#include <ProtectedConformation.hh>

Inheritance diagram for protocols::environment::ProtectedConformation:

Public Member Functions
	ProtectedConformation (ProtectedConformation const &src)

	ProtectedConformation (EnvironmentCAP, core::conformation::Conformation const &)

	~ProtectedConformation () override

EnvironmentCAP	environment () const

void	env_destruction ()

bool	is_protected () const override

core::conformation::ResidueOP	match_variants (core::Size seqpos, core::conformation::Residue const &in_rsd) const

SequenceAnnotationCOP	resolver () const

SequenceAnnotationCOP	annotations () const

core::conformation::ConformationOP	clone () const override
	clone the conformation More...

Conformation &	operator= (Conformation const &src) override
	equals operator More...

void	set_torsion (TorsionID const &id, core::Real const setting) override
	Sets the AtomTree DOF and the torsion OR rigid-body offset in the corresponding Residue or Jump. More...

void	set_jump (AtomID const &, core::kinematics::Jump const &) override
	set a jump More...

void	set_jump (int const , core::kinematics::Jump const &) override
	Sets the jump <jump_number> to <new_jump> More...

void	set_secstruct (core::Size const seqpos, char const setting) override
	Sets the secondary structure of the position <seqpos> to <setting> More...

void	replace_residue (core::Size const seqpos, core::conformation::Residue const &new_rsd, utility::vector1< std::pair< std::string, std::string > > const &atom_pairs) override
	function to replace a residue based on superposition on the specified input atom pairs More...

void	replace_residue (core::Size const seqpos, core::conformation::Residue const &new_rsd, bool const orient_backbone) override
	replace residue More...

void	set_stub_transform (core::id::StubID const &stub_id1, core::id::StubID const &stub_id2, core::kinematics::RT const &target_rt) override
	Set the transform between two stubs – only works if there's a jump between the two sets of stubatoms. More...

void	set_dof (DOF_ID const &id, core::Real const setting) override
	Sets the AtomTree degree of freedom (DOF) <id> to <setting> More...

void	set_torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4, core::Real const setting, bool const quiet=false) override
	Sets the torsion angle defined by <atom[1-4]> to <setting> More...

void	set_bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, core::Real const setting) override
	Sets the bond angle defined by <atom[1-3]> to <setting> More...

void	set_bond_length (AtomID const &atom1, AtomID const &atom2, core::Real const setting) override
	Sets the cond length between <atom1> and <atom2> to <setting> More...

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

void	fold_tree (FoldTree const &) override
	Sets the FoldTree to <fold_tree_in> More...

void	chain_endings (utility::vector1< core::Size > const &) override
	Sets the list of (chain number) chain endings. More...

void	insert_chain_ending (core::Size const ) override
	Marks <seqpos> as the end of a new (chain number) chain. More...

void	delete_chain_ending (core::Size const ) override
	Deletes <seqpos> from the list of (chain number) chain endings. More...

void	reset_chain_endings () override
	Resets chain data so that the Conformation is marked as a single (chain number) chain. More...

void	chains_from_termini () override
	Rederive the (chain number) chains from the termini/polymer status. More...

void	append_residue_by_jump (core::conformation::Residue const &, core::Size const, std::string const &="", std::string const &="", bool const _=false) override
	Append a new residue by a jump. More...

void	append_polymer_residue_after_seqpos (core::conformation::Residue const &, core::Size const, bool const) override
	glues to seqpos and perhaps also seqpos+1 More...

void	safely_append_polymer_residue_after_seqpos (core::conformation::Residue const &, core::Size const, bool const) override
	glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary More...

void	prepend_polymer_residue_before_seqpos (core::conformation::Residue const &, core::Size const, bool const) override
	glues to seqpos and perhaps also seqpos-1 More...

void	safely_prepend_polymer_residue_before_seqpos (core::conformation::Residue const &, core::Size const, bool const) override
	glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary More...

void	delete_polymer_residue (core::Size const ) override
	Delete polymer residue at the given sequence position. More...

void	delete_residue_slow (core::Size const ) override
	Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. More...

void	delete_residue_range_slow (core::Size const range_begin, core::Size const range_end) override
	Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue. More...

void	declare_chemical_bond (core::Size const, std::string const &, core::Size const, std::string const &) override
	Declare that a chemical bond exists between two residues. More...

