#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::OptionCollectionCOP	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

◆ FullModelPoseBuilder()

core::import_pose::FullModelPoseBuilder::FullModelPoseBuilder ( )

◆ ~FullModelPoseBuilder()

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

inline

Member Function Documentation

◆ build()

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(), core::import_pose::initialize_pose_and_other_poses_from_options_and_input_poses(), and protocols::recces::pose_setup_from_file().

◆ fill_full_model_info() [1/4]

void core::import_pose::FullModelPoseBuilder::fill_full_model_info ( core::pose::Pose & pose )

private

Referenced by build().

◆ fill_full_model_info() [2/4]

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

private

◆ fill_full_model_info() [3/4]

void core::import_pose::FullModelPoseBuilder::fill_full_model_info ( utility::vector1< core::pose::Pose * > & pose_pointers )

private

◆ fill_full_model_info() [4/4]

void core::import_pose::FullModelPoseBuilder::fill_full_model_info ( utility::vector1< core::pose::PoseOP > & pose_ops )

private

◆ initialize_full_model_parameters()

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().

◆ 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(), core::import_pose::initialize_pose_and_other_poses_from_options_and_input_poses(), and protocols::recces::pose_setup_from_file().

◆ initialize_input_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().

◆ set_alignment_anchor_res()

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().

◆ set_block_stack_above_res()

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().

◆ set_block_stack_below_res()

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().

◆ set_bulge_res()

void core::import_pose::FullModelPoseBuilder::set_bulge_res ( utility::vector1< Size > const & bulge_res )

inline

References bulge_res_.

Referenced by initialize_further_from_options().

◆ set_calc_rms_res()

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().

◆ set_constraint_file()

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

inline

References constraint_file_.

Referenced by initialize_further_from_options().

◆ set_cutpoint_closed()

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

inline

References cutpoint_closed_.

Referenced by initialize_further_from_options().

◆ set_cutpoint_open_in_full_model()

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().

◆ set_cyclize_res()

void core::import_pose::FullModelPoseBuilder::set_cyclize_res ( utility::vector1< Size > const & cyclize_res )

inline

References cyclize_res_.

Referenced by initialize_further_from_options().

◆ set_disulfide_file()

void core::import_pose::FullModelPoseBuilder::set_disulfide_file ( std::string const & disulfide_file )

inline

References disulfide_file_.

Referenced by initialize_further_from_options().

◆ set_extra_minimize_jump_res()

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().

◆ set_extra_minimize_res()

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().

◆ set_fasta_file()

void core::import_pose::FullModelPoseBuilder::set_fasta_file ( std::string const & fasta_file )

inline

References fasta_file_.

◆ set_fiveprime_res()

void core::import_pose::FullModelPoseBuilder::set_fiveprime_res ( utility::vector1< Size > const & fiveprime_res )

inline

References fiveprime_res_.

Referenced by initialize_further_from_options().

◆ set_full_model_parameters()

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

inline

References full_model_parameters_.

◆ set_global_seq_file()

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().

◆ set_input_poses()

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

inline

References input_poses_.

Referenced by core::import_pose::initialize_pose_and_other_poses_from_options_and_input_poses(), and protocols::recces::pose_setup_from_file().

◆ set_input_resnum_and_chain_and_segid()

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().

◆ set_jump_res()

void core::import_pose::FullModelPoseBuilder::set_jump_res ( utility::vector1< Size > const & jump_res )

inline

References jump_res_.

Referenced by initialize_further_from_options().

◆ set_options()

void core::import_pose::FullModelPoseBuilder::set_options ( utility::options::OptionCollection const & options )

References options_.

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

◆ set_preferred_root_res()

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().

◆ set_rna_anti_chi()

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().

◆ set_rna_north_sugar()

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().

◆ set_rna_sample_sugar()

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().

◆ set_rna_south_sugar()

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().

◆ set_rna_syn_chi()

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().

◆ set_sample_res()

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

inline

References sample_res_.

Referenced by initialize_further_from_options().

◆ set_terminal_res()

void core::import_pose::FullModelPoseBuilder::set_terminal_res ( utility::vector1< Size > const & terminal_res )

inline

References terminal_res_.

Referenced by initialize_further_from_options().

◆ set_twoprime_res()

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

inline

References twoprime_res_.

Referenced by initialize_further_from_options().

◆ set_virtual_sugar_res()

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().

◆ set_working_res()

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

◆ alignment_anchor_res_

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

private

Referenced by set_alignment_anchor_res().

◆ block_stack_above_res_

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

private

Referenced by set_block_stack_above_res().

◆ block_stack_below_res_

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

private

Referenced by set_block_stack_below_res().

◆ bulge_res_

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

private

Referenced by set_bulge_res().

◆ calc_rms_res_

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

private

Referenced by set_calc_rms_res().

◆ constraint_file_

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

private

Referenced by set_constraint_file().

◆ cutpoint_closed_

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

private

Referenced by set_cutpoint_closed().

◆ cutpoint_open_in_full_model_

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

private

Referenced by initialize_full_model_parameters(), and set_cutpoint_open_in_full_model().

◆ cyclize_res_

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

private

Referenced by set_cyclize_res().

◆ disulfide_file_

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

private

Referenced by set_disulfide_file().

◆ extra_minimize_jump_res_

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

private

Referenced by set_extra_minimize_jump_res().

◆ extra_minimize_res_

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

private

Referenced by set_extra_minimize_res().

◆ fasta_file_

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

private

Referenced by initialize_full_model_parameters(), and set_fasta_file().

◆ fiveprime_res_

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

private

Referenced by set_fiveprime_res().

◆ full_model_parameters_

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

private

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

◆ global_seq_file_

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

private

Referenced by set_global_seq_file().

◆ input_poses_

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().

◆ input_resnum_and_chain_and_segid_

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().

◆ jump_res_

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

private

Referenced by set_extra_minimize_jump_res(), and set_jump_res().

◆ options_

utility::options::OptionCollectionCOP core::import_pose::FullModelPoseBuilder::options_

private

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

◆ preferred_root_res_

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

private

Referenced by set_preferred_root_res().

◆ rna_anti_chi_

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

private

Referenced by set_rna_anti_chi().

◆ rna_north_sugar_

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

private

Referenced by set_rna_north_sugar().

◆ rna_sample_sugar_

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

private

Referenced by set_rna_sample_sugar().

◆ rna_south_sugar_

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

private

Referenced by set_rna_south_sugar().

◆ rna_syn_chi_

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

private

Referenced by set_rna_syn_chi().

◆ sample_res_

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

private

Referenced by set_sample_res().

◆ terminal_res_

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

private

Referenced by set_terminal_res().

◆ twoprime_res_

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

private

Referenced by set_twoprime_res().

◆ virtual_sugar_res_

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

private

Referenced by set_virtual_sugar_res().

◆ working_res_

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

private

Referenced by set_working_res().

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

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

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ FullModelPoseBuilder()

◆ ~FullModelPoseBuilder()

Member Function Documentation

◆ build()

◆ fill_full_model_info() [1/4]

◆ fill_full_model_info() [2/4]

◆ fill_full_model_info() [3/4]

◆ fill_full_model_info() [4/4]

◆ initialize_full_model_parameters()

◆ initialize_further_from_options()

◆ initialize_input_poses_from_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_fasta_file()

◆ set_fiveprime_res()

◆ set_full_model_parameters()

◆ set_global_seq_file()

◆ set_input_poses()

◆ set_input_resnum_and_chain_and_segid()

◆ set_jump_res()

◆ set_options()

◆ 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()

◆ set_working_res()

Member Data Documentation

◆ alignment_anchor_res_

◆ block_stack_above_res_

◆ block_stack_below_res_

◆ bulge_res_

◆ calc_rms_res_

◆ constraint_file_

◆ cutpoint_closed_

◆ cutpoint_open_in_full_model_

◆ cyclize_res_

◆ disulfide_file_

◆ extra_minimize_jump_res_

◆ extra_minimize_res_

◆ fasta_file_

◆ fiveprime_res_

◆ full_model_parameters_

◆ global_seq_file_

◆ input_poses_

◆ input_resnum_and_chain_and_segid_

◆ jump_res_

◆ options_

◆ preferred_root_res_

◆ rna_anti_chi_

◆ rna_north_sugar_

◆ rna_sample_sugar_

◆ rna_south_sugar_

◆ rna_syn_chi_

◆ sample_res_

◆ terminal_res_

◆ twoprime_res_

◆ virtual_sugar_res_

◆ working_res_