#include <StepWiseProteinPoseSetup.hh>

Inheritance diagram for protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup:

[legend]

Public Member Functions
	StepWiseProteinPoseSetup (utility::vector1< core::Size > const &moving_res_list, std::string const &desired_sequence, utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP > &input_streams_with_residue_info, utility::vector1< core::Size > const &cutpoint_open, utility::vector1< core::Size > const &cutpoint_closed)

	~StepWiseProteinPoseSetup () override

void	apply (core::pose::Pose &pose_to_visualize) override
	Apply the minimizer to one pose. More...

std::string	get_name () const override
	Each derived class must specify its name. The class name. More...

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP &	working_parameters ()

void	set_fixed_res (utility::vector1< core::Size > const &fixed_res)

void	set_extra_minimize_res (utility::vector1< core::Size > const &setting)

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

void	set_virtual_res (utility::vector1< core::Size > const &set_virtual_res_list)

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

void	set_superimpose_res (utility::vector1< core::Size > const &superimpose_res)

void	set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)

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

void	set_bridge_res (utility::vector1< core::Size > const &bridge_res)

void	set_parin_favorite_output (bool const &setting)

void	set_rsd_set (core::chemical::ResidueTypeSetCAP &rsd_set)

void	set_cst_file (std::string const &cst_file)

void	set_disulfide_file (std::string const &disulfide_file)

void	set_align_file (std::string const &align_file)

void	set_add_peptide_plane_variants (bool const &setting)

void	set_remove_nterminus_variant (bool const &setting)

void	set_remove_cterminus_variant (bool const &setting)

void	align_pose (core::pose::Pose &pose) const

bool	ready_to_align () const

void	set_dump (bool const dump)

void	set_add_virt_res (bool const setting)

void	set_secstruct (std::string const &secstruct)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual MoverOP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

virtual MoverOP	clone () const
	Return a clone of the Mover object. More...

virtual bool	reinitialize_for_each_job () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	Generates a new Mover object freshly created with the default ctor. More...

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

void	set_type (std::string const &setting)
	Set the 'type' string. More...

std::string	get_type () const

void	type (const std::string &type_in)
	Set the 'type' string. More...

std::string const &	type () const
	Get the set 'type' string. More...

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

virtual void	set_current_tag (std::string const &new_tag)

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

virtual core::Real	last_proposal_density_ratio ()

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	Import_pose (core::pose::Pose &import_pose, protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP &stream)

void	check_moving_res_in_chain (core::Size const &start_chain, core::Size const &end_chain, core::Size const &num_chains, core::Size &which_chain_has_moving_res)

void	figure_out_working_sequence_and_mapping ()

void	setup_secstruct (core::pose::Pose &pose) const

void	figure_out_jump_partners ()

core::Size	which_chain (core::Size const &i)

bool	already_connected (std::pair< core::Size, core::Size > const &potential_chain_partner, utility::vector1< std::pair< core::Size, core::Size > > const &chain_partners) const

bool	already_connected (core::Size const start_chain, core::Size const stop_chain, utility::vector1< std::pair< core::Size, core::Size > > const &chain_partners, utility::vector1< bool > already_checked) const

void	figure_out_cuts ()

void	make_pose (core::pose::Pose &pose)

void	make_full_pose (core::pose::Pose &pose)

void	setup_constraints (core::pose::Pose &pose)

void	setup_disulfides (core::pose::Pose &pose)

void	initialize_pose_from_streams (core::pose::Pose &pose)

void	figure_out_Prepend_Internal (core::pose::Pose const &pose)

void	figure_out_partition_definition (core::pose::Pose const &pose)

void	figure_out_gap_size_and_first_chain_break_res ()

void	reroot_fold_tree (core::pose::Pose &pose)

void	apply_cutpoint_variants (core::pose::Pose &pose) const

void	check_close_chain_break (core::pose::Pose const &pose) const

void	apply_bulge_variants (core::pose::Pose &pose) const

void	apply_terminus_variants_at_protein_rna_boundaries (core::pose::Pose &pose) const

void	setup_working_native_pose ()

void	get_working_pose (core::pose::Pose const &pose, core::pose::Pose &working_pose)

void	align_poses (core::pose::Pose &pose)

utility::vector1< core::Size > const	apply_full_to_sub_mapping (utility::vector1< core::Size > &res_vector) const

void	apply_virtual_phosphate_variants (core::pose::Pose &pose) const

void	apply_peptide_plane_variants_OLD (core::pose::Pose &pose) const

void	apply_peptide_plane_variants (core::pose::Pose &pose) const

void	add_terminal_res_repulsion (core::pose::Pose &pose) const

void	apply_virtual_res_variant (core::pose::Pose &pose) const

void	initialize_phi_psi_offsets (core::pose::Pose const &pose)

void	save_phi_psi_offsets (core::pose::Pose const &start_pose, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &slice_res)

void	fix_phi_psi_offsets (core::pose::Pose &pose) const

void	copy_rna_chi (core::pose::Pose &pose, core::pose::Pose const &import_pose, utility::vector1< core::Size > const &input_res, utility::vector1< core::Size > const &slice_res)

void	check_superimpose_res (core::pose::Pose const &pose)

bool	is_working_cutpoint_closed (core::Size const res, std::map< core::Size, core::Size > &full_to_sub) const

std::string	get_stepwise_jump_atom (core::chemical::ResidueType const &rsd)

void	add_aa_virt_rsd_as_root (core::pose::Pose &pose)

void	setup_full_model_info (core::pose::Pose &pose) const

Private Attributes
utility::vector1< core::Size > const &	moving_res_list_

std::string const	desired_sequence_

core::chemical::ResidueTypeSetCAP	rsd_set_

utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP >	input_streams_with_residue_info_

utility::vector1< core::Size > const	cutpoint_open_

utility::vector1< core::Size > const	cutpoint_closed_

ObjexxFCL::FArray1D< bool >	is_cutpoint_

std::string	secstruct_

utility::vector1< core::Size >	fixed_res_

utility::vector1< core::Size >	virtual_res_list_

utility::vector1< core::Size >	terminal_res_

utility::vector1< core::Size >	superimpose_res_

utility::vector1< core::Size >	calc_rms_res_

utility::vector1< core::Size >	bulge_res_

utility::vector1< core::Size >	jump_res_

utility::vector1< core::Size >	bridge_res_

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP	working_parameters_

ObjexxFCL::FArray1D< core::Real >	phi_offsets_

ObjexxFCL::FArray1D< core::Real >	psi_offsets_

utility::vector1< std::pair< core::Size, core::Size > >	jump_partners_

utility::vector1< core::Size >	cuts_

utility::vector1< core::Size >	extra_minimize_res_

bool	virtualize_5prime_phosphates_

bool	add_peptide_plane_variants_

bool	remove_nterminus_variant_

bool	remove_cterminus_variant_

bool	parin_favorite_output_

bool	add_virt_res_

std::string	cst_file_

std::string	disulfide_file_

core::scoring::constraints::ConstraintSetOP	cst_set_

core::pose::PoseOP	working_native_pose

std::string	align_file_

bool	ready_to_align_

core::pose::PoseOP	working_align_pose_

core::id::AtomID_Map< core::id::AtomID >	alignment_atom_id_map_

bool	dump_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	Overload this static method if you access options within the mover. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Constructor & Destructor Documentation

◆ StepWiseProteinPoseSetup()

protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::StepWiseProteinPoseSetup	(	utility::vector1< core::Size > const &	moving_res_list,
		std::string const &	desired_sequence,
		utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP > &	input_streams_with_residue_info,
		utility::vector1< core::Size > const &	cutpoint_open,
		utility::vector1< core::Size > const &	cutpoint_closed
	)

References cutpoint_closed_, cutpoint_open_, and is_cutpoint_.

◆ ~StepWiseProteinPoseSetup()

protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::~StepWiseProteinPoseSetup ( )

overridedefault

Member Function Documentation

◆ add_aa_virt_rsd_as_root()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_aa_virt_rsd_as_root ( core::pose::Pose & pose )

private

References core::chemical::ResidueTypeBase::aa(), core::chemical::aa_vrt, core::pose::Pose::append_residue_by_jump(), core::conformation::ResidueFactory::create_residue(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), protocols::TR(), core::pose::virtual_type_for_pose(), and working_parameters_.

Referenced by apply(), and setup_working_native_pose().

◆ add_terminal_res_repulsion()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_terminal_res_repulsion ( core::pose::Pose & pose ) const

private

References core::pose::Pose::constraint_set(), core::chemical::rna::first_base_atom_index(), core::pose::Pose::fold_tree(), core::pose::Pose::residue_type(), core::kinematics::FoldTree::root(), core::pose::Pose::size(), working_parameters_, and core::pose::Pose::xyz().

Referenced by apply().

◆ align_pose()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::align_pose ( core::pose::Pose & pose ) const

References alignment_atom_id_map_, ready_to_align_, core::scoring::superimpose_pose(), and working_align_pose_.

Referenced by align_poses().

◆ align_poses()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::align_poses ( core::pose::Pose & pose )

private

References align_file_, align_pose(), alignment_atom_id_map_, protocols::stepwise::modeler::align::create_alignment_id_map_legacy(), protocols::moves::Mover::get_native_pose(), get_working_pose(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), ready_to_align_, rsd_set_, core::pose::Pose::size(), core::scoring::superimpose_pose(), protocols::TR(), working_align_pose_, working_native_pose, and working_parameters_.

Referenced by apply().

◆ already_connected() [1/2]

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::already_connected	(	core::Size const	start_chain,
		core::Size const	stop_chain,
		utility::vector1< std::pair< core::Size, core::Size > > const &	chain_partners,
		utility::vector1< bool >	already_checked
	)		const

private

References already_connected().

◆ already_connected() [2/2]

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::already_connected	(	std::pair< core::Size, core::Size > const &	potential_chain_partner,
		utility::vector1< std::pair< core::Size, core::Size > > const &	chain_partners
	)		const

private

Referenced by already_connected(), and figure_out_jump_partners().

◆ apply()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply ( core::pose::Pose & pose_to_visualize )

overridevirtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

References add_aa_virt_rsd_as_root(), add_peptide_plane_variants_, add_terminal_res_repulsion(), add_virt_res_, align_poses(), apply_bulge_variants(), apply_cutpoint_variants(), apply_full_to_sub_mapping(), apply_peptide_plane_variants(), apply_virtual_phosphate_variants(), apply_virtual_res_variant(), bridge_res_, calc_rms_res_, check_close_chain_break(), figure_out_cuts(), figure_out_gap_size_and_first_chain_break_res(), figure_out_jump_partners(), figure_out_partition_definition(), figure_out_Prepend_Internal(), figure_out_working_sequence_and_mapping(), fixed_res_, initialize_pose_from_streams(), make_pose(), reroot_fold_tree(), setup_constraints(), setup_disulfides(), setup_full_model_info(), setup_secstruct(), setup_working_native_pose(), superimpose_res_, virtualize_5prime_phosphates_, working_native_pose, and working_parameters_.

◆ apply_bulge_variants()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_bulge_variants ( core::pose::Pose & pose ) const

private

References core::pose::add_variant_type_to_pose_residue(), core::chemical::BULGE, bulge_res_, core::pose::full_model_info::full_to_sub(), and working_parameters_.

Referenced by apply().

◆ apply_cutpoint_variants()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_cutpoint_variants ( core::pose::Pose & pose ) const

private

References core::id::BB, core::pose::correctly_add_cutpoint_variants(), cutpoint_closed_, core::pose::Pose::fold_tree(), core::pose::full_model_info::full_to_sub(), core::conformation::Residue::mainchain_torsions(), core::pose::Pose::residue(), core::pose::Pose::set_torsion(), core::pose::Pose::size(), protocols::TR(), and working_parameters_.

Referenced by apply().

◆ apply_full_to_sub_mapping()

utility::vector1< core::Size > const protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_full_to_sub_mapping ( utility::vector1< core::Size > & res_vector ) const

private

References working_parameters_.

Referenced by apply().

◆ apply_peptide_plane_variants()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_peptide_plane_variants ( core::pose::Pose & pose ) const

private

References add_peptide_plane_variants_, core::pose::add_variant_type_to_pose_residue(), core::chemical::C_METHYLAMIDATION, core::pose::full_model_info::full_to_sub(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_protein(), is_working_cutpoint_closed(), core::chemical::LOWER_TERMINUS_VARIANT, core::chemical::N_ACETYLATION, core::pose::Pose::residue_type(), core::chemical::UPPER_TERMINUS_VARIANT, and working_parameters_.

Referenced by apply().

◆ apply_peptide_plane_variants_OLD()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_peptide_plane_variants_OLD ( core::pose::Pose & pose ) const

private

References add_peptide_plane_variants_.

◆ apply_terminus_variants_at_protein_rna_boundaries()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_terminus_variants_at_protein_rna_boundaries ( core::pose::Pose & pose ) const

private

References core::pose::add_variant_type_to_pose_residue(), core::chemical::ResidueTypeBase::is_protein(), core::chemical::ResidueTypeBase::is_RNA(), core::chemical::LOWER_TERMINUS_VARIANT, core::pose::Pose::residue_type(), core::pose::Pose::size(), and core::chemical::UPPER_TERMINUS_VARIANT.

◆ apply_virtual_phosphate_variants()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_virtual_phosphate_variants ( core::pose::Pose & pose ) const

private

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_UPPER, core::pose::full_model_info::full_to_sub(), core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::ResidueTypeBase::is_RNA(), is_working_cutpoint_closed(), core::pose::Pose::residue_type(), core::chemical::VIRTUAL_PHOSPHATE, and working_parameters_.

Referenced by apply().

◆ apply_virtual_res_variant()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::apply_virtual_res_variant ( core::pose::Pose & pose ) const

private

References core::pose::add_variant_type_to_pose_residue(), core::pose::full_model_info::full_to_sub(), virtual_res_list_, core::chemical::VIRTUAL_RESIDUE_VARIANT, and working_parameters_.

Referenced by apply().

◆ check_close_chain_break()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::check_close_chain_break ( core::pose::Pose const & pose ) const

private

References protocols::stepwise::legacy::modeler::protein::is_close_chain_break(), and working_parameters_.

Referenced by apply().

◆ check_moving_res_in_chain()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::check_moving_res_in_chain	(	core::Size const &	start_chain,
		core::Size const &	end_chain,
		core::Size const &	num_chains,
		core::Size &	which_chain_has_moving_res
	)

private

◆ check_superimpose_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::check_superimpose_res ( core::pose::Pose const & pose )

private

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::root(), protocols::TR(), and working_parameters_.

◆ copy_rna_chi()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::copy_rna_chi	(	core::pose::Pose &	pose,
		core::pose::Pose const &	import_pose,
		utility::vector1< core::Size > const &	input_res,
		utility::vector1< core::Size > const &	slice_res
	)

private

References core::pose::Pose::chi(), core::pose::full_model_info::full_to_sub(), core::chemical::ResidueTypeBase::is_RNA(), core::pose::Pose::residue_type(), core::pose::Pose::set_chi(), and working_parameters_.

Referenced by initialize_pose_from_streams().

◆ figure_out_cuts()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_cuts ( )

private

References cuts_, core::pose::full_model_info::full_to_sub(), and working_parameters_.

Referenced by apply().

◆ figure_out_gap_size_and_first_chain_break_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_gap_size_and_first_chain_break_res ( )

private

References BRIDGE_RES, cutpoint_open_, core::pose::full_model_info::full_to_sub(), protocols::TR(), and working_parameters_.

Referenced by apply().

◆ figure_out_jump_partners()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_jump_partners ( )

private

References already_connected(), BRIDGE_RES, core::pose::full_model_info::full_to_sub(), jump_partners_, jump_res_, moving_res_list_, protocols::TR(), which_chain(), and working_parameters_.

Referenced by apply().

◆ figure_out_partition_definition()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_partition_definition ( core::pose::Pose const & pose )

private

References protocols::stepwise::modeler::figure_out_moving_partition_res(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::partition_by_residue(), core::pose::Pose::size(), core::pose::full_model_info::sub_to_full(), protocols::TR(), and working_parameters_.

Referenced by apply().

◆ figure_out_Prepend_Internal()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_Prepend_Internal ( core::pose::Pose const & pose )

private

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::size(), and working_parameters_.

Referenced by apply().

◆ figure_out_working_sequence_and_mapping()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::figure_out_working_sequence_and_mapping ( )

private

References BRIDGE_RES, bridge_res_, protocols::stepwise::legacy::modeler::protein::convert_to_vector1(), desired_sequence_, core::pose::full_model_info::full_to_sub(), input_streams_with_residue_info_, is_cutpoint_, MOVING_RES, moving_res_list_, core::pose::rna::remove_and_store_bracketed(), core::pose::rna::remove_bracketed(), protocols::TR(), and working_parameters_.

Referenced by apply().

◆ fix_phi_psi_offsets()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::fix_phi_psi_offsets ( core::pose::Pose & pose ) const

private

References protocols::stepwise::legacy::modeler::protein::get_pretend_phi_explicit(), protocols::stepwise::legacy::modeler::protein::get_pretend_psi_explicit(), core::chemical::ResidueTypeBase::is_protein(), core::pose::Pose::phi(), phi_offsets_, core::pose::Pose::psi(), psi_offsets_, core::pose::Pose::residue_type(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::size().

◆ get_name()

std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_name ( ) const

overridevirtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

◆ get_stepwise_jump_atom()

std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_stepwise_jump_atom ( core::chemical::ResidueType const & rsd )

private

References core::chemical::ResidueTypeBase::is_protein(), and core::chemical::ResidueTypeBase::is_RNA().

Referenced by make_pose().

◆ get_working_pose()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::get_working_pose	(	core::pose::Pose const &	pose,
		core::pose::Pose &	working_pose
	)

private

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::conformation::Residue::clone(), core::pose::Pose::fold_tree(), core::pose::rna::make_phosphate_nomenclature_matches_mini(), core::pose::Pose::residue(), core::pose::Pose::sequence(), core::pose::Pose::size(), and working_parameters_.

Referenced by align_poses(), and setup_working_native_pose().

◆ Import_pose()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::Import_pose	(	core::pose::Pose &	import_pose,
		protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP &	stream
	)

private

◆ initialize_phi_psi_offsets()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::initialize_phi_psi_offsets ( core::pose::Pose const & pose )

private

References protocols::stepwise::legacy::modeler::protein::get_pretend_phi_explicit(), protocols::stepwise::legacy::modeler::protein::get_pretend_psi_explicit(), core::chemical::ResidueTypeBase::is_protein(), phi_offsets_, psi_offsets_, core::pose::Pose::residue_type(), and core::pose::Pose::size().

Referenced by initialize_pose_from_streams().

◆ initialize_pose_from_streams()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::initialize_pose_from_streams ( core::pose::Pose & pose )

private

References align_file_, copy_rna_chi(), dump_, core::pose::Pose::dump_pdb(), protocols::moves::Mover::get_native_pose(), initialize_phi_psi_offsets(), input_streams_with_residue_info_, rsd_set_, save_phi_psi_offsets(), and working_parameters_.

Referenced by apply().

◆ is_working_cutpoint_closed()

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::is_working_cutpoint_closed	(	core::Size const	res,
		std::map< core::Size, core::Size > &	full_to_sub
	)		const

private

References cutpoint_closed_, and core::pose::full_model_info::full_to_sub().

Referenced by apply_peptide_plane_variants(), and apply_virtual_phosphate_variants().

◆ make_full_pose()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_full_pose ( core::pose::Pose & pose )

private

References core::pose::Pose::annotated_sequence(), desired_sequence_, core::pose::make_pose_from_sequence(), remove_cterminus_variant_, core::pose::remove_lower_terminus_type_from_pose_residue(), remove_nterminus_variant_, core::pose::remove_upper_terminus_type_from_pose_residue(), rsd_set_, core::pose::Pose::size(), and protocols::TR().

Referenced by make_pose(), setup_constraints(), and setup_disulfides().

◆ make_pose()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::make_pose ( core::pose::Pose & pose )

private

◆ ready_to_align()

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::ready_to_align ( ) const

References ready_to_align_.

◆ reroot_fold_tree()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::reroot_fold_tree ( core::pose::Pose & pose )

private

References desired_sequence_, core::pose::Pose::fold_tree(), core::kinematics::FoldTree::possible_root(), core::kinematics::FoldTree::reorder(), core::pose::Pose::size(), protocols::TR(), and working_parameters_.

Referenced by apply().

◆ save_phi_psi_offsets()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::save_phi_psi_offsets	(	core::pose::Pose const &	start_pose,
		utility::vector1< core::Size > const &	input_res,
		utility::vector1< core::Size > const &	slice_res
	)

private

References core::pose::full_model_info::full_to_sub(), protocols::stepwise::legacy::modeler::protein::get_pretend_phi_explicit(), protocols::stepwise::legacy::modeler::protein::get_pretend_psi_explicit(), core::chemical::ResidueTypeBase::is_protein(), phi_offsets_, psi_offsets_, core::pose::Pose::residue_type(), and working_parameters_.

Referenced by initialize_pose_from_streams().

◆ set_add_peptide_plane_variants()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_add_peptide_plane_variants ( bool const & setting )

References add_peptide_plane_variants_.

◆ set_add_virt_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_add_virt_res ( bool const setting )

References add_virt_res_.

