#include <ProtectedConformation.hh>

Public Member Functions
	ProtectedConformation (ProtectedConformation const &src)

virtual	~ProtectedConformation ()

EnvironmentCAP	environment () const

void	env_destruction ()

virtual bool	is_protected () const

SequenceAnnotationCOP	resolver () const

SequenceAnnotationCOP	annotations () const

virtual core::conformation::ConformationOP	clone () const

virtual Conformation &	operator= (Conformation const &src)

virtual void	set_torsion (TorsionID const &id, core::Real const setting)

virtual void	set_jump (AtomID const &, core::kinematics::Jump const &)

virtual void	set_jump (int const, core::kinematics::Jump const &)

virtual void	set_secstruct (Size const seqpos, char const setting)

virtual void	replace_residue (Size const seqpos, core::conformation::Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs)

virtual void	set_stub_transform (core::id::StubID const &stub_id1, core::id::StubID const &stub_id2, core::kinematics::RT const &target_rt)

virtual void	set_dof (DOF_ID const &id, core::Real const setting)

virtual void	set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, core::Real const setting, bool quiet=false)

virtual void	set_bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, core::Real const setting)

virtual void	set_bond_length (AtomID const &atom1, AtomID const &atom2, core::Real const setting)

virtual void	insert_fragment (core::id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz)

virtual void	contains_carbohydrate_residues (bool const )

virtual void	fold_tree (FoldTree const &)

virtual void	chain_endings (utility::vector1< Size > const &)

virtual void	insert_chain_ending (Size const )

virtual void	delete_chain_ending (Size const )

virtual void	reset_chain_endings ()

virtual void	chains_from_termini ()

virtual void	append_residue_by_jump (core::conformation::Residue const &, Size const, std::string const &="", std::string const &="", bool const =false)

virtual void	append_polymer_residue_after_seqpos (core::conformation::Residue const &, Size const, bool const )

virtual void	safely_append_polymer_residue_after_seqpos (core::conformation::Residue const &, Size const, bool const )

virtual void	prepend_polymer_residue_before_seqpos (core::conformation::Residue const &, Size const, bool const )

virtual void	safely_prepend_polymer_residue_before_seqpos (core::conformation::Residue const &, Size const, bool const )

virtual void	delete_polymer_residue (Size const )

virtual void	delete_residue_slow (Size const )

virtual void	delete_residue_range_slow (Size const range_begin, Size const range_end)

virtual void	declare_chemical_bond (Size const, std::string const &, Size const, std::string const &)

virtual void	insert_conformation_by_jump (Conformation const &, Size const, Size const, Size const, Size const, std::string const &="", std::string const &="")

virtual void	rebuild_polymer_bond_dependent_atoms (Size const )

virtual void	insert_ideal_geometry_at_polymer_bond (Size const seqpos)

virtual void	insert_ideal_geometry_at_residue_connection (Size const pos1, Size const connid1)

virtual void	set_polymeric_connection (Size, Size)

virtual void	fix_disulfides (utility::vector1< std::pair< Size, Size > >)

virtual void	set_xyz (AtomID const &id, core::PointPosition const &position)

virtual void	batch_set_xyz (utility::vector1< AtomID > const &id, utility::vector1< core::PointPosition > const &position)

virtual void	reset_move_data ()

virtual void	clear ()

virtual void	fill_missing_atoms (core::id::AtomID_Mask missing)

virtual bool	same_type_as_me (Conformation const &other, bool recurse) const

Public Member Functions inherited from core::conformation::Conformation
	Conformation ()

virtual	~Conformation ()

	Conformation (Conformation const &src)

void	clear ()

void	debug_residue_torsions (bool verbose=false) const

void	show_residue_connections () const

void	show_residue_connections (std::ostream &os) const

bool	sequence_matches (Conformation const &other) const

Size	size () const

bool	empty () const

bool	is_residue_typeset (std::string tag) const

bool	is_fullatom () const

bool	is_centroid () const

bool	is_membrane () const

bool	contains_carbohydrate_residues () const

void	contains_carbohydrate_residues (bool const setting)

Size	chain_end (Size const chain) const

Size	chain_begin (Size const chain) const

Size	num_chains () const

utility::vector1< Size > const &	chain_endings () const

void	chain_endings (utility::vector1< Size > const &endings)

void	insert_chain_ending (Size const seqpos)

void	delete_chain_ending (Size const seqpos)

void	reset_chain_endings ()

void	chains_from_termini ()

char	secstruct (Size const seqpos) const

void	setup_membrane (utility::vector1< std::pair< int, int > > embres_map, int membrane)

membrane::MembraneInfoOP	membrane ()

virtual FoldTree const &	fold_tree () const

AtomTree const &	atom_tree () const

chemical::AA const &	aa (Size const seqpos) const

Residue const &	residue (Size const seqpos) const

chemical::ResidueType const &	residue_type (Size const seqpos) const

ResidueCAPs	const_residues () const

void	insert_residue_by_jump (Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false)

void	append_residue_by_bond (conformation::Residue const &new_rsd, bool const build_ideal_geometry=false, int connection_index=0, Size anchor_residue=0, int anchor_connection_index=0, bool const start_new_chain=false, bool const lookup_bond_length=false)

void	append_polymer_residue_after_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)

void	safely_append_polymer_residue_after_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)

void	prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)

void	safely_prepend_polymer_residue_before_seqpos (Residue const &new_rsd, Size const seqpos, bool const build_ideal_geometry)

virtual void	replace_residue (Size const seqpos, Residue const &new_rsd, bool const orient_backbone)

void	delete_polymer_residue (Size const seqpos)

void	delete_residue_slow (Size const seqpos)

void	delete_residue_range_slow (Size const range_begin, Size const range_end)

virtual utility::vector1< bool >	get_residue_mask () const

virtual Real	get_residue_weight (core::Size, core::Size) const

void	detect_bonds ()

void	detect_pseudobonds ()

void	declare_chemical_bond (Size const seqpos1, std::string const &atom_name1, Size const seqpos2, std::string const &atom_name2)

void	rebuild_polymer_bond_dependent_atoms (Size const seqpos)

void	rebuild_residue_connection_dependent_atoms (Size const seqpos, Size const connid)

AtomID	inter_residue_connection_partner (Size const seqpos, int const connection_index) const

utility::vector1 < core::id::AtomID >	bonded_neighbor_all_res (core::id::AtomID atomid, bool virt=false) const

void	fill_missing_atoms (id::AtomID_Mask missing)

bool	atom_is_backbone_norefold (Size const pos, Size const atomno) const

void	set_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2, kinematics::RT const &target_rt)

kinematics::RT	get_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2) const

void	set_jump_atom_stub_id (id::StubID const &id)

kinematics::Stub	stub_from_id (id::StubID const &id) const

kinematics::Stub	upstream_jump_stub (int const jump_number) const

kinematics::Stub	downstream_jump_stub (int const jump_number) const

void	set_polymeric_connection (Size res_id_lower, Size res_id_upper)

void	update_polymeric_connection (Size const lower_seqpos)

virtual void	detect_disulfides ()

void	fix_disulfides (utility::vector1< std::pair< Size, Size > > disulf_bonds)

void	copy_segment (Size const size, Conformation const &src, Size const begin, Size const src_begin)

void	insert_fragment (id::StubID const &instub_id, FragRT const &outstub_transforms, FragXYZ const &frag_xyz)

Real	dof (DOF_ID const &id) const

Real	torsion (TorsionID const &id) const

Real	torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4) const

Real	bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3) const

Real	bond_length (AtomID const &atom1, AtomID const &atom2) const

const Jump &	jump (int const jump_number) const

const Jump &	jump (AtomID const &id) const

PointPosition const &	xyz (AtomID const &id) const

virtual void	set_xyz (AtomID const &id, PointPosition const &position)

virtual void	batch_set_xyz (utility::vector1< AtomID > const &id, utility::vector1< PointPosition > const &position)

virtual void	batch_get_xyz (utility::vector1< AtomID > const &id, utility::vector1< PointPosition > &position) const

void	insert_ideal_geometry_at_polymer_bond (Size const seqpos)

void	insert_ideal_geometry_at_residue_connection (Size const pos1, Size const connid1)

void	update_actcoords ()

void	update_actcoord (Size resid)

void	update_orbital_coords (Residue &rsd) const

void	update_orbital_coords (Size resid)

DOF_ID	dof_id_from_torsion_id (TorsionID const &id) const

id::AtomID	jump_atom_id (int const jump_number) const

bool	get_torsion_angle_atom_ids (TorsionID const &tor_id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const

void	update_domain_map (DomainMap &domain_map) const

bool	structure_moved () const

void	reset_structure_moved () const

void	reset_move_data ()

utility::signals::Link	attach_connection_obs (MemFn fn, Ptr ptr) const

bool	detach_connection_obs (MemFn fn, Ptr ptr) const

utility::signals::Link	attach_general_obs (MemFn fn, Ptr ptr) const

bool	detach_general_obs (MemFn fn, Ptr ptr) const

utility::signals::Link	attach_identity_obs (MemFn fn, Ptr ptr) const

bool	detach_identity_obs (MemFn fn, Ptr ptr) const

utility::signals::Link	attach_length_obs (MemFn fn, Ptr ptr) const

bool	detach_length_obs (MemFn fn, Ptr ptr) const

utility::signals::Link	attach_xyz_obs (MemFn fn, Ptr ptr) const

bool	detach_xyz_obs (MemFn fn, Ptr ptr) const

void	clear_observers ()

void	receive_observers_from (Conformation const &src)

void	debug_pause (bool const flag) const

bool	debug_pause () const

void	buffer_signals ()

void	block_signals ()

void	unblock_signals ()

bool	buffering_signals () const

bool	blocking_signals () const

Private Types
typedef core::conformation::Conformation	Parent

typedef core::environment::SequenceAnnotationCOP	SequenceAnnotationCOP

Private Member Functions
	ProtectedConformation (EnvironmentCAP, core::conformation::Conformation const &)

bool	verify (core::id::TorsionID const &)

bool	verify (core::id::DOF_ID const &)

bool	verify_jump (core::id::AtomID const &)

bool	verify_backbone (Size const &seqpos)

bool	verify_residue (Size const &seqpos)

void	fail_verification (std::string const &str)

void	fork_annotation ()

void	attach_annotation (SequenceAnnotationCOP)

void	push_passport (core::environment::DofPassportCOP)

void	pop_passport ()

bool	has_passport () const

void	set_environment (EnvironmentCAP)

Private Attributes
std::stack < core::environment::DofPassportCOP >	unlocks_

SequenceAnnotationCOP	annotations_

EnvironmentCAP	env_

bool	environment_exists_

Friends
class	DofUnlock

class	Environment

class	EnvClaimBroker

Additional Inherited Members
Public Types inherited from core::conformation::Conformation
typedef kinematics::Jump	Jump

typedef kinematics::FoldTree	FoldTree

typedef kinematics::FoldTreeOP	FoldTreeOP

typedef kinematics::AtomTree	AtomTree

typedef kinematics::AtomTreeOP	AtomTreeOP

typedef id::AtomID	AtomID

typedef id::AtomID_Mask	AtomID_Mask

typedef id::DOF_ID	DOF_ID

typedef id::TorsionID	TorsionID

typedef kinematics::DomainMap	DomainMap

typedef core::conformation::signals::ConnectionEvent	ConnectionEvent

typedef core::conformation::signals::GeneralEvent	GeneralEvent

typedef core::conformation::signals::IdentityEvent	IdentityEvent

typedef core::conformation::signals::LengthEvent	LengthEvent

typedef core::conformation::signals::XYZEvent	XYZEvent

typedef std::map< id::AtomID, Vector >	FragXYZ

typedef std::map< id::StubID, kinematics::RT >	FragRT

Protected Attributes inherited from core::conformation::Conformation
ResidueOPs	residues_

Member Typedef Documentation

typedef core::conformation::Conformation protocols::environment::ProtectedConformation::Parent

private

typedef core::environment::SequenceAnnotationCOP protocols::environment::ProtectedConformation::SequenceAnnotationCOP

private

Constructor & Destructor Documentation

protocols::environment::ProtectedConformation::ProtectedConformation ( ProtectedConformation const & src )

References environment().

Referenced by clone().

protocols::environment::ProtectedConformation::~ProtectedConformation ( )

virtual

References environment(), and environment_exists_.

protocols::environment::ProtectedConformation::ProtectedConformation	(	EnvironmentCAP	env,
		core::conformation::Conformation const &	src
	)

private

References environment().

Member Function Documentation

SequenceAnnotationCOP protocols::environment::ProtectedConformation::annotations ( ) const

inline

References resolver().

Referenced by attach_annotation().

void protocols::environment::ProtectedConformation::append_polymer_residue_after_seqpos	(	core::conformation::Residue const &	,
		Size const	,
		bool const
	)

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::append_residue_by_jump	(	core::conformation::Residue const &	,
		Size const	,
		std::string const &	= `""`,
		std::string const &	= `""`,
		bool const	= `false`
	)

virtual

Reimplemented from core::conformation::Conformation.

References fail_verification().

void protocols::environment::ProtectedConformation::attach_annotation ( SequenceAnnotationCOP annotations )

private

References annotations(), and annotations_.

void protocols::environment::ProtectedConformation::batch_set_xyz	(	utility::vector1< AtomID > const &	id,
		utility::vector1< core::PointPosition > const &	position
	)

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::chain_endings ( utility::vector1< Size > const & )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::chains_from_termini ( )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::clear ( )

virtual

References fail_verification().

core::conformation::ConformationOP protocols::environment::ProtectedConformation::clone ( ) const

virtual

Reimplemented from core::conformation::Conformation.

References ProtectedConformation().

void protocols::environment::ProtectedConformation::contains_carbohydrate_residues ( bool const )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::declare_chemical_bond	(	Size const	,
		std::string const &	,
		Size const	,
		std::string const &
	)

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::delete_chain_ending ( Size const )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::delete_polymer_residue ( Size const )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::delete_residue_range_slow	(	Size const	range_begin,
		Size const	range_end
	)

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::delete_residue_slow ( Size const )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::env_destruction ( )

inline

References environment_exists_.

EnvironmentCAP protocols::environment::ProtectedConformation::environment ( ) const

References env_, and environment_exists_.

Referenced by fail_verification(), ProtectedConformation(), protocols::environment::Environment::start(), verify(), and ~ProtectedConformation().

void protocols::environment::ProtectedConformation::fail_verification ( std::string const & str )

inlineprivate

References environment(), protocols::environment::get_mover_name(), and unlocks_.

Referenced by append_polymer_residue_after_seqpos(), append_residue_by_jump(), batch_set_xyz(), chain_endings(), chains_from_termini(), clear(), contains_carbohydrate_residues(), declare_chemical_bond(), delete_chain_ending(), delete_polymer_residue(), delete_residue_range_slow(), delete_residue_slow(), fill_missing_atoms(), fix_disulfides(), fold_tree(), insert_chain_ending(), insert_conformation_by_jump(), insert_ideal_geometry_at_polymer_bond(), insert_ideal_geometry_at_residue_connection(), prepend_polymer_residue_before_seqpos(), rebuild_polymer_bond_dependent_atoms(), replace_residue(), reset_chain_endings(), reset_move_data(), safely_append_polymer_residue_after_seqpos(), safely_prepend_polymer_residue_before_seqpos(), set_bond_angle(), set_bond_length(), set_dof(), set_jump(), set_polymeric_connection(), set_secstruct(), set_stub_transform(), set_torsion(), set_torsion_angle(), and set_xyz().

void protocols::environment::ProtectedConformation::fill_missing_atoms ( core::id::AtomID_Mask missing )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::fix_disulfides ( utility::vector1< std::pair< Size, Size > > )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::fold_tree ( FoldTree const & )

virtual

Reimplemented from core::conformation::Conformation.

References fail_verification().

void protocols::environment::ProtectedConformation::fork_annotation ( )

private

References annotations_, runtime_assert, and tr.

bool protocols::environment::ProtectedConformation::has_passport ( ) const

privatevirtual

Reimplemented from core::conformation::Conformation.

References unlocks_.

void protocols::environment::ProtectedConformation::insert_chain_ending ( Size const )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::insert_conformation_by_jump	(	Conformation const &	,
		Size const	,
		Size const	,
		Size const	,
		Size const	,
		std::string const &	= `""`,
		std::string const &	= `""`
	)

virtual

Reimplemented from core::conformation::Conformation.

References fail_verification().

void protocols::environment::ProtectedConformation::insert_fragment	(	core::id::StubID const &	instub_id,
		FragRT const &	outstub_transforms,
		FragXYZ const &	frag_xyz
	)

virtual

References runtime_assert.

void protocols::environment::ProtectedConformation::insert_ideal_geometry_at_polymer_bond ( Size const seqpos )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::insert_ideal_geometry_at_residue_connection	(	Size const	pos1,
		Size const	connid1
	)

virtual

References fail_verification().

virtual bool protocols::environment::ProtectedConformation::is_protected ( ) const

inlinevirtual

Reimplemented from core::conformation::Conformation.

Conformation & protocols::environment::ProtectedConformation::operator= ( Conformation const & src )

virtual

Reimplemented from core::conformation::Conformation.

References annotations_, env_, core::conformation::Conformation::operator=(), and unlocks_.

void protocols::environment::ProtectedConformation::pop_passport ( )

privatevirtual

Reimplemented from core::conformation::Conformation.

References unlocks_.

void protocols::environment::ProtectedConformation::prepend_polymer_residue_before_seqpos	(	core::conformation::Residue const &	,
		Size const	,
		bool const
	)

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::push_passport ( core::environment::DofPassportCOP passport )

privatevirtual

Reimplemented from core::conformation::Conformation.

References unlocks_.

void protocols::environment::ProtectedConformation::rebuild_polymer_bond_dependent_atoms ( Size const )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::replace_residue	(	Size const	seqpos,
		core::conformation::Residue const &	new_rsd,
		utility::vector1< std::pair< std::string, std::string > > const &	atom_pairs
	)

virtual

Reimplemented from core::conformation::Conformation.

References fail_verification(), core::conformation::Conformation::replace_residue(), utility::to_string(), and verify_backbone().

void protocols::environment::ProtectedConformation::reset_chain_endings ( )

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::reset_move_data ( )

virtual

References fail_verification().

SequenceAnnotationCOP protocols::environment::ProtectedConformation::resolver ( ) const

References annotations_.

Referenced by annotations().

void protocols::environment::ProtectedConformation::safely_append_polymer_residue_after_seqpos	(	core::conformation::Residue const &	,
		Size const	,
		bool const
	)

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::safely_prepend_polymer_residue_before_seqpos	(	core::conformation::Residue const &	,
		Size const	,
		bool const
	)

virtual

References fail_verification().

bool protocols::environment::ProtectedConformation::same_type_as_me	(	Conformation const &	other,
		bool	recurse
	)		const

virtual

Reimplemented from core::conformation::Conformation.

References core::conformation::Conformation::same_type_as_me().

void protocols::environment::ProtectedConformation::set_bond_angle	(	AtomID const &	atom1,
		AtomID const &	atom2,
		AtomID const &	atom3,
		core::Real const	setting
	)

virtual

Reimplemented from core::conformation::Conformation.

References core::conformation::Conformation::atom_tree(), core::kinematics::AtomTree::bond_angle_dof_id(), fail_verification(), core::conformation::Conformation::set_bond_angle(), utility::to_string(), and verify().

void protocols::environment::ProtectedConformation::set_bond_length	(	AtomID const &	atom1,
		AtomID const &	atom2,
		core::Real const	setting
	)

virtual

Reimplemented from core::conformation::Conformation.

References core::conformation::Conformation::atom_tree(), core::kinematics::AtomTree::bond_length_dof_id(), fail_verification(), core::conformation::Conformation::set_bond_length(), utility::to_string(), and verify().

void protocols::environment::ProtectedConformation::set_dof	(	DOF_ID const &	id,
		core::Real const	setting
	)

virtual

Reimplemented from core::conformation::Conformation.

References fail_verification(), core::conformation::Conformation::set_dof(), utility::to_string(), and verify().

void protocols::environment::ProtectedConformation::set_environment ( EnvironmentCAP env )

private

References env_.

void protocols::environment::ProtectedConformation::set_jump	(	AtomID const &	id,
		core::kinematics::Jump const &	new_jump
	)

virtual

Reimplemented from core::conformation::Conformation.

References fail_verification(), core::conformation::Conformation::set_jump(), utility::to_string(), and verify_jump().

Referenced by set_jump().

void protocols::environment::ProtectedConformation::set_jump	(	int const	jump_number,
		core::kinematics::Jump const &	new_jump
	)

virtual

Reimplemented from core::conformation::Conformation.

References core::conformation::Conformation::jump_atom_id(), and set_jump().

void protocols::environment::ProtectedConformation::set_polymeric_connection	(	Size	,
		Size
	)

virtual

References fail_verification().

void protocols::environment::ProtectedConformation::set_secstruct	(	Size const	seqpos,
		char const	setting
	)

virtual

Reimplemented from core::conformation::Conformation.

References fail_verification(), core::conformation::Conformation::set_secstruct(), and verify_backbone().

void protocols::environment::ProtectedConformation::set_stub_transform	(	core::id::StubID const &	stub_id1,
		core::id::StubID const &	stub_id2,
		core::kinematics::RT const &	target_rt
	)

virtual

References core::conformation::Conformation::atom_tree(), fail_verification(), core::conformation::Conformation::set_stub_transform(), utility::to_string(), and verify_jump().

void protocols::environment::ProtectedConformation::set_torsion	(	TorsionID const &	id,
		core::Real const	setting
	)

virtual

Reimplemented from core::conformation::Conformation.

References fail_verification(), core::conformation::Conformation::set_torsion(), utility::to_string(), and verify().

void protocols::environment::ProtectedConformation::set_torsion_angle	(	AtomID const &	atom1,
		AtomID const &	atom2,
		AtomID const &	atom3,
		AtomID const &	atom4,
		core::Real const	setting,
		bool	quiet = `false`
	)