#include <StepWisePoseSetup.hh>

Inheritance diagram for protocols::swa::StepWisePoseSetup:

Collaboration diagram for protocols::swa::StepWisePoseSetup:

Public Member Functions
	StepWisePoseSetup (utility::vector1< core::Size > const &moving_res_list, std::string const &desired_sequence, utility::vector1< InputStreamWithResidueInfoOP > &input_streams_with_residue_info, utility::vector1< core::Size > const &cutpoint_open, utility::vector1< core::Size > const &cutpoint_closed)

	~StepWisePoseSetup ()

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

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

StepWiseJobParametersOP &	job_parameters ()

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

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)

bool	ready_to_align () const

void	set_dump (bool const dump)

void	set_secstruct (std::string const secstruct)

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

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

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

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

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...

void	set_current_tag (std::string const &new_tag)

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	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...

void	type (const std::string &type_in)

virtual MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

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...

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 bool	reinitialize_for_each_job () const
	this function informs 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
	this function informs 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
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

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

jobdist::BasicJobCOP	get_current_job () const

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

void	check_moving_res_in_chain (Size const &start_chain, Size const &end_chain, Size const &num_chains, 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 ()

Size	which_chain (Size const &i)

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

bool	already_connected (Size const start_chain, Size const stop_chain, utility::vector1< std::pair< Size, 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< Size > const	apply_full_to_sub_mapping (utility::vector1< 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 (Size const res, std::map< Size, Size > &full_to_sub) const

std::string	get_swa_jump_atom (core::conformation::Residue const &rsd)

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

std::string const	desired_sequence_

core::chemical::ResidueTypeSetCAP	rsd_set_

utility::vector1 < InputStreamWithResidueInfoOP >	input_streams_with_residue_info_

utility::vector1< Size > const	cutpoint_open_

utility::vector1< Size > const	cutpoint_closed_

utility::vector1< Size >	fixed_res_

utility::vector1< Size >	virtual_res_list_

utility::vector1< Size >	terminal_res_

utility::vector1< Size >	superimpose_res_

utility::vector1< Size >	calc_rms_res_

utility::vector1< Size >	bulge_res_

utility::vector1< Size >	jump_res_

utility::vector1< Size >	bridge_res_

ObjexxFCL::FArray1D< bool >	is_cutpoint_

std::string	secstruct_

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_

StepWiseJobParametersOP	job_parameters_

bool	virtualize_5prime_phosphates_

bool	add_peptide_plane_variants_

bool	remove_nterminus_variant_

bool	remove_cterminus_variant_

bool	parin_favorite_output_

std::string	cst_file_

std::string	disulfide_file_

core::scoring::constraints::ConstraintSetOP	cst_set_

core::pose::PoseOP	working_native_pose

Size const	BRIDGE_RES_

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::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...

Detailed Description

Definition at line 53 of file StepWisePoseSetup.hh.

Constructor & Destructor Documentation

protocols::swa::StepWisePoseSetup::StepWisePoseSetup	(	utility::vector1< core::Size > const &	moving_res_list,
		std::string const &	desired_sequence,
		utility::vector1< InputStreamWithResidueInfoOP > &	input_streams_with_residue_info,
		utility::vector1< core::Size > const &	cutpoint_open,
		utility::vector1< core::Size > const &	cutpoint_closed
	)

Definition at line 99 of file StepWisePoseSetup.cc.

References cutpoint_closed_, cutpoint_open_, and is_cutpoint_.

protocols::swa::StepWisePoseSetup::~StepWisePoseSetup ( )

Definition at line 140 of file StepWisePoseSetup.cc.

Member Function Documentation

void protocols::swa::StepWisePoseSetup::add_terminal_res_repulsion ( core::pose::Pose & pose) const

private

Definition at line 1496 of file StepWisePoseSetup.cc.

