Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Types | Private Member Functions | Private Attributes | Friends | List of all members
protocols::environment::ProtectedConformation Class Reference

#include <ProtectedConformation.hh>

Inheritance diagram for protocols::environment::ProtectedConformation:
Inheritance graph
[legend]

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...
 
Conformationoperator= (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< boolget_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 Jumpjump (int jump_number) const
 Returns the Jump with jump number <jump_number> More...
 
const Jumpjump (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

Constructor & Destructor Documentation

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

Member Function Documentation

SequenceAnnotationCOP protocols::environment::ProtectedConformation::annotations ( ) const
inline
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
EnvironmentCAP protocols::environment::ProtectedConformation::environment ( ) const
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
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
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
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
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 
)
overridevirtual

Sets the torsion angle defined by <atom[1-4]> to <setting>

Reimplemented from core::conformation::Conformation.

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

References core::id::PHI, and core::id::RB1.

bool protocols::environment::ProtectedConformation::verify ( core::id::TorsionID const &  id)
inlineprivate

References core::id::DOF_ID::valid().

Referenced by set_torsion().

bool protocols::environment::ProtectedConformation::verify ( core::id::DOF_ID const &  id)
inlineprivate

References core::scoring::env.

bool protocols::environment::ProtectedConformation::verify_backbone ( core::Size const &  seqpos)
inlineprivate
bool protocols::environment::ProtectedConformation::verify_jump ( core::id::AtomID const &  a_id)
inlineprivate

References core::id::RB1, and core::id::RB6.

Referenced by set_jump().

Friends And Related Function Documentation

friend class DofUnlock
friend
friend class EnvClaimBroker
friend
friend class Environment
friend

Member Data Documentation

SequenceAnnotationCOP protocols::environment::ProtectedConformation::annotations_
private

Referenced by operator=().

EnvironmentCAP protocols::environment::ProtectedConformation::env_
private

Referenced by environment(), and operator=().

bool protocols::environment::ProtectedConformation::environment_exists_
private
std::stack<core::environment::DofPassportCOP> protocols::environment::ProtectedConformation::unlocks_
private

Referenced by operator=().


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