void	insert_conformation_by_jump (Conformation const &, core::Size const, core::Size const, core::Size const, core::Size const, std::string const &="", std::string const &="") override
	Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump. More...

void	rebuild_polymer_bond_dependent_atoms (core::Size const ) override
	Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1. More...

void	insert_ideal_geometry_at_polymer_bond (core::Size const seqpos) override

void	insert_ideal_geometry_at_residue_connection (core::Size const pos1, core::Size const connid1) override

void	set_polymeric_connection (core::Size, core::Size) override
	identify polymeric connections More...

void	fix_disulfides (utility::vector1< std::pair< core::Size, core::Size > > const &) override
	Assigns disulfide bonds based on a pre-determined list. More...

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

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

void	reset_move_data () override
	forget all the structure modifications More...

void	clear ()

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

bool	same_type_as_me (Conformation const &other, bool const recurse) const override
	determine the type of the ConformationOP More...

Public Member Functions inherited from core::conformation::Conformation
iterator	begin () noexcept

const_iterator	begin () const noexcept

iterator	end () noexcept

const_iterator	end () const noexcept

	Conformation ()
	constructor More...

	~Conformation () override
	default destructor More...

	Conformation (Conformation const &src)
	copy constructor More...

virtual void	detached_copy (Conformation const &src)
	copy the other conformation into this, but make sure that the two share no possibly-non-bitwise-const data nor do they refer to each other (as the AtomTree does with its topological observer system). More...

void	clear ()
	clear data More...

ConformationCOP	get_self_ptr () const
	self pointers More...

ConformationOP	get_self_ptr ()

ConformationCAP	get_self_weak_ptr () const

ConformationAP	get_self_weak_ptr ()

void	debug_residue_torsions (bool verbose=false) const
	debugging More...

void	show_residue_connections () const
	Show residue connections for debugging purposes. More...

void	show_residue_connections (std::ostream &os) const
	Show residue connections for debugging purposes. More...

bool	sequence_matches (Conformation const &other) const
	do the names of all residues in this and src match? More...

Size	size () const
	Returns the number of residues in the Conformation. More...

bool	empty () const
	Returns true if this conformation does not have any residues. More...

core::chemical::ResidueTypeSetCOP	residue_type_set_for_conf (core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const
	Return the appropriate ResidueTypeSet for the Conformation If mode is INVALID_t (the default), then return the typeset for the majority mode of the Conformation. Note: This may be a GlobalResidueTypeSet, if the Conformation doesn't have a specific PoseResidueTypeSet. More...

core::chemical::PoseResidueTypeSetOP	modifiable_residue_type_set_for_conf (core::chemical::TypeSetMode mode=core::chemical::INVALID_t) const
	Return a clone of the Conformation-specific PoseResidueTypeSet (note this is const) Modifications to this RTS won't be seen in the Conformation unless you pass it back in with reset_residue_type_set_for_conf() Should always return a non-null pointer: will create a new PoseResidueTypeSet if the Conformation doesn't have it already. More...

void	reset_residue_type_set_for_conf (core::chemical::PoseResidueTypeSetCOP new_set, core::chemical::TypeSetMode mode=core::chemical::INVALID_t)
	Reset the Conformation-specific PoseResidueTypeSet for the appropriate mode to the given RTS. (If the given mode is INVALID_t (the recommended default) the mode will be auto-determined from the RTS.) More...

core::chemical::TypeSetMode	residue_typeset_mode (bool majority=true) const
	What mode of ResidueTypeSet is this Conformation made of? If majority is true, it will be the mode of the ResidueTypes for most residues in the pose. If majority is false, core::chemical::MIXED_t will be returned for conformations with ResidueTypes of multiple modes. More...

bool	is_fullatom () const
	convenience test for residue_type_set mode More...

bool	is_centroid () const
	convenience test for residue_type_set mode More...

bool	is_mixed_mode () const
	convenience test for residue_type_set mode More...

bool	is_membrane () const
	convenience test for if the conformation contains information for a membrane protein More...

bool	contains_carbohydrate_residues () const
	Return true if this conformation contains any carbohydrate residues. More...

void	contains_carbohydrate_residues (bool setting)
	Set whether this conformation contains any carbohydrate residues. More...

Size	chain_end (Size chain) const
	Returns the position number of the last residue in chain number <chain> More...