References core::pose::Pose::constraint_set(), core::scoring::rna::first_base_atom_index(), core::pose::Pose::fold_tree(), job_parameters_, core::pose::Pose::residue(), core::kinematics::FoldTree::root(), core::pose::Pose::total_residue(), and core::pose::Pose::xyz().

Referenced by apply().

void protocols::swa::StepWisePoseSetup::align_pose ( core::pose::Pose & pose)

Definition at line 1276 of file StepWisePoseSetup.cc.

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

Referenced by align_poses().

void protocols::swa::StepWisePoseSetup::align_poses ( core::pose::Pose & pose)

private

Definition at line 1217 of file StepWisePoseSetup.cc.

References align_file_, align_pose(), alignment_atom_id_map_, protocols::swa::create_alignment_id_map(), protocols::moves::Mover::get_native_pose(), get_working_pose(), job_parameters_, core::import_pose::pose_from_pdb(), ready_to_align_, rsd_set_, core::scoring::superimpose_pose(), core::pose::Pose::total_residue(), working_align_pose_, and working_native_pose.

Referenced by apply().

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

private

Definition at line 453 of file StepWisePoseSetup.cc.

Referenced by already_connected(), and figure_out_jump_partners().

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

private

Definition at line 462 of file StepWisePoseSetup.cc.

References already_connected().

void protocols::swa::StepWisePoseSetup::apply ( core::pose::Pose & pose_to_visualize)

virtual

Apply the minimizer to one pose.

Implements protocols::moves::Mover.

Definition at line 151 of file StepWisePoseSetup.cc.

References add_peptide_plane_variants_, add_terminal_res_repulsion(), 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(), job_parameters_, make_pose(), reroot_fold_tree(), setup_constraints(), setup_disulfides(), setup_secstruct(), setup_working_native_pose(), superimpose_res_, terminal_res_, virtualize_5prime_phosphates_, and working_native_pose.

void protocols::swa::StepWisePoseSetup::apply_bulge_variants ( core::pose::Pose & pose) const

private

Definition at line 1091 of file StepWisePoseSetup.cc.

References core::pose::add_variant_type_to_pose_residue(), bulge_res_, and job_parameters_.

Referenced by apply().

void protocols::swa::StepWisePoseSetup::apply_cutpoint_variants ( core::pose::Pose & pose) const

private

Definition at line 1044 of file StepWisePoseSetup.cc.

References core::pose::add_variant_type_to_pose_residue(), core::id::BB, protocols::swa::rna::Correctly_position_cutpoint_phosphate_torsions(), cutpoint_closed_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::is_RNA(), job_parameters_, core::pose::Pose::residue(), core::pose::Pose::set_torsion(), and core::pose::Pose::total_residue().

Referenced by apply().

utility::vector1< Size > const protocols::swa::StepWisePoseSetup::apply_full_to_sub_mapping ( utility::vector1< Size > & res_vector) const

private

Definition at line 1285 of file StepWisePoseSetup.cc.

References job_parameters_.

Referenced by apply().

void protocols::swa::StepWisePoseSetup::apply_peptide_plane_variants ( core::pose::Pose & pose) const

private

Definition at line 1441 of file StepWisePoseSetup.cc.

References add_peptide_plane_variants_, core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::has_variant_type(), core::conformation::Residue::is_protein(), is_working_cutpoint_closed(), job_parameters_, and core::pose::Pose::residue().

Referenced by apply().

void protocols::swa::StepWisePoseSetup::apply_peptide_plane_variants_OLD ( core::pose::Pose & pose) const

private

Definition at line 1409 of file StepWisePoseSetup.cc.

References add_peptide_plane_variants_.

void protocols::swa::StepWisePoseSetup::apply_terminus_variants_at_protein_rna_boundaries ( core::pose::Pose & pose) const

private

Definition at line 1110 of file StepWisePoseSetup.cc.