◆ set_align_file()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_align_file ( std::string const & align_file )

References align_file_.

◆ set_bridge_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_bridge_res ( utility::vector1< core::Size > const & bridge_res )

References bridge_res_.

◆ set_bulge_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_bulge_res ( utility::vector1< core::Size > const & bulge_res )

References bulge_res_.

◆ set_calc_rms_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_calc_rms_res ( utility::vector1< core::Size > const & calc_rms_res )

References calc_rms_res_.

◆ set_cst_file()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_cst_file ( std::string const & cst_file )

References cst_file_.

◆ set_disulfide_file()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_disulfide_file ( std::string const & disulfide_file )

References disulfide_file_.

◆ set_dump()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_dump ( bool const dump )

References dump_.

◆ set_extra_minimize_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_extra_minimize_res ( utility::vector1< core::Size > const & setting )

inline

References extra_minimize_res_.

◆ set_fixed_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_fixed_res ( utility::vector1< core::Size > const & fixed_res )

References fixed_res_.

◆ set_jump_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_jump_res ( utility::vector1< core::Size > const & jump_res )

References jump_res_.

◆ set_parin_favorite_output()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_parin_favorite_output ( bool const & setting )

inline

References parin_favorite_output_.

◆ set_remove_cterminus_variant()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_remove_cterminus_variant ( bool const & setting )

inline

References remove_cterminus_variant_.

◆ set_remove_nterminus_variant()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_remove_nterminus_variant ( bool const & setting )

inline

References remove_nterminus_variant_.

◆ set_rsd_set()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_rsd_set ( core::chemical::ResidueTypeSetCAP & rsd_set )

References rsd_set_.

◆ set_secstruct()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_secstruct ( std::string const & secstruct )

References secstruct_.

◆ set_superimpose_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_superimpose_res ( utility::vector1< core::Size > const & superimpose_res )

References superimpose_res_.

◆ set_terminal_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_terminal_res ( utility::vector1< core::Size > const & terminal_res )

References terminal_res_.

◆ set_virtual_res()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::set_virtual_res ( utility::vector1< core::Size > const & set_virtual_res_list )

References virtual_res_list_.

◆ setup_constraints()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_constraints ( core::pose::Pose & pose )

private

References core::scoring::atom_pair_constraint, core::pose::Pose::constraint_set(), protocols::stepwise::modeler::constraint_set_slice(), core::scoring::coordinate_constraint, cst_file_, cst_set_, make_full_pose(), and working_parameters_.

Referenced by apply().

◆ setup_disulfides()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_disulfides ( core::pose::Pose & pose )

private

References core::pose::Pose::annotated_sequence(), core::pose::Pose::conformation(), core::chemical::DISULFIDE, disulfide_file_, core::io::raw_data::DisulfideFile::disulfides(), core::conformation::Conformation::fix_disulfides(), core::pose::full_model_info::full_to_sub(), core::chemical::ResidueTypeBase::has_variant_type(), make_full_pose(), core::pose::Pose::residue_type(), core::pose::Pose::size(), protocols::TR(), and working_parameters_.

Referenced by apply().

◆ setup_full_model_info()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_full_model_info ( core::pose::Pose & pose ) const

private

References BRIDGE_RES, core::pose::full_model_info::CALC_RMS, calc_rms_res_, cutpoint_open_, desired_sequence_, core::pose::full_model_info::EXTRA_MINIMIZE, extra_minimize_res_, core::pose::copydofs::FIXED_DOMAIN, fixed_res_, core::pose::full_model_info::INPUT_DOMAIN, MOVING_RES, core::pose::full_model_info::set_full_model_info(), and working_parameters_.

Referenced by apply(), and setup_working_native_pose().

◆ setup_secstruct()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_secstruct ( core::pose::Pose & pose ) const

private

References desired_sequence_, secstruct_, core::pose::Pose::set_secstruct(), core::pose::Pose::size(), and working_parameters_.

Referenced by apply().

◆ setup_working_native_pose()

void protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::setup_working_native_pose ( )

private

References add_aa_virt_rsd_as_root(), add_virt_res_, protocols::moves::Mover::get_native_pose(), get_working_pose(), setup_full_model_info(), protocols::TR(), and working_native_pose.

Referenced by apply().

◆ which_chain()

Size protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::which_chain ( core::Size const & i )

private

References core::pose::full_model_info::full_to_sub(), and working_parameters_.

Referenced by figure_out_jump_partners().

◆ working_parameters()

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP & protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::working_parameters ( )

References working_parameters_.

Member Data Documentation

◆ add_peptide_plane_variants_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_peptide_plane_variants_

private

Referenced by apply(), apply_peptide_plane_variants(), apply_peptide_plane_variants_OLD(), and set_add_peptide_plane_variants().

◆ add_virt_res_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::add_virt_res_

private

Referenced by apply(), set_add_virt_res(), and setup_working_native_pose().

◆ align_file_

std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::align_file_

private

Referenced by align_poses(), initialize_pose_from_streams(), and set_align_file().

◆ alignment_atom_id_map_

core::id::AtomID_Map< core::id::AtomID > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::alignment_atom_id_map_

private

Referenced by align_pose(), and align_poses().

◆ bridge_res_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::bridge_res_

private

Referenced by apply(), figure_out_working_sequence_and_mapping(), and set_bridge_res().

◆ bulge_res_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::bulge_res_

private

Referenced by apply_bulge_variants(), and set_bulge_res().

◆ calc_rms_res_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::calc_rms_res_

private

Referenced by apply(), set_calc_rms_res(), and setup_full_model_info().

◆ cst_file_

std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::cst_file_

private

Referenced by set_cst_file(), and setup_constraints().

◆ cst_set_

core::scoring::constraints::ConstraintSetOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::cst_set_

private

Referenced by setup_constraints().

◆ cutpoint_closed_

utility::vector1< core::Size > const protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::cutpoint_closed_

private

Referenced by apply_cutpoint_variants(), is_working_cutpoint_closed(), and StepWiseProteinPoseSetup().

◆ cutpoint_open_

utility::vector1< core::Size > const protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::cutpoint_open_

private

Referenced by figure_out_gap_size_and_first_chain_break_res(), setup_full_model_info(), and StepWiseProteinPoseSetup().

◆ cuts_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::cuts_

private

Referenced by figure_out_cuts(), and make_pose().

◆ desired_sequence_

std::string const protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::desired_sequence_

private

Referenced by figure_out_working_sequence_and_mapping(), make_full_pose(), reroot_fold_tree(), setup_full_model_info(), and setup_secstruct().

◆ disulfide_file_

std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::disulfide_file_

private

Referenced by set_disulfide_file(), and setup_disulfides().

◆ dump_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::dump_

private

Referenced by initialize_pose_from_streams(), and set_dump().

◆ extra_minimize_res_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::extra_minimize_res_

private

Referenced by set_extra_minimize_res(), and setup_full_model_info().

◆ fixed_res_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::fixed_res_

private

Referenced by apply(), set_fixed_res(), and setup_full_model_info().

◆ input_streams_with_residue_info_

utility::vector1< protocols::stepwise::modeler::protein::InputStreamWithResidueInfoOP > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::input_streams_with_residue_info_

private

Referenced by figure_out_working_sequence_and_mapping(), and initialize_pose_from_streams().

◆ is_cutpoint_

ObjexxFCL::FArray1D< bool > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::is_cutpoint_

private

Referenced by figure_out_working_sequence_and_mapping(), and StepWiseProteinPoseSetup().

◆ jump_partners_

utility::vector1< std::pair< core::Size, core::Size > > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::jump_partners_

private

Referenced by figure_out_jump_partners(), and make_pose().

◆ jump_res_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::jump_res_

private

Referenced by figure_out_jump_partners(), and set_jump_res().

◆ moving_res_list_

utility::vector1< core::Size > const& protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::moving_res_list_

private

Referenced by figure_out_jump_partners(), and figure_out_working_sequence_and_mapping().

◆ parin_favorite_output_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::parin_favorite_output_

private

Referenced by set_parin_favorite_output().

◆ phi_offsets_

ObjexxFCL::FArray1D< core::Real > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::phi_offsets_

private

Referenced by fix_phi_psi_offsets(), initialize_phi_psi_offsets(), and save_phi_psi_offsets().

◆ psi_offsets_

ObjexxFCL::FArray1D< core::Real > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::psi_offsets_

private

Referenced by fix_phi_psi_offsets(), initialize_phi_psi_offsets(), and save_phi_psi_offsets().

◆ ready_to_align_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::ready_to_align_

private

Referenced by align_pose(), align_poses(), and ready_to_align().

◆ remove_cterminus_variant_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::remove_cterminus_variant_

private

Referenced by make_full_pose(), and set_remove_cterminus_variant().

◆ remove_nterminus_variant_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::remove_nterminus_variant_

private

Referenced by make_full_pose(), and set_remove_nterminus_variant().

◆ rsd_set_

core::chemical::ResidueTypeSetCAP protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::rsd_set_

private

Referenced by align_poses(), initialize_pose_from_streams(), make_full_pose(), and set_rsd_set().

◆ secstruct_

std::string protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::secstruct_

private

Referenced by set_secstruct(), and setup_secstruct().

◆ superimpose_res_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::superimpose_res_

private

Referenced by apply(), and set_superimpose_res().

◆ terminal_res_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::terminal_res_

private

Referenced by set_terminal_res().

◆ virtual_res_list_

utility::vector1< core::Size > protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::virtual_res_list_

private

Referenced by apply_virtual_res_variant(), and set_virtual_res().

◆ virtualize_5prime_phosphates_

bool protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::virtualize_5prime_phosphates_

private

Referenced by apply().

◆ working_align_pose_

core::pose::PoseOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::working_align_pose_

private

Referenced by align_pose(), and align_poses().

◆ working_native_pose

core::pose::PoseOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::working_native_pose

private

Referenced by align_poses(), apply(), and setup_working_native_pose().

◆ working_parameters_

stepwise::modeler::working_parameters::StepWiseWorkingParametersOP protocols::stepwise::legacy::modeler::protein::StepWiseProteinPoseSetup::working_parameters_

private

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

src/protocols/stepwise/legacy/modeler/protein/StepWiseProteinPoseSetup.hh
src/protocols/stepwise/legacy/modeler/protein/StepWiseProteinPoseSetup.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ StepWiseProteinPoseSetup()

◆ ~StepWiseProteinPoseSetup()

Member Function Documentation

◆ add_aa_virt_rsd_as_root()

◆ add_terminal_res_repulsion()

◆ align_pose()

◆ align_poses()

◆ already_connected() [1/2]

◆ already_connected() [2/2]

◆ apply()

◆ apply_bulge_variants()

◆ apply_cutpoint_variants()

◆ apply_full_to_sub_mapping()

◆ apply_peptide_plane_variants()

◆ apply_peptide_plane_variants_OLD()

◆ apply_terminus_variants_at_protein_rna_boundaries()

◆ apply_virtual_phosphate_variants()

◆ apply_virtual_res_variant()

◆ check_close_chain_break()

◆ check_moving_res_in_chain()

◆ check_superimpose_res()

◆ copy_rna_chi()

◆ figure_out_cuts()

◆ figure_out_gap_size_and_first_chain_break_res()

◆ figure_out_jump_partners()

◆ figure_out_partition_definition()

◆ figure_out_Prepend_Internal()

◆ figure_out_working_sequence_and_mapping()

◆ fix_phi_psi_offsets()

◆ get_name()

◆ get_stepwise_jump_atom()

◆ get_working_pose()

◆ Import_pose()

◆ initialize_phi_psi_offsets()

◆ initialize_pose_from_streams()

◆ is_working_cutpoint_closed()

◆ make_full_pose()

◆ make_pose()

◆ ready_to_align()

◆ reroot_fold_tree()

◆ save_phi_psi_offsets()

◆ set_add_peptide_plane_variants()

◆ set_add_virt_res()

◆ set_align_file()

◆ set_bridge_res()

◆ set_bulge_res()

◆ set_calc_rms_res()

◆ set_cst_file()

◆ set_disulfide_file()

◆ set_dump()

◆ set_extra_minimize_res()

◆ set_fixed_res()

◆ set_jump_res()

◆ set_parin_favorite_output()

◆ set_remove_cterminus_variant()

◆ set_remove_nterminus_variant()

◆ set_rsd_set()

◆ set_secstruct()

◆ set_superimpose_res()

◆ set_terminal_res()

◆ set_virtual_res()

◆ setup_constraints()

◆ setup_disulfides()

◆ setup_full_model_info()

◆ setup_secstruct()

◆ setup_working_native_pose()

◆ which_chain()

◆ working_parameters()

Member Data Documentation

◆ add_peptide_plane_variants_

◆ add_virt_res_

◆ align_file_

◆ alignment_atom_id_map_

◆ bridge_res_

◆ bulge_res_