Size	chain_begin (Size chain) const
	Returns the position number of the first residue in chain number <chain> More...

Size	num_chains () const
	Returns the number of chains. More...

utility::vector1< Size > const &	chain_endings () const
	Returns the list of (chain number) chain endings. More...

char	secstruct (Size seqpos) const
	Returns the secondary structure the position <seqpos> More...

void	set_membrane_info (membrane::MembraneInfoOP mem_info)
	Setup a Membrane Info object in Conformation - pos & topology. More...

membrane::MembraneInfoOP	membrane_info ()
	Returns the const MembraneInfo object in conformation. More...

membrane::MembraneInfoOP	membrane_info () const
	Returns the const MembraneInfo object in conformation. More...

void	update_membrane_position (Vector center, Vector normal)
	Update Normal, Center in the Membrane. More...

void	check_valid_membrane () const
	Check that a new membrane position is valid. More...

carbohydrates::GlycanTreeSetCOP	glycan_tree_set () const
	Get the glycan tree set. Nullptr if not present. More...

void	setup_glycan_trees ()
	Setup glycan trees and attach length observer. More...

void	clear_glycan_trees ()
	Safely detaches any tree observers and clears it to null. More...

virtual FoldTree const &	fold_tree () const
	Returns the conformation's FoldTree. More...

AtomTree const &	atom_tree () const
	Returns the conformation's AtomTree. More...

chemical::AA const &	aa (Size seqpos) const
	Returns the AA enum for position <seqpos> More...

std::string	annotated_sequence (bool show_all_variants) const
	Returns the variant-tagged string representing the residue types that make up a conformation; e.g. M[MET:N-Terminus-Variant]CDH[HIS_D]LLR[ARG:C-Terminus-Variant]. More...

Residue const &	residue (Size seqpos) const
	access one of the residues More...

basic::datacache::BasicDataCache const &	residue_data (Size seqpos) const
	Read access to the datacache array stored inside a Residue object. Also accessible to the user by calling residue( seqpos ).data_ptr() directly. More...

basic::datacache::BasicDataCache &	residue_data (Size seqpos)
	Write access to the datacache array stored inside a Residue object. Although the Conformation very deliberately does not grant users write access to the whole of its Residue objects, it will grant users access to the Residue objects data cache. So while the coordinates and dihedrals of the Residue will not be changable e.g. during the setup-for-scoring phase, data derived from those coordinates and dihedrals and which ends up living in the Residue will be changable. More...

ResidueCOP	residue_cop (Size seqpos) const
	access one of the residues, using COP More...

chemical::ResidueType const &	residue_type (Size seqpos) const
	access one of the residue's types – avoids coord/torsion update More...

chemical::ResidueTypeCOP	residue_type_ptr (Size seqpos) const
	access one of the residue's types as a COP – avoids coord/torsion update More...

ResidueCOPs	const_residues () const
	Inefficient – constructs copy of residues_. More...

void	insert_residue_by_jump (Residue const &new_rsd_in, Size seqpos, Size anchor_pos, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false)
	Insert a new residue by jump. If new_chain is "true", then seqpos must be the last residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) More...

void	insert_residue_by_bond (Residue const &new_rsd_in, Size const seqpos, Size anchor_pos, bool const build_ideal_geometry=false, std::string const &anchor_atom="", std::string const &root_atom="", bool new_chain=false, bool const lookup_bond_length=false)
	Insert a new residue by jump. If new_chain is "true", then seqpos must be the last residue of one chain (i.e. residue(seqpos).chain() != residue(seqpos+1).chain() ) More...

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)
	Append a new residue by a bond. More...

virtual utility::vector1< bool >	get_residue_mask () const
	returns a mask of residues to be used in scoring More...

virtual Real	get_residue_weight (core::Size, core::Size) const
	returns a residue-pair weight More...

void	detect_bonds ()

void	detect_pseudobonds ()

virtual void	sever_chemical_bond (Size seqpos1, Size res1_resconn_index, Size seqpos2, Size res2_resconn_index)
	Sever the chemical bond between two residues by stating that the connections for those residues are "incomplete" (i.e. in a state where these residues are not ready to be scored). More...

void	rebuild_polymer_bond_dependent_atoms_this_residue_only (Size const seqpos)
	Rebuilds the atoms that are dependent on polymer bonds for the specified residue only. More...

void	rebuild_residue_connection_dependent_atoms (Size seqpos, Size connid)

AtomID	inter_residue_connection_partner (Size seqpos, int connection_index) const
	This returns the AtomID of the atom in the other residue to which the "connection_index"-th connection of residue seqpos is connected to. More...

AtomID	resolve_partial_atom_id (PartialAtomID const &partial_id) const
	Resolve a partial atom ID into an AtomID that is specific for this Conformation. More...

bool	is_bonded (core::id::AtomID const &atomid1, core::id::AtomID const &atomid2, bool virt=false, bool skip_canonical_and_solvent=false) const
	Returns a boolean for two atomIDs to be bonded. More...

utility::vector1 < core::id::AtomID >	bonded_neighbor_all_res (core::id::AtomID const &atomid, bool virt=false, bool skip_canonical_and_solvent=false, bool intra_res=true, bool inter_res=true) const
	Get all atoms bonded to another. More...

bool	atom_is_backbone_norefold (Size pos, Size atomno) const
	returns true if atom is part of backbone. More...

kinematics::RT	get_stub_transform (id::StubID const &stub_id1, id::StubID const &stub_id2) const
	get the transform between two stubs More...

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 jump_number) const
	The upstream and downstream Stubs are the coordinate frames between which this jump is transforming. More...

kinematics::Stub	downstream_jump_stub (int jump_number) const
	The upstream and downstream Stubs are the coordinate frames between which this jump is transforming. More...

void	set_noncanonical_connection (Size res_id_lower, Size lr_conn_id, Size res_id_upper, Size ur_conn_id)
	Create an arbitrary covalent connection between two residues. More...

void	update_polymeric_connection (Size lower_seqpos, bool update_connection_dep_atoms=false)
	Update the polymer connection status between lower_seqpos and lower_seqpos+1 based on chainID's and termini. If update_connection_dep_atoms is true, positions of atoms dependent on the polymer connection are updated. More...

virtual void	update_noncanonical_connection (Size lower_seqpos, Size lr_conn_id, Size upper_seqpos, Size ur_conn_id)
	Update the connection status between the lower_seqpos residue's lr_conn_id connection ID and the upper_seqpos residue's ur_conn_id connection ID. More...

virtual void	detect_disulfides (utility::vector1< Size > const &disulf_one=utility::vector1< core::Size >(), utility::vector1< Size > const &disulf_two=utility::vector1< core::Size >())
	Detect existing disulfides from the protein structure using suggestions from the FileData (or not!) More...

void	create_new_parameters_set ()
	Create a new (empty) ParametersSet object and add its owning pointer to the current Conformation object. More...

void	add_parameters_set (ParametersSetOP newset)
	Add a (predefined) ParametersSet object (via its owning pointer) to the current Conformation object. More...

core::Size	n_parameters_sets () const
	Get the number of parameters sets defined for this Conformation. More...

void	clear_parameters_set_list ()
	Delete the list of ParametersSetOP objects. More...

ParametersSetOP	parameters_set (core::Size const index)
	Access one of the ParametersSets objects linked to this Conformation. More...

ParametersSetCOP	parameters_set (core::Size const index) const
	Const access to one of the ParametersSets objects linked to this Conformation. More...

void	copy_segment (Size size, Conformation const &src, Size begin, Size src_begin)
	copy a stretch of coordinates/torsions from another Conformation More...

Real	dof (DOF_ID const &id) const
	Returns the AtomTree degree of freedom (DOF) <id> More...

Real	torsion (TorsionID const &id) const
	Return the torsion angle OR rigid-body offset for <id> More...

Real	torsion_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3, AtomID const &atom4) const
	Returns the torsion angle defined by <atom[1-4]> in Radians. More...

Real	bond_angle (AtomID const &atom1, AtomID const &atom2, AtomID const &atom3) const
	Returns the bond angle defined by <atom[1-3]> through the AtomTree. More...

Real	bond_length (AtomID const &atom1, AtomID const &atom2) const
	Returns the bond length between <atom1> and <atom2> through the AtomTree. More...

core::Vector	bond_orientation (AtomID const &atom1, AtomID const &atom2) const
	Return the normalized vector of the bond between these two atoms. More...

core::Vector	bond_orientation (core::id::TorsionID const torsion) const
	Return the normalized vector of the bond about which this torsion angle twists. More...

const Jump &	jump (int jump_number) const
	Returns the Jump with jump number <jump_number> More...

const Jump &	jump (AtomID const &id) const
	access a jump More...

PointPosition const &	xyz (AtomID const &id) const
	access xyz coordinates of an atom More...

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

virtual void	apply_transform_Rx_plus_v (numeric::xyzMatrix< Real > const &R, Vector const &v)

void	update_actcoords ()

void	update_actcoord (Size resid)

void	update_orbital_coords (Residue &rsd) const

void	update_orbital_coords (Size resid)

id::DOF_ID	dof_id_from_atom_ids (id::AtomID const &id1, id::AtomID const &id2, id::AtomID const &id3, id::AtomID const &id4) const
	Get the DOF_ID corresponding to the torsion angle defined by these four atoms. More...

id::DOF_ID	dof_id_from_atom_ids (id::AtomID const &id1, id::AtomID const &id2, id::AtomID const &id3) const
	Get the DOF_ID corresponding to the bond angle defined by these three atoms. More...

id::DOF_ID	dof_id_from_atom_ids (id::AtomID const &id1, id::AtomID const &id2) const
	Get the DOF_ID corresponding to the bond distance defined by these two atoms. More...

id::DOF_ID	dof_id_from_atom_ids (utility::vector1< id::AtomID > const &ids) const
	Get the DOF_ID defined by these atoms. More...

DOF_ID	dof_id_from_torsion_id (TorsionID const &id) const
	Get the DOF_ID corresponding to this TorsionID. More...

id::AtomID	jump_atom_id (int jump_number) const

bool	get_torsion_angle_atom_ids (TorsionID const &tor_id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const
	get four atoms which defined this torsion More...

bool	get_jump_atom_ids (core::Size jump_number, AtomID &upstream_id, AtomID &downstream_id) const
	get two atoms connect by jump More...

bool	atoms_are_bonded (AtomID const &id1, AtomID const &id2) const
	Helper method to determine whether two atoms have a chemical bond linking them. More...

void	update_domain_map (DomainMap &domain_map) const
	Generate a domain_map from the current dof/xyz moved data. More...

bool	structure_moved () const
	has the structure moved since the last call to reset_move_data or reset_structure_moved More...

void	reset_structure_moved () const
	reset the structure_moved_ bool More...

void	align_virtual_atoms_in_carbohydrate_residue (uint const sequence_position)
	Set coordinates of virtual atoms (used as angle reference points) within a saccharide residue of this conformation. More...

template<typename MemFn , typename Ptr >
utility::signals::Link	attach_connection_obs (MemFn fn, Ptr ptr) const
	attach ConnectionEvent observer function More...

template<typename MemFn , typename Ptr >
bool	detach_connection_obs (MemFn fn, Ptr ptr) const
	detach ConnectionEvent observer function More...

template<typename MemFn , typename Ptr >
utility::signals::Link	attach_general_obs (MemFn fn, Ptr ptr) const
	attach GeneralEvent observer function More...

template<typename MemFn , typename Ptr >
bool	detach_general_obs (MemFn fn, Ptr ptr) const
	detach GeneralEvent observer function More...

template<typename MemFn , typename Ptr >
utility::signals::Link	attach_identity_obs (MemFn fn, Ptr ptr) const
	attach IdentityEvent observer function More...

template<typename MemFn , typename Ptr >
bool	detach_identity_obs (MemFn fn, Ptr ptr) const
	detach IdentityEvent observer function More...

template<typename MemFn , typename Ptr >
utility::signals::Link	attach_length_obs (MemFn fn, Ptr ptr) const
	attach LengthEvent observer function More...

template<typename MemFn , typename Ptr >
bool	detach_length_obs (MemFn fn, Ptr ptr) const
	detach LengthEvent observer function More...

template<typename MemFn , typename Ptr >
utility::signals::Link	attach_xyz_obs (MemFn fn, Ptr ptr) const
	attach XYZEvent observer function More...

template<typename MemFn , typename Ptr >
bool	detach_xyz_obs (MemFn fn, Ptr ptr) const
	detach XYZEvent observer function More...

void	clear_observers ()
	clear all observers More...

void	receive_observers_from (Conformation const &src)
	fire a ConnectionEvent::TRANSFER to transfer observers from some source Conformation More...

void	debug_pause (bool flag) const
	wait for stdin after sending a GeneralEvent signal More...

bool	debug_pause () const
	waiting for stdin after sending a GeneralEvent signal? More...

void	buffer_signals ()
	block signals from being sent and buffer them to be sent after unblocking More...

void	block_signals ()
	block signals from being sent More...

void	unblock_signals ()
	allow signals to be sent More...

bool	buffering_signals () const
	are signals being blocked and buffered? More...

bool	blocking_signals () const
	are signals being blocked? More...

bool	backbone_torsion_angle_atoms (TorsionID const &id, AtomID &id1, AtomID &id2, AtomID &id3, AtomID &id4) const
	get four backbone atoms which define this backbone torsion More...

Private Types
typedef core::conformation::Conformation	Parent

typedef core::environment::SequenceAnnotationCOP	SequenceAnnotationCOP

Private Member Functions
bool	verify (core::id::TorsionID const &)

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

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

bool	verify_backbone (core::Size const &seqpos)

void	fail_verification (std::string const &mod_type, core::Size const &seqpos=0) const

void	fail_verification (core::id::DOF_ID const &id, std::string const &mod_type) const

void	replace_residue_sandbox (core::Size seqpos, core::conformation::Residue const &new_rsd, bool)

void	push_passport (core::environment::DofPassportCOP) override

core::environment::DofPassportCOP	pop_passport () override

bool	has_passport () const override

void	set_environment (EnvironmentCAP)

void	attach_annotation (SequenceAnnotationCOP)

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::PartialAtomID	PartialAtomID

typedef core::conformation::parametric::ParametersSet	ParametersSet

typedef core::conformation::parametric::ParametersSetOP	ParametersSetOP

typedef core::conformation::parametric::ParametersSetCOP	ParametersSetCOP

typedef core::conformation::parametric::Parameters	Parameters

typedef core::conformation::parametric::ParametersOP	ParametersOP

typedef core::conformation::parametric::ParametersOP	ParametersCOP

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

typedef Size	size_type

typedef ptrdiff_t	difference_type

typedef boost::indirect_iterator < ResidueOPs::const_iterator, Residue const >	const_iterator

typedef boost::indirect_iterator < ResidueOPs::iterator, Residue const >	iterator

Protected Member Functions inherited from core::conformation::Conformation
Residue const &	const_residue_ (Size seqpos) const
	Returns a constant residue reference without triggering coordinate/torsion update. More...

void	force_update_residue_torsions () const
	Force updating of residue torsions. More...

void	force_update_residue_coordinates () const
	Force updating of residue coordinates. More...

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 core::scoring::env, and environment().

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

References core::scoring::env, and environment().

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

override

References core::scoring::env, environment(), and environment_exists_.

Member Function Documentation

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

inline

References resolver().

Referenced by protocols::environment::claims::EnvLabelSelector::apply().

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

overridevirtual

glues to seqpos and perhaps also seqpos+1

Fires a LengthEvent::RESIDUE_PREPEND signal at seqpos + 1 due to insert_polymer_residue() call.

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Append a new residue by a jump.

add a residue into residues_ container, update its seqpos, chainid as well fold tree and atoms. Fires a LengthEvent::RESIDUE_APPEND signal.

Reimplemented from core::conformation::Conformation.

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

private

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

override

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

overridevirtual

Sets the list of (chain number) chain endings.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Remarks: All positions must be strictly less than the number of residues in the Conformation, otherwise the routine will fail fast. Note that the last residue position is not counted as a chain end.

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Rederive the (chain number) chains from the termini/polymer status.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Reimplemented from core::conformation::Conformation.

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

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

overridevirtual

clone the conformation

make a copy of this conformation( allocate actual memory for it )

Reimplemented from core::conformation::Conformation.

void protocols::environment::ProtectedConformation::declare_chemical_bond	(	core::Size const	seqpos1,
		std::string const &	atom_name1,
		core::Size const	seqpos2,
		std::string const &	atom_name2
	)

overridevirtual

Declare that a chemical bond exists between two residues.

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Deletes <seqpos> from the list of (chain number) chain endings.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Remarks: The last residue position is not counted as a chain ending.

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Delete polymer residue at the given sequence position.

delete a polymer residues Fires a LengthEvent::RESIDUE_DELETE signal.

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue.

Like above but only one call to setup_atom_tree Fires a LengthEvent::RESIDUE_DELETE signal.

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Slow method that relies on FoldTree::delete_seqpos, rebuilds atomtree, can handle jumps/root residue.

Delete a residue from the Conformation the slow way – triggers a rebuild of the atomtree Fires a LengthEvent::RESIDUE_DELETE signal.

Note: Could be upstream and/or downstream of a jump or chemical edge, or the root of the tree; Not well-tested. Expect funny behavior in new or different situations (email pbrad.nosp@m.ley@.nosp@m.fhcrc.nosp@m..org)

LOGIC: uses fold_tree.delete_seqpos to handle shifting the topology around if necessary, then calls setup_atom_tree

Reimplemented from core::conformation::Conformation.

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

inline

References environment_exists_.

Referenced by protocols::environment::Environment::~Environment().

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

References env_, and environment_exists_.

Referenced by ProtectedConformation(), and ~ProtectedConformation().

void protocols::environment::ProtectedConformation::fail_verification	(	std::string const &	mod_type,
		core::Size const &	seqpos = `0`
	)		const

inlineprivate

References core::id::PHI.

Referenced by set_jump(), set_secstruct(), and set_torsion().

void protocols::environment::ProtectedConformation::fail_verification	(	core::id::DOF_ID const &	id,
		std::string const &	mod_type
	)		const

inlineprivate

References protocols::environment::get_mover_name().

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

overridevirtual

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Assigns disulfide bonds based on a pre-determined list.

Note: works in centroid and full-atom modes

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Sets the FoldTree to <fold_tree_in>

setup atom tree as well from the fold tree

Reimplemented from core::conformation::Conformation.

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

overrideprivatevirtual

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Marks <seqpos> as the end of a new (chain number) chain.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Remarks: The last residue position is not counted as a chain ending. Also increases the chain ID number by 1 for all residues upstream from seqpos.

Reimplemented from core::conformation::Conformation.

void protocols::environment::ProtectedConformation::insert_conformation_by_jump	(	Conformation const &	conf,
		core::Size const	insert_seqpos,
		core::Size const	insert_jumppos,
		core::Size const	anchor_pos,
		core::Size const	anchor_jump_number,
		std::string const &	anchor_atom = `""`,
		std::string const &	root_atom = `""`
	)

overridevirtual

Insert one conformation into another. See FoldTree::insert_fold_tree_by_jump.

Calls residue append observers AFTER addition of all residues

Insert one conformation into another. Some tricky issues: (1) residue connections: assume all residue connections within conf carry over, after renumbering residues positions (2) jump numbers: see FoldTree::insert_fold_tree_by_jump (3) chains: chain endings are inserted before insert_seqpos, and after insert_seqpos+conf.size()-1 ie. at the beginning and ending of the inserted conformation; all internal chain endings from conf are used (4) atom_tree: setup_atom_tree is called to rebuild from scratch using the fold_tree (5) Residue append observers are notified AFTER addition of ALL residues into the conformation)

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Set two bond angles and a bond length. DOES NOT DO ANY DIHEDRALS – NOT EVEN OMEGA IF IT'S A PROTEIN

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Set two bond angles and a bond length. DOES NOT DO ANY DIHEDRALS – NOT EVEN OMEGA IF IT'S A PROTEIN

Reimplemented from core::conformation::Conformation.

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

inlineoverridevirtual

Reimplemented from core::conformation::Conformation.

ResidueOP protocols::environment::ProtectedConformation::match_variants	(	core::Size	seqpos,
		core::conformation::Residue const &	in_rsd
	)		const

References protocols::environment::add_variant(), core::chemical::ResidueProperties::get_list_of_variants(), core::chemical::ResidueProperties::get_variant_from_string(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueTypeBase::properties(), protocols::environment::rm_variant(), protocols::environment::tr(), and core::conformation::Residue::type().

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

overridevirtual

equals operator

If lengths & sequence of source and target are different, will fire a LengthEvent::INVALIDATE signal and then an IdentityEvent::INVALIDATE signal.

Reimplemented from core::conformation::Conformation.

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

DofPassportCOP protocols::environment::ProtectedConformation::pop_passport ( )

overrideprivatevirtual

Reimplemented from core::conformation::Conformation.

