#include <AllowInsert.hh>

Public Member Functions
	AllowInsert (core::pose::Pose const &pose)

virtual	~AllowInsert ()

AllowInsert &	operator= (AllowInsert const &src)

	AllowInsert (AllowInsert const &src)

virtual AllowInsertOP	clone () const

bool	get (Size const &i) const

bool	get (core::id::AtomID const &atom_id) const

bool	get (core::id::TorsionID const &torsion_id, core::conformation::Conformation const &conformation) const

Size	get_domain (Size const &i) const

bool	has_domain (core::id::AtomID const &atom_id) const

Size	get_domain (core::id::AtomID const &atom_id) const

void	set_domain (Size const &i, Size const &setting)

void	set_domain (core::id::AtomID const &atom_id, Size const &setting)

void	set_domain (Size const &setting)

void	and_allow_insert (AllowInsertOP allow_insert_in)

core::Size	nres () const

void	set_phosphate_domain (core::Size const &i, core::pose::Pose const &pose, Size const &setting)

void	set_phosphate (core::Size const &i, core::pose::Pose const &pose, bool const &setting)

void	set (Size const &i, bool const &setting)

void	set (core::id::AtomID const &atom_id, bool const &setting)

void	set (bool const &setting)

void	show ()

std::map< core::id::AtomID, Size > const &	calculated_atom_id_domain_map ()

std::map< core::id::AtomID, Size > const &	calculate_atom_id_domain_map (core::pose::Pose const &pose)

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

void	calculate_atom_id_map (core::pose::Pose const &pose, std::map< core::Size, core::Size > const &res_map, core::kinematics::FoldTree const &scratch_fold_tree, std::map< core::id::AtomID, core::id::AtomID > &atom_id_map)

void	set_force_ideal_chainbreak (bool const &setting)

void	append_residue (core::pose::Pose const &pose, Size const &i, bool const &setting)

Private Member Functions
void	initialize (core::pose::Pose const &pose)

Private Attributes
std::map< core::id::AtomID, Size >	allow_insert_

std::map < core::id::NamedAtomID, core::id::AtomID >	named_atom_id_map_

utility::vector1 < utility::vector1 < core::id::AtomID > >	atom_ids_in_res_

std::map< core::id::AtomID, Size >	calculated_atom_id_domain_map_

std::map< core::id::AtomID, core::id::AtomID >	map_to_original_

core::Size	nres_

bool	force_ideal_chainbreak_

Constructor & Destructor Documentation

protocols::toolbox::AllowInsert::AllowInsert ( core::pose::Pose const & pose )

References initialize().

Referenced by clone().

protocols::toolbox::AllowInsert::~AllowInsert ( )

virtual

protocols::toolbox::AllowInsert::AllowInsert ( AllowInsert const & src )

Member Function Documentation

void protocols::toolbox::AllowInsert::and_allow_insert ( AllowInsertOP allow_insert_in )

References allow_insert_.

void protocols::toolbox::AllowInsert::append_residue	(	core::pose::Pose const &	pose,
		Size const &	i,
		bool const &	setting
	)

References allow_insert_, atom_id_to_named_atom_id(), atom_ids_in_res_, protocols::toolbox::FIXED_DOMAIN, j, map_to_original_, named_atom_id_map_, core::conformation::Residue::natoms(), nres_, and core::pose::Pose::residue().

std::map< AtomID, Size > const & protocols::toolbox::AllowInsert::calculate_atom_id_domain_map ( core::pose::Pose const & pose )

References calculated_atom_id_domain_map_, get_domain(), j, core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by initialize(), and renumber_after_variant_changes().

void protocols::toolbox::AllowInsert::calculate_atom_id_map	(	core::pose::Pose const &	pose,
		std::map< core::Size, core::Size > const &	res_map,
		core::kinematics::FoldTree const &	scratch_fold_tree,
		std::map< core::id::AtomID, core::id::AtomID > &	atom_id_map
	)

References core::id::AtomID::atomno(), core::kinematics::FoldTree::is_cutpoint(), j, map_to_original_, core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::id::AtomID::rsd().

std::map< AtomID, Size > const & protocols::toolbox::AllowInsert::calculated_atom_id_domain_map ( )

References calculated_atom_id_domain_map_.

AllowInsertOP protocols::toolbox::AllowInsert::clone ( ) const

virtual

References AllowInsert().

bool protocols::toolbox::AllowInsert::get ( Size const & i ) const

References get_domain().

bool protocols::toolbox::AllowInsert::get ( core::id::AtomID const & atom_id ) const

References get_domain().

bool protocols::toolbox::AllowInsert::get	(	core::id::TorsionID const &	torsion_id,
		core::conformation::Conformation const &	conformation
	)		const

References get_domain(), and core::conformation::Conformation::get_torsion_angle_atom_ids().

Size protocols::toolbox::AllowInsert::get_domain ( Size const & i ) const

References atom_ids_in_res_, j, nres_, and utility_exit_with_message.

Referenced by calculate_atom_id_domain_map(), and get().

Size protocols::toolbox::AllowInsert::get_domain ( core::id::AtomID const & atom_id ) const

References allow_insert_, map_to_original_, and utility_exit_with_message.

bool protocols::toolbox::AllowInsert::has_domain ( core::id::AtomID const & atom_id ) const

References map_to_original_.

void protocols::toolbox::AllowInsert::initialize ( core::pose::Pose const & pose )

private

References allow_insert_, atom_ids_in_res_, core::chemical::ResidueType::atom_name(), calculate_atom_id_domain_map(), j, map_to_original_, named_atom_id_map_, core::chemical::ResidueType::natoms(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by AllowInsert().

core::Size protocols::toolbox::AllowInsert::nres ( ) const

inline

References nres_.

AllowInsert & protocols::toolbox::AllowInsert::operator= ( AllowInsert const & src )

References allow_insert_, atom_ids_in_res_, calculated_atom_id_domain_map_, force_ideal_chainbreak_, map_to_original_, named_atom_id_map_, and nres_.

void protocols::toolbox::AllowInsert::renumber_after_variant_changes ( core::pose::Pose const & pose )

References core::chemical::ResidueType::atom_name(), calculate_atom_id_domain_map(), force_ideal_chainbreak_, core::chemical::ResidueType::is_coarse(), core::chemical::ResidueType::is_RNA(), j, map_to_original_, named_atom_id_map_, core::chemical::ResidueType::natoms(), nres_, core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and utility_exit_with_message.

void protocols::toolbox::AllowInsert::set	(	Size const &	i,
		bool const &	setting
	)

References set_domain().

void protocols::toolbox::AllowInsert::set	(	core::id::AtomID const &	atom_id,
		bool const &	setting
	)

References set_domain().

void protocols::toolbox::AllowInsert::set ( bool const & setting )

References set_domain().

void protocols::toolbox::AllowInsert::set_domain	(	Size const &	i,
		Size const &	setting
	)

References atom_ids_in_res_, and j.

Referenced by set(), and set_phosphate_domain().

void protocols::toolbox::AllowInsert::set_domain	(	core::id::AtomID const &	atom_id,
		Size const &	setting
	)

References allow_insert_, map_to_original_, and utility_exit_with_message.

void protocols::toolbox::AllowInsert::set_domain ( Size const & setting )

References allow_insert_.

void protocols::toolbox::AllowInsert::set_force_ideal_chainbreak ( bool const & setting )

inline

References force_ideal_chainbreak_.

void protocols::toolbox::AllowInsert::set_phosphate	(	core::Size const &	i,
		core::pose::Pose const &	pose,
		bool const &	setting
	)

References set_phosphate_domain().

void protocols::toolbox::AllowInsert::set_phosphate_domain	(	core::Size const &	i,
		core::pose::Pose const &	pose,
		Size const &	setting
	)

References core::chemical::rna::atoms_involved_in_phosphate_torsion, core::conformation::Residue::is_coarse(), named_atom_id_to_atom_id(), core::pose::Pose::residue(), and set_domain().

Referenced by set_phosphate().

void protocols::toolbox::AllowInsert::show ( )

References allow_insert_, atom_ids_in_res_, protocols::abinitio::abscript::I, j, and nres_.

Member Data Documentation

std::map< core::id::AtomID, Size > protocols::toolbox::AllowInsert::allow_insert_

private

Referenced by and_allow_insert(), append_residue(), get_domain(), initialize(), operator=(), set_domain(), and show().

utility::vector1< utility::vector1< core::id::AtomID > > protocols::toolbox::AllowInsert::atom_ids_in_res_

private

Referenced by append_residue(), get_domain(), initialize(), operator=(), set_domain(), and show().

std::map< core::id::AtomID, Size > protocols::toolbox::AllowInsert::calculated_atom_id_domain_map_

private

Referenced by calculate_atom_id_domain_map(), calculated_atom_id_domain_map(), and operator=().

bool protocols::toolbox::AllowInsert::force_ideal_chainbreak_

private

Referenced by operator=(), renumber_after_variant_changes(), and set_force_ideal_chainbreak().

std::map< core::id::AtomID, core::id::AtomID > protocols::toolbox::AllowInsert::map_to_original_

private

Referenced by append_residue(), calculate_atom_id_map(), get_domain(), has_domain(), initialize(), operator=(), renumber_after_variant_changes(), and set_domain().

std::map< core::id::NamedAtomID, core::id::AtomID > protocols::toolbox::AllowInsert::named_atom_id_map_

private

Referenced by append_residue(), initialize(), operator=(), and renumber_after_variant_changes().

core::Size protocols::toolbox::AllowInsert::nres_

private

Referenced by append_residue(), get_domain(), nres(), operator=(), renumber_after_variant_changes(), and show().

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

symlinks/rosetta/src/protocols/toolbox/AllowInsert.hh
symlinks/rosetta/src/protocols/toolbox/AllowInsert.cc

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation