options().

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

References fiveprime_res_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_full_model_parameters ( core::pose::full_model_info::FullModelParametersOP const &  full_model_parameters )

inline

References full_model_parameters_.

void core::import_pose::FullModelPoseBuilder::set_global_seq_file ( std::string const &  global_seq_file )

inline

References global_seq_file_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_input_poses ( utility::vector1< pose::PoseOP >  input_poses )

inline

References input_poses_.

Referenced by protocols::recces::pose_setup_from_file().

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

References input_resnum_and_chain_and_segid_.

Referenced by initialize_further_from_options().

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

References options_.

Referenced by core::import_pose::initialize_pose_and_other_poses_from_options(), and core::import_pose::initialize_pose_and_other_poses_from_options_and_input_poses().

void core::import_pose::FullModelPoseBuilder::set_preferred_root_res ( utility::vector1< Size > const &  preferred_root_res )

inline

References preferred_root_res_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_rna_anti_chi ( utility::vector1< Size > const &  rna_anti_chi )

inline

References rna_anti_chi_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_rna_north_sugar ( utility::vector1< Size > const &  rna_north_sugar )

inline

References rna_north_sugar_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_rna_sample_sugar ( utility::vector1< Size > const &  rna_sample_sugar )

inline

References rna_sample_sugar_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_rna_south_sugar ( utility::vector1< Size > const &  rna_south_sugar )

inline

References rna_south_sugar_.

Referenced by initialize_further_from_options().

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

References terminal_res_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_twoprime_res ( utility::vector1< Size > const &  twoprime_res )

inline

References twoprime_res_.

Referenced by initialize_further_from_options().

void core::import_pose::FullModelPoseBuilder::set_virtual_sugar_res ( utility::vector1< Size > const &  virtual_sugar_res )

inline

References virtual_sugar_res_.

Referenced by initialize_further_from_options().

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

Referenced by fill_full_model_info(), and set_alignment_anchor_res().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::block_stack_above_res_

private

Referenced by fill_full_model_info(), and set_block_stack_above_res().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::block_stack_below_res_

private

Referenced by fill_full_model_info(), and set_block_stack_below_res().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::bulge_res_

private

Referenced by fill_full_model_info(), and set_bulge_res().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::calc_rms_res_

private

Referenced by fill_full_model_info(), and set_calc_rms_res().

std::string core::import_pose::FullModelPoseBuilder::constraint_file_ = ""

private

Referenced by fill_full_model_info(), and set_constraint_file().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::cutpoint_closed_

private

Referenced by fill_full_model_info(), and set_cutpoint_closed().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::cutpoint_open_in_full_model_

private

Referenced by fill_full_model_info(), initialize_full_model_parameters(), and set_cutpoint_open_in_full_model().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::cyclize_res_

private

Referenced by fill_full_model_info(), and set_cyclize_res().

std::string core::import_pose::FullModelPoseBuilder::disulfide_file_ = ""

private

Referenced by fill_full_model_info(), and set_disulfide_file().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::extra_minimize_jump_res_

private

Referenced by fill_full_model_info(), and set_extra_minimize_jump_res().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::extra_minimize_res_

private

Referenced by fill_full_model_info(), and set_extra_minimize_res().

std::string core::import_pose::FullModelPoseBuilder::fasta_file_ = ""

private

Referenced by initialize_full_model_parameters(), and set_fasta_file().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::fiveprime_res_

private

Referenced by fill_full_model_info(), and set_fiveprime_res().

core::pose::full_model_info::FullModelParametersOP core::import_pose::FullModelPoseBuilder::full_model_parameters_ = nullptr

private

Referenced by fill_full_model_info(), initialize_full_model_parameters(), initialize_further_from_options(), and set_full_model_parameters().

std::string core::import_pose::FullModelPoseBuilder::global_seq_file_ = ""

private

Referenced by fill_full_model_info(), and set_global_seq_file().

utility::vector1< pose::PoseOP > core::import_pose::FullModelPoseBuilder::input_poses_

private

Referenced by build(), initialize_full_model_parameters(), initialize_input_poses_from_options(), and set_input_poses().

std::tuple< utility::vector1< Size >, utility::vector1< char >, utility::vector1< std::string > > core::import_pose::FullModelPoseBuilder::input_resnum_and_chain_and_segid_

private

Referenced by build(), and set_input_resnum_and_chain_and_segid().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::jump_res_

private

Referenced by fill_full_model_info(), set_extra_minimize_jump_res(), and set_jump_res().

utility::options::OptionCollection core::import_pose::FullModelPoseBuilder::options_

private

Referenced by fill_full_model_info(), initialize_full_model_parameters(), initialize_further_from_options(), initialize_input_poses_from_options(), and set_options().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::preferred_root_res_

private

Referenced by fill_full_model_info(), and set_preferred_root_res().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::rna_anti_chi_

private

Referenced by fill_full_model_info(), and set_rna_anti_chi().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::rna_north_sugar_

private

Referenced by fill_full_model_info(), and set_rna_north_sugar().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::rna_sample_sugar_

private

Referenced by fill_full_model_info(), and set_rna_sample_sugar().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::rna_south_sugar_

private

Referenced by fill_full_model_info(), and set_rna_south_sugar().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::rna_syn_chi_

private

Referenced by fill_full_model_info(), and set_rna_syn_chi().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::sample_res_

private

Referenced by fill_full_model_info(), and set_sample_res().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::terminal_res_

private

Referenced by fill_full_model_info(), and set_terminal_res().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::twoprime_res_

private

Referenced by fill_full_model_info(), and set_twoprime_res().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::virtual_sugar_res_

private

Referenced by fill_full_model_info(), and set_virtual_sugar_res().

utility::vector1< Size > core::import_pose::FullModelPoseBuilder::working_res_

private

Referenced by fill_full_model_info(), and set_working_res().

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

• src/core/import_pose/FullModelPoseBuilder.hh
• src/core/import_pose/FullModelPoseBuilder.cc