References core::pose::add_variant_type_to_pose_residue(), core::conformation::Residue::is_protein(), core::conformation::Residue::is_RNA(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

void protocols::swa::StepWisePoseSetup::apply_virtual_phosphate_variants ( core::pose::Pose & pose) const

private

Definition at line 1383 of file StepWisePoseSetup.cc.

References core::pose::add_variant_type_to_pose_residue(), core::chemical::CUTPOINT_UPPER, core::chemical::ResidueType::has_variant_type(), core::conformation::Residue::is_RNA(), is_working_cutpoint_closed(), job_parameters_, core::pose::Pose::residue(), and core::conformation::Residue::type().

Referenced by apply().

void protocols::swa::StepWisePoseSetup::apply_virtual_res_variant ( core::pose::Pose & pose) const

private

Definition at line 1476 of file StepWisePoseSetup.cc.

References core::pose::add_variant_type_to_pose_residue(), job_parameters_, and virtual_res_list_.

Referenced by apply().

void protocols::swa::StepWisePoseSetup::check_close_chain_break ( core::pose::Pose const & pose) const

private

Definition at line 1126 of file StepWisePoseSetup.cc.

References protocols::swa::Is_close_chain_break(), and job_parameters_.

Referenced by apply().

void protocols::swa::StepWisePoseSetup::check_moving_res_in_chain	(	Size const &	start_chain,
		Size const &	end_chain,
		Size const &	num_chains,
		Size &	which_chain_has_moving_res
	)

private

void protocols::swa::StepWisePoseSetup::check_superimpose_res ( core::pose::Pose const & pose)

private

Definition at line 1140 of file StepWisePoseSetup.cc.

References protocols::swa::Contain_seq_num(), core::pose::Pose::fold_tree(), job_parameters_, and core::kinematics::FoldTree::root().

void protocols::swa::StepWisePoseSetup::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

Definition at line 735 of file StepWisePoseSetup.cc.

References core::pose::Pose::chi(), core::conformation::Residue::is_RNA(), job_parameters_, core::pose::Pose::residue(), and core::pose::Pose::set_chi().

Referenced by initialize_pose_from_streams().

void protocols::swa::StepWisePoseSetup::figure_out_cuts ( )

private

Definition at line 499 of file StepWisePoseSetup.cc.

References cuts_, and job_parameters_.

Referenced by apply().

void protocols::swa::StepWisePoseSetup::figure_out_gap_size_and_first_chain_break_res ( )

private

Definition at line 990 of file StepWisePoseSetup.cc.

References BRIDGE_RES_, cutpoint_open_, and job_parameters_.

Referenced by apply().

void protocols::swa::StepWisePoseSetup::figure_out_jump_partners ( )

private

Definition at line 343 of file StepWisePoseSetup.cc.

References already_connected(), BRIDGE_RES_, protocols::swa::Contain_seq_num(), job_parameters_, jump_partners_, jump_res_, moving_res_list_, and which_chain().

Referenced by apply().

void protocols::swa::StepWisePoseSetup::figure_out_partition_definition ( core::pose::Pose const & pose)

private

Definition at line 790 of file StepWisePoseSetup.cc.

References core::pose::Pose::fold_tree(), job_parameters_, core::kinematics::FoldTree::partition_by_residue(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::swa::StepWisePoseSetup::figure_out_Prepend_Internal ( core::pose::Pose const & pose)

private

Definition at line 1295 of file StepWisePoseSetup.cc.

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), job_parameters_, and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::swa::StepWisePoseSetup::figure_out_working_sequence_and_mapping ( )

private

Definition at line 231 of file StepWisePoseSetup.cc.

References bridge_res_, BRIDGE_RES_, desired_sequence_, input_streams_with_residue_info_, is_cutpoint_, job_parameters_, and moving_res_list_.

Referenced by apply().

void protocols::swa::StepWisePoseSetup::fix_phi_psi_offsets ( core::pose::Pose & pose) const

private

Definition at line 719 of file StepWisePoseSetup.cc.