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

overridevirtual

glues to seqpos and perhaps also seqpos-1

Fires a LengthEvent::RESIDUE_PREPEND signal.

Reimplemented from core::conformation::Conformation.

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

overrideprivatevirtual

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Rebuild the atoms ( like HN(seqpos), OC(seqpos+1) ) that are dependent on the polymer bond between seqpos and seqpos+1.

rebuilds the atoms that are dependent on the bond between seqpos and seqpos+1 for their torsion offset

Reimplemented from core::conformation::Conformation.

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

overridevirtual

function to replace a residue based on superposition on the specified input atom pairs

Note: NOTE: at the moment, only superposition on 3 atoms works Fires an IdentityEvent signal.

Reimplemented from core::conformation::Conformation.

void protocols::environment::ProtectedConformation::replace_residue	(	core::Size const	seqpos,
		core::conformation::Residue const &	new_rsd_in,
		bool const	orient_backbone
	)

overridevirtual

replace residue

replace a residue Fires an IdentityEvent signal.

Reimplemented from core::conformation::Conformation.

void protocols::environment::ProtectedConformation::replace_residue_sandbox	(	core::Size	seqpos,
		core::conformation::Residue const &	new_rsd,
		bool	p
	)

private

References protocols::environment::collect_dofs(), protocols::environment::get_mover_name(), core::id::THETA, protocols::environment::tr(), and core::conformation::Residue::type().

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

overridevirtual

Resets chain data so that the Conformation is marked as a single (chain number) chain.

See the documentation of Pose::num_chains() for details about chain numbers, chain letters and jumps.

Reimplemented from core::conformation::Conformation.

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

overridevirtual

forget all the structure modifications

called after domain map information is transferred to the Energies class

Reimplemented from core::conformation::Conformation.

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

Referenced by annotations().

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

overridevirtual

glues to seqpos and perhaps also seqpos+1, removes termini variants if necessary

Reimplemented from core::conformation::Conformation.

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

overridevirtual

glues to seqpos and perhaps also seqpos-1, removes termini variants if necessary

Fires a LengthEvent::RESIDUE_PREPEND signal.

Reimplemented from core::conformation::Conformation.

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

overridevirtual

determine the type of the ConformationOP

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
	)

overridevirtual

Sets the bond angle defined by <atom[1-3]> to <setting>

Note: in radians!!

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Sets the cond length between <atom1> and <atom2> to <setting>

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Sets the AtomTree degree of freedom (DOF) <id> to <setting>

Reimplemented from core::conformation::Conformation.

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

private

References core::scoring::env.

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

overridevirtual

set a jump

Reimplemented from core::conformation::Conformation.

References fail_verification(), core::id::RB1, core::conformation::Conformation::set_jump(), and verify_jump().

Referenced by set_jump().

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

overridevirtual

Sets the jump <jump_number> to <new_jump>

Reimplemented from core::conformation::Conformation.

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

void protocols::environment::ProtectedConformation::set_polymeric_connection	(	core::Size	res_id_lower,
		core::Size	res_id_upper
	)

overridevirtual

identify polymeric connections

The lower residue connects to the upper residue through its upper_connect connection The upper residue connects to the lower residue through its lower_connect connection

Reimplemented from core::conformation::Conformation.

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

overridevirtual

Sets the secondary structure of the position <seqpos> to <setting>

Sets secondary structure character of a sequence position. Will resize the secondary structure array if the requested sequence position is larger than the length of the array.

Reimplemented from core::conformation::Conformation.

References core::id::BB, core::conformation::Conformation::dof_id_from_torsion_id(), fail_verification(), core::id::phi_torsion(), 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
	)

overridevirtual

Set the transform between two stubs – only works if there's a jump between the two sets of stubatoms.

Reimplemented from core::conformation::Conformation.

References core::id::RB1, core::id::to_string(), and protocols::environment::tr().

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

overridevirtual

Sets the AtomTree DOF and the torsion OR rigid-body offset in the corresponding Residue or Jump.

Remarks: This is a poorly named method, as it can also be used to set jump rigid-body offsets. ~Labonte

Reimplemented from core::conformation::Conformation.

References core::conformation::Conformation::dof_id_from_torsion_id(), fail_verification(), core::conformation::Conformation::set_torsion(), 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 const	quiet = `false`
	)