References protocols::swa::protein::get_pretend_phi_explicit(), protocols::swa::protein::get_pretend_psi_explicit(), core::conformation::Residue::is_protein(), core::pose::Pose::phi(), phi_offsets_, core::pose::Pose::psi(), psi_offsets_, core::pose::Pose::residue(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::total_residue().

std::string protocols::swa::StepWisePoseSetup::get_name ( ) const

virtual

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

Implements protocols::moves::Mover.

Definition at line 144 of file StepWisePoseSetup.cc.

std::string protocols::swa::StepWisePoseSetup::get_swa_jump_atom ( core::conformation::Residue const & rsd)

private

Definition at line 637 of file StepWisePoseSetup.cc.

References core::conformation::Residue::is_protein(), and core::conformation::Residue::is_RNA().

Referenced by make_pose().

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

private

Definition at line 1163 of file StepWisePoseSetup.cc.

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::pose::Pose::fold_tree(), job_parameters_, protocols::rna::make_phosphate_nomenclature_matches_mini(), core::pose::Pose::sequence(), and core::pose::Pose::total_residue().

Referenced by align_poses(), and setup_working_native_pose().

void protocols::swa::StepWisePoseSetup::Import_pose	(	core::pose::Pose &	import_pose,
		InputStreamWithResidueInfoOP &	stream
	)

private

void protocols::swa::StepWisePoseSetup::initialize_phi_psi_offsets ( core::pose::Pose const & pose)

private

Definition at line 680 of file StepWisePoseSetup.cc.

References protocols::swa::protein::get_pretend_phi_explicit(), protocols::swa::protein::get_pretend_psi_explicit(), core::conformation::Residue::is_protein(), phi_offsets_, psi_offsets_, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

Referenced by initialize_pose_from_streams().

void protocols::swa::StepWisePoseSetup::initialize_pose_from_streams ( core::pose::Pose & pose)

private

Definition at line 751 of file StepWisePoseSetup.cc.

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_, job_parameters_, rsd_set_, and save_phi_psi_offsets().

Referenced by apply().

bool protocols::swa::StepWisePoseSetup::is_working_cutpoint_closed	(	Size const	res,
		std::map< Size, Size > &	full_to_sub
	)		const

private

Definition at line 1366 of file StepWisePoseSetup.cc.

References cutpoint_closed_.

Referenced by apply_peptide_plane_variants(), and apply_virtual_phosphate_variants().

StepWiseJobParametersOP & protocols::swa::StepWisePoseSetup::job_parameters ( )

Definition at line 1290 of file StepWisePoseSetup.cc.

References job_parameters_.

void protocols::swa::StepWisePoseSetup::make_full_pose ( core::pose::Pose & pose)

private

Definition at line 515 of file StepWisePoseSetup.cc.

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_, and core::pose::Pose::total_residue().

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

void protocols::swa::StepWisePoseSetup::make_pose ( core::pose::Pose & pose)

private

Definition at line 528 of file StepWisePoseSetup.cc.

References cuts_, core::pose::Pose::fold_tree(), get_swa_jump_atom(), core::conformation::Residue::is_protein(), job_parameters_, jump_partners_, make_full_pose(), protocols::swa::pdbslice(), core::pose::Pose::residue(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), and core::pose::Pose::total_residue().

Referenced by apply().

bool protocols::swa::StepWisePoseSetup::ready_to_align ( ) const

Definition at line 1682 of file StepWisePoseSetup.cc.

References ready_to_align_.

void protocols::swa::StepWisePoseSetup::reroot_fold_tree ( core::pose::Pose & pose)

private

Definition at line 849 of file StepWisePoseSetup.cc.

References desired_sequence_, core::pose::Pose::fold_tree(), job_parameters_, protocols::rna::possible_root(), core::kinematics::FoldTree::reorder(), core::kinematics::FoldTree::root(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::swa::StepWisePoseSetup::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

Definition at line 701 of file StepWisePoseSetup.cc.

References protocols::swa::protein::get_pretend_phi_explicit(), protocols::swa::protein::get_pretend_psi_explicit(), core::conformation::Residue::is_protein(), job_parameters_, phi_offsets_, psi_offsets_, and core::pose::Pose::residue().

Referenced by initialize_pose_from_streams().

void protocols::swa::StepWisePoseSetup::set_add_peptide_plane_variants ( bool const & setting)

Definition at line 1658 of file StepWisePoseSetup.cc.

References add_peptide_plane_variants_.

void protocols::swa::StepWisePoseSetup::set_align_file ( std::string const align_file)

Definition at line 1652 of file StepWisePoseSetup.cc.

References align_file_.

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

Definition at line 1627 of file StepWisePoseSetup.cc.

References bridge_res_.

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

Definition at line 1621 of file StepWisePoseSetup.cc.

References bulge_res_.

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

Definition at line 1664 of file StepWisePoseSetup.cc.

References calc_rms_res_.

void protocols::swa::StepWisePoseSetup::set_cst_file ( std::string const cst_file)

Definition at line 1639 of file StepWisePoseSetup.cc.

References cst_file_.

void protocols::swa::StepWisePoseSetup::set_disulfide_file ( std::string const disulfide_file)

Definition at line 1646 of file StepWisePoseSetup.cc.

References disulfide_file_.

void protocols::swa::StepWisePoseSetup::set_dump ( bool const dump)

Definition at line 1676 of file StepWisePoseSetup.cc.

References dump_.

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

Definition at line 1598 of file StepWisePoseSetup.cc.

References fixed_res_.

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

Definition at line 1604 of file StepWisePoseSetup.cc.

References jump_res_.

void protocols::swa::StepWisePoseSetup::set_parin_favorite_output ( bool const & setting)

inline

Definition at line 100 of file StepWisePoseSetup.hh.

References parin_favorite_output_.

void protocols::swa::StepWisePoseSetup::set_remove_cterminus_variant ( bool const & setting)

inline

Definition at line 121 of file StepWisePoseSetup.hh.

References remove_cterminus_variant_.

void protocols::swa::StepWisePoseSetup::set_remove_nterminus_variant ( bool const & setting)

inline

Definition at line 118 of file StepWisePoseSetup.hh.

References remove_nterminus_variant_.

void protocols::swa::StepWisePoseSetup::set_rsd_set ( core::chemical::ResidueTypeSetCAP & rsd_set)

Definition at line 1633 of file StepWisePoseSetup.cc.

References rsd_set_.

void protocols::swa::StepWisePoseSetup::set_secstruct ( std::string const secstruct)

Definition at line 1689 of file StepWisePoseSetup.cc.

References secstruct_.

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

Definition at line 1670 of file StepWisePoseSetup.cc.

References superimpose_res_.

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

Definition at line 1615 of file StepWisePoseSetup.cc.

References terminal_res_.

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

Definition at line 1610 of file StepWisePoseSetup.cc.

References virtual_res_list_.

void protocols::swa::StepWisePoseSetup::setup_constraints ( core::pose::Pose & pose)

private

Definition at line 650 of file StepWisePoseSetup.cc.

References core::scoring::atom_pair_constraint, core::pose::Pose::constraint_set(), protocols::swa::constraint_set_slice(), core::scoring::coordinate_constraint, cst_file_, cst_set_, core::scoring::constraints::ConstraintIO::get_instance(), job_parameters_, make_full_pose(), core::scoring::constraints::ConstraintIO::read_constraints(), and core::scoring::ScoreFunction::set_weight().

Referenced by apply().

void protocols::swa::StepWisePoseSetup::setup_disulfides ( core::pose::Pose & pose)

private

Definition at line 598 of file StepWisePoseSetup.cc.

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::chemical::ResidueType::has_variant_type(), job_parameters_, make_full_pose(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::swa::StepWisePoseSetup::setup_secstruct ( core::pose::Pose & pose) const

private

Definition at line 1570 of file StepWisePoseSetup.cc.

References desired_sequence_, job_parameters_, secstruct_, core::pose::Pose::set_secstruct(), and core::pose::Pose::total_residue().

Referenced by apply().

void protocols::swa::StepWisePoseSetup::setup_working_native_pose ( )

private

Definition at line 1201 of file StepWisePoseSetup.cc.

References protocols::moves::Mover::get_native_pose(), get_working_pose(), and working_native_pose.

Referenced by apply().

Size protocols::swa::StepWisePoseSetup::which_chain ( Size const & i)

private

Definition at line 439 of file StepWisePoseSetup.cc.

References job_parameters_.

Referenced by figure_out_jump_partners().

Member Data Documentation

bool protocols::swa::StepWisePoseSetup::add_peptide_plane_variants_

private

Definition at line 300 of file StepWisePoseSetup.hh.

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

std::string protocols::swa::StepWisePoseSetup::align_file_

private

Definition at line 312 of file StepWisePoseSetup.hh.

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

core::id::AtomID_Map< core::id::AtomID > protocols::swa::StepWisePoseSetup::alignment_atom_id_map_

private

Definition at line 315 of file StepWisePoseSetup.hh.

Referenced by align_pose(), and align_poses().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::bridge_res_

private

Definition at line 287 of file StepWisePoseSetup.hh.

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

Size const protocols::swa::StepWisePoseSetup::BRIDGE_RES_

private

Definition at line 310 of file StepWisePoseSetup.hh.

Referenced by figure_out_gap_size_and_first_chain_break_res(), figure_out_jump_partners(), and figure_out_working_sequence_and_mapping().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::bulge_res_

private

Definition at line 285 of file StepWisePoseSetup.hh.

Referenced by apply_bulge_variants(), and set_bulge_res().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::calc_rms_res_

private

Definition at line 284 of file StepWisePoseSetup.hh.

Referenced by apply(), and set_calc_rms_res().

std::string protocols::swa::StepWisePoseSetup::cst_file_

private

Definition at line 305 of file StepWisePoseSetup.hh.

Referenced by set_cst_file(), and setup_constraints().

core::scoring::constraints::ConstraintSetOP protocols::swa::StepWisePoseSetup::cst_set_

private

Definition at line 307 of file StepWisePoseSetup.hh.

Referenced by setup_constraints().

utility::vector1< Size > const protocols::swa::StepWisePoseSetup::cutpoint_closed_

private

Definition at line 279 of file StepWisePoseSetup.hh.

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

utility::vector1< Size > const protocols::swa::StepWisePoseSetup::cutpoint_open_

private

Definition at line 278 of file StepWisePoseSetup.hh.

Referenced by figure_out_gap_size_and_first_chain_break_res(), and StepWisePoseSetup().

utility::vector1< core::Size > protocols::swa::StepWisePoseSetup::cuts_

private

Definition at line 295 of file StepWisePoseSetup.hh.

Referenced by figure_out_cuts(), and make_pose().

std::string const protocols::swa::StepWisePoseSetup::desired_sequence_

private

Definition at line 273 of file StepWisePoseSetup.hh.

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

std::string protocols::swa::StepWisePoseSetup::disulfide_file_

private

Definition at line 306 of file StepWisePoseSetup.hh.

Referenced by set_disulfide_file(), and setup_disulfides().

bool protocols::swa::StepWisePoseSetup::dump_

private

Definition at line 316 of file StepWisePoseSetup.hh.

Referenced by initialize_pose_from_streams(), and set_dump().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::fixed_res_

private

Definition at line 280 of file StepWisePoseSetup.hh.

Referenced by apply(), and set_fixed_res().

utility::vector1< InputStreamWithResidueInfoOP > protocols::swa::StepWisePoseSetup::input_streams_with_residue_info_

private

Definition at line 276 of file StepWisePoseSetup.hh.

Referenced by figure_out_working_sequence_and_mapping(), and initialize_pose_from_streams().

ObjexxFCL::FArray1D< bool > protocols::swa::StepWisePoseSetup::is_cutpoint_

private

Definition at line 288 of file StepWisePoseSetup.hh.

Referenced by figure_out_working_sequence_and_mapping(), and StepWisePoseSetup().

StepWiseJobParametersOP protocols::swa::StepWisePoseSetup::job_parameters_

private

utility::vector1< std::pair< core::Size, core::Size > > protocols::swa::StepWisePoseSetup::jump_partners_

private

Definition at line 294 of file StepWisePoseSetup.hh.

Referenced by figure_out_jump_partners(), and make_pose().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::jump_res_

private

Definition at line 286 of file StepWisePoseSetup.hh.

Referenced by figure_out_jump_partners(), and set_jump_res().

utility::vector1< core::Size > const& protocols::swa::StepWisePoseSetup::moving_res_list_

private

Definition at line 272 of file StepWisePoseSetup.hh.

Referenced by figure_out_jump_partners(), and figure_out_working_sequence_and_mapping().

bool protocols::swa::StepWisePoseSetup::parin_favorite_output_

private

Definition at line 303 of file StepWisePoseSetup.hh.

Referenced by set_parin_favorite_output().

ObjexxFCL::FArray1D< core::Real > protocols::swa::StepWisePoseSetup::phi_offsets_

private

Definition at line 291 of file StepWisePoseSetup.hh.

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

ObjexxFCL::FArray1D< core::Real > protocols::swa::StepWisePoseSetup::psi_offsets_

private

Definition at line 292 of file StepWisePoseSetup.hh.

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

bool protocols::swa::StepWisePoseSetup::ready_to_align_

private

Definition at line 313 of file StepWisePoseSetup.hh.

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

bool protocols::swa::StepWisePoseSetup::remove_cterminus_variant_

private

Definition at line 302 of file StepWisePoseSetup.hh.

Referenced by make_full_pose(), and set_remove_cterminus_variant().

bool protocols::swa::StepWisePoseSetup::remove_nterminus_variant_

private

Definition at line 301 of file StepWisePoseSetup.hh.

Referenced by make_full_pose(), and set_remove_nterminus_variant().

core::chemical::ResidueTypeSetCAP protocols::swa::StepWisePoseSetup::rsd_set_

private

Definition at line 274 of file StepWisePoseSetup.hh.

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

std::string protocols::swa::StepWisePoseSetup::secstruct_

private

Definition at line 289 of file StepWisePoseSetup.hh.

Referenced by set_secstruct(), and setup_secstruct().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::superimpose_res_

private

Definition at line 283 of file StepWisePoseSetup.hh.

Referenced by apply(), and set_superimpose_res().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::terminal_res_

private

Definition at line 282 of file StepWisePoseSetup.hh.

Referenced by apply(), and set_terminal_res().

utility::vector1< Size > protocols::swa::StepWisePoseSetup::virtual_res_list_

private

Definition at line 281 of file StepWisePoseSetup.hh.

Referenced by apply_virtual_res_variant(), and set_virtual_res().

bool protocols::swa::StepWisePoseSetup::virtualize_5prime_phosphates_

private

Definition at line 299 of file StepWisePoseSetup.hh.

Referenced by apply().

core::pose::PoseOP protocols::swa::StepWisePoseSetup::working_align_pose_

private

Definition at line 314 of file StepWisePoseSetup.hh.

Referenced by align_pose(), and align_poses().

core::pose::PoseOP protocols::swa::StepWisePoseSetup::working_native_pose

private

Definition at line 308 of file StepWisePoseSetup.hh.

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

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

src/protocols/swa/StepWisePoseSetup.hh
src/protocols/swa/StepWisePoseSetup